TY - JOUR T1 - Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. JF - Front Immunol Y1 - 2024 A1 - Niarakis, Anna A1 - Ostaszewski, Marek A1 - Mazein, Alexander A1 - Kuperstein, Inna A1 - Kutmon, Martina A1 - Gillespie, Marc E A1 - Funahashi, Akira A1 - Acencio, Marcio Luis A1 - Hemedan, Ahmed A1 - Aichem, Michael A1 - Klein, Karsten A1 - Czauderna, Tobias A1 - Burtscher, Felicia A1 - Yamada, Takahiro G A1 - Hiki, Yusuke A1 - Hiroi, Noriko F A1 - Hu, Finterly A1 - Pham, Nhung A1 - Ehrhart, Friederike A1 - Willighagen, Egon L A1 - Valdeolivas, Alberto A1 - Dugourd, Aurélien A1 - Messina, Francesco A1 - Esteban-Medina, Marina A1 - Peña-Chilet, Maria A1 - Rian, Kinza A1 - Soliman, Sylvain A1 - Aghamiri, Sara Sadat A1 - Puniya, Bhanwar Lal A1 - Naldi, Aurélien A1 - Helikar, Tomáš A1 - Singh, Vidisha A1 - Fernández, Marco Fariñas A1 - Bermudez, Viviam A1 - Tsirvouli, Eirini A1 - Montagud, Arnau A1 - Noël, Vincent A1 - Ponce-de-Leon, Miguel A1 - Maier, Dieter A1 - Bauch, Angela A1 - Gyori, Benjamin M A1 - Bachman, John A A1 - Luna, Augustin A1 - Piñero, Janet A1 - Furlong, Laura I A1 - Balaur, Irina A1 - Rougny, Adrien A1 - Jarosz, Yohan A1 - Overall, Rupert W A1 - Phair, Robert A1 - Perfetto, Livia A1 - Matthews, Lisa A1 - Rex, Devasahayam Arokia Balaya A1 - Orlic-Milacic, Marija A1 - Gomez, Luis Cristobal Monraz A1 - De Meulder, Bertrand A1 - Ravel, Jean Marie A1 - Jassal, Bijay A1 - Satagopam, Venkata A1 - Wu, Guanming A1 - Golebiewski, Martin A1 - Gawron, Piotr A1 - Calzone, Laurence A1 - Beckmann, Jacques S A1 - Evelo, Chris T A1 - D'Eustachio, Peter A1 - Schreiber, Falk A1 - Saez-Rodriguez, Julio A1 - Dopazo, Joaquin A1 - Kuiper, Martin A1 - Valencia, Alfonso A1 - Wolkenhauer, Olaf A1 - Kitano, Hiroaki A1 - Barillot, Emmanuel A1 - Auffray, Charles A1 - Balling, Rudi A1 - Schneider, Reinhard KW - Computer Simulation KW - COVID-19 KW - drug repositioning KW - Humans KW - SARS-CoV-2 KW - Systems biology AB -

INTRODUCTION: The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing.

METHODS: Extensive community work allowed an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework can link biomolecules from omics data analysis and computational modelling to dysregulated pathways in a cell-, tissue- or patient-specific manner. Drug repurposing using text mining and AI-assisted analysis identified potential drugs, chemicals and microRNAs that could target the identified key factors.

RESULTS: Results revealed drugs already tested for anti-COVID-19 efficacy, providing a mechanistic context for their mode of action, and drugs already in clinical trials for treating other diseases, never tested against COVID-19.

DISCUSSION: The key advance is that the proposed framework is versatile and expandable, offering a significant upgrade in the arsenal for virus-host interactions and other complex pathologies.

VL - 14 ER - TY - JOUR T1 - The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. JF - J Transl Med Y1 - 2024 A1 - Esteban-Medina, Marina A1 - Loucera, Carlos A1 - Rian, Kinza A1 - Velasco, Sheyla A1 - Olivares-González, Lorena A1 - Rodrigo, Regina A1 - Dopazo, Joaquin A1 - Peña-Chilet, Maria KW - Animals KW - Mice KW - Retinitis pigmentosa KW - Signal Transduction AB -

BACKGROUND: Retinitis pigmentosa is the prevailing genetic cause of blindness in developed nations with no effective treatments. In the pursuit of unraveling the intricate dynamics underlying this complex disease, mechanistic models emerge as a tool of proven efficiency rooted in systems biology, to elucidate the interplay between RP genes and their mechanisms. The integration of mechanistic models and drug-target interactions under the umbrella of machine learning methodologies provides a multifaceted approach that can boost the discovery of novel therapeutic targets, facilitating further drug repurposing in RP.

METHODS: By mapping Retinitis Pigmentosa-related genes (obtained from Orphanet, OMIM and HPO databases) onto KEGG signaling pathways, a collection of signaling functional circuits encompassing Retinitis Pigmentosa molecular mechanisms was defined. Next, a mechanistic model of the so-defined disease map, where the effects of interventions can be simulated, was built. Then, an explainable multi-output random forest regressor was trained using normal tissue transcriptomic data to learn causal connections between targets of approved drugs from DrugBank and the functional circuits of the mechanistic disease map. Selected target genes involvement were validated on rd10 mice, a murine model of Retinitis Pigmentosa.

RESULTS: A mechanistic functional map of Retinitis Pigmentosa was constructed resulting in 226 functional circuits belonging to 40 KEGG signaling pathways. The method predicted 109 targets of approved drugs in use with a potential effect over circuits corresponding to nine hallmarks identified. Five of those targets were selected and experimentally validated in rd10 mice: Gabre, Gabra1 (GABARα1 protein), Slc12a5 (KCC2 protein), Grin1 (NR1 protein) and Glr2a. As a result, we provide a resource to evaluate the potential impact of drug target genes in Retinitis Pigmentosa.

CONCLUSIONS: The possibility of building actionable disease models in combination with machine learning algorithms to learn causal drug-disease interactions opens new avenues for boosting drug discovery. Such mechanistically-based hypotheses can guide and accelerate the experimental validations prioritizing drug target candidates. In this work, a mechanistic model describing the functional disease map of Retinitis Pigmentosa was developed, identifying five promising therapeutic candidates targeted by approved drug. Further experimental validation will demonstrate the efficiency of this approach for a systematic application to other rare diseases.

VL - 22 IS - 1 ER - TY - JOUR T1 - Case report: Analysis of phage therapy failure in a patient with a Pseudomonas aeruginosa prosthetic vascular graft infection JF - Front Med (Lausanne) Y1 - 2023 A1 - Blasco, Lucia A1 - López-Hernández, Inmaculada A1 - Rodríguez-Fernández, Miguel A1 - Perez-Florido, Javier A1 - Casimiro-Soriguer, Carlos S AB -

Clinical case of a patient with a multidrug-resistant prosthetic vascular graft infection which was treated with a cocktail of phages (PT07, 14/01, and PNM) in combination with ceftazidime-avibactam (CZA). After the application of the phage treatment and in absence of antimicrobial therapy, a new bloodstream infection (BSI) with a septic residual limb metastasis occurred, now involving a wild-type strain being susceptible to ß-lactams and quinolones. Clinical strains were analyzed by microbiology and whole genome sequencing techniques. In relation with phage administration, the clinical isolates of before phage therapy (HE2011471) and post phage therapy (HE2105886) showed a clonal relationship but with important genomic changes which could be involved in the resistance to this therapy. Finally, phenotypic studies showed a decrease in Minimum Inhibitory Concentration (MIC) to ß-lactams and quinolones as well as an increase of the biofilm production and phage resistant mutants in the clinical isolate of post phage therapy.

VL - 10 UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10235614/ ER - TY - BOOK T1 - Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder T2 - Lecture Notes in Computer Science. Computational Methods in Systems Biology Y1 - 2023 A1 - Gundogdu, Pelin A1 - Payá-Milans, Miriam A1 - Alamo-Alvarez, Inmaculada A1 - Nepomuceno-Chamorro, Isabel A. A1 - Dopazo, Joaquin A1 - Loucera, Carlos JF - Lecture Notes in Computer Science. Computational Methods in Systems Biology PB - Springer Nature Switzerland CY - Cham VL - 14137 SN - 978-3-031-42696-4 UR - https://link.springer.com/chapter/10.1007/978-3-031-42697-1_5 ER - TY - JOUR T1 - A Comprehensive Analysis of 21 Actionable Pharmacogenes in the Spanish Population: From Genetic Characterisation to Clinical Impact. JF - Pharmaceutics Y1 - 2023 A1 - Núñez-Torres, Rocío A1 - Pita, Guillermo A1 - Peña-Chilet, Maria A1 - López-López, Daniel A1 - Zamora, Jorge A1 - Roldán, Gema A1 - Herráez, Belén A1 - Alvarez, Nuria A1 - Alonso, María Rosario A1 - Dopazo, Joaquin A1 - González-Neira, Anna AB -

The implementation of pharmacogenetics (PGx) is a main milestones of precision medicine nowadays in order to achieve safer and more effective therapies. Nevertheless, the implementation of PGx diagnostics is extremely slow and unequal worldwide, in part due to a lack of ethnic PGx information. We analysed genetic data from 3006 Spanish individuals obtained by different high-throughput (HT) techniques. Allele frequencies were determined in our population for the main 21 actionable PGx genes associated with therapeutical changes. We found that 98% of the Spanish population harbours at least one allele associated with a therapeutical change and, thus, there would be a need for a therapeutical change in a mean of 3.31 of the 64 associated drugs. We also identified 326 putative deleterious variants that were not previously related with PGx in 18 out of the 21 main PGx genes evaluated and a total of 7122 putative deleterious variants for the 1045 PGx genes described. Additionally, we performed a comparison of the main HT diagnostic techniques, revealing that after whole genome sequencing, genotyping with the PGx HT array is the most suitable solution for PGx diagnostics. Finally, all this information was integrated in the Collaborative Spanish Variant Server to be available to and updated by the scientific community.

VL - 15 IS - 4 ER - TY - JOUR T1 - Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer. JF - Int J Mol Sci Y1 - 2023 A1 - Cubuk, Cankut A1 - Loucera, Carlos A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

The reprogramming of metabolism is a recognized cancer hallmark. It is well known that different signaling pathways regulate and orchestrate this reprogramming that contributes to cancer initiation and development. However, recent evidence is accumulating, suggesting that several metabolites could play a relevant role in regulating signaling pathways. To assess the potential role of metabolites in the regulation of signaling pathways, both metabolic and signaling pathway activities of Breast invasive Carcinoma (BRCA) have been modeled using mechanistic models. Gaussian Processes, powerful machine learning methods, were used in combination with SHapley Additive exPlanations (SHAP), a recent methodology that conveys causality, to obtain potential causal relationships between the production of metabolites and the regulation of signaling pathways. A total of 317 metabolites were found to have a strong impact on signaling circuits. The results presented here point to the existence of a complex crosstalk between signaling and metabolic pathways more complex than previously was thought.

VL - 24 IS - 8 ER - TY - JOUR T1 - A crowdsourcing database for the copy-number variation of the Spanish population. JF - Hum Genomics Y1 - 2023 A1 - López-López, Daniel A1 - Roldán, Gema A1 - Fernandez-Rueda, Jose L A1 - Bostelmann, Gerrit A1 - Carmona, Rosario A1 - Aquino, Virginia A1 - Perez-Florido, Javier A1 - Ortuno, Francisco A1 - Pita, Guillermo A1 - Núñez-Torres, Rocío A1 - González-Neira, Anna A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

BACKGROUND: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants.

RESULTS: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/ .

CONCLUSION: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.

VL - 17 IS - 1 ER - TY - JOUR T1 - Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis. JF - Cell Rep Y1 - 2023 A1 - Pellegrinelli, Vanessa A1 - Figueroa-Juárez, Elizabeth A1 - Samuelson, Isabella A1 - U-Din, Mueez A1 - Rodriguez-Fdez, Sonia A1 - Virtue, Samuel A1 - Leggat, Jennifer A1 - Cubuk, Cankut A1 - Peirce, Vivian J A1 - Niemi, Tarja A1 - Campbell, Mark A1 - Rodriguez-Cuenca, Sergio A1 - Dopazo, Joaquin A1 - Carobbio, Stefania A1 - Virtanen, Kirsi A A1 - Vidal-Puig, Antonio AB -

The relevance of extracellular matrix (ECM) remodeling is reported in white adipose tissue (AT) and obesity-related dysfunctions, but little is known about the importance of ECM remodeling in brown AT (BAT) function. Here, we show that a time course of high-fat diet (HFD) feeding progressively impairs diet-induced thermogenesis concomitantly with the development of fibro-inflammation in BAT. Higher markers of fibro-inflammation are associated with lower cold-induced BAT activity in humans. Similarly, when mice are housed at thermoneutrality, inactivated BAT features fibro-inflammation. We validate the pathophysiological relevance of BAT ECM remodeling in response to temperature challenges and HFD using a model of a primary defect in the collagen turnover mediated by partial ablation of the Pepd prolidase. Pepd-heterozygous mice display exacerbated dysfunction and BAT fibro-inflammation at thermoneutrality and in HFD. Our findings show the relevance of ECM remodeling in BAT activation and provide a mechanism for BAT dysfunction in obesity.

VL - 42 IS - 6 ER - TY - JOUR T1 - Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia. JF - Int J Mol Sci Y1 - 2023 A1 - Perez-Florido, Javier A1 - Casimiro-Soriguer, Carlos S A1 - Ortuno, Francisco A1 - Fernandez-Rueda, Jose L A1 - Aguado, Andrea A1 - Lara, María A1 - Riazzo, Cristina A1 - Rodriguez-Iglesias, Manuel A A1 - Camacho-Martinez, Pedro A1 - Merino-Diaz, Laura A1 - Pupo-Ledo, Inmaculada A1 - de Salazar, Adolfo A1 - Viñuela, Laura A1 - Fuentes, Ana A1 - Chueca, Natalia A1 - García, Federico A1 - Dopazo, Joaquin A1 - Lepe, Jose A AB -

Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.

VL - 24 IS - 3 ER - TY - JOUR T1 - Evidence of the association between increased use of direct oral anticoagulants and a reduction in the rate of atrial fibrillation-related stroke and major bleeding at the population level (2012-2019). JF - Med Clin (Barc) Y1 - 2023 A1 - Loucera, Carlos A1 - Carmona, Rosario A1 - Bostelmann, Gerrit A1 - Muñoyerro-Muñiz, Dolores A1 - Villegas, Román A1 - Gonzalez-Manzanares, Rafael A1 - Dopazo, Joaquin A1 - Anguita, Manuel AB -

BACKGROUND: The introduction of direct-acting oral anticoagulants (DOACs) has shown to decrease atrial fibrillation (AF)-related stroke and bleeding rates in clinical studies, but there is no certain evidence about their effects at the population level. Our aim was to assess changes in AF-related stroke and major bleeding rates between 2012 and 2019 in Andalusia (Spain), and the association between DOACs use and events rates at the population level.

METHODS: All patients with an AF diagnosis from 2012 to 2019 were identified using the Andalusian Health Population Base, that provides clinical information on all Andalusian people. Annual ischemic and hemorrhagic stroke, major bleeding rates, and used antithrombotic treatments were determined. Marginal hazard ratios (HR) were calculated for each treatment.

RESULTS: A total of 95,085 patients with an AF diagnosis were identified. Mean age was 76.1±10.2 years (49.7% women). An increase in the use of DOACs was observed throughout the study period in both males and females (p<0.001). The annual rate of ischemic stroke decreased by one third, while that of hemorrhagic stroke and major bleeding decreased 2-3-fold from 2012 to 2019. Marginal HR was lower than 0.50 for DOACs compared to VKA for all ischemic or hemorrhagic events.

CONCLUSIONS: In this contemporary population-based study using clinical and administrative databases in Andalusia, a significant reduction in the incidence of AF-related ischemic and hemorrhagic stroke and major bleeding was observed between 2012 and 2019. The increased use of DOACs seems to be associated with this reduction.

ER - TY - JOUR T1 - Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging. JF - Commun Biol Y1 - 2023 A1 - Sola-García, Alejandro A1 - Cáliz-Molina, María Ángeles A1 - Espadas, Isabel A1 - Petr, Michael A1 - Panadero-Morón, Concepción A1 - González-Morán, Daniel A1 - Martín-Vázquez, María Eugenia A1 - Narbona-Pérez, Álvaro Jesús A1 - López-Noriega, Livia A1 - Martínez-Corrales, Guillermo A1 - López-Fernández-Sobrino, Raúl A1 - Carmona-Marin, Lina M A1 - Martínez-Force, Enrique A1 - Yanes, Oscar A1 - Vinaixa, Maria A1 - López-López, Daniel A1 - Reyes, José Carlos A1 - Dopazo, Joaquin A1 - Martín, Franz A1 - Gauthier, Benoit R A1 - Scheibye-Knudsen, Morten A1 - Capilla-González, Vivian A1 - Martín-Montalvo, Alejandro AB -

ATP-citrate lyase is a central integrator of cellular metabolism in the interface of protein, carbohydrate, and lipid metabolism. The physiological consequences as well as the molecular mechanisms orchestrating the response to long-term pharmacologically induced Acly inhibition are unknown. We report here that the Acly inhibitor SB-204990 improves metabolic health and physical strength in wild-type mice when fed with a high-fat diet, while in mice fed with healthy diet results in metabolic imbalance and moderated insulin resistance. By applying a multiomic approach using untargeted metabolomics, transcriptomics, and proteomics, we determined that, in vivo, SB-204990 plays a role in the regulation of molecular mechanisms associated with aging, such as energy metabolism, mitochondrial function, mTOR signaling, and folate cycle, while global alterations on histone acetylation are absent. Our findings indicate a mechanism for regulating molecular pathways of aging that prevents the development of metabolic abnormalities associated with unhealthy dieting. This strategy might be explored for devising therapeutic approaches to prevent metabolic diseases.

VL - 6 IS - 1 ER - TY - JOUR T1 - microRNAs-mediated regulation of insulin signaling in white adipose tissue during aging: Role of caloric restriction. JF - Aging Cell Y1 - 2023 A1 - Corrales, Patricia A1 - Martin-Taboada, Marina A1 - Vivas-García, Yurena A1 - Torres, Lucia A1 - Ramirez-Jimenez, Laura A1 - Lopez, Yamila A1 - Horrillo, Daniel A1 - Vila-Bedmar, Rocio A1 - Barber-Cano, Eloisa A1 - Izquierdo-Lahuerta, Adriana A1 - Peña-Chilet, Maria A1 - Martínez, Carmen A1 - Dopazo, Joaquin A1 - Ros, Manuel A1 - Medina-Gomez, Gema AB -

Caloric restriction is a non-pharmacological intervention known to ameliorate the metabolic defects associated with aging, including insulin resistance. The levels of miRNA expression may represent a predictive tool for aging-related alterations. In order to investigate the role of miRNAs underlying insulin resistance in adipose tissue during the early stages of aging, 3- and 12-month-old male animals fed ad libitum, and 12-month-old male animals fed with a 20% caloric restricted diet were used. In this work we demonstrate that specific miRNAs may contribute to the impaired insulin-stimulated glucose metabolism specifically in the subcutaneous white adipose tissue, through the regulation of target genes implicated in the insulin signaling cascade. Moreover, the expression of these miRNAs is modified by caloric restriction in middle-aged animals, in accordance with the improvement of the metabolic state. Overall, our work demonstrates that alterations in posttranscriptional gene expression because of miRNAs dysregulation might represent an endogenous mechanism by which insulin response in the subcutaneous fat depot is already affected at middle age. Importantly, caloric restriction could prevent this modulation, demonstrating that certain miRNAs could constitute potential biomarkers of age-related metabolic alterations.

ER - TY - JOUR T1 - Rapid degeneration of iPSC-derived motor neurons lacking Gdap1 engages a mitochondrial-sustained innate immune response. JF - Cell Death Discov Y1 - 2023 A1 - León, Marian A1 - Prieto, Javier A1 - Molina-Navarro, María Micaela A1 - Garcia-Garcia, Francisco A1 - Barneo-Muñoz, Manuela A1 - Ponsoda, Xavier A1 - Sáez, Rosana A1 - Palau, Francesc A1 - Dopazo, Joaquin A1 - Izpisua Belmonte, Juan Carlos A1 - Torres, Josema AB -

Charcot-Marie-Tooth disease is a chronic hereditary motor and sensory polyneuropathy targeting Schwann cells and/or motor neurons. Its multifactorial and polygenic origin portrays a complex clinical phenotype of the disease with a wide range of genetic inheritance patterns. The disease-associated gene GDAP1 encodes for a mitochondrial outer membrane protein. Mouse and insect models with mutations in Gdap1 have reproduced several traits of the human disease. However, the precise function in the cell types affected by the disease remains unknown. Here, we use induced-pluripotent stem cells derived from a Gdap1 knockout mouse model to better understand the molecular and cellular phenotypes of the disease caused by the loss-of-function of this gene. Gdap1-null motor neurons display a fragile cell phenotype prone to early degeneration showing (1) altered mitochondrial morphology, with an increase in the fragmentation of these organelles, (2) activation of autophagy and mitophagy, (3) abnormal metabolism, characterized by a downregulation of Hexokinase 2 and ATP5b proteins, (4) increased reactive oxygen species and elevated mitochondrial membrane potential, and (5) increased innate immune response and p38 MAP kinase activation. Our data reveals the existence of an underlying Redox-inflammatory axis fueled by altered mitochondrial metabolism in the absence of Gdap1. As this biochemical axis encompasses a wide variety of druggable targets, our results may have implications for developing therapies using combinatorial pharmacological approaches and improving therefore human welfare. A Redox-immune axis underlying motor neuron degeneration caused by the absence of Gdap1. Our results show that Gdap1 motor neurons have a fragile cellular phenotype that is prone to degeneration. Gdap1 iPSCs differentiated into motor neurons showed an altered metabolic state: decreased glycolysis and increased OXPHOS. These alterations may lead to hyperpolarization of mitochondria and increased ROS levels. Excessive amounts of ROS might be the cause of increased mitophagy, p38 activation and inflammation as a cellular response to oxidative stress. The p38 MAPK pathway and the immune response may, in turn, have feedback mechanisms, leading to the induction of apoptosis and senescence, respectively. CAC, citric acid cycle; ETC, electronic transport chain; Glc, glucose; Lac, lactate; Pyr, pyruvate.

VL - 9 IS - 1 ER - TY - JOUR T1 - Real-world evidence with a retrospective cohort of 15,968 COVID-19 hospitalized patients suggests 21 new effective treatments. JF - Virol J Y1 - 2023 A1 - Loucera, Carlos A1 - Carmona, Rosario A1 - Esteban-Medina, Marina A1 - Bostelmann, Gerrit A1 - Muñoyerro-Muñiz, Dolores A1 - Villegas, Román A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

PURPOSE: Despite the extensive vaccination campaigns in many countries, COVID-19 is still a major worldwide health problem because of its associated morbidity and mortality. Therefore, finding efficient treatments as fast as possible is a pressing need. Drug repurposing constitutes a convenient alternative when the need for new drugs in an unexpected medical scenario is urgent, as is the case with COVID-19.

METHODS: Using data from a central registry of electronic health records (the Andalusian Population Health Database), the effect of prior consumption of drugs for other indications previous to the hospitalization with respect to patient outcomes, including survival and lymphocyte progression, was studied on a retrospective cohort of 15,968 individuals, comprising all COVID-19 patients hospitalized in Andalusia between January and November 2020.

RESULTS: Covariate-adjusted hazard ratios and analysis of lymphocyte progression curves support a significant association between consumption of 21 different drugs and better patient survival. Contrarily, one drug, furosemide, displayed a significant increase in patient mortality.

CONCLUSIONS: In this study we have taken advantage of the availability of a regional clinical database to study the effect of drugs, which patients were taking for other indications, on their survival. The large size of the database allowed us to control covariates effectively.

VL - 20 IS - 1 ER - TY - JOUR T1 - SigPrimedNet: A Signaling-Informed Neural Network for scRNA-seq Annotation of Known and Unknown Cell Types. JF - Biology (Basel) Y1 - 2023 A1 - Gundogdu, Pelin A1 - Alamo, Inmaculada A1 - Nepomuceno-Chamorro, Isabel A A1 - Dopazo, Joaquin A1 - Loucera, Carlos AB -

Single-cell RNA sequencing is increasing our understanding of the behavior of complex tissues or organs, by providing unprecedented details on the complex cell type landscape at the level of individual cells. Cell type definition and functional annotation are key steps to understanding the molecular processes behind the underlying cellular communication machinery. However, the exponential growth of scRNA-seq data has made the task of manually annotating cells unfeasible, due not only to an unparalleled resolution of the technology but to an ever-increasing heterogeneity of the data. Many supervised and unsupervised methods have been proposed to automatically annotate cells. Supervised approaches for cell-type annotation outperform unsupervised methods except when new (unknown) cell types are present. Here, we introduce SigPrimedNet an artificial neural network approach that leverages (i) efficient training by means of a sparsity-inducing signaling circuits-informed layer, (ii) feature representation learning through supervised training, and (iii) unknown cell-type identification by fitting an anomaly detection method on the learned representation. We show that SigPrimedNet can efficiently annotate known cell types while keeping a low false-positive rate for unseen cells across a set of publicly available datasets. In addition, the learned representation acts as a proxy for signaling circuit activity measurements, which provide useful estimations of the cell functionalities.

VL - 12 IS - 4 ER - TY - JOUR T1 - Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival. JF - Viruses Y1 - 2022 A1 - Loucera, Carlos A1 - Perez-Florido, Javier A1 - Casimiro-Soriguer, Carlos S A1 - Ortuno, Francisco M A1 - Carmona, Rosario A1 - Bostelmann, Gerrit A1 - Martínez-González, L Javier A1 - Muñoyerro-Muñiz, Dolores A1 - Villegas, Román A1 - Rodríguez-Baño, Jesús A1 - Romero-Gómez, Manuel A1 - Lorusso, Nicola A1 - Garcia-León, Javier A1 - Navarro-Marí, Jose M A1 - Camacho-Martinez, Pedro A1 - Merino-Diaz, Laura A1 - Salazar, Adolfo de A1 - Viñuela, Laura A1 - Lepe, Jose A A1 - García, Federico A1 - Dopazo, Joaquin KW - COVID-19 KW - Genome, Viral KW - Humans KW - mutation KW - Pandemics KW - Phylogeny KW - SARS-CoV-2 AB -

OBJECTIVES: More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain.

METHODS: A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis.

RESULTS: A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins.

CONCLUSIONS: This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.

VL - 14 IS - 9 ER - TY - JOUR T1 - CIBERER: Spanish National Network for Research on Rare Diseases: a highly productive collaborative initiative. JF - Clin Genet Y1 - 2022 A1 - Luque, Juan A1 - Mendes, Ingrid A1 - Gómez, Beatriz A1 - Morte, Beatriz A1 - de Heredia, Miguel López A1 - Herreras, Enrique A1 - Corrochano, Virginia A1 - Bueren, Juan A1 - Gallano, Pia A1 - Artuch, Rafael A1 - Fillat, Cristina A1 - Pérez-Jurado, Luis A A1 - Montoliu, Lluis A1 - Carracedo, Ángel A1 - Millán, José M A1 - Webb, Susan M A1 - Palau, Francesc A1 - Lapunzina, Pablo AB -

CIBER (Center for Biomedical Network Research; Centro de Investigación Biomédica En Red) is a public national consortium created in 2006 under the umbrella of the Spanish National Institute of Health Carlos III (ISCIII). This innovative research structure comprises 11 different specific areas dedicated to the main public health priorities in the National Health System. CIBERER, the thematic area of CIBER focused on Rare Diseases currently consists of 75 research groups belonging to universities, research centers and hospitals of the entire country. CIBERER's mission is to be a center prioritizing and favoring collaboration and cooperation between biomedical and clinical research groups, with special emphasis on the aspects of genetic, molecular, biochemical and cellular research of rare diseases. This research is the basis for providing new tools for the diagnosis and therapy of low-prevalence diseases, in line with the International Rare Diseases Research Consortium (IRDiRC) objectives, thus favoring translational research between the scientific environment of the laboratory and the clinical setting of health centers. In this paper, we intend to review CIBERER's 15-year journey and summarize the main results obtained in terms of internationalization, scientific production, contributions towards the discovery of new therapies and novel genes associated to diseases, cooperation with patients' associations and many other topics related to rare disease research. This article is protected by copyright. All rights reserved.

ER - TY - JOUR T1 - Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling. JF - Hum Mol Genet Y1 - 2022 A1 - López-Sánchez, Macarena A1 - Loucera, Carlos A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

Recent studies have demonstrated a relevant role of the host genetics in the COVID-19 prognosis. Most of the 7000 rare diseases described to date have a genetic component, typically highly penetrant. However, this vast spectrum of genetic variability remains yet unexplored with respect to possible interactions with COVID-19. Here, a mathematical mechanistic model of the COVID-19 molecular disease mechanism has been used to detect potential interactions between rare disease genes and the COVID-19 infection process and downstream consequences. Out of the 2518 disease genes analyzed, causative of 3854 rare diseases, a total of 254 genes have a direct effect on the COVID-19 molecular disease mechanism and 207 have an indirect effect revealed by a significant strong correlation. This remarkable potential of interaction occurs for more than 300 rare diseases. Mechanistic modeling of COVID-19 disease map has allowed a holistic systematic analysis of the potential interactions between the loss of function in known rare disease genes and the pathological consequences of COVID-19 infection. The results identify links between disease genes and COVID-19 hallmarks and demonstrate the usefulness of the proposed approach for future preventive measures in some rare diseases.

ER - TY - JOUR T1 - Endoglin and MMP14 Contribute to Ewing Sarcoma Spreading by Modulation of Cell-Matrix Interactions. JF - Int J Mol Sci Y1 - 2022 A1 - Puerto-Camacho, Pilar A1 - Diaz-Martin, Juan A1 - Olmedo-Pelayo, Joaquín A1 - Bolado-Carrancio, Alfonso A1 - Salguero-Aranda, Carmen A1 - Jordán-Pérez, Carmen A1 - Esteban-Medina, Marina A1 - Alamo-Alvarez, Inmaculada A1 - Delgado-Bellido, Daniel A1 - Lobo-Selma, Laura A1 - Dopazo, Joaquin A1 - Sastre, Ana A1 - Alonso, Javier A1 - Grünewald, Thomas G P A1 - Bernabeu, Carmelo A1 - Byron, Adam A1 - Brunton, Valerie G A1 - Amaral, Ana Teresa A1 - de Alava, Enrique KW - Bone Neoplasms KW - Endoglin KW - Humans KW - Matrix Metalloproteinase 14 KW - Proteomics KW - Receptors, Growth Factor KW - Sarcoma, Ewing KW - Signal Transduction AB -

Endoglin (ENG) is a mesenchymal stem cell (MSC) marker typically expressed by active endothelium. This transmembrane glycoprotein is shed by matrix metalloproteinase 14 (MMP14). Our previous work demonstrated potent preclinical activity of first-in-class anti-ENG antibody-drug conjugates as a nascent strategy to eradicate Ewing sarcoma (ES), a devastating rare bone/soft tissue cancer with a putative MSC origin. We also defined a correlation between ENG and MMP14 expression in ES. Herein, we show that ENG expression is significantly associated with a dismal prognosis in a large cohort of ES patients. Moreover, both ENG/MMP14 are frequently expressed in primary ES tumors and metastasis. To deepen in their functional relevance in ES, we conducted transcriptomic and proteomic profiling of in vitro ES models that unveiled a key role of ENG and MMP14 in cell mechano-transduction. Migration and adhesion assays confirmed that loss of ENG disrupts actin filament assembly and filopodia formation, with a concomitant effect on cell spreading. Furthermore, we observed that ENG regulates cell-matrix interaction through activation of focal adhesion signaling and protein kinase C expression. In turn, loss of MMP14 contributed to a more adhesive phenotype of ES cells by modulating the transcriptional extracellular matrix dynamics. Overall, these results suggest that ENG and MMP14 exert a significant role in mediating correct spreading machinery of ES cells, impacting the aggressiveness of the disease.

VL - 23 IS - 15 ER - TY - JOUR T1 - Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. JF - BioData Min Y1 - 2022 A1 - Gundogdu, Pelin A1 - Loucera, Carlos A1 - Alamo-Alvarez, Inmaculada A1 - Dopazo, Joaquin A1 - Nepomuceno, Isabel AB -

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) data provide valuable insights into cellular heterogeneity which is significantly improving the current knowledge on biology and human disease. One of the main applications of scRNA-seq data analysis is the identification of new cell types and cell states. Deep neural networks (DNNs) are among the best methods to address this problem. However, this performance comes with the trade-off for a lack of interpretability in the results. In this work we propose an intelligible pathway-driven neural network to correctly solve cell-type related problems at single-cell resolution while providing a biologically meaningful representation of the data.

RESULTS: In this study, we explored the deep neural networks constrained by several types of prior biological information, e.g. signaling pathway information, as a way to reduce the dimensionality of the scRNA-seq data. We have tested the proposed biologically-based architectures on thousands of cells of human and mouse origin across a collection of public datasets in order to check the performance of the model. Specifically, we tested the architecture across different validation scenarios that try to mimic how unknown cell types are clustered by the DNN and how it correctly annotates cell types by querying a database in a retrieval problem. Moreover, our approach demonstrated to be comparable to other less interpretable DNN approaches constrained by using protein-protein interactions gene regulation data. Finally, we show how the latent structure learned by the network could be used to visualize and to interpret the composition of human single cell datasets.

CONCLUSIONS: Here we demonstrate how the integration of pathways, which convey fundamental information on functional relationships between genes, with DNNs, that provide an excellent classification framework, results in an excellent alternative to learn a biologically meaningful representation of scRNA-seq data. In addition, the introduction of prior biological knowledge in the DNN reduces the size of the network architecture. Comparative results demonstrate a superior performance of this approach with respect to other similar approaches. As an additional advantage, the use of pathways within the DNN structure enables easy interpretability of the results by connecting features to cell functionalities by means of the pathway nodes, as demonstrated with an example with human melanoma tumor cells.

VL - 15 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34980200?dopt=Abstract ER - TY - JOUR T1 - Novel genes and sex differences in COVID-19 severity. JF - Hum Mol Genet Y1 - 2022 A1 - Cruz, Raquel A1 - Almeida, Silvia Diz-de A1 - Heredia, Miguel López A1 - Quintela, Inés A1 - Ceballos, Francisco C A1 - Pita, Guillermo A1 - Lorenzo-Salazar, José M A1 - González-Montelongo, Rafaela A1 - Gago-Domínguez, Manuela A1 - Porras, Marta Sevilla A1 - Castaño, Jair Antonio Tenorio A1 - Nevado, Julián A1 - Aguado, Jose María A1 - Aguilar, Carlos A1 - Aguilera-Albesa, Sergio A1 - Almadana, Virginia A1 - Almoguera, Berta A1 - Alvarez, Nuria A1 - Andreu-Bernabeu, Álvaro A1 - Arana-Arri, Eunate A1 - Arango, Celso A1 - Arranz, María J A1 - Artiga, Maria-Jesus A1 - Baptista-Rosas, Raúl C A1 - Barreda-Sánchez, María A1 - Belhassen-Garcia, Moncef A1 - Bezerra, Joao F A1 - Bezerra, Marcos A C A1 - Boix-Palop, Lucía A1 - Brión, Maria A1 - Brugada, Ramón A1 - Bustos, Matilde A1 - Calderón, Enrique J A1 - Carbonell, Cristina A1 - Castano, Luis A1 - Castelao, Jose E A1 - Conde-Vicente, Rosa A1 - Cordero-Lorenzana, M Lourdes A1 - Cortes-Sanchez, Jose L A1 - Corton, Marta A1 - Darnaude, M Teresa A1 - De Martino-Rodríguez, Alba A1 - Campo-Pérez, Victor A1 - Bustamante, Aranzazu Diaz A1 - Domínguez-Garrido, Elena A1 - Luchessi, André D A1 - Eirós, Rocío A1 - Sanabria, Gladys Mercedes Estigarribia A1 - Fariñas, María Carmen A1 - Fernández-Robelo, Uxía A1 - Fernández-Rodríguez, Amanda A1 - Fernández-Villa, Tania A1 - Gil-Fournier, Belén A1 - Gómez-Arrue, Javier A1 - Álvarez, Beatriz González A1 - Quirós, Fernan Gonzalez Bernaldo A1 - González-Peñas, Javier A1 - Gutiérrez-Bautista, Juan F A1 - Herrero, María José A1 - Herrero-Gonzalez, Antonio A1 - Jimenez-Sousa, María A A1 - Lattig, María Claudia A1 - Borja, Anabel Liger A1 - Lopez-Rodriguez, Rosario A1 - Mancebo, Esther A1 - Martín-López, Caridad A1 - Martín, Vicente A1 - Martinez-Nieto, Oscar A1 - Martinez-Lopez, Iciar A1 - Martinez-Resendez, Michel F A1 - Martinez-Perez, Ángel A1 - Mazzeu, Juliana A A1 - Macías, Eleuterio Merayo A1 - Minguez, Pablo A1 - Cuerda, Victor Moreno A1 - Silbiger, Vivian N A1 - Oliveira, Silviene F A1 - Ortega-Paino, Eva A1 - Parellada, Mara A1 - Paz-Artal, Estela A1 - Santos, Ney P C A1 - Pérez-Matute, Patricia A1 - Perez, Patricia A1 - Pérez-Tomás, M Elena A1 - Perucho, Teresa A1 - Pinsach-Abuin, Mel Lina A1 - Pompa-Mera, Ericka N A1 - Porras-Hurtado, Gloria L A1 - Pujol, Aurora A1 - León, Soraya Ramiro A1 - Resino, Salvador A1 - Fernandes, Marianne R A1 - Rodríguez-Ruiz, Emilio A1 - Rodriguez-Artalejo, Fernando A1 - Rodriguez-Garcia, José A A1 - Ruiz-Cabello, Francisco A1 - Ruiz-Hornillos, Javier A1 - Ryan, Pablo A1 - Soria, José Manuel A1 - Souto, Juan Carlos A1 - Tamayo, Eduardo A1 - Tamayo-Velasco, Alvaro A1 - Taracido-Fernandez, Juan Carlos A1 - Teper, Alejandro A1 - Torres-Tobar, Lilian A1 - Urioste, Miguel A1 - Valencia-Ramos, Juan A1 - Yáñez, Zuleima A1 - Zarate, Ruth A1 - Nakanishi, Tomoko A1 - Pigazzini, Sara A1 - Degenhardt, Frauke A1 - Butler-Laporte, Guillaume A1 - Maya-Miles, Douglas A1 - Bujanda, Luis A1 - Bouysran, Youssef A1 - Palom, Adriana A1 - Ellinghaus, David A1 - Martínez-Bueno, Manuel A1 - Rolker, Selina A1 - Amitrano, Sara A1 - Roade, Luisa A1 - Fava, Francesca A1 - Spinner, Christoph D A1 - Prati, Daniele A1 - Bernardo, David A1 - García, Federico A1 - Darcis, Gilles A1 - Fernández-Cadenas, Israel A1 - Holter, Jan Cato A1 - Banales, Jesus M A1 - Frithiof, Robert A1 - Duga, Stefano A1 - Asselta, Rosanna A1 - Pereira, Alexandre C A1 - Romero-Gómez, Manuel A1 - Nafría-Jiménez, Beatriz A1 - Hov, Johannes R A1 - Migeotte, Isabelle A1 - Renieri, Alessandra A1 - Planas, Anna M A1 - Ludwig, Kerstin U A1 - Buti, Maria A1 - Rahmouni, Souad A1 - Alarcón-Riquelme, Marta E A1 - Schulte, Eva C A1 - Franke, Andre A1 - Karlsen, Tom H A1 - Valenti, Luca A1 - Zeberg, Hugo A1 - Richards, Brent A1 - Ganna, Andrea A1 - Boada, Mercè A1 - Rojas, Itziar A1 - Ruiz, Agustín A1 - Sánchez, Pascual A1 - Real, Luis Miguel A1 - Guillén-Navarro, Encarna A1 - Ayuso, Carmen A1 - González-Neira, Anna A1 - Riancho, José A A1 - Rojas-Martinez, Augusto A1 - Flores, Carlos A1 - Lapunzina, Pablo A1 - Carracedo, Ángel AB -

Here we describe the results of a genome-wide study conducted in 11 939 COVID-19 positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (p < 5x10-8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (p = 1.3x10-22 and p = 8.1x10-12, respectively), and for variants in 9q21.32 near TLE1 only among females (p = 4.4x10-8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (p = 2.7x10-8) and ARHGAP33 (p = 1.3x10-8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, p = 4.1x10-8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥ 60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.

ER - TY - JOUR T1 - An SPM-Enriched Marine Oil Supplement Shifted Microglia Polarization toward M2, Ameliorating Retinal Degeneration in Mice. JF - Antioxidants (Basel) Y1 - 2022 A1 - Olivares-González, Lorena A1 - Velasco, Sheyla A1 - Gallego, Idoia A1 - Esteban-Medina, Marina A1 - Puras, Gustavo A1 - Loucera, Carlos A1 - Martínez-Romero, Alicia A1 - Peña-Chilet, Maria A1 - Pedraz, José Luis A1 - Rodrigo, Regina AB -

Retinitis pigmentosa (RP) is the most common inherited retinal dystrophy causing progressive vision loss. It is accompanied by chronic and sustained inflammation, including M1 microglia activation. This study evaluated the effect of an essential fatty acid (EFA) supplement containing specialized pro-resolving mediators (SPMs), on retinal degeneration and microglia activation in mice, a model of RP, as well as on LPS-stimulated BV2 cells. The EFA supplement was orally administered to mice from postnatal day (P)9 to P18. At P18, the electrical activity of the retina was examined by electroretinography (ERG) and innate behavior in response to light were measured. Retinal degeneration was studied via histology including the TUNEL assay and microglia immunolabeling. Microglia polarization (M1/M2) was assessed by flow cytometry, qPCR, ELISA and histology. Redox status was analyzed by measuring antioxidant enzymes and markers of oxidative damage. Interestingly, the EFA supplement ameliorated retinal dysfunction and degeneration by improving ERG recording and sensitivity to light, and reducing photoreceptor cell loss. The EFA supplement reduced inflammation and microglia activation attenuating M1 markers as well as inducing a shift to the M2 phenotype in mouse retinas and LPS-stimulated BV2 cells. It also reduced oxidative stress markers of lipid peroxidation and carbonylation. These findings could open up new therapeutic opportunities based on resolving inflammation with oral supplementation with SPMs such as the EFA supplement.

VL - 12 IS - 1 ER - TY - JOUR T1 - Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. JF - Sci Rep Y1 - 2022 A1 - Casimiro-Soriguer, Carlos S A1 - Loucera, Carlos A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.

VL - 12 IS - 1 ER - TY - JOUR T1 - A comprehensive database for integrated analysis of omics data in autoimmune diseases. JF - BMC Bioinformatics Y1 - 2021 A1 - Martorell-Marugán, Jordi A1 - López-Domínguez, Raúl A1 - García-Moreno, Adrián A1 - Toro-Domínguez, Daniel A1 - Villatoro-García, Juan Antonio A1 - Barturen, Guillermo A1 - Martín-Gómez, Adoración A1 - Troule, Kevin A1 - Gómez-López, Gonzalo A1 - Al-Shahrour, Fátima A1 - González-Rumayor, Víctor A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin A1 - Saez-Rodriguez, Julio A1 - Alarcón-Riquelme, Marta E A1 - Carmona-Sáez, Pedro KW - Autoimmune Diseases KW - Computational Biology KW - Databases, Factual KW - Humans AB -

BACKGROUND: Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanisms of these diseases. Nevertheless, data from different cohorts and pathologies are stored independently in public repositories and a unified resource is imperative to assist researchers in this field.

RESULTS: Here, we present Autoimmune Diseases Explorer ( https://adex.genyo.es ), a database that integrates 82 curated transcriptomics and methylation studies covering 5609 samples for some of the most common autoimmune diseases. The database provides, in an easy-to-use environment, advanced data analysis and statistical methods for exploring omics datasets, including meta-analysis, differential expression or pathway analysis.

CONCLUSIONS: This is the first omics database focused on autoimmune diseases. This resource incorporates homogeneously processed data to facilitate integrative analyses among studies.

VL - 22 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34167460?dopt=Abstract ER - TY - JOUR T1 - COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. JF - Mol Syst Biol Y1 - 2021 A1 - Ostaszewski, Marek A1 - Niarakis, Anna A1 - Mazein, Alexander A1 - Kuperstein, Inna A1 - Phair, Robert A1 - Orta-Resendiz, Aurelio A1 - Singh, Vidisha A1 - Aghamiri, Sara Sadat A1 - Acencio, Marcio Luis A1 - Glaab, Enrico A1 - Ruepp, Andreas A1 - Fobo, Gisela A1 - Montrone, Corinna A1 - Brauner, Barbara A1 - Frishman, Goar A1 - Monraz Gómez, Luis Cristóbal A1 - Somers, Julia A1 - Hoch, Matti A1 - Kumar Gupta, Shailendra A1 - Scheel, Julia A1 - Borlinghaus, Hanna A1 - Czauderna, Tobias A1 - Schreiber, Falk A1 - Montagud, Arnau A1 - Ponce de Leon, Miguel A1 - Funahashi, Akira A1 - Hiki, Yusuke A1 - Hiroi, Noriko A1 - Yamada, Takahiro G A1 - Dräger, Andreas A1 - Renz, Alina A1 - Naveez, Muhammad A1 - Bocskei, Zsolt A1 - Messina, Francesco A1 - Börnigen, Daniela A1 - Fergusson, Liam A1 - Conti, Marta A1 - Rameil, Marius A1 - Nakonecnij, Vanessa A1 - Vanhoefer, Jakob A1 - Schmiester, Leonard A1 - Wang, Muying A1 - Ackerman, Emily E A1 - Shoemaker, Jason E A1 - Zucker, Jeremy A1 - Oxford, Kristie A1 - Teuton, Jeremy A1 - Kocakaya, Ebru A1 - Summak, Gökçe Yağmur A1 - Hanspers, Kristina A1 - Kutmon, Martina A1 - Coort, Susan A1 - Eijssen, Lars A1 - Ehrhart, Friederike A1 - Rex, Devasahayam Arokia Balaya A1 - Slenter, Denise A1 - Martens, Marvin A1 - Pham, Nhung A1 - Haw, Robin A1 - Jassal, Bijay A1 - Matthews, Lisa A1 - Orlic-Milacic, Marija A1 - Senff Ribeiro, Andrea A1 - Rothfels, Karen A1 - Shamovsky, Veronica A1 - Stephan, Ralf A1 - Sevilla, Cristoffer A1 - Varusai, Thawfeek A1 - Ravel, Jean-Marie A1 - Fraser, Rupsha A1 - Ortseifen, Vera A1 - Marchesi, Silvia A1 - Gawron, Piotr A1 - Smula, Ewa A1 - Heirendt, Laurent A1 - Satagopam, Venkata A1 - Wu, Guanming A1 - Riutta, Anders A1 - Golebiewski, Martin A1 - Owen, Stuart A1 - Goble, Carole A1 - Hu, Xiaoming A1 - Overall, Rupert W A1 - Maier, Dieter A1 - Bauch, Angela A1 - Gyori, Benjamin M A1 - Bachman, John A A1 - Vega, Carlos A1 - Grouès, Valentin A1 - Vazquez, Miguel A1 - Porras, Pablo A1 - Licata, Luana A1 - Iannuccelli, Marta A1 - Sacco, Francesca A1 - Nesterova, Anastasia A1 - Yuryev, Anton A1 - de Waard, Anita A1 - Turei, Denes A1 - Luna, Augustin A1 - Babur, Ozgun A1 - Soliman, Sylvain A1 - Valdeolivas, Alberto A1 - Esteban-Medina, Marina A1 - Peña-Chilet, Maria A1 - Rian, Kinza A1 - Helikar, Tomáš A1 - Puniya, Bhanwar Lal A1 - Modos, Dezso A1 - Treveil, Agatha A1 - Olbei, Marton A1 - De Meulder, Bertrand A1 - Ballereau, Stephane A1 - Dugourd, Aurélien A1 - Naldi, Aurélien A1 - Noël, Vincent A1 - Calzone, Laurence A1 - Sander, Chris A1 - Demir, Emek A1 - Korcsmaros, Tamas A1 - Freeman, Tom C A1 - Augé, Franck A1 - Beckmann, Jacques S A1 - Hasenauer, Jan A1 - Wolkenhauer, Olaf A1 - Wilighagen, Egon L A1 - Pico, Alexander R A1 - Evelo, Chris T A1 - Gillespie, Marc E A1 - Stein, Lincoln D A1 - Hermjakob, Henning A1 - D'Eustachio, Peter A1 - Saez-Rodriguez, Julio A1 - Dopazo, Joaquin A1 - Valencia, Alfonso A1 - Kitano, Hiroaki A1 - Barillot, Emmanuel A1 - Auffray, Charles A1 - Balling, Rudi A1 - Schneider, Reinhard KW - Antiviral Agents KW - Computational Biology KW - Computer Graphics KW - COVID-19 KW - Cytokines KW - Data Mining KW - Databases, Factual KW - Gene Expression Regulation KW - Host Microbial Interactions KW - Humans KW - Immunity, Cellular KW - Immunity, Humoral KW - Immunity, Innate KW - Lymphocytes KW - Metabolic Networks and Pathways KW - Myeloid Cells KW - Protein Interaction Mapping KW - SARS-CoV-2 KW - Signal Transduction KW - Software KW - Transcription Factors KW - Viral Proteins AB -

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

VL - 17 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34664389?dopt=Abstract ER - TY - JOUR T1 - CSVS, a crowdsourcing database of the Spanish population genetic variability. JF - Nucleic Acids Res Y1 - 2021 A1 - Peña-Chilet, Maria A1 - Roldán, Gema A1 - Perez-Florido, Javier A1 - Ortuno, Francisco M A1 - Carmona, Rosario A1 - Aquino, Virginia A1 - López-López, Daniel A1 - Loucera, Carlos A1 - Fernandez-Rueda, Jose L A1 - Gallego, Asunción A1 - Garcia-Garcia, Francisco A1 - González-Neira, Anna A1 - Pita, Guillermo A1 - Núñez-Torres, Rocío A1 - Santoyo-López, Javier A1 - Ayuso, Carmen A1 - Minguez, Pablo A1 - Avila-Fernandez, Almudena A1 - Corton, Marta A1 - Moreno-Pelayo, Miguel Ángel A1 - Morin, Matías A1 - Gallego-Martinez, Alvaro A1 - Lopez-Escamez, Jose A A1 - Borrego, Salud A1 - Antiňolo, Guillermo A1 - Amigo, Jorge A1 - Salgado-Garrido, Josefa A1 - Pasalodos-Sanchez, Sara A1 - Morte, Beatriz A1 - Carracedo, Ángel A1 - Alonso, Ángel A1 - Dopazo, Joaquin KW - Alleles KW - Chromosome Mapping KW - Crowdsourcing KW - Databases, Genetic KW - Exome KW - Gene Frequency KW - Genetic Variation KW - Genetics, Population KW - Genome, Human KW - Genomics KW - Humans KW - Internet KW - Precision Medicine KW - Software KW - Spain AB -

The knowledge of the genetic variability of the local population is of utmost importance in personalized medicine and has been revealed as a critical factor for the discovery of new disease variants. Here, we present the Collaborative Spanish Variability Server (CSVS), which currently contains more than 2000 genomes and exomes of unrelated Spanish individuals. This database has been generated in a collaborative crowdsourcing effort collecting sequencing data produced by local genomic projects and for other purposes. Sequences have been grouped by ICD10 upper categories. A web interface allows querying the database removing one or more ICD10 categories. In this way, aggregated counts of allele frequencies of the pseudo-control Spanish population can be obtained for diseases belonging to the category removed. Interestingly, in addition to pseudo-control studies, some population studies can be made, as, for example, prevalence of pharmacogenomic variants, etc. In addition, this genomic data has been used to define the first Spanish Genome Reference Panel (SGRP1.0) for imputation. This is the first local repository of variability entirely produced by a crowdsourcing effort and constitutes an example for future initiatives to characterize local variability worldwide. CSVS is also part of the GA4GH Beacon network. CSVS can be accessed at: http://csvs.babelomics.org/.

VL - 49 IS - D1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32990755?dopt=Abstract ER - TY - JOUR T1 - De novo small deletion affecting transcription start site of short isoform of AUTS2 gene in a patient with syndromic neurodevelopmental defects. JF - Am J Med Genet A Y1 - 2021 A1 - Martinez-Delgado, Beatriz A1 - Lopez-Martin, Estrella A1 - Lara-Herguedas, Julián A1 - Monzon, Sara A1 - Cuesta, Isabel A1 - Juliá, Miguel A1 - Aquino, Virginia A1 - Rodriguez-Martin, Carlos A1 - Damian, Alejandra A1 - Gonzalo, Irene A1 - Gomez-Mariano, Gema A1 - Baladron, Beatriz A1 - Cazorla, Rosario A1 - Iglesias, Gema A1 - Roman, Enriqueta A1 - Ros, Purificacion A1 - Tutor, Pablo A1 - Mellor, Susana A1 - Jimenez, Carlos A1 - Cabrejas, Maria Jose A1 - Gonzalez-Vioque, Emiliano A1 - Alonso, Javier A1 - Bermejo-Sánchez, Eva A1 - Posada, Manuel KW - Child, Preschool KW - Cytoskeletal Proteins KW - Dwarfism KW - Exons KW - Gene Expression Regulation KW - Genetic Association Studies KW - Humans KW - Male KW - Neurodevelopmental Disorders KW - Protein Isoforms KW - RNA, Messenger KW - Sequence Deletion KW - Syndrome KW - Transcription Factors KW - Transcription Initiation Site KW - Transcription, Genetic AB -

Disruption of the autism susceptibility candidate 2 (AUTS2) gene through genomic rearrangements, copy number variations (CNVs), and intragenic deletions and mutations, has been recurrently involved in syndromic forms of developmental delay and intellectual disability, known as AUTS2 syndrome. The AUTS2 gene plays an important role in regulation of neuronal migration, and when altered, associates with a variable phenotype from severely to mildly affected patients. The more severe phenotypes significantly correlate with the presence of defects affecting the C-terminus part of the gene. This article reports a new patient with a syndromic neurodevelopmental disorder, who presents a deletion of 30 nucleotides in the exon 9 of the AUTS2 gene. Importantly, this deletion includes the transcription start site for the AUTS2 short transcript isoform, which has an important role in brain development. Gene expression analysis of AUTS2 full-length and short isoforms revealed that the deletion found in this patient causes a remarkable reduction in the expression level, not only of the short isoform, but also of the full AUTS2 transcripts. This report adds more evidence for the role of mutated AUTS2 short transcripts in the development of a severe phenotype in the AUTS2 syndrome.

VL - 185 IS - 3 ER - TY - JOUR T1 - Deciphering Genomic Heterogeneity and the Internal Composition of Tumour Activities through a Hierarchical Factorisation Model JF - Mathematics Y1 - 2021 A1 - Carbonell-Caballero, José A1 - López-Quílez, Antonio A1 - Conesa, David A1 - Dopazo, Joaquin VL - 9 UR - https://www.mdpi.com/2227-7390/9/21/2833https://www.mdpi.com/2227-7390/9/21/2833/pdf IS - 21 JO - Mathematics ER - TY - JOUR T1 - A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. JF - Mol Oncol Y1 - 2021 A1 - Moura, David S A1 - Peña-Chilet, Maria A1 - Cordero Varela, Juan Antonio A1 - Alvarez-Alegret, Ramiro A1 - Agra-Pujol, Carolina A1 - Izquierdo, Francisco A1 - Ramos, Rafael A1 - Ortega-Medina, Luis A1 - Martin-Davila, Francisco A1 - Castilla-Ramirez, Carolina A1 - Hernandez-Leon, Carmen Nieves A1 - Romagosa, Cleofe A1 - Vaz Salgado, Maria Angeles A1 - Lavernia, Javier A1 - Bagué, Silvia A1 - Mayodormo-Aranda, Empar A1 - Vicioso, Luis A1 - Hernández Barceló, Jose Emilio A1 - Rubio-Casadevall, Jordi A1 - de Juan, Ana A1 - Fiaño-Valverde, Maria Concepcion A1 - Hindi, Nadia A1 - Lopez-Alvarez, Maria A1 - Lacerenza, Serena A1 - Dopazo, Joaquin A1 - Gutierrez, Antonio A1 - Alvarez, Rosa A1 - Valverde, Claudia A1 - Martinez-Trufero, Javier A1 - Martin-Broto, Javier AB -

Predictive biomarkers of trabectedin represent an unmet need in advanced soft-tissue sarcomas (STS). DNA damage repair (DDR) genes, involved in homologous recombination or nucleotide excision repair, had been previously described as biomarkers of trabectedin resistance or sensitivity, respectively. The majority of these studies only focused on specific factors (ERCC1, ERCC5, and BRCA1) and did not evaluate several other DDR-related genes that could have a relevant role for trabectedin efficacy. In this retrospective translational study, 118 genes involved in DDR were evaluated to determine, by transcriptomics, a predictive gene signature of trabectedin efficacy. A six-gene predictive signature of trabectedin efficacy was built in a series of 139 tumor samples from patients with advanced STS. Patients in the high-risk gene signature group showed a significantly worse progression-free survival compared with patients in the low-risk group (2.1 vs 6.0 months, respectively). Differential gene expression analysis defined new potential predictive biomarkers of trabectedin sensitivity (PARP3 and CCNH) or resistance (DNAJB11 and PARP1). Our study identified a new gene signature that significantly predicts patients with higher probability to respond to treatment with trabectedin. Targeting some genes of this signature emerges as a potential strategy to enhance trabectedin efficacy.

VL - 15 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33983674?dopt=Abstract ER - TY - JOUR T1 - Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data JF - Computational and Structural Biotechnology Journal Y1 - 2021 A1 - Rian, Kinza A1 - Hidalgo, Marta R. A1 - Cubuk, Cankut A1 - Falco, Matias M. A1 - Loucera, Carlos A1 - Esteban-Medina, Marina A1 - Alamo-Alvarez, Inmaculada A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin VL - 19 UR - https://linkinghub.elsevier.com/retrieve/pii/S2001037021002038 JO - Computational and Structural Biotechnology Journal ER - TY - JOUR T1 - Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system developmentAbstractBackgroundResultsConclusionsGraphic abstract JF - Clinical Epigenetics Y1 - 2021 A1 - Villalba-Benito, Leticia A1 - López-López, Daniel A1 - Torroglosa, Ana A1 - Casimiro-Soriguer, Carlos S. A1 - Luzón-Toro, Berta A1 - Fernández, Raquel María A1 - Moya-Jiménez, María José A1 - Antiňolo, Guillermo A1 - Dopazo, Joaquin A1 - Borrego, Salud VL - 13 UR - http://link.springer.com/article/10.1186/s13148-021-01040-6/fulltext.html IS - 1 JO - Clin Epigenet ER - TY - JOUR T1 - Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences. JF - Gigascience Y1 - 2021 A1 - Ortuno, Francisco M A1 - Loucera, Carlos A1 - Casimiro-Soriguer, Carlos S A1 - Lepe, Jose A A1 - Camacho Martinez, Pedro A1 - Merino Diaz, Laura A1 - de Salazar, Adolfo A1 - Chueca, Natalia A1 - García, Federico A1 - Perez-Florido, Javier A1 - Dopazo, Joaquin KW - Genome, Viral KW - Phylogeny KW - SARS-CoV-2 KW - Whole Genome Sequencing AB -

BACKGROUND: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.

RESULTS: We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (<20%).

CONCLUSIONS: Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.

VL - 10 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34865008?dopt=Abstract ER - TY - JOUR T1 - Immunotherapy in nonsmall-cell lung cancer: current status and future prospects for liquid biopsy. JF - Cancer Immunol Immunother Y1 - 2021 A1 - Brozos-Vázquez, Elena María A1 - Díaz-Peña, Roberto A1 - García-González, Jorge A1 - León-Mateos, Luis A1 - Mondelo-Macía, Patricia A1 - Peña-Chilet, Maria A1 - López-López, Rafael KW - Animals KW - Biomarkers, Tumor KW - Carcinoma, Non-Small-Cell Lung KW - Cell-Free Nucleic Acids KW - Exosomes KW - Humans KW - Immunotherapy KW - Liquid Biopsy KW - Lung Neoplasms AB -

Immunotherapy has been one of the great advances in the recent years for the treatment of advanced tumors, with nonsmall-cell lung cancer (NSCLC) being one of the cancers that has benefited most from this approach. Currently, the only validated companion diagnostic test for first-line immunotherapy in metastatic NSCLC patients is testing for programmed death ligand 1 (PD-L1) expression in tumor tissues. However, not all patients experience an effective response with the established selection criteria and immune checkpoint inhibitors (ICIs). Liquid biopsy offers a noninvasive opportunity to monitor disease in patients with cancer and identify those who would benefit the most from immunotherapy. This review focuses on the use of liquid biopsy in immunotherapy treatment of NSCLC patients. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and exosomes are promising tools for developing new biomarkers. We discuss the current application and future implementation of these parameters to improve therapeutic decision-making and identify the patients who will benefit most from immunotherapy.

VL - 70 IS - 5 ER - TY - JOUR T1 - Implementing Personalized Medicine in COVID-19 in Andalusia: An Opportunity to Transform the Healthcare System. JF - J Pers Med Y1 - 2021 A1 - Dopazo, Joaquin A1 - Maya-Miles, Douglas A1 - García, Federico A1 - Lorusso, Nicola A1 - Calleja, Miguel Ángel A1 - Pareja, María Jesús A1 - López-Miranda, José A1 - Rodríguez-Baño, Jesús A1 - Padillo, Javier A1 - Túnez, Isaac A1 - Romero-Gómez, Manuel AB -

The COVID-19 pandemic represents an unprecedented opportunity to exploit the advantages of personalized medicine for the prevention, diagnosis, treatment, surveillance and management of a new challenge in public health. COVID-19 infection is highly variable, ranging from asymptomatic infections to severe, life-threatening manifestations. Personalized medicine can play a key role in elucidating individual susceptibility to the infection as well as inter-individual variability in clinical course, prognosis and response to treatment. Integrating personalized medicine into clinical practice can also transform health care by enabling the design of preventive and therapeutic strategies tailored to individual profiles, improving the detection of outbreaks or defining transmission patterns at an increasingly local level. SARS-CoV2 genome sequencing, together with the assessment of specific patient genetic variants, will support clinical decision-makers and ultimately better ways to fight this disease. Additionally, it would facilitate a better stratification and selection of patients for clinical trials, thus increasing the likelihood of obtaining positive results. Lastly, defining a national strategy to implement in clinical practice all available tools of personalized medicine in COVID-19 could be challenging but linked to a positive transformation of the health care system. In this review, we provide an update of the achievements, promises, and challenges of personalized medicine in the fight against COVID-19 from susceptibility to natural history and response to therapy, as well as from surveillance to control measures and vaccination. We also discuss strategies to facilitate the adoption of this new paradigm for medical and public health measures during and after the pandemic in health care systems.

VL - 11 IS - 6 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34073493?dopt=Abstract ER - TY - JOUR T1 - Mechanistic modeling of the SARS-CoV-2 disease map. JF - BioData Min Y1 - 2021 A1 - Rian, Kinza A1 - Esteban-Medina, Marina A1 - Hidalgo, Marta R A1 - Cubuk, Cankut A1 - Falco, Matias M A1 - Loucera, Carlos A1 - Gunyel, Devrim A1 - Ostaszewski, Marek A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin AB -

Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral infection, covering from the entry and replication mechanisms to the downstream consequences as inflammation and antigenic response, can be inferred from gene expression experiments. Moreover, the effect of potential interventions, such as knock-downs, or drug effects (currently the system models the effect of more than 8000 DrugBank drugs) can be studied. This freely available tool not only provides an unprecedentedly detailed view of the mechanisms of viral invasion and the consequences in the cell but has also the potential of becoming an invaluable asset in the search for efficient antiviral treatments.

VL - 14 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33478554?dopt=Abstract ER - TY - JOUR T1 - Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development. JF - Cancers (Basel) Y1 - 2021 A1 - Millán-Esteban, David A1 - Peña-Chilet, Maria A1 - García-Casado, Zaida A1 - Manrique-Silva, Esperanza A1 - Requena, Celia A1 - Bañuls, José A1 - Lopez-Guerrero, Jose Antonio A1 - Rodríguez-Hernández, Aranzazu A1 - Traves, Víctor A1 - Dopazo, Joaquin A1 - Virós, Amaya A1 - Kumar, Rajiv A1 - Nagore, Eduardo AB -

According to the divergent pathway model, cutaneous melanoma comprises a nevogenic group with a propensity to melanocyte proliferation and another one associated with cumulative solar damage (CSD). While characterized clinically and epidemiologically, the differences in the molecular profiles between the groups have remained primarily uninvestigated. This study has used a custom gene panel and bioinformatics tools to investigate the potential molecular differences in a thoroughly characterized cohort of 119 melanoma patients belonging to nevogenic and CSD groups. We found that the nevogenic melanomas had a restricted set of mutations, with the prominently mutated gene being . The CSD melanomas, in contrast, showed mutations in a diverse group of genes that included , , , and . We thus provide evidence that nevogenic and CSD melanomas constitute different biological entities and highlight the need to explore new targeted therapies.

VL - 13 IS - 20 ER - TY - JOUR T1 - The NCI Genomic Data Commons JF - Nature Genetics Y1 - 2021 A1 - Heath, Allison P. A1 - Ferretti, Vincent A1 - Agrawal, Stuti A1 - An, Maksim A1 - Angelakos, James C. A1 - Arya, Renuka A1 - Bajari, Rosita A1 - Baqar, Bilal A1 - Barnowski, Justin H. B. A1 - Burt, Jeffrey A1 - Catton, Ann A1 - Chan, Brandon F. A1 - Chu, Fay A1 - Cullion, Kim A1 - Davidsen, Tanja A1 - Do, Phuong-My A1 - Dompierre, Christian A1 - Ferguson, Martin L. A1 - Fitzsimons, Michael S. A1 - Ford, Michael A1 - Fukuma, Miyuki A1 - Gaheen, Sharon A1 - Ganji, Gajanan L. A1 - Garcia, Tzintzuni I. A1 - George, Sameera S. A1 - Gerhard, Daniela S. A1 - Gerthoffert, Francois A1 - Gomez, Fauzi A1 - Han, Kang A1 - Hernandez, Kyle M. A1 - Issac, Biju A1 - Jackson, Richard A1 - Jensen, Mark A. A1 - Joshi, Sid A1 - Kadam, Ajinkya A1 - Khurana, Aishmit A1 - Kim, Kyle M. J. A1 - Kraft, Victoria E. A1 - Li, Shenglai A1 - Lichtenberg, Tara M. A1 - Lodato, Janice A1 - Lolla, Laxmi A1 - Martinov, Plamen A1 - Mazzone, Jeffrey A. A1 - Miller, Daniel P. A1 - Miller, Ian A1 - Miller, Joshua S. A1 - Miyauchi, Koji A1 - Murphy, Mark W. A1 - Nullet, Thomas A1 - Ogwara, Rowland O. A1 - Ortuño, Francisco M. A1 - Pedrosa, Jesús A1 - Pham, Phuong L. A1 - Popov, Maxim Y. A1 - Porter, James J. A1 - Powell, Raymond A1 - Rademacher, Karl A1 - Reid, Colin P. A1 - Rich, Samantha A1 - Rogel, Bessie A1 - Sahni, Himanso A1 - Savage, Jeremiah H. A1 - Schmitt, Kyle A. A1 - Simmons, Trevar J. A1 - Sislow, Joseph A1 - Spring, Jonathan A1 - Stein, Lincoln A1 - Sullivan, Sean A1 - Tang, Yajing A1 - Thiagarajan, Mathangi A1 - Troyer, Heather D. A1 - Wang, Chang A1 - Wang, Zhining A1 - West, Bedford L. A1 - Wilmer, Alex A1 - Wilson, Shane A1 - Wu, Kaman A1 - Wysocki, William P. A1 - Xiang, Linda A1 - Yamada, Joseph T. A1 - Yang, Liming A1 - Yu, Christine A1 - Yung, Christina K. A1 - Zenklusen, Jean Claude A1 - Zhang, Junjun A1 - Zhang, Zhenyu A1 - Zhao, Yuanheng A1 - Zubair, Ariz A1 - Staudt, Louis M. A1 - Grossman, Robert L. UR - http://www.nature.com/articles/s41588-021-00791-5 JO - Nat Genet ER - TY - JOUR T1 - Orchestrating and sharing large multimodal data for transparent and reproducible research. JF - Nat Commun Y1 - 2021 A1 - Mammoliti, Anthony A1 - Smirnov, Petr A1 - Nakano, Minoru A1 - Safikhani, Zhaleh A1 - Eeles, Christopher A1 - Seo, Heewon A1 - Nair, Sisira Kadambat A1 - Mer, Arvind S A1 - Smith, Ian A1 - Ho, Chantal A1 - Beri, Gangesh A1 - Kusko, Rebecca A1 - Lin, Eva A1 - Yu, Yihong A1 - Martin, Scott A1 - Hafner, Marc A1 - Haibe-Kains, Benjamin AB -

Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon. However, the intrinsic complexity and continuous growth of biomedical data makes it increasingly difficult to process, analyze, and share with the community in a FAIR (findable, accessible, interoperable, and reusable) manner. To overcome these issues, we created a cloud-based platform called ORCESTRA ( orcestra.ca ), which provides a flexible framework for the reproducible processing of multimodal biomedical data. It enables processing of clinical, genomic and perturbation profiles of cancer samples through automated processing pipelines that are user-customizable. ORCESTRA creates integrated and fully documented data objects with persistent identifiers (DOI) and manages multiple dataset versions, which can be shared for future studies.

VL - 12 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34608132?dopt=Abstract ER - TY - JOUR T1 - Phylogenetic Analysis of the 2020 West Nile Virus (WNV) Outbreak in Andalusia (Spain) JF - Viruses Y1 - 2021 A1 - Casimiro-Soriguer, Carlos S. A1 - Perez-Florido, Javier A1 - Fernandez-Rueda, Jose L. A1 - Pedrosa-Corral, Irene A1 - Guillot-Sulay, Vicente A1 - Lorusso, Nicola A1 - Martinez-Gonzalez, Luis Javier A1 - Navarro-Marí, Jose M. A1 - Dopazo, Joaquin A1 - Sanbonmatsu-Gámez, Sara VL - 13 UR - https://www.mdpi.com/1999-4915/13/5/836 IS - 5 JO - Viruses ER - TY - JOUR T1 - Real world evidence of calcifediol or vitamin D prescription and mortality rate of COVID-19 in a retrospective cohort of hospitalized Andalusian patients. JF - Sci Rep Y1 - 2021 A1 - Loucera, Carlos A1 - Peña-Chilet, Maria A1 - Esteban-Medina, Marina A1 - Muñoyerro-Muñiz, Dolores A1 - Villegas, Román A1 - López-Miranda, José A1 - Rodríguez-Baño, Jesús A1 - Túnez, Isaac A1 - Bouillon, Roger A1 - Dopazo, Joaquin A1 - Quesada Gomez, Jose Manuel KW - Calcifediol KW - COVID-19 KW - Female KW - Humans KW - Kaplan-Meier Estimate KW - Male KW - Retrospective Studies KW - Spain KW - Survival Analysis KW - Vitamin D AB -

COVID-19 is a major worldwide health problem because of acute respiratory distress syndrome, and mortality. Several lines of evidence have suggested a relationship between the vitamin D endocrine system and severity of COVID-19. We present a survival study on a retrospective cohort of 15,968 patients, comprising all COVID-19 patients hospitalized in Andalusia between January and November 2020. Based on a central registry of electronic health records (the Andalusian Population Health Database, BPS), prescription of vitamin D or its metabolites within 15-30 days before hospitalization were recorded. The effect of prescription of vitamin D (metabolites) for other indication previous to the hospitalization was studied with respect to patient survival. Kaplan-Meier survival curves and hazard ratios support an association between prescription of these metabolites and patient survival. Such association was stronger for calcifediol (Hazard Ratio, HR = 0.67, with 95% confidence interval, CI, of [0.50-0.91]) than for cholecalciferol (HR = 0.75, with 95% CI of [0.61-0.91]), when prescribed 15 days prior hospitalization. Although the relation is maintained, there is a general decrease of this effect when a longer period of 30 days prior hospitalization is considered (calcifediol HR = 0.73, with 95% CI [0.57-0.95] and cholecalciferol HR = 0.88, with 95% CI [0.75, 1.03]), suggesting that association was stronger when the prescription was closer to the hospitalization.

VL - 11 IS - 1 ER - TY - JOUR T1 - Reporting guidelines for human microbiome research: the STORMS checklist. JF - Nat Med Y1 - 2021 A1 - Mirzayi, Chloe A1 - Renson, Audrey A1 - Zohra, Fatima A1 - Elsafoury, Shaimaa A1 - Geistlinger, Ludwig A1 - Kasselman, Lora J A1 - Eckenrode, Kelly A1 - van de Wijgert, Janneke A1 - Loughman, Amy A1 - Marques, Francine Z A1 - MacIntyre, David A A1 - Arumugam, Manimozhiyan A1 - Azhar, Rimsha A1 - Beghini, Francesco A1 - Bergstrom, Kirk A1 - Bhatt, Ami A1 - Bisanz, Jordan E A1 - Braun, Jonathan A1 - Bravo, Hector Corrada A1 - Buck, Gregory A A1 - Bushman, Frederic A1 - Casero, David A1 - Clarke, Gerard A1 - Collado, Maria Carmen A1 - Cotter, Paul D A1 - Cryan, John F A1 - Demmer, Ryan T A1 - Devkota, Suzanne A1 - Elinav, Eran A1 - Escobar, Juan S A1 - Fettweis, Jennifer A1 - Finn, Robert D A1 - Fodor, Anthony A A1 - Forslund, Sofia A1 - Franke, Andre A1 - Furlanello, Cesare A1 - Gilbert, Jack A1 - Grice, Elizabeth A1 - Haibe-Kains, Benjamin A1 - Handley, Scott A1 - Herd, Pamela A1 - Holmes, Susan A1 - Jacobs, Jonathan P A1 - Karstens, Lisa A1 - Knight, Rob A1 - Knights, Dan A1 - Koren, Omry A1 - Kwon, Douglas S A1 - Langille, Morgan A1 - Lindsay, Brianna A1 - McGovern, Dermot A1 - McHardy, Alice C A1 - McWeeney, Shannon A1 - Mueller, Noel T A1 - Nezi, Luigi A1 - Olm, Matthew A1 - Palm, Noah A1 - Pasolli, Edoardo A1 - Raes, Jeroen A1 - Redinbo, Matthew R A1 - Rühlemann, Malte A1 - Balfour Sartor, R A1 - Schloss, Patrick D A1 - Schriml, Lynn A1 - Segal, Eran A1 - Shardell, Michelle A1 - Sharpton, Thomas A1 - Smirnova, Ekaterina A1 - Sokol, Harry A1 - Sonnenburg, Justin L A1 - Srinivasan, Sujatha A1 - Thingholm, Louise B A1 - Turnbaugh, Peter J A1 - Upadhyay, Vaibhav A1 - Walls, Ramona L A1 - Wilmes, Paul A1 - Yamada, Takuji A1 - Zeller, Georg A1 - Zhang, Mingyu A1 - Zhao, Ni A1 - Zhao, Liping A1 - Bao, Wenjun A1 - Culhane, Aedin A1 - Devanarayan, Viswanath A1 - Dopazo, Joaquin A1 - Fan, Xiaohui A1 - Fischer, Matthias A1 - Jones, Wendell A1 - Kusko, Rebecca A1 - Mason, Christopher E A1 - Mercer, Tim R A1 - Sansone, Susanna-Assunta A1 - Scherer, Andreas A1 - Shi, Leming A1 - Thakkar, Shraddha A1 - Tong, Weida A1 - Wolfinger, Russ A1 - Hunter, Christopher A1 - Segata, Nicola A1 - Huttenhower, Curtis A1 - Dowd, Jennifer B A1 - Jones, Heidi E A1 - Waldron, Levi KW - Computational Biology KW - Dysbiosis KW - Humans KW - Microbiota KW - Observational Studies as Topic KW - Research Design KW - Translational Science, Biomedical AB -

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

VL - 27 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34789871?dopt=Abstract ER - TY - JOUR T1 - Schuurs–Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review JF - Genes Y1 - 2021 A1 - Tenorio-Castaño, Jair A1 - Morte, Beatriz A1 - Nevado, Julián A1 - Martínez-Glez, Víctor A1 - Santos-Simarro, Fernando A1 - García-Miñaur, Sixto A1 - Palomares-Bralo, María A1 - Pacio-Míguez, Marta A1 - Gómez, Beatriz A1 - Arias, Pedro A1 - Alcochea, Alba A1 - Carrión, Juan A1 - Arias, Patricia A1 - Almoguera, Berta A1 - López-Grondona, Fermina A1 - Lorda-Sanchez, Isabel A1 - Galán-Gómez, Enrique A1 - Valenzuela, Irene A1 - Méndez Perez, María A1 - Cuscó, Ivón A1 - Barros, Francisco A1 - Pié, Juan A1 - Ramos, Sergio A1 - Ramos, Feliciano A1 - Kuechler, Alma A1 - Tizzano, Eduardo A1 - Ayuso, Carmen A1 - Kaiser, Frank A1 - Pérez-Jurado, Luis A1 - Carracedo, Ángel A1 - Lapunzina, Pablo VL - 12 UR - https://www.mdpi.com/2073-4425/12/5/738https://www.mdpi.com/2073-4425/12/5/738/pdf IS - 5 JO - Genes ER - TY - JOUR T1 - Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism. JF - Mol Med Y1 - 2021 A1 - Méndez-Salazar, Eder Orlando A1 - Vázquez-Mellado, Janitzia A1 - Casimiro-Soriguer, Carlos S A1 - Dopazo, Joaquin A1 - Cubuk, Cankut A1 - Zamudio-Cuevas, Yessica A1 - Francisco-Balderas, Adriana A1 - Martínez-Flores, Karina A1 - Fernández-Torres, Javier A1 - Lozada-Pérez, Carlos A1 - Pineda, Carlos A1 - Sánchez-González, Austreberto A1 - Silveira, Luis H A1 - Burguete-García, Ana I A1 - Orbe-Orihuela, Citlalli A1 - Lagunas-Martínez, Alfredo A1 - Vazquez-Gomez, Alonso A1 - López-Reyes, Alberto A1 - Palacios-González, Berenice A1 - Martínez-Nava, Gabriela Angélica KW - Biodiversity KW - Computational Biology KW - Dysbiosis KW - Gastrointestinal Microbiome KW - Gout KW - Humans KW - Metagenome KW - metagenomics KW - Protein Interaction Mapping KW - Protein Interaction Maps KW - Uric Acid AB -

OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.

METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.

RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.

CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.

VL - 27 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34030623?dopt=Abstract ER - TY - JOUR T1 - Uniform genomic data analysis in the NCI Genomic Data CommonsAbstract JF - Nature Communications Y1 - 2021 A1 - Zhang, Zhenyu A1 - Hernandez, Kyle A1 - Savage, Jeremiah A1 - Li, Shenglai A1 - Miller, Dan A1 - Agrawal, Stuti A1 - Ortuno, Francisco A1 - Staudt, Louis M. A1 - Heath, Allison A1 - Grossman, Robert L. VL - 12 UR - http://www.nature.com/articles/s41467-021-21254-9 IS - 1 JO - Nat Commun ER - TY - JOUR T1 - A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. JF - PLoS Comput Biol Y1 - 2021 A1 - Garrido-Rodriguez, Martín A1 - López-López, Daniel A1 - Ortuno, Francisco M A1 - Peña-Chilet, Maria A1 - Muñoz, Eduardo A1 - Calzado, Marco A A1 - Dopazo, Joaquin KW - Algorithms KW - Cell Line, Tumor KW - Computational Biology KW - Databases, Factual KW - Gene Expression Profiling KW - Genomics KW - High-Throughput Nucleotide Sequencing KW - Humans KW - Models, Theoretical KW - mutation KW - RNA-seq KW - Signal Transduction KW - Software KW - Transcriptome KW - whole exome sequencing KW - Workflow AB -

MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available.

VL - 17 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33571195?dopt=Abstract ER - TY - JOUR T1 - Association of a single nucleotide polymorphism in the ubxn6 gene with long-term non-progression phenotype in HIV-positive individuals. JF - Clin Microbiol Infect Y1 - 2020 A1 - Díez-Fuertes, F A1 - De La Torre-Tarazona, H E A1 - Calonge, E A1 - Pernas, M A1 - Bermejo, M A1 - García-Pérez, J A1 - Álvarez, A A1 - Capa, L A1 - García-García, F A1 - Saumoy, M A1 - Riera, M A1 - Boland-Auge, A A1 - López-Galíndez, C A1 - Lathrop, M A1 - Dopazo, J A1 - Sakuntabhai, A A1 - Alcamí, J KW - Adaptor Proteins, Vesicular Transport KW - Autophagy-Related Proteins KW - Caveolin 1 KW - Cohort Studies KW - Dendritic Cells KW - Disease Progression KW - Gene Frequency KW - Gene Knockdown Techniques KW - Genetic Association Studies KW - HeLa Cells KW - HIV Infections KW - HIV Long-Term Survivors KW - HIV-1 KW - Humans KW - Macrophages KW - Oligonucleotide Array Sequence Analysis KW - Phenotype KW - Polymorphism, Single Nucleotide KW - whole exome sequencing AB -

OBJECTIVES: The long-term non-progressors (LTNPs) are a heterogeneous group of HIV-positive individuals characterized by their ability to maintain high CD4 T-cell counts and partially control viral replication for years in the absence of antiretroviral therapy. The present study aims to identify host single nucleotide polymorphisms (SNPs) associated with non-progression in a cohort of 352 individuals.

METHODS: DNA microarrays and exome sequencing were used for genotyping about 240 000 functional polymorphisms throughout more than 20 000 human genes. The allele frequencies of 85 LTNPs were compared with a control population. SNPs associated with LTNPs were confirmed in a population of typical progressors. Functional analyses in the affected gene were carried out through knockdown experiments in HeLa-P4, macrophages and dendritic cells.

RESULTS: Several SNPs located within the major histocompatibility complex region previously related to LTNPs were confirmed in this new cohort. The SNP rs1127888 (UBXN6) surpassed the statistical significance of these markers after Bonferroni correction (q = 2.11 × 10). An uncommon allelic frequency of rs1127888 among LTNPs was confirmed by comparison with typical progressors and other publicly available populations. UBXN6 knockdown experiments caused an increase in CAV1 expression and its accumulation in the plasma membrane. In vitro infection of different cell types with HIV-1 replication-competent recombinant viruses caused a reduction of the viral replication capacity compared with their corresponding wild-type cells expressing UBXN6.

CONCLUSIONS: A higher prevalence of Ala31Thr in UBXN6 was found among LTNPs within its N-terminal region, which is crucial for UBXN6/VCP protein complex formation. UBXN6 knockdown affected CAV1 turnover and HIV-1 replication capacity.

VL - 26 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/31158522?dopt=Abstract ER - TY - JOUR T1 - Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. JF - Cell Syst Y1 - 2020 A1 - Yang, Mi A1 - Petralia, Francesca A1 - Li, Zhi A1 - Li, Hongyang A1 - Ma, Weiping A1 - Song, Xiaoyu A1 - Kim, Sunkyu A1 - Lee, Heewon A1 - Yu, Han A1 - Lee, Bora A1 - Bae, Seohui A1 - Heo, Eunji A1 - Kaczmarczyk, Jan A1 - Stępniak, Piotr A1 - Warchoł, Michał A1 - Yu, Thomas A1 - Calinawan, Anna P A1 - Boutros, Paul C A1 - Payne, Samuel H A1 - Reva, Boris A1 - Boja, Emily A1 - Rodriguez, Henry A1 - Stolovitzky, Gustavo A1 - Guan, Yuanfang A1 - Kang, Jaewoo A1 - Wang, Pei A1 - Fenyö, David A1 - Saez-Rodriguez, Julio KW - Crowdsourcing KW - Female KW - Genomics KW - Humans KW - Machine Learning KW - Male KW - Neoplasms KW - Phosphoproteins KW - Proteins KW - Proteomics KW - Transcriptome AB -

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information.

VL - 11 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32710834?dopt=Abstract ER - TY - JOUR T1 - Drug repurposing for COVID-19 using machine learning and mechanistic models of signal transduction circuits related to SARS-CoV-2 infection. JF - Signal Transduct Target Ther Y1 - 2020 A1 - Loucera, Carlos A1 - Esteban-Medina, Marina A1 - Rian, Kinza A1 - Falco, Matias M A1 - Dopazo, Joaquin A1 - Peña-Chilet, Maria KW - Computational Chemistry KW - COVID-19 KW - drug repositioning KW - Humans KW - Machine Learning KW - Molecular Docking Simulation KW - Molecular Targeted Therapy KW - Proteins KW - SARS-CoV-2 KW - Signal Transduction VL - 5 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33311438?dopt=Abstract ER - TY - JOUR T1 - The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. JF - F1000Res Y1 - 2020 A1 - Salgado, David A1 - Armean, Irina M A1 - Baudis, Michael A1 - Beltran, Sergi A1 - Capella-Gutíerrez, Salvador A1 - Carvalho-Silva, Denise A1 - Dominguez Del Angel, Victoria A1 - Dopazo, Joaquin A1 - Furlong, Laura I A1 - Gao, Bo A1 - Garcia, Leyla A1 - Gerloff, Dietlind A1 - Gut, Ivo A1 - Gyenesei, Attila A1 - Habermann, Nina A1 - Hancock, John M A1 - Hanauer, Marc A1 - Hovig, Eivind A1 - Johansson, Lennart F A1 - Keane, Thomas A1 - Korbel, Jan A1 - Lauer, Katharina B A1 - Laurie, Steve A1 - Leskošek, Brane A1 - Lloyd, David A1 - Marqués-Bonet, Tomás A1 - Mei, Hailiang A1 - Monostory, Katalin A1 - Piñero, Janet A1 - Poterlowicz, Krzysztof A1 - Rath, Ana A1 - Samarakoon, Pubudu A1 - Sanz, Ferran A1 - Saunders, Gary A1 - Sie, Daoud A1 - Swertz, Morris A A1 - Tsukanov, Kirill A1 - Valencia, Alfonso A1 - Vidak, Marko A1 - Yenyxe González, Cristina A1 - Ylstra, Bauke A1 - Béroud, Christophe KW - Computational Biology KW - DNA Copy Number Variations KW - High-Throughput Nucleotide Sequencing KW - Humans AB -

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While "High-Throughput" sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR's recently established with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

VL - 9 U1 - https://www.ncbi.nlm.nih.gov/pubmed/34367618?dopt=Abstract ER - TY - JOUR T1 - Immune Cell Associations with Cancer Risk. JF - iScience Y1 - 2020 A1 - Palomero, Luis A1 - Galván-Femenía, Ivan A1 - de Cid, Rafael A1 - Espín, Roderic A1 - Barnes, Daniel R A1 - Blommaert, Eline A1 - Gil-Gil, Miguel A1 - Falo, Catalina A1 - Stradella, Agostina A1 - Ouchi, Dan A1 - Roso-Llorach, Albert A1 - Violan, Concepció A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin A1 - Extremera, Ana Isabel A1 - García-Valero, Mar A1 - Herranz, Carmen A1 - Mateo, Francesca A1 - Mereu, Elisabetta A1 - Beesley, Jonathan A1 - Chenevix-Trench, Georgia A1 - Roux, Cecilia A1 - Mak, Tak A1 - Brunet, Joan A1 - Hakem, Razq A1 - Gorrini, Chiara A1 - Antoniou, Antonis C A1 - Lázaro, Conxi A1 - Pujana, Miquel Angel AB -

Proper immune system function hinders cancer development, but little is known about whether genetic variants linked to cancer risk alter immune cells. Here, we report 57 cancer risk loci associated with differences in immune and/or stromal cell contents in the corresponding tissue. Predicted target genes show expression and regulatory associations with immune features. Polygenic risk scores also reveal associations with immune and/or stromal cell contents, and breast cancer scores show consistent results in normal and tumor tissue. SH2B3 links peripheral alterations of several immune cell types to the risk of this malignancy. Pleiotropic SH2B3 variants are associated with breast cancer risk in BRCA1/2 mutation carriers. A retrospective case-cohort study indicates a positive association between blood counts of basophils, leukocytes, and monocytes and age at breast cancer diagnosis. These findings broaden our knowledge of the role of the immune system in cancer and highlight promising prevention strategies for individuals at high risk.

VL - 23 IS - 7 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32622267?dopt=Abstract ER - TY - JOUR T1 - Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscapeAbstract JF - NAR Cancer Y1 - 2020 A1 - Falco, Matias M A1 - Peña-Chilet, Maria A1 - Loucera, Carlos A1 - Hidalgo, Marta R A1 - Dopazo, Joaquin VL - 2 UR - https://academic.oup.com/narcancer/article/doi/10.1093/narcan/zcaa011/5862620http://academic.oup.com/narcancer/article-pdf/2/2/zcaa011/33428092/zcaa011.pdfhttp://academic.oup.com/narcancer/article-pdf/2/2/zcaa011/33428092/zcaa011.pdf IS - 2 ER - TY - JOUR T1 - Nivolumab and sunitinib combination in advanced soft tissue sarcomas: a multicenter, single-arm, phase Ib/II trial. JF - J Immunother Cancer Y1 - 2020 A1 - Martin-Broto, Javier A1 - Hindi, Nadia A1 - Grignani, Giovanni A1 - Martinez-Trufero, Javier A1 - Redondo, Andres A1 - Valverde, Claudia A1 - Stacchiotti, Silvia A1 - Lopez-Pousa, Antonio A1 - D'Ambrosio, Lorenzo A1 - Gutierrez, Antonio A1 - Perez-Vega, Herminia A1 - Encinas-Tobajas, Victor A1 - de Alava, Enrique A1 - Collini, Paola A1 - Peña-Chilet, Maria A1 - Dopazo, Joaquin A1 - Carrasco-Garcia, Irene A1 - Lopez-Alvarez, Maria A1 - Moura, David S A1 - Lopez-Martin, Jose A KW - Adult KW - Aged KW - Antineoplastic Agents, Immunological KW - Female KW - Humans KW - Male KW - Middle Aged KW - Nivolumab KW - Sarcoma KW - Sunitinib KW - Young Adult AB -

BACKGROUND: Sarcomas exhibit low expression of factors related to immune response, which could explain the modest activity of PD-1 inhibitors. A potential strategy to convert a cold into an inflamed microenvironment lies on a combination therapy. As tumor angiogenesis promotes immunosuppression, we designed a phase Ib/II trial to test the double inhibition of angiogenesis (sunitinib) and PD-1/PD-L1 axis (nivolumab).

METHODS: This single-arm, phase Ib/II trial enrolled adult patients with selected subtypes of sarcoma. Phase Ib established two dose levels: level 0 with sunitinib 37.5 mg daily from day 1, plus nivolumab 3 mg/kg intravenously on day 15, and then every 2 weeks; and level -1 with sunitinib 37.5 mg on the first 14 days (induction) and then 25 mg per day plus nivolumab on the same schedule. The primary endpoint was to determine the recommended dose for phase II (phase I) and the 6-month progression-free survival rate, according to Response Evaluation Criteria in Solid Tumors 1.1 (phase II).

RESULTS: From May 2017 to April 2019, 68 patients were enrolled: 16 in phase Ib and 52 in phase II. The recommended dose of sunitinib for phase II was 37.5 mg as induction and then 25 mg in combination with nivolumab. After a median follow-up of 17 months (4-26), the 6-month progression-free survival rate was 48% (95% CI 41% to 55%). The most common grade 3-4 adverse events included transaminitis (17.3%) and neutropenia (11.5%).

CONCLUSIONS: Sunitinib plus nivolumab is an active scheme with manageable toxicity in the treatment of selected patients with advanced soft tissue sarcoma, with almost half of patients free of progression at 6 months. NCT03277924.

VL - 8 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33203665?dopt=Abstract ER - TY - JOUR T1 - Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. JF - J Med Genet Y1 - 2020 A1 - Bogliolo, Massimo A1 - Pujol, Roser A1 - Aza-Carmona, Miriam A1 - Muñoz-Subirana, Núria A1 - Rodriguez-Santiago, Benjamin A1 - Casado, José Antonio A1 - Rio, Paula A1 - Bauser, Christopher A1 - Reina-Castillón, Judith A1 - Lopez-Sanchez, Marcos A1 - Gonzalez-Quereda, Lidia A1 - Gallano, Pia A1 - Catalá, Albert A1 - Ruiz-Llobet, Ana A1 - Badell, Isabel A1 - Diaz-Heredia, Cristina A1 - Hladun, Raquel A1 - Senent, Leonort A1 - Argiles, Bienvenida A1 - Bergua Burgues, Juan Miguel A1 - Bañez, Fatima A1 - Arrizabalaga, Beatriz A1 - López Almaraz, Ricardo A1 - Lopez, Monica A1 - Figuera, Ángela A1 - Molinés, Antonio A1 - Pérez de Soto, Inmaculada A1 - Hernando, Inés A1 - Muñoz, Juan Antonio A1 - Del Rosario Marin, Maria A1 - Balmaña, Judith A1 - Stjepanovic, Neda A1 - Carrasco, Estela A1 - Cuesta, Isabel A1 - Cosuelo, José Miguel A1 - Regueiro, Alexandra A1 - Moraleda Jimenez, José A1 - Galera-Miñarro, Ana Maria A1 - Rosiñol, Laura A1 - Carrió, Anna A1 - Beléndez-Bieler, Cristina A1 - Escudero Soto, Antonio A1 - Cela, Elena A1 - de la Mata, Gregorio A1 - Fernández-Delgado, Rafael A1 - Garcia-Pardos, Maria Carmen A1 - Sáez-Villaverde, Raquel A1 - Barragaño, Marta A1 - Portugal, Raquel A1 - Lendinez, Francisco A1 - Hernadez, Ines A1 - Vagace, José Manue A1 - Tapia, Maria A1 - Nieto, José A1 - Garcia, Marta A1 - Gonzalez, Macarena A1 - Vicho, Cristina A1 - Galvez, Eva A1 - Valiente, Alberto A1 - Antelo, Maria Luisa A1 - Ancliff, Phil A1 - García, Francisco A1 - Dopazo, Joaquin A1 - Sevilla, Julian A1 - Paprotka, Tobias A1 - Pérez-Jurado, Luis Alberto A1 - Bueren, Juan A1 - Surralles, Jordi KW - Cell Line KW - DNA Copy Number Variations KW - DNA Repair KW - DNA-Binding Proteins KW - Fanconi Anemia KW - Fanconi Anemia Complementation Group A Protein KW - Female KW - Gene Knockout Techniques KW - Genetic Predisposition to Disease KW - Humans KW - Male KW - Mutation, Missense KW - Polymorphism, Single Nucleotide KW - whole exome sequencing AB -

PURPOSE: Patients with Fanconi anaemia (FA), a rare DNA repair genetic disease, exhibit chromosome fragility, bone marrow failure, malformations and cancer susceptibility. FA molecular diagnosis is challenging since FA is caused by point mutations and large deletions in 22 genes following three heritability patterns. To optimise FA patients' characterisation, we developed a simplified but effective methodology based on whole exome sequencing (WES) and functional studies.

METHODS: 68 patients with FA were analysed by commercial WES services. Copy number variations were evaluated by sequencing data analysis with RStudio. To test missense variants, wt FANCA cDNA was cloned and variants were introduced by site-directed mutagenesis. Vectors were then tested for their ability to complement DNA repair defects of a FANCA-KO human cell line generated by TALEN technologies.

RESULTS: We identified 93.3% of mutated alleles including large deletions. We determined the pathogenicity of three FANCA missense variants and demonstrated that two variants reported in mutations databases as 'affecting functions' are SNPs. Deep analysis of sequencing data revealed patients' true mutations, highlighting the importance of functional analysis. In one patient, no pathogenic variant could be identified in any of the 22 known FA genes, and in seven patients, only one deleterious variant could be identified (three patients each with FANCA and FANCD2 and one patient with FANCE mutations) CONCLUSION: WES and proper bioinformatics analysis are sufficient to effectively characterise patients with FA regardless of the rarity of their complementation group, type of mutations, mosaic condition and DNA source.

VL - 57 IS - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/31586946?dopt=Abstract ER - TY - JOUR T1 - Pazopanib for treatment of typical solitary fibrous tumours: a multicentre, single-arm, phase 2 trial. JF - Lancet Oncol Y1 - 2020 A1 - Martin-Broto, Javier A1 - Cruz, Josefina A1 - Penel, Nicolas A1 - Le Cesne, Axel A1 - Hindi, Nadia A1 - Luna, Pablo A1 - Moura, David S A1 - Bernabeu, Daniel A1 - de Alava, Enrique A1 - Lopez-Guerrero, Jose Antonio A1 - Dopazo, Joaquin A1 - Peña-Chilet, Maria A1 - Gutierrez, Antonio A1 - Collini, Paola A1 - Karanian, Marie A1 - Redondo, Andres A1 - Lopez-Pousa, Antonio A1 - Grignani, Giovanni A1 - Diaz-Martin, Juan A1 - Marcilla, David A1 - Fernandez-Serra, Antonio A1 - Gonzalez-Aguilera, Cristina A1 - Casali, Paolo G A1 - Blay, Jean-Yves A1 - Stacchiotti, Silvia KW - Aged KW - Female KW - Follow-Up Studies KW - Humans KW - Indazoles KW - Male KW - Middle Aged KW - Neoplasm Metastasis KW - Prognosis KW - Prospective Studies KW - Protein Kinase Inhibitors KW - Pyrimidines KW - Response Evaluation Criteria in Solid Tumors KW - Solitary Fibrous Tumors KW - Sulfonamides KW - Survival Rate AB -

BACKGROUND: Solitary fibrous tumour is an ultra-rare sarcoma, which encompasses different clinicopathological subgroups. The dedifferentiated subgroup shows an aggressive course with resistance to pazopanib, whereas in the malignant subgroup, pazopanib shows higher activity than in previous studies with chemotherapy. We designed a trial to test pazopanib activity in two different cohorts of solitary fibrous tumour: the malignant-dedifferentiated cohort, which was previously published, and the typical cohort, which is presented here.

METHODS: In this single-arm, phase 2 trial, adult patients (aged ≥18 years) diagnosed with confirmed metastatic or unresectable typical solitary fibrous tumour of any location, who had progressed in the previous 6 months (by Choi criteria or Response Evaluation Criteria in Solid Tumors [RECIST]) and an Eastern Cooperative Oncology Group (ECOG) performance status of 0-2 were enrolled at 11 tertiary hospitals in Italy, France, and Spain. Patients received pazopanib 800 mg once daily, taken orally, until progression, unacceptable toxicity, withdrawal of consent, non-compliance, or a delay in pazopanib administration of longer than 3 weeks. The primary endpoint was proportion of patients achieving an overall response measured by Choi criteria in patients who received at least 1 month of treatment with at least one radiological assessment. All patients who received at least one dose of the study drug were included in the safety analyses. This study is registered in ClinicalTrials.gov, NCT02066285, and with the European Clinical Trials Database, EudraCT 2013-005456-15.

FINDINGS: From June 26, 2014, to Dec 13, 2018, of 40 patients who were assessed, 34 patients were enrolled and 31 patients were included in the response analysis. Median follow-up was 18 months (IQR 14-34), and 18 (58%) of 31 patients had a partial response, 12 (39%) had stable disease, and one (3%) showed progressive disease according to Choi criteria and central review. The proportion of overall response based on Choi criteria was 58% (95% CI 34-69). There were no deaths caused by toxicity, and the most frequent adverse events were diarrhoea (18 [53%] of 34 patients), fatigue (17 [50%]), and hypertension (17 [50%]).

INTERPRETATION: To our knowledge, this is the first prospective trial of pazopanib for advanced typical solitary fibrous tumour. The manageable toxicity and activity shown by pazopanib in this cohort suggest that this drug could be considered as first-line treatment for advanced typical solitary fibrous tumour.

FUNDING: Spanish Group for Research on Sarcomas (GEIS), Italian Sarcoma Group (ISG), French Sarcoma Group (FSG), GlaxoSmithKline, and Novartis.

VL - 21 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32066540?dopt=Abstract ER - TY - JOUR T1 - Platform to study intracellular polystyrene nanoplastic pollution and clinical outcomes. JF - Stem Cells Y1 - 2020 A1 - Bojic, Sanja A1 - Falco, Matias M A1 - Stojkovic, Petra A1 - Ljujic, Biljana A1 - Gazdic Jankovic, Marina A1 - Armstrong, Lyle A1 - Markovic, Nebojsa A1 - Dopazo, Joaquin A1 - Lako, Majlinda A1 - Bauer, Roman A1 - Stojkovic, Miodrag KW - Environmental Pollution KW - Humans KW - Induced Pluripotent Stem Cells KW - Intracellular Space KW - Nanoparticles KW - Plastics KW - Polystyrenes KW - Transcriptome KW - Treatment Outcome AB -

Increased pollution by plastics has become a serious global environmental problem, but the concerns for human health have been raised after reported presence of microplastics (MPs) and nanoplastics (NPs) in food and beverages. Unfortunately, few studies have investigate the potentially harmful effects of MPs/NPs on early human development and human health. Therefore, we used a new platform to study possible effects of polystyrene NPs (PSNPs) on the transcription profile of preimplantation human embryos and human induced pluripotent stem cells (hiPSCs). Two pluripotency genes, LEFTY1 and LEFTY2, which encode secreted ligands of the transforming growth factor-beta, were downregulated, while CA4 and OCLM, which are related to eye development, were upregulated in both samples. The gene set enrichment analysis showed that the development of atrioventricular heart valves and the dysfunction of cellular components, including extracellular matrix, were significantly affected after exposure of hiPSCs to PSNPs. Finally, using the HiPathia method, which uncovers disease mechanisms and predicts clinical outcomes, we determined the APOC3 circuit, which is responsible for increased risk for ischemic cardiovascular disease. These results clearly demonstrate that better understanding of NPs bioactivities and its implications for human health is of extreme importance. Thus, the presented platform opens further aspects to study interactions between different environmental and intracellular pollutions with the aim to decipher the mechanism and origin of human diseases.

VL - 38 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32614127?dopt=Abstract ER - TY - JOUR T1 - SMN1 copy-number and sequence variant analysis from next-generation sequencing data. JF - Hum Mutat Y1 - 2020 A1 - López-López, Daniel A1 - Loucera, Carlos A1 - Carmona, Rosario A1 - Aquino, Virginia A1 - Salgado, Josefa A1 - Pasalodos, Sara A1 - Miranda, María A1 - Alonso, Ángel A1 - Dopazo, Joaquin KW - Base Sequence KW - DNA Copy Number Variations KW - High-Throughput Nucleotide Sequencing KW - Humans KW - Reproducibility of Results KW - Software KW - Survival of Motor Neuron 1 Protein AB -

Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.

VL - 41 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33058415?dopt=Abstract ER - TY - JOUR T1 - Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. JF - Genes (Basel) Y1 - 2020 A1 - León, Carlos A1 - Garcia-Garcia, Francisco A1 - Llames, Sara A1 - García-Pérez, Eva A1 - Carretero, Marta A1 - Arriba, María Del Carmen A1 - Dopazo, Joaquin A1 - Del Rio, Marcela A1 - Escamez, Maria José A1 - Martínez-Santamaría, Lucía KW - Animals KW - Diabetes Mellitus, Experimental KW - Gene Expression Profiling KW - Gene Expression Regulation KW - Gene ontology KW - Humans KW - Metabolic Networks and Pathways KW - Mice KW - Mice, Nude KW - Microarray Analysis KW - Molecular Sequence Annotation KW - Principal Component Analysis KW - Signal Transduction KW - Skin KW - Skin Transplantation KW - Skin Ulcer KW - Streptozocin KW - Tissue Engineering KW - Transcriptome KW - Transplantation, Heterologous KW - Wound Healing AB -

Defective healing leading to cutaneous ulcer formation is one of the most feared complications of diabetes due to its consequences on patients' quality of life and on the healthcare system. A more in-depth analysis of the underlying molecular pathophysiology is required to develop effective healing-promoting therapies for those patients. Major architectural and functional differences with human epidermis limit extrapolation of results coming from rodents and other small mammal-healing models. Therefore, the search for reliable humanized models has become mandatory. Previously, we developed a diabetes-induced delayed humanized wound healing model that faithfully recapitulated the major histological features of such skin repair-deficient condition. Herein, we present the results of a transcriptomic and functional enrichment analysis followed by a mechanistic analysis performed in such humanized wound healing model. The deregulation of genes implicated in functions such as angiogenesis, apoptosis, and inflammatory signaling processes were evidenced, confirming published data in diabetic patients that in fact might also underlie some of the histological features previously reported in the delayed skin-humanized healing model. Altogether, these molecular findings support the utility of such preclinical model as a valuable tool to gain insight into the molecular basis of the delayed diabetic healing with potential impact in the translational medicine field.

VL - 12 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33396192?dopt=Abstract ER - TY - JOUR T1 - Transparency and reproducibility in artificial intelligence. JF - Nature Y1 - 2020 A1 - Haibe-Kains, Benjamin A1 - Adam, George Alexandru A1 - Hosny, Ahmed A1 - Khodakarami, Farnoosh A1 - Waldron, Levi A1 - Wang, Bo A1 - McIntosh, Chris A1 - Goldenberg, Anna A1 - Kundaje, Anshul A1 - Greene, Casey S A1 - Broderick, Tamara A1 - Hoffman, Michael M A1 - Leek, Jeffrey T A1 - Korthauer, Keegan A1 - Huber, Wolfgang A1 - Brazma, Alvis A1 - Pineau, Joelle A1 - Tibshirani, Robert A1 - Hastie, Trevor A1 - Ioannidis, John P A A1 - Quackenbush, John A1 - Aerts, Hugo J W L KW - Algorithms KW - Artificial Intelligence KW - Reproducibility of Results VL - 586 IS - 7829 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33057217?dopt=Abstract ER - TY - JOUR T1 - Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. JF - Biol Direct Y1 - 2019 A1 - Casimiro-Soriguer, Carlos S A1 - Loucera, Carlos A1 - Perez Florido, Javier A1 - López-López, Daniel A1 - Dopazo, Joaquin KW - biomarkers KW - Cities KW - Drug Resistance, Microbial KW - Machine Learning KW - Metabolome KW - Metagenome KW - metagenomics KW - Microbiota AB -

BACKGROUND: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

RESULTS: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification.

CONCLUSIONS: We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances.

REVIEWERS: Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.

VL - 14 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/31429791?dopt=Abstract ER - TY - JOUR T1 - Exploring the druggable space around the Fanconi anemia pathway using machine learning and mechanistic models. JF - BMC Bioinformatics Y1 - 2019 A1 - Esteban-Medina, Marina A1 - Peña-Chilet, Maria A1 - Loucera, Carlos A1 - Dopazo, Joaquin KW - Databases, Factual KW - Fanconi Anemia KW - Genomics KW - Humans KW - Machine Learning KW - Phenotype KW - Proteins KW - Signal Transduction AB -

BACKGROUND: In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensionality, given the disbalance between samples and candidate genes. And this is especially dramatic in scenarios in which the availability of samples is difficult, such as the case of rare diseases.

RESULTS: The application of multi-output regression machine learning methodologies to predict the potential effect of external proteins over the signaling circuits that trigger Fanconi anemia related cell functionalities, inferred with a mechanistic model, allowed us to detect over 20 potential therapeutic targets.

CONCLUSIONS: The use of artificial intelligence methods for the prediction of potentially causal relationships between proteins of interest and cell activities related with disease-related phenotypes opens promising avenues for the systematic search of new targets in rare diseases.

VL - 20 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/31266445?dopt=Abstract ER - TY - JOUR T1 - Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. JF - Br J Dermatol Y1 - 2019 A1 - Chacón-Solano, E A1 - León, C A1 - Díaz, F A1 - García-García, F A1 - García, M A1 - Escámez, M J A1 - Guerrero-Aspizua, S A1 - Conti, C J A1 - Mencía, Á A1 - Martínez-Santamaría, L A1 - Llames, S A1 - Pévida, M A1 - Carbonell-Caballero, J A1 - Puig-Butillé, J A A1 - Maseda, R A1 - Puig, S A1 - de Lucas, R A1 - Baselga, E A1 - Larcher, F A1 - Dopazo, J A1 - Del Rio, M KW - Adolescent KW - Adult KW - Biopsy KW - Blister KW - Case-Control Studies KW - Cells, Cultured KW - Child KW - Child, Preschool KW - Epidermolysis Bullosa KW - Epidermolysis Bullosa Dystrophica KW - Extracellular Matrix KW - Extracellular Matrix Proteins KW - Female KW - Fibroblasts KW - Fibrosis KW - Gene Expression Regulation KW - Healthy Volunteers KW - Humans KW - Infant KW - Infant, Newborn KW - Male KW - Middle Aged KW - mutation KW - Periodontal Diseases KW - Photosensitivity Disorders KW - Primary Cell Culture KW - RNA-seq KW - Skin KW - Xeroderma Pigmentosum KW - Young Adult AB -

BACKGROUND: Recessive dystrophic epidermolysis bullosa (RDEB), Kindler syndrome (KS) and xeroderma pigmentosum complementation group C (XPC) are three cancer-prone genodermatoses whose causal genetic mutations cannot fully explain, on their own, the array of associated phenotypic manifestations. Recent evidence highlights the role of the stromal microenvironment in the pathology of these disorders.

OBJECTIVES: To investigate, by means of comparative gene expression analysis, the role played by dermal fibroblasts in the pathogenesis of RDEB, KS and XPC.

METHODS: We conducted RNA-Seq analysis, which included a thorough examination of the differentially expressed genes, a functional enrichment analysis and a description of affected signalling circuits. Transcriptomic data were validated at the protein level in cell cultures, serum samples and skin biopsies.

RESULTS: Interdisease comparisons against control fibroblasts revealed a unifying signature of 186 differentially expressed genes and four signalling pathways in the three genodermatoses. Remarkably, some of the uncovered expression changes suggest a synthetic fibroblast phenotype characterized by the aberrant expression of extracellular matrix (ECM) proteins. Western blot and immunofluorescence in situ analyses validated the RNA-Seq data. In addition, enzyme-linked immunosorbent assay revealed increased circulating levels of periostin in patients with RDEB.

CONCLUSIONS: Our results suggest that the different causal genetic defects converge into common changes in gene expression, possibly due to injury-sensitive events. These, in turn, trigger a cascade of reactions involving abnormal ECM deposition and underexpression of antioxidant enzymes. The elucidated expression signature provides new potential biomarkers and common therapeutic targets in RDEB, XPC and KS. What's already known about this topic? Recessive dystrophic epidermolysis bullosa (RDEB), Kindler syndrome (KS) and xeroderma pigmentosum complementation group C (XPC) are three genodermatoses with high predisposition to cancer development. Although their causal genetic mutations mainly affect epithelia, the dermal microenvironment likely contributes to the physiopathology of these disorders. What does this study add? We disclose a large overlapping transcription profile between XPC, KS and RDEB fibroblasts that points towards an activated phenotype with high matrix-synthetic capacity. This common signature seems to be independent of the primary causal deficiency, but reflects an underlying derangement of the extracellular matrix via transforming growth factor-β signalling activation and oxidative state imbalance. What is the translational message? This study broadens the current knowledge about the pathology of these diseases and highlights new targets and biomarkers for effective therapeutic intervention. It is suggested that high levels of circulating periostin could represent a potential biomarker in RDEB.

VL - 181 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/30693469?dopt=Abstract ER - TY - JOUR T1 - Pazopanib for treatment of advanced malignant and dedifferentiated solitary fibrous tumour: a multicentre, single-arm, phase 2 trial. JF - Lancet Oncol Y1 - 2019 A1 - Martin-Broto, Javier A1 - Stacchiotti, Silvia A1 - Lopez-Pousa, Antonio A1 - Redondo, Andres A1 - Bernabeu, Daniel A1 - de Alava, Enrique A1 - Casali, Paolo G A1 - Italiano, Antoine A1 - Gutierrez, Antonio A1 - Moura, David S A1 - Peña-Chilet, Maria A1 - Diaz-Martin, Juan A1 - Biscuola, Michele A1 - Taron, Miguel A1 - Collini, Paola A1 - Ranchere-Vince, Dominique A1 - Garcia Del Muro, Xavier A1 - Grignani, Giovanni A1 - Dumont, Sarah A1 - Martinez-Trufero, Javier A1 - Palmerini, Emanuela A1 - Hindi, Nadia A1 - Sebio, Ana A1 - Dopazo, Joaquin A1 - Dei Tos, Angelo Paolo A1 - LeCesne, Axel A1 - Blay, Jean-Yves A1 - Cruz, Josefina KW - Adult KW - Aged KW - Angiogenesis Inhibitors KW - Antineoplastic Agents KW - Female KW - Humans KW - Indazoles KW - Male KW - Middle Aged KW - Multivariate Analysis KW - Pyrimidines KW - Response Evaluation Criteria in Solid Tumors KW - Soft Tissue Neoplasms KW - Solitary Fibrous Tumors KW - Sulfonamides KW - Survival Analysis AB -

BACKGROUND: A solitary fibrous tumour is a rare soft-tissue tumour with three clinicopathological variants: typical, malignant, and dedifferentiated. Preclinical experiments and retrospective studies have shown different sensitivities of solitary fibrous tumour to chemotherapy and antiangiogenics. We therefore designed a trial to assess the activity of pazopanib in a cohort of patients with malignant or dedifferentiated solitary fibrous tumour. The clinical and translational results are presented here.

METHODS: In this single-arm, phase 2 trial, adult patients (aged ≥ 18 years) with histologically confirmed metastatic or unresectable malignant or dedifferentiated solitary fibrous tumour at any location, who had progressed (by RECIST and Choi criteria) in the previous 6 months and had an ECOG performance status of 0-2, were enrolled at 16 third-level hospitals with expertise in sarcoma care in Spain, Italy, and France. Patients received pazopanib 800 mg once daily, taken orally without food, at least 1 h before or 2 h after a meal, until progression or intolerance. The primary endpoint of the study was overall response measured by Choi criteria in the subset of the intention-to-treat population (patients who received at least 1 month of treatment with at least one radiological assessment). All patients who received at least one dose of the study drug were included in the safety analyses. This study is registered with ClinicalTrials.gov, number NCT02066285, and with the European Clinical Trials Database, EudraCT number 2013-005456-15.

FINDINGS: From June 26, 2014, to Nov 24, 2016, of 40 patients assessed, 36 were enrolled (34 with malignant solitary fibrous tumour and two with dedifferentiated solitary fibrous tumour). Median follow-up was 27 months (IQR 16-31). Based on central radiology review, 18 (51%) of 35 evaluable patients had partial responses, nine (26%) had stable disease, and eight (23%) had progressive disease according to Choi criteria. Further enrolment of patients with dedifferentiated solitary fibrous tumour was stopped after detection of early and fast progressions in a planned interim analysis. 51% (95% CI 34-69) of 35 patients achieved an overall response according to Choi criteria. Ten (29%) of 35 patients died. There were no deaths related to adverse events and the most frequent grade 3 or higher adverse events were hypertension (11 [31%] of 36 patients), neutropenia (four [11%]), increased concentrations of alanine aminotransferase (four [11%]), and increased concentrations of bilirubin (three [8%]).

INTERPRETATION: To our knowledge, this is the first trial of pazopanib for treatment of malignant solitary fibrous tumour showing activity in this patient group. The manageable toxicity profile and the activity shown by pazopanib suggests that this drug could be an option for systemic treatment of advanced malignant solitary fibrous tumour, and provides a benchmark for future trials.

FUNDING: Spanish Group for Research on Sarcomas (GEIS), Italian Sarcoma Group (ISG), French Sarcoma Group (FSG), GlaxoSmithKline, and Novartis.

VL - 20 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/30578023?dopt=Abstract ER - TY - JOUR T1 - PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources. JF - BMC Bioinformatics Y1 - 2019 A1 - Perez-Gil, Daniel A1 - Lopez, Francisco J A1 - Dopazo, Joaquin A1 - Marin-Garcia, Pablo A1 - Rendon, Augusto A1 - Medina, Ignacio KW - Computational Biology KW - Databases, Factual KW - Software KW - User-Computer Interface AB -

BACKGROUND: Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data.

RESULTS: In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTful web service API offered by CellBase. This package offers a fast and user-friendly access to biological information without the need of installing any local database. In addition, a series of command-line tools are provided to perform common bioinformatic tasks, such as variant annotation. CellBase data is always available by a high-availability cluster and queries have been tuned to ensure a real-time performance.

CONCLUSION: PyCellBase is an open-source Python package that provides an efficient access to heterogeneous biological information. It allows to perform tasks that require a comprehensive set of knowledge resources, as for example variant annotation. Queries can be easily fine-tuned to retrieve the desired information of particular biological features. PyCellBase offers the convenience of an object-oriented scripting language and provides the ability to integrate the obtained results into other Python applications and pipelines.

VL - 20 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/30922213?dopt=Abstract ER - TY - JOUR T1 - Using mechanistic models for the clinical interpretation of complex genomic variation JF - Scientific Reports Y1 - 2019 A1 - Peña-Chilet, Maria A1 - Esteban-Medina, Marina A1 - Falco, Matias M. A1 - Rian, Kinza A1 - Hidalgo, Marta R. A1 - Loucera, Carlos A1 - Dopazo, Joaquin VL - 9 UR - http://www.nature.com/articles/s41598-019-55454-7http://www.nature.com/articles/s41598-019-55454-7.pdfhttp://www.nature.com/articles/s41598-019-55454-7.pdfhttp://www.nature.com/articles/s41598-019-55454-7 IS - 1 JO - Sci Rep ER - TY - JOUR T1 - A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection JF - Nature Communications Y1 - 2018 A1 - Fourati, Slim A1 - Talla, Aarthi A1 - Mahmoudian, Mehrad A1 - Burkhart, Joshua G. A1 - Klén, Riku A1 - Henao, Ricardo A1 - Yu, Thomas A1 - Aydın, Zafer A1 - Yeung, Ka Yee A1 - Ahsen, Mehmet Eren A1 - Almugbel, Reem A1 - Jahandideh, Samad A1 - Liang, Xiao A1 - Nordling, Torbjörn E. M. A1 - Shiga, Motoki A1 - Stanescu, Ana A1 - Vogel, Robert A1 - Pandey, Gaurav A1 - Chiu, Christopher A1 - McClain, Micah T. A1 - Woods, Christopher W. A1 - Ginsburg, Geoffrey S. A1 - Elo, Laura L. A1 - Tsalik, Ephraim L. A1 - Mangravite, Lara M. A1 - Sieberts, Solveig K. VL - 9 UR - http://www.nature.com/articles/s41467-018-06735-8http://www.nature.com/articles/s41467-018-06735-8.pdfhttp://www.nature.com/articles/s41467-018-06735-8.pdfhttp://www.nature.com/articles/s41467-018-06735-8 IS - 1 JO - Nat Commun ER - TY - JOUR T1 - Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. JF - Sci Rep Y1 - 2018 A1 - López, M A1 - Rueda, A A1 - Florido, J P A1 - Blasco, L A1 - Fernández-García, L A1 - Trastoy, R A1 - Fernández-Cuenca, F A1 - Martínez-Martínez, L A1 - Vila, J A1 - Pascual, A A1 - Bou, G A1 - Tomas, M KW - Acinetobacter baumannii KW - Acinetobacter Infections KW - Bacteriophages KW - Cross Infection KW - Humans KW - Plasmids KW - Quorum Sensing KW - Retrospective Studies AB -

In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit (ICU) in 2000 (9 strains referred to collectively as Ab_GEIH-2000) and 2010 (9 strains referred to collectively as Ab_GEIH-2010), during the GEIH-REIPI project (Umbrella BioProject PRJNA422585). We observed two main molecular differences between the Ab_GEIH-2010 and the Ab_GEIH-2000 collections, acquired over the course of the decade long sampling interval and involving the mobilome: i) a plasmid harbouring genes for bla ß-lactamase and abKA/abkB proteins of a toxin-antitoxin system; and ii) two temperate bacteriophages, Ab105-1ϕ (63 proteins) and Ab105-2ϕ (93 proteins), containing important viral defence proteins. Moreover, all Ab_GEIH-2010 strains contained a Quorum functional network of Quorum Sensing (QS) and Quorum Quenching (QQ) mechanisms, including a new QQ enzyme, AidA, which acts as a bacterial defence mechanism against the exogenous 3-oxo-C12-HSL. Interestingly, the infective capacity of the bacteriophages isolated in this study (Ab105-1ϕ and Ab105-2ϕ) was higher in the Ab_GEIH-2010 strains (carrying a functional Quorum network) than in the Ab_GEIH-2000 strains (carrying a deficient Quorum network), in which the bacteriophages showed little or no infectivity. This is the first study about the evolution of the Quorum network and the mobilome in clinical strains of Acinetobacter baumannii during a decade.

VL - 8 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/29410443?dopt=Abstract ER - TY - JOUR T1 - Genomics of the origin and evolution of Citrus. JF - Nature Y1 - 2018 A1 - Wu, Guohong Albert A1 - Terol, Javier A1 - Ibañez, Victoria A1 - López-García, Antonio A1 - Pérez-Román, Estela A1 - Borredá, Carles A1 - Domingo, Concha A1 - Tadeo, Francisco R A1 - Carbonell-Caballero, José A1 - Alonso, Roberto A1 - Curk, Franck A1 - Du, Dongliang A1 - Ollitrault, Patrick A1 - Roose, Mikeal L A1 - Dopazo, Joaquin A1 - Gmitter, Frederick G A1 - Rokhsar, Daniel S A1 - Talon, Manuel KW - Asia, Southeastern KW - Biodiversity KW - citrus KW - Crop Production KW - Evolution, Molecular KW - Genetic Speciation KW - Genome, Plant KW - Genomics KW - Haplotypes KW - Heterozygote KW - History, Ancient KW - Human Migration KW - Hybridization, Genetic KW - Phylogeny AB -

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.

VL - 554 IS - 7692 U1 - https://www.ncbi.nlm.nih.gov/pubmed/29414943?dopt=Abstract ER - TY - JOUR T1 - LRH-1 agonism favours an immune-islet dialogue which protects against diabetes mellitus. JF - Nat Commun Y1 - 2018 A1 - Cobo-Vuilleumier, Nadia A1 - Lorenzo, Petra I A1 - Rodríguez, Noelia García A1 - Herrera Gómez, Irene de Gracia A1 - Fuente-Martin, Esther A1 - López-Noriega, Livia A1 - Mellado-Gil, José Manuel A1 - Romero-Zerbo, Silvana-Yanina A1 - Baquié, Mathurin A1 - Lachaud, Christian Claude A1 - Stifter, Katja A1 - Perdomo, German A1 - Bugliani, Marco A1 - De Tata, Vincenzo A1 - Bosco, Domenico A1 - Parnaud, Geraldine A1 - Pozo, David A1 - Hmadcha, Abdelkrim A1 - Florido, Javier P A1 - Toscano, Miguel G A1 - de Haan, Peter A1 - Schoonjans, Kristina A1 - Sánchez Palazón, Luis A1 - Marchetti, Piero A1 - Schirmbeck, Reinhold A1 - Martín-Montalvo, Alejandro A1 - Meda, Paolo A1 - Soria, Bernat A1 - Bermúdez-Silva, Francisco-Javier A1 - St-Onge, Luc A1 - Gauthier, Benoit R KW - Animals KW - Apoptosis KW - Cell Communication KW - Cell Survival KW - Diabetes Mellitus, Experimental KW - Diabetes Mellitus, Type 2 KW - Female KW - Gene Expression Regulation KW - Humans KW - Hypoglycemic Agents KW - Immunity, Innate KW - insulin KW - Insulin-Secreting Cells KW - Islets of Langerhans KW - Islets of Langerhans Transplantation KW - Macrophages KW - Male KW - Mice KW - Mice, Inbred C57BL KW - Phenalenes KW - Receptors, Cytoplasmic and Nuclear KW - Streptozocin KW - T-Lymphocytes, Regulatory KW - Transplantation, Heterologous AB -

Type 1 diabetes mellitus (T1DM) is due to the selective destruction of islet beta cells by immune cells. Current therapies focused on repressing the immune attack or stimulating beta cell regeneration still have limited clinical efficacy. Therefore, it is timely to identify innovative targets to dampen the immune process, while promoting beta cell survival and function. Liver receptor homologue-1 (LRH-1) is a nuclear receptor that represses inflammation in digestive organs, and protects pancreatic islets against apoptosis. Here, we show that BL001, a small LRH-1 agonist, impedes hyperglycemia progression and the immune-dependent inflammation of pancreas in murine models of T1DM, and beta cell apoptosis in islets of type 2 diabetic patients, while increasing beta cell mass and insulin secretion. Thus, we suggest that LRH-1 agonism favors a dialogue between immune and islet cells, which could be druggable to protect against diabetes mellitus.

VL - 9 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/29662071?dopt=Abstract ER - TY - JOUR T1 - The modular network structure of the mutational landscape of Acute Myeloid Leukemia. JF - PLoS One Y1 - 2018 A1 - Ibáñez, Mariam A1 - Carbonell-Caballero, José A1 - Such, Esperanza A1 - García-Alonso, Luz A1 - Liquori, Alessandro A1 - López-Pavía, María A1 - LLop, Marta A1 - Alonso, Carmen A1 - Barragán, Eva A1 - Gómez-Seguí, Inés A1 - Neef, Alexander A1 - Hervás, David A1 - Montesinos, Pau A1 - Sanz, Guillermo A1 - Sanz, Miguel Angel A1 - Dopazo, Joaquin A1 - Cervera, José KW - Adult KW - Aged KW - Cytodiagnosis KW - Female KW - Gene Regulatory Networks KW - Genetic Association Studies KW - Genetic Heterogeneity KW - Humans KW - Karyotype KW - Leukemia, Myeloid, Acute KW - Male KW - Middle Aged KW - mutation KW - Neoplasm Proteins KW - Nucleophosmin KW - Prognosis KW - whole exome sequencing AB -

Acute myeloid leukemia (AML) is associated with the sequential accumulation of acquired genetic alterations. Although at diagnosis cytogenetic alterations are frequent in AML, roughly 50% of patients present an apparently normal karyotype (NK), leading to a highly heterogeneous prognosis. Due to this significant heterogeneity, it has been suggested that different molecular mechanisms may trigger the disease with diverse prognostic implications. We performed whole-exome sequencing (WES) of tumor-normal matched samples of de novo AML-NK patients lacking mutations in NPM1, CEBPA or FLT3-ITD to identify new gene mutations with potential prognostic and therapeutic relevance to patients with AML. Novel candidate-genes, together with others previously described, were targeted resequenced in an independent cohort of 100 de novo AML patients classified in the cytogenetic intermediate-risk (IR) category. A mean of 4.89 mutations per sample were detected in 73 genes, 35 of which were mutated in more than one patient. After a network enrichment analysis, we defined a single in silico model and established a set of seed-genes that may trigger leukemogenesis in patients with normal karyotype. The high heterogeneity of gene mutations observed in AML patients suggested that a specific alteration could not be as essential as the interaction of deregulated pathways.

VL - 13 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/30303964?dopt=Abstract ER - TY - JOUR T1 - HGVA: the Human Genome Variation Archive. JF - Nucleic Acids Res Y1 - 2017 A1 - Lopez, Javier A1 - Coll, Jacobo A1 - Haimel, Matthias A1 - Kandasamy, Swaathi A1 - Tárraga, Joaquín A1 - Furio-Tari, Pedro A1 - Bari, Wasim A1 - Bleda, Marta A1 - Rueda, Antonio A1 - Gräf, Stefan A1 - Rendon, Augusto A1 - Dopazo, Joaquin A1 - Medina, Ignacio KW - Genetic Variation KW - Genome, Human KW - Humans KW - Internet KW - Software KW - User-Computer Interface AB -

High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets.

VL - 45 UR - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx445 IS - W1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/28535294?dopt=Abstract ER - TY - JOUR T1 - Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation. JF - Hum Mutat Y1 - 2017 A1 - Matalonga, Leslie A1 - Bravo, Miren A1 - Serra-Peinado, Carla A1 - García-Pelegrí, Elisabeth A1 - Ugarteburu, Olatz A1 - Vidal, Silvia A1 - Llambrich, Maria A1 - Quintana, Ester A1 - Fuster-Jorge, Pedro A1 - Gonzalez-Bravo, Maria Nieves A1 - Beltran, Sergi A1 - Dopazo, Joaquin A1 - Garcia-Garcia, Francisco A1 - Foulquier, François A1 - Matthijs, Gert A1 - Mills, Philippa A1 - Ribes, Antonia A1 - Egea, Gustavo A1 - Briones, Paz A1 - Tort, Frederic A1 - Girós, Marisa KW - Abnormalities, Multiple KW - Alleles KW - Amino Acid Substitution KW - Brain KW - Congenital Disorders of Glycosylation KW - Genotype KW - Humans KW - Magnetic Resonance Imaging KW - Male KW - mutation KW - Phenotype KW - Vesicular Transport Proteins KW - Whole Genome Sequencing AB -

Congenital disorders of glycosylation (CDG) are a heterogeneous and rapidly growing group of diseases caused by abnormal glycosylation of proteins and/or lipids. Mutations in genes involved in the homeostasis of the endoplasmic reticulum (ER), the Golgi apparatus (GA), and the vesicular trafficking from the ER to the ER-Golgi intermediate compartment (ERGIC) have been found to be associated with CDG. Here, we report a patient with defects in both N- and O-glycosylation combined with a delayed vesicular transport in the GA due to mutations in TRAPPC11, a subunit of the TRAPPIII complex. TRAPPIII is implicated in the anterograde transport from the ER to the ERGIC as well as in the vesicle export from the GA. This report expands the spectrum of genetic alterations associated with CDG, providing new insights for the diagnosis and the understanding of the physiopathological mechanisms underlying glycosylation disorders.

VL - 38 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27862579?dopt=Abstract ER - TY - JOUR T1 - Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. JF - Bioinformatics Y1 - 2017 A1 - Carbonell-Caballero, José A1 - Amadoz, Alicia A1 - Alonso, Roberto A1 - Hidalgo, Marta R A1 - Cubuk, Cankut A1 - Conesa, David A1 - López-Quílez, Antonio A1 - Dopazo, Joaquin KW - Animals KW - Genetic Variation KW - Genome KW - Genomics KW - Genotype KW - Humans KW - Models, Statistical KW - Quality Control KW - Reproducibility of Results KW - Software AB -

Motivation: Current plant and animal genomic studies are often based on newly assembled genomes that have not been properly consolidated. In this scenario, misassembled regions can easily lead to false-positive findings. Despite quality control scores are included within genotyping protocols, they are usually employed to evaluate individual sample quality rather than reference sequence reliability. We propose a statistical model that combines quality control scores across samples in order to detect incongruent patterns at every genomic region. Our model is inherently robust since common artifact signals are expected to be shared between independent samples over misassembled regions of the genome.

Results: The reliability of our protocol has been extensively tested through different experiments and organisms with accurate results, improving state-of-the-art methods. Our analysis demonstrates synergistic relations between quality control scores and allelic variability estimators, that improve the detection of misassembled regions, and is able to find strong artifact signals even within the human reference assembly. Furthermore, we demonstrated how our model can be trained to properly rank the confidence of a set of candidate variants obtained from new independent samples.

Availability and implementation: This tool is freely available at http://gitlab.com/carbonell/ces.

Contact: jcarbonell.cipf@gmail.com or joaquin.dopazo@juntadeandalucia.es.

Supplementary information: Supplementary data are available at Bioinformatics online.

VL - 33 UR - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx482 IS - 22 U1 - https://www.ncbi.nlm.nih.gov/pubmed/28961772?dopt=Abstract ER - TY - JOUR T1 - Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes JF - Genome Biology Y1 - 2017 A1 - Gui, Hongsheng A1 - Schriemer, Duco A1 - Cheng, William W. A1 - Chauhan, Rajendra K. A1 - Antiňolo, Guillermo A1 - Berrios, Courtney A1 - Bleda, Marta A1 - Brooks, Alice S. A1 - Brouwer, Rutger W. W. A1 - Burns, Alan J. A1 - Cherny, Stacey S. A1 - Dopazo, Joaquin A1 - Eggen, Bart J. L. A1 - Griseri, Paola A1 - Jalloh, Binta A1 - Le, Thuy-Linh A1 - Lui, Vincent C. H. A1 - Luzón-Toro, Berta A1 - Matera, Ivana A1 - Ngan, Elly S. W. A1 - Pelet, Anna A1 - Ruiz-Ferrer, Macarena A1 - Sham, Pak C. A1 - Shepherd, Iain T. A1 - So, Man-Ting A1 - Sribudiani, Yunia A1 - Tang, Clara S. M. A1 - van den Hout, Mirjam C. G. N. A1 - van der Linde, Herma C. A1 - van Ham, Tjakko J. A1 - van IJcken, Wilfred F. J. A1 - Verheij, Joke B. G. M. A1 - Amiel, Jeanne A1 - Borrego, Salud A1 - Ceccherini, Isabella A1 - Chakravarti, Aravinda A1 - Lyonnet, Stanislas A1 - Tam, Paul K. H. A1 - Garcia-Barceló, Maria-Mercè A1 - Hofstra, Robert M. W. VL - 18 UR - http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1174-6http://link.springer.com/content/pdf/10.1186/s13059-017-1174-6.pdf IS - 1 JO - Genome Biol ER - TY - JOUR T1 - Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. JF - Genome biology Y1 - 2017 A1 - Gui, Hongsheng A1 - Schriemer, Duco A1 - Cheng, William W A1 - Chauhan, Rajendra K A1 - Antiňolo, Guillermo A1 - Berrios, Courtney A1 - Bleda, Marta A1 - Brooks, Alice S A1 - Brouwer, Rutger W W A1 - Burns, Alan J A1 - Cherny, Stacey S A1 - Dopazo, Joaquin A1 - Eggen, Bart J L A1 - Griseri, Paola A1 - Jalloh, Binta A1 - Le, Thuy-Linh A1 - Lui, Vincent C H A1 - Luzón-Toro, Berta A1 - Matera, Ivana A1 - Ngan, Elly S W A1 - Pelet, Anna A1 - Ruiz-Ferrer, Macarena A1 - Sham, Pak C A1 - Shepherd, Iain T A1 - So, Man-Ting A1 - Sribudiani, Yunia A1 - Tang, Clara S M A1 - van den Hout, Mirjam C G N A1 - van der Linde, Herma C A1 - van Ham, Tjakko J A1 - van IJcken, Wilfred F J A1 - Verheij, Joke B G M A1 - Amiel, Jeanne A1 - Borrego, Salud A1 - Ceccherini, Isabella A1 - Chakravarti, Aravinda A1 - Lyonnet, Stanislas A1 - Tam, Paul K H A1 - Garcia-Barceló, Maria-Mercè A1 - Hofstra, Robert Mw KW - Hirschprung KW - Rare Disease KW - WES AB - BACKGROUND: Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human. RESULTS: We performed de novo mutation (DNM) screening on 24 HSCR trios. We identify 28 DNMs in 21 different genes. Eight of the DNMs we identified occur in RET, the main HSCR gene, and the remaining 20 DNMs reside in genes not reported in the ENS. Knockdown of all 12 genes with missense or loss-of-function DNMs showed that the orthologs of four genes (DENND3, NCLN, NUP98, and TBATA) are indispensable for ENS development in zebrafish, and these results were confirmed by CRISPR knockout. These genes are also expressed in human and mouse gut and/or ENS progenitors. Importantly, the encoded proteins are linked to neuronal processes shared by the central nervous system and the ENS. CONCLUSIONS: Our data open new fields of investigation into HSCR pathology and provide novel insights into the development of the ENS. Moreover, the study demonstrates that functional analyses of genes carrying DNMs are warranted to delineate the full genetic architecture of rare complex diseases. VL - 18 UR - http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1174-6 ER - TY - JOUR T1 - 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. JF - Molecular biology and evolution Y1 - 2016 A1 - Joaquín Dopazo A1 - Amadoz, Alicia A1 - Bleda, Marta A1 - García-Alonso, Luz A1 - Alemán, Alejandro A1 - Garcia-Garcia, Francisco A1 - Rodriguez, Juan A A1 - Daub, Josephine T A1 - Muntané, Gerard A1 - Antonio Rueda A1 - Vela-Boza, Alicia A1 - López-Domingo, Francisco J A1 - Florido, Javier P A1 - Arce, Pablo A1 - Ruiz-Ferrer, Macarena A1 - Méndez-Vidal, Cristina A1 - Arnold, Todd E A1 - Spleiss, Olivia A1 - Alvarez-Tejado, Miguel A1 - Navarro, Arcadi A1 - Bhattacharya, Shomi S A1 - Borrego, Salud A1 - Santoyo-López, Javier A1 - Antiňolo, Guillermo KW - disease KW - NGS KW - polymorphisms KW - Population genomics KW - prioritization KW - SNP AB - Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalogue of local variability motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population. Like in other studies, a considerable number of rare variants were found (almost one third of the described variants). There were also relevant differences in allelic frequencies in polymorphic variants, including about 10,000 polymorphisms private to the Spanish population. The allelic frequencies of variants conferring susceptibility to complex diseases (including cancer, schizophrenia, Alzheimer disease, type 2 diabetes and other pathologies) were overall similar to those of other populations. However, the trend is the opposite for variants linked to Mendelian and rare diseases (including several retinal degenerative dystrophies and cardiomyopathies) that show marked frequency differences between populations. Interestingly, a correspondence between differences in allelic frequencies and disease prevalence was found, highlighting the relevance of frequency differences in disease risk. These differences are also observed in variants that disrupt known drug binding sites, suggesting an important role for local variability in population-specific drug resistances or adverse effects. We have made the Spanish population variant server web page that contains population frequency information for the complete list of 170,888 variant positions we found publicly available (http://spv.babelomics.org/), We show that it if fundamental to determine population-specific variant frequencies in order to distinguish real disease associations from population-specific polymorphisms. UR - https://mbe.oxfordjournals.org/content/early/2016/02/17/molbev.msw005.full ER - TY - JOUR T1 - Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy. JF - The Journal of molecular diagnostics : JMD Y1 - 2016 A1 - Lupo, Vincenzo A1 - Garcia-Garcia, Francisco A1 - Sancho, Paula A1 - Tello, Cristina A1 - García-Romero, Mar A1 - Villarreal, Liliana A1 - Alberti, Antonia A1 - Sivera, Rafael A1 - Joaquín Dopazo A1 - Pascual-Pascual, Samuel I A1 - Márquez-Infante, Celedonio A1 - Casasnovas, Carlos A1 - Sevilla, Teresa A1 - Espinós, Carmen KW - Charcot-Marie-Tooth KW - CMT KW - Diagnostic KW - NGS KW - Panels KW - rare diseases KW - Targeted resequencing AB - Charcot-Marie-Tooth disease is characterized by broad genetic heterogeneity with >50 known disease-associated genes. Mutations in some of these genes can cause a pure motor form of hereditary motor neuropathy, the genetics of which are poorly characterized. We designed a panel comprising 56 genes associated with Charcot-Marie-Tooth disease/hereditary motor neuropathy. We validated this diagnostic tool by first testing 11 patients with pathological mutations. A cohort of 33 affected subjects was selected for this study. The DNAJB2 c.352+1G>A mutation was detected in two cases; novel changes and/or variants with low frequency (<1%) were found in 12 cases. There were no candidate variants in 18 cases, and amplification failed for one sample. The DNAJB2 c.352+1G>A mutation was also detected in three additional families. On haplotype analysis, all of the patients from these five families shared the same haplotype; therefore, the DNAJB2 c.352+1G>A mutation may be a founder event. Our gene panel allowed us to perform a very rapid and cost-effective screening of genes involved in Charcot-Marie-Tooth disease/hereditary motor neuropathy. Our diagnostic strategy was robust in terms of both coverage and read depth for all of the genes and patient samples. These findings demonstrate the difficulty in achieving a definitive molecular diagnosis because of the complexity of interpreting new variants and the genetic heterogeneity that is associated with these neuropathies. UR - http://www.sciencedirect.com/science/article/pii/S1525157815002615 ER - TY - JOUR T1 - Dysfunctional mitochondrial fission impairs cell reprogramming. JF - Cell Cycle Y1 - 2016 A1 - Prieto, Javier A1 - León, Marian A1 - Ponsoda, Xavier A1 - Garcia-Garcia, Francisco A1 - Bort, Roque A1 - Serna, Eva A1 - Barneo-Muñoz, Manuela A1 - Palau, Francesc A1 - Dopazo, Joaquin A1 - López-García, Carlos A1 - Torres, Josema KW - Animals KW - Cell Cycle Checkpoints KW - Cellular Reprogramming KW - DNA Damage KW - G2 Phase KW - Gene Knockdown Techniques KW - Mice KW - Mitochondrial Dynamics KW - Mitosis KW - Nerve Tissue Proteins KW - Pluripotent Stem Cells KW - Transcription Factors AB -

We have recently shown that mitochondrial fission is induced early in reprogramming in a Drp1-dependent manner; however, the identity of the factors controlling Drp1 recruitment to mitochondria was unexplored. To investigate this, we used a panel of RNAi targeting factors involved in the regulation of mitochondrial dynamics and we observed that MiD51, Gdap1 and, to a lesser extent, Mff were found to play key roles in this process. Cells derived from Gdap1-null mice were used to further explore the role of this factor in cell reprogramming. Microarray data revealed a prominent down-regulation of cell cycle pathways in Gdap1-null cells early in reprogramming and cell cycle profiling uncovered a G2/M growth arrest in Gdap1-null cells undergoing reprogramming. High-Content analysis showed that this growth arrest was DNA damage-independent. We propose that lack of efficient mitochondrial fission impairs cell reprogramming by interfering with cell cycle progression in a DNA damage-independent manner.

VL - 15 IS - 23 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27753531?dopt=Abstract ER - TY - JOUR T1 - Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). JF - Nature communications Y1 - 2016 A1 - Lagarde, Julien A1 - Uszczynska-Ratajczak, Barbara A1 - Santoyo-López, Javier A1 - Gonzalez, Jose Manuel A1 - Tapanari, Electra A1 - Mudge, Jonathan M A1 - Steward, Charles A A1 - Wilming, Laurens A1 - Tanzer, Andrea A1 - Howald, Cédric A1 - Chrast, Jacqueline A1 - Vela-Boza, Alicia A1 - Antonio Rueda A1 - López-Domingo, Francisco J A1 - Dopazo, Joaquin A1 - Reymond, Alexandre A1 - Guigó, Roderic A1 - Harrow, Jennifer AB - Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing. We apply RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts. About 60% of the targeted loci are extended in either 5’ or 3’, often reaching genomic hallmarks of gene boundaries. Analysis of the novel transcripts suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions. Overall, we show that RACE-Seq is an effective tool to annotate an organism’s deep transcriptome, and compares favourably to other targeted sequencing techniques. VL - 7 UR - http://www.nature.com/articles/ncomms12339 ER - TY - JOUR T1 - Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq) JF - Nature Communications Y1 - 2016 A1 - Lagarde, Julien A1 - Uszczynska-Ratajczak, Barbara A1 - Santoyo-López, Javier A1 - Gonzalez, Jose Manuel A1 - Tapanari, Electra A1 - Mudge, Jonathan M. A1 - Steward, Charles A. A1 - Wilming, Laurens A1 - Tanzer, Andrea A1 - Howald, Cédric A1 - Chrast, Jacqueline A1 - Vela-Boza, Alicia A1 - Rueda, Antonio A1 - Lopez-Domingo, Francisco J. A1 - Dopazo, Joaquin A1 - Reymond, Alexandre A1 - Guigó, Roderic A1 - Harrow, Jennifer VL - 7 UR - http://www.nature.com/articles/ncomms12339http://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339 IS - 1 JO - Nat Commun ER - TY - JOUR T1 - Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. JF - Transl Psychiatry Y1 - 2016 A1 - Sanchez-Mut, J V A1 - Heyn, H A1 - Vidal, E A1 - Moran, S A1 - Sayols, S A1 - Delgado-Morales, R A1 - Schultz, M D A1 - Ansoleaga, B A1 - Garcia-Esparcia, P A1 - Pons-Espinal, M A1 - de Lagran, M M A1 - Dopazo, J A1 - Rabano, A A1 - Avila, J A1 - Dierssen, M A1 - Lott, I A1 - Ferrer, I A1 - Ecker, J R A1 - Esteller, M KW - Adult KW - Aged KW - Aged, 80 and over KW - DNA Methylation KW - Epigenomics KW - Female KW - Humans KW - Male KW - Middle Aged KW - neurodegenerative diseases KW - Prefrontal Cortex KW - Tissue Array Analysis AB -

Different neurodegenerative disorders often show similar lesions, such as the presence of amyloid plaques, TAU-neurotangles and synuclein inclusions. The genetically inherited forms are rare, so we wondered whether shared epigenetic aberrations, such as those affecting DNA methylation, might also exist. The studied samples were gray matter samples from the prefrontal cortex of control and neurodegenerative disease-associated cases. We performed the DNA methylation analyses of Alzheimer's disease, dementia with Lewy bodies, Parkinson's disease and Alzheimer-like neurodegenerative profile associated with Down's syndrome samples. The DNA methylation landscapes obtained show that neurodegenerative diseases share similar aberrant CpG methylation shifts targeting a defined gene set. Our findings suggest that neurodegenerative disorders might have similar pathogenetic mechanisms that subsequently evolve into different clinical entities. The identified aberrant DNA methylation changes can be used as biomarkers of the disorders and as potential new targets for the development of new therapies.

VL - 6 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26784972?dopt=Abstract ER - TY - JOUR T1 - Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. JF - Sci Rep Y1 - 2016 A1 - Corton, M A1 - Avila-Fernández, A A1 - Campello, L A1 - Sánchez, M A1 - Benavides, B A1 - López-Molina, M I A1 - Fernández-Sánchez, L A1 - Sánchez-Alcudia, R A1 - da Silva, L R J A1 - Reyes, N A1 - Martín-Garrido, E A1 - Zurita, O A1 - Fernández-San José, P A1 - Pérez-Carro, R A1 - García-García, F A1 - Dopazo, J A1 - García-Sandoval, B A1 - Cuenca, N A1 - Ayuso, C KW - Aged KW - Animals KW - Co-Repressor Proteins KW - Codon, Nonsense KW - Cohort Studies KW - Comparative Genomic Hybridization KW - Consanguinity KW - DNA Mutational Analysis KW - Exome KW - Eye Proteins KW - Female KW - Gene Expression Regulation KW - Genes, Recessive KW - Homeodomain Proteins KW - Homozygote KW - Humans KW - Male KW - Mice KW - Middle Aged KW - Polymorphism, Single Nucleotide KW - Protein Interaction Mapping KW - Retina KW - Retinal Dystrophies KW - Retinal Rod Photoreceptor Cells KW - Retinitis pigmentosa KW - Spain KW - Trans-Activators KW - Transcription Factors AB -

Retinitis pigmentosa (RP), the most frequent form of inherited retinal dystrophy is characterized by progressive photoreceptor degeneration. Many genes have been implicated in RP development, but several others remain to be identified. Using a combination of homozygosity mapping, whole-exome and targeted next-generation sequencing, we found a novel homozygous nonsense mutation in SAMD11 in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families. SAMD11 is ortholog to the mouse major retinal SAM domain (mr-s) protein that is implicated in CRX-mediated transcriptional regulation in the retina. Accordingly, protein-protein network analysis revealed a significant interaction of SAMD11 with CRX. Immunoblotting analysis confirmed strong expression of SAMD11 in human retina. Immunolocalization studies revealed SAMD11 was detected in the three nuclear layers of the human retina and interestingly differential expression between cone and rod photoreceptors was observed. Our study strongly implicates SAMD11 as novel cause of RP playing an important role in the pathogenesis of human degeneration of photoreceptors.

VL - 6 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27734943?dopt=Abstract ER - TY - JOUR T1 - Integrating transcriptomic and metabolomic analysis to understand natural leaf senescence in sunflower. JF - Plant Biotechnol J Y1 - 2016 A1 - Moschen, Sebastián A1 - Bengoa Luoni, Sofía A1 - Di Rienzo, Julio A A1 - Caro, María Del Pilar A1 - Tohge, Takayuki A1 - Watanabe, Mutsumi A1 - Hollmann, Julien A1 - Gonzalez, Sergio A1 - Rivarola, Máximo A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Hopp, Horacio Esteban A1 - Hoefgen, Rainer A1 - Fernie, Alisdair R A1 - Paniego, Norma A1 - Fernandez, Paula A1 - Heinz, Ruth A KW - Gas Chromatography-Mass Spectrometry KW - Gene Expression Profiling KW - Gene Expression Regulation, Plant KW - Gene ontology KW - Genes, Plant KW - Helianthus KW - Ions KW - metabolomics KW - Oligonucleotide Array Sequence Analysis KW - Plant Leaves KW - Principal Component Analysis KW - RNA, Messenger KW - Transcription Factors AB -

Leaf senescence is a complex process, which has dramatic consequences on crop yield. In sunflower, gap between potential and actual yields reveals the economic impact of senescence. Indeed, sunflower plants are incapable of maintaining their green leaf area over sustained periods. This study characterizes the leaf senescence process in sunflower through a systems biology approach integrating transcriptomic and metabolomic analyses: plants being grown under both glasshouse and field conditions. Our results revealed a correspondence between profile changes detected at the molecular, biochemical and physiological level throughout the progression of leaf senescence measured at different plant developmental stages. Early metabolic changes were detected prior to anthesis and before the onset of the first senescence symptoms, with more pronounced changes observed when physiological and molecular variables were assessed under field conditions. During leaf development, photosynthetic activity and cell growth processes decreased, whereas sucrose, fatty acid, nucleotide and amino acid metabolisms increased. Pathways related to nutrient recycling processes were also up-regulated. Members of the NAC, AP2-EREBP, HB, bZIP and MYB transcription factor families showed high expression levels, and their expression level was highly correlated, suggesting their involvement in sunflower senescence. The results of this study thus contribute to the elucidation of the molecular mechanisms involved in the onset and progression of leaf senescence in sunflower leaves as well as to the identification of candidate genes involved in this process.

VL - 14 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26132509?dopt=Abstract ER - TY - JOUR T1 - The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. JF - PLoS One Y1 - 2016 A1 - Ibáñez, Mariam A1 - Carbonell-Caballero, José A1 - García-Alonso, Luz A1 - Such, Esperanza A1 - Jiménez-Almazán, Jorge A1 - Vidal, Enrique A1 - Barragán, Eva A1 - López-Pavía, María A1 - LLop, Marta A1 - Martín, Iván A1 - Gómez-Seguí, Inés A1 - Montesinos, Pau A1 - Sanz, Miguel A A1 - Dopazo, Joaquin A1 - Cervera, José KW - Exome KW - Gene Regulatory Networks KW - Genome, Human KW - Humans KW - INDEL Mutation KW - Leukemia, Promyelocytic, Acute KW - mutation KW - Mutation Rate KW - Polymorphism, Single Nucleotide KW - Reproducibility of Results AB -

Preliminary Acute Promyelocytic Leukemia (APL) whole exome sequencing (WES) studies have identified a huge number of somatic mutations affecting more than a hundred different genes mainly in a non-recurrent manner, suggesting that APL is a heterogeneous disease with secondary relevant changes not yet defined. To extend our knowledge of subtle genetic alterations involved in APL that might cooperate with PML/RARA in the leukemogenic process, we performed a comprehensive analysis of somatic mutations in APL combining WES with sequencing of a custom panel of targeted genes by next-generation sequencing. To select a reduced subset of high confidence candidate driver genes, further in silico analysis were carried out. After prioritization and network analysis we found recurrent deleterious mutations in 8 individual genes (STAG2, U2AF1, SMC1A, USP9X, IKZF1, LYN, MYCBP2 and PTPN11) with a strong potential of being involved in APL pathogenesis. Our network analysis of multiple mutations provides a reliable approach to prioritize genes for additional analysis, improving our knowledge of the leukemogenesis interactome. Additionally, we have defined a functional module in the interactome of APL. The hypothesis is that the number, or the specific combinations, of mutations harbored in each patient might not be as important as the disturbance caused in biological key functions, triggered by several not necessarily recurrent mutations.

VL - 11 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26886259?dopt=Abstract ER - TY - JOUR T1 - Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease. JF - Brain Y1 - 2016 A1 - Sevilla, Teresa A1 - Lupo, Vincenzo A1 - Martínez-Rubio, Dolores A1 - Sancho, Paula A1 - Sivera, Rafael A1 - Chumillas, María J A1 - García-Romero, Mar A1 - Pascual-Pascual, Samuel I A1 - Muelas, Nuria A1 - Dopazo, Joaquin A1 - Vílchez, Juan J A1 - Palau, Francesc A1 - Espinós, Carmen KW - Adult KW - Aged KW - Animals KW - Axons KW - Charcot-Marie-Tooth Disease KW - Female KW - gene expression KW - Humans KW - Infant KW - Male KW - Mice KW - Middle Aged KW - mutation KW - Pedigree KW - Phenotype KW - Sciatic Nerve KW - Sural Nerve KW - Transcription Factors KW - Young Adult AB -

Charcot-Marie-Tooth disease (CMT) is a complex disorder with wide genetic heterogeneity. Here we present a new axonal Charcot-Marie-Tooth disease form, associated with the gene microrchidia family CW-type zinc finger 2 (MORC2). Whole-exome sequencing in a family with autosomal dominant segregation identified the novel MORC2 p.R190W change in four patients. Further mutational screening in our axonal Charcot-Marie-Tooth disease clinical series detected two additional sporadic cases, one patient who also carried the same MORC2 p.R190W mutation and another patient that harboured a MORC2 p.S25L mutation. Genetic and in silico studies strongly supported the pathogenicity of these sequence variants. The phenotype was variable and included patients with congenital or infantile onset, as well as others whose symptoms started in the second decade. The patients with early onset developed a spinal muscular atrophy-like picture, whereas in the later onset cases, the initial symptoms were cramps, distal weakness and sensory impairment. Weakness and atrophy progressed in a random and asymmetric fashion and involved limb girdle muscles, leading to a severe incapacity in adulthood. Sensory loss was always prominent and proportional to disease severity. Electrophysiological studies were consistent with an asymmetric axonal motor and sensory neuropathy, while fasciculations and myokymia were recorded rather frequently by needle electromyography. Sural nerve biopsy revealed pronounced multifocal depletion of myelinated fibres with some regenerative clusters and occasional small onion bulbs. Morc2 is expressed in both axons and Schwann cells of mouse peripheral nerve. Different roles in biological processes have been described for MORC2. As the silencing of Charcot-Marie-Tooth disease genes have been associated with DNA damage response, it is tempting to speculate that a deregulation of this pathway may be linked to the axonal degeneration observed in MORC2 neuropathy, thus adding a new pathogenic mechanism to the long list of causes of Charcot-Marie-Tooth disease.

VL - 139 IS - Pt 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26497905?dopt=Abstract ER - TY - JOUR T1 - Progress in pharmacogenetics: consortiums and new strategies. JF - Drug Metab Pers Ther Y1 - 2016 A1 - Maroñas, Olalla A1 - Latorre, Ana A1 - Dopazo, Joaquin A1 - Pirmohamed, Munir A1 - Rodríguez-Antona, Cristina A1 - Siest, Gérard A1 - Carracedo, Ángel A1 - LLerena, Adrián KW - Cooperative Behavior KW - Genome-Wide Association Study KW - High-Throughput Screening Assays KW - Humans KW - Patient Care Team KW - pharmacogenetics KW - Polymorphism, Single Nucleotide KW - Precision Medicine AB -

Pharmacogenetics (PGx), as a field dedicated to achieving the goal of personalized medicine (PM), is devoted to the study of genes involved in inter-individual response to drugs. Due to its nature, PGx requires access to large samples; therefore, in order to progress, the formation of collaborative consortia seems to be crucial. Some examples of this collective effort are the European Society of Pharmacogenomics and personalized Therapy and the Ibero-American network of Pharmacogenetics. As an emerging field, one of the major challenges that PGx faces is translating their discoveries from research bench to bedside. The development of genomic high-throughput technologies is generating a revolution and offers the possibility of producing vast amounts of genome-wide single nucleotide polymorphisms for each patient. Moreover, there is a need of identifying and replicating associations of new biomarkers, and, in addition, a greater effort must be invested in developing regulatory organizations to accomplish a correct standardization. In this review, we outline the current progress in PGx using examples to highlight both the importance of polymorphisms and the research strategies for their detection. These concepts need to be applied together with a proper dissemination of knowledge to improve clinician and patient understanding, in a multidisciplinary team-based approach.

VL - 31 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26913460?dopt=Abstract ER - TY - JOUR T1 - Serum metabolomic profiling facilitates the non-invasive identification of metabolic biomarkers associated with the onset and progression of non-small cell lung cancer. JF - Oncotarget Y1 - 2016 A1 - Puchades-Carrasco, Leonor A1 - Jantus-Lewintre, Eloisa A1 - Pérez-Rambla, Clara A1 - Garcia-Garcia, Francisco A1 - Lucas, Rut A1 - Calabuig, Silvia A1 - Blasco, Ana A1 - Dopazo, Joaquin A1 - Camps, Carlos A1 - Pineda-Lucena, Antonio KW - Adult KW - Aged KW - Biomarkers, Tumor KW - Carcinoma, Non-Small-Cell Lung KW - Disease Progression KW - Female KW - Humans KW - Lung Neoplasms KW - Male KW - metabolomics KW - Middle Aged KW - Proton Magnetic Resonance Spectroscopy AB -

Lung cancer (LC) is responsible for most cancer deaths. One of the main factors contributing to the lethality of this disease is the fact that a large proportion of patients are diagnosed at advanced stages when a clinical intervention is unlikely to succeed. In this study, we evaluated the potential of metabolomics by 1H-NMR to facilitate the identification of accurate and reliable biomarkers to support the early diagnosis and prognosis of non-small cell lung cancer (NSCLC).We found that the metabolic profile of NSCLC patients, compared with healthy individuals, is characterized by statistically significant changes in the concentration of 18 metabolites representing different amino acids, organic acids and alcohols, as well as different lipids and molecules involved in lipid metabolism. Furthermore, the analysis of the differences between the metabolic profiles of NSCLC patients at different stages of the disease revealed the existence of 17 metabolites involved in metabolic changes associated with disease progression.Our results underscore the potential of metabolomics profiling to uncover pathophysiological mechanisms that could be useful to objectively discriminate NSCLC patients from healthy individuals, as well as between different stages of the disease.

VL - 7 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26883203?dopt=Abstract ER - TY - JOUR T1 - Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. JF - Hum Genet Y1 - 2016 A1 - Lucariello, Mario A1 - Vidal, Enrique A1 - Vidal, Silvia A1 - Saez, Mauricio A1 - Roa, Laura A1 - Huertas, Dori A1 - Pineda, Mercè A1 - Dalfó, Esther A1 - Dopazo, Joaquin A1 - Jurado, Paola A1 - Armstrong, Judith A1 - Esteller, Manel KW - Adolescent KW - Adult KW - Animals KW - Caenorhabditis elegans KW - Carrier Proteins KW - Cell Cycle Proteins KW - Child KW - Child, Preschool KW - DNA Mutational Analysis KW - Exome KW - Female KW - Forkhead Transcription Factors KW - Genetic Variation KW - High-Throughput Nucleotide Sequencing KW - Humans KW - Methyl-CpG-Binding Protein 2 KW - mutation KW - Nerve Tissue Proteins KW - Protein Serine-Threonine Kinases KW - Receptors, Nicotinic KW - Rett Syndrome AB -

Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.

VL - 135 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27541642?dopt=Abstract ER - TY - JOUR T1 - BRCA1 Alternative splicing landscape in breast tissue samples. JF - BMC cancer Y1 - 2015 A1 - Romero, Atocha A1 - Garcia-Garcia, Francisco A1 - López-Perolio, Irene A1 - Ruiz de Garibay, Gorka A1 - García-Sáenz, José A A1 - Garre, Pilar A1 - Ayllón, Patricia A1 - Benito, Esperanza A1 - Joaquín Dopazo A1 - Díaz-Rubio, Eduardo A1 - Caldés, Trinidad A1 - de la Hoya, Miguel AB - BACKGROUND: BRCA1 is a key protein in cell network, involved in DNA repair pathways and cell cycle. Recently, the ENIGMA consortium has reported a high number of alternative splicing (AS) events at this locus in blood-derived samples. However, BRCA1 splicing pattern in breast tissue samples is unknown. Here, we provide an accurate description of BRCA1 splicing events distribution in breast tissue samples. METHODS: BRCA1 splicing events were scanned in 70 breast tumor samples, 4 breast samples from healthy individuals and in 72 blood-derived samples by capillary electrophoresis (capillary EP). Molecular subtype was identified in all tumor samples. Splicing events were considered predominant if their relative expression level was at least the 10% of the full-length reference signal. RESULTS: 54 BRCA1 AS events were identified, 27 of them were annotated as predominant in at least one sample. Δ5q, Δ13, Δ9, Δ5 and ▼1aA were significantly more frequently annotated as predominant in breast tumor samples than in blood-derived samples. Predominant splicing events were, on average, more frequent in tumor samples than in normal breast tissue samples (P = 0.010). Similarly, likely inactivating splicing events (PTC-NMDs, Non-Coding, Δ5 and Δ18) were more frequently annotated as predominant in tumor than in normal breast samples (P = 0.020), whereas there were no significant differences for other splicing events (No-Fs) frequency distribution between tumor and normal breast samples (P = 0.689). CONCLUSIONS: Our results complement recent findings by the ENIGMA consortium, demonstrating that BRCA1 AS, despite its tremendous complexity, is similar in breast and blood samples, with no evidences for tissue specific AS events. Further on, we conclude that somatic inactivation of BRCA1 through spliciogenic mutations is, at best, a rare mechanism in breast carcinogenesis, albeit our data detects an excess of likely inactivating AS events in breast tumor samples. VL - 15 UR - http://www.biomedcentral.com/1471-2407/15/219 ER - TY - JOUR T1 - Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. JF - Nature methods Y1 - 2015 A1 - Ewing, Adam D A1 - Houlahan, Kathleen E A1 - Hu, Yin A1 - Ellrott, Kyle A1 - Caloian, Cristian A1 - Yamaguchi, Takafumi N A1 - Bare, J Christopher A1 - P’ng, Christine A1 - Waggott, Daryl A1 - Sabelnykova, Veronica Y A1 - Kellen, Michael R A1 - Norman, Thea C A1 - Haussler, David A1 - Friend, Stephen H A1 - Stolovitzky, Gustavo A1 - Margolin, Adam A A1 - Stuart, Joshua M A1 - Boutros, Paul C ED - ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants ED - Liu Xi ED - Ninad Dewal ED - Yu Fan ED - Wenyi Wang ED - David Wheeler ED - Andreas Wilm ED - Grace Hui Ting ED - Chenhao Li ED - Denis Bertrand ED - Niranjan Nagarajan ED - Qing-Rong Chen ED - Chih-Hao Hsu ED - Ying Hu ED - Chunhua Yan ED - Warren Kibbe ED - Daoud Meerzaman ED - Kristian Cibulskis ED - Mara Rosenberg ED - Louis Bergelson ED - Adam Kiezun ED - Amie Radenbaugh ED - Anne-Sophie Sertier ED - Anthony Ferrari ED - Laurie Tonton ED - Kunal Bhutani ED - Nancy F Hansen ED - Difei Wang ED - Lei Song ED - Zhongwu Lai ED - Liao, Yang ED - Shi, Wei ED - Carbonell-Caballero, José ED - Joaquín Dopazo ED - Cheryl C K Lau ED - Justin Guinney KW - cancer KW - NGS KW - variant calling AB - The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/. UR - http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3407.html ER - TY - JOUR T1 - Differential Features Between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models. JF - J Invest Dermatol Y1 - 2015 A1 - Carretero, M A1 - Guerrero-Aspizua, S A1 - Illera, N A1 - Galvez, V A1 - Navarro, M A1 - García-García, F A1 - Dopazo, J A1 - Jorcano, J L A1 - Larcher, F A1 - Del Rio, M AB -

Psoriasis (PS) and atopic dermatitis (AD) are chronic and relapsing inflammatory diseases of the skin affecting a large number of patients worldwide. Psoriasis is characterized by a Th1/Th17 immunological response whereas acute AD lesions exhibit Th2-dominant inflammation. Current single gene and signaling pathways-based models of inflammatory skin diseases are incomplete. Previous work allowed us to model psoriasis in skin-humanized mice through proper combinations of inflammatory cell components and disruption of barrier function. Herein we describe and characterize an animal model for AD using similar bioengineered-based approaches, by intradermal injection of human Th2 lymphocytes in regenerated human skin after partial removal of stratum corneum. In the present work we have extensively compared this model with the previous and an improved version of the PS model, in which Th17/Th1 lymphocytes replace exogenous cytokines. Comparative expression analyses revealed marked differences in specific epidermal proliferation and differentiation markers and immune-related molecules including antimicrobial peptides. Likewise, the composition of the dermal inflammatory infiltrate presented important differences. Availability of accurate and reliable animal models for these diseases will contribute to the understanding of the pathogenesis and provide valuable tools for drug development and testing.Journal of Investigative Dermatology accepted article preview online, 23 September 2015. doi:10.1038/jid.2015.362.

U1 - https://www.ncbi.nlm.nih.gov/pubmed/26398345?dopt=Abstract ER - TY - JOUR T1 - The EGR2 gene is involved in axonal Charcot-Marie-Tooth disease. JF - Eur J Neurol Y1 - 2015 A1 - Sevilla, T A1 - Sivera, R A1 - Martínez-Rubio, D A1 - Lupo, V A1 - Chumillas, M J A1 - Calpena, E A1 - Dopazo, J A1 - Vílchez, J J A1 - Palau, F A1 - Espinós, C KW - Adult KW - Aged KW - Aged, 80 and over KW - Axons KW - Charcot-Marie-Tooth Disease KW - Early Growth Response Protein 2 KW - Exome KW - Female KW - Humans KW - Male KW - Middle Aged KW - mutation KW - Pedigree KW - Phenotype KW - Severity of Illness Index KW - Young Adult AB -

BACKGROUND AND PURPOSE: A three-generation family affected by axonal Charcot-Marie-Tooth disease (CMT) was investigated with the aim of discovering genetic defects and to further characterize the phenotype.

METHODS: The clinical, nerve conduction studies and muscle magnetic resonance images of the patients were reviewed. A whole exome sequencing was performed and the changes were investigated by genetic studies, in silico analysis and luciferase reporter assays.

RESULTS: A novel c.1226G>A change (p.R409Q) in the EGR2 gene was identified. Patients presented with a typical, late-onset axonal CMT phenotype with variable severity that was confirmed in the ancillary tests. The in silico studies showed that the residue R409 is an evolutionary conserved amino acid. The p.R409Q mutation, which is predicted as probably damaging, would alter the conformation of the protein slightly and would cause a decrease of gene expression.

CONCLUSIONS: This is the first report of an EGR2 mutation presenting as an axonal CMT phenotype with variable severity. This study broadens the phenotype of the EGR2-related neuropathies and suggests that the genetic testing of patients suffering from axonal CMT should include the EGR2 gene.

VL - 22 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26204789?dopt=Abstract ER - TY - JOUR T1 - Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease. JF - Scientific reports Y1 - 2015 A1 - Luzón-Toro, Berta A1 - Gui, Hongsheng A1 - Ruiz-Ferrer, Macarena A1 - Sze-Man Tang, Clara A1 - Fernández, Raquel M A1 - Sham, Pak-Chung A1 - Torroglosa, Ana A1 - Kwong-Hang Tam, Paul A1 - Espino-Paisán, Laura A1 - Cherny, Stacey S A1 - Bleda, Marta A1 - Enguix-Riego, María Del Valle A1 - Joaquín Dopazo A1 - Antiňolo, Guillermo A1 - Garcia-Barceló, Maria-Mercè A1 - Borrego, Salud KW - babelomics KW - Hirschprung KW - NGS KW - prioritization AB - Hirschsprung disease (HSCR; OMIM 142623) is a developmental disorder characterized by aganglionosis along variable lengths of the distal gastrointestinal tract, which results in intestinal obstruction. Interactions among known HSCR genes and/or unknown disease susceptibility loci lead to variable severity of phenotype. Neither linkage nor genome-wide association studies have efficiently contributed to completely dissect the genetic pathways underlying this complex genetic disorder. We have performed whole exome sequencing of 16 HSCR patients from 8 unrelated families with SOLID platform. Variants shared by affected relatives were validated by Sanger sequencing. We searched for genes recurrently mutated across families. Only variations in the FAT3 gene were significantly enriched in five families. Within-family analysis identified compound heterozygotes for AHNAK and several genes (N = 23) with heterozygous variants that co-segregated with the phenotype. Network and pathway analyses facilitated the discovery of polygenic inheritance involving FAT3, HSCR known genes and their gene partners. Altogether, our approach has facilitated the detection of more than one damaging variant in biologically plausible genes that could jointly contribute to the phenotype. Our data may contribute to the understanding of the complex interactions that occur during enteric nervous system development and the etiopathology of familial HSCR. VL - 5 UR - http://www.nature.com/articles/srep16473 ER - TY - JOUR T1 - Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease JF - Scientific Reports Y1 - 2015 A1 - Luzón-Toro, Berta A1 - Gui, Hongsheng A1 - Ruiz-Ferrer, Macarena A1 - Sze-Man Tang, Clara A1 - Fernández, Raquel M. A1 - Sham, Pak-Chung A1 - Torroglosa, Ana A1 - Kwong-Hang Tam, Paul A1 - Espino-Paisán, Laura A1 - Cherny, Stacey S. A1 - Bleda, Marta A1 - Enguix-Riego, María Del Valle A1 - Dopazo, Joaquin A1 - Antiňolo, Guillermo A1 - Garcia-Barceló, Maria-Mercè A1 - Borrego, Salud VL - 5 UR - http://www.nature.com/articles/srep16473http://www.nature.com/articles/srep16473.pdfhttp://www.nature.com/articles/srep16473.pdfhttp://www.nature.com/articles/srep16473 IS - 1 JO - Sci Rep ER - TY - JOUR T1 - Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas JF - BMC Medical Genomics Y1 - 2015 A1 - Luzón-Toro, Berta A1 - Bleda, Marta A1 - Navarro, Elena A1 - García-Alonso, Luz A1 - Ruiz-Ferrer, Macarena A1 - Medina, Ignacio A1 - Martín-Sánchez, Marta A1 - Gonzalez, Cristina Y. A1 - Fernández, Raquel M. A1 - Torroglosa, Ana A1 - Antiňolo, Guillermo A1 - Dopazo, Joaquin A1 - Borrego, Salud AB - The molecular mechanisms leading to sporadic medullary thyroid carcinoma (sMTC) and juvenile papillary thyroid carcinoma (PTC), two rare tumours of the thyroid gland, remain poorly understood. Genetic studies on thyroid carcinomas have been conducted, although just a few loci have been systematically associated. Given the difficulties to obtain single-loci associations, this work expands its scope to the study of epistatic interactions that could help to understand the genetic architecture of complex diseases and explain new heritable components of genetic risk. VL - 8 UR - https://doi.org/10.1186/s12920-015-0160-7 ER - TY - JOUR T1 - Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas. JF - BMC medical genomics Y1 - 2015 A1 - Luzón-Toro, Berta A1 - Bleda, Marta A1 - Navarro, Elena A1 - García-Alonso, Luz A1 - Ruiz-Ferrer, Macarena A1 - Medina, Ignacio A1 - Martín-Sánchez, Marta A1 - Gonzalez, Cristina Y A1 - Fernández, Raquel M A1 - Torroglosa, Ana A1 - Antiňolo, Guillermo A1 - Dopazo, Joaquin A1 - Borrego, Salud KW - epistasis KW - GWAS KW - Thyroid cancer AB - BACKGROUND: The molecular mechanisms leading to sporadic medullary thyroid carcinoma (sMTC) and juvenile papillary thyroid carcinoma (PTC), two rare tumours of the thyroid gland, remain poorly understood. Genetic studies on thyroid carcinomas have been conducted, although just a few loci have been systematically associated. Given the difficulties to obtain single-loci associations, this work expands its scope to the study of epistatic interactions that could help to understand the genetic architecture of complex diseases and explain new heritable components of genetic risk. METHODS: We carried out the first screening for epistasis by Multifactor-Dimensionality Reduction (MDR) in genome-wide association study (GWAS) on sMTC and juvenile PTC, to identify the potential simultaneous involvement of pairs of variants in the disease. RESULTS: We have identified two significant epistatic gene interactions in sMTC (CHFR-AC016582.2 and C8orf37-RNU1-55P) and three in juvenile PTC (RP11-648k4.2-DIO1, RP11-648k4.2-DMGDH and RP11-648k4.2-LOXL1). Interestingly, each interacting gene pair included a non-coding RNA, providing thus support to the relevance that these elements are increasingly gaining to explain carcinoma development and progression. CONCLUSIONS: Overall, this study contributes to the understanding of the genetic basis of thyroid carcinoma susceptibility in two different case scenarios such as sMTC and juvenile PTC. VL - 8 UR - http://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-015-0160-7 ER - TY - JOUR T1 - Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation. JF - BMC genomics Y1 - 2015 A1 - Terol, Javier A1 - Ibañez, Victoria A1 - Carbonell, José A1 - Alonso, Roberto A1 - Estornell, Leandro H A1 - Licciardello, Concetta A1 - Gut, Ivo G A1 - Joaquín Dopazo A1 - Talon, Manuel AB - BACKGROUND: Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. RESULTS: Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5’ end of the deletion. The Arrufatina Mule displayed "dissimilar" 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. CONCLUSIONS: Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements. VL - 16 UR - http://www.biomedcentral.com/1471-2164/16/69 ER - TY - JOUR T1 - Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation JF - BMC Genomics Y1 - 2015 A1 - Terol, Javier A1 - Ibañez, Victoria A1 - Carbonell, José A1 - Alonso, Roberto A1 - Estornell, Leandro H. A1 - Licciardello, Concetta A1 - Gut, Ivo G. A1 - Dopazo, Joaquin A1 - Talon, Manuel AB - Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. VL - 16 UR - https://doi.org/10.1186/s12864-015-1280-3 ER - TY - JOUR T1 - PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. JF - Nucleic Acids Res Y1 - 2015 A1 - Minguez, Pablo A1 - Letunic, Ivica A1 - Parca, Luca A1 - García-Alonso, Luz A1 - Dopazo, Joaquin A1 - Huerta-Cepas, Jaime A1 - Bork, Peer KW - Databases, Protein KW - Internet KW - Protein Interaction Mapping KW - Protein Processing, Post-Translational AB -

The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs. We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting proteins. In order to make data available for understudied organisms, PTMcode v2 (http://ptmcode.embl.de) includes a new strategy to propagate PTMs from validated modified sites through orthologous proteins. The second release of PTMcode covers 19 eukaryotic species from which we collected more than 300,000 experimentally verified PTMs (>1,300,000 propagated) of 69 types extracting the post-translational regulation of >100,000 proteins and >100,000 interactions. In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs.

VL - 43 IS - Database issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/25361965?dopt=Abstract ER - TY - JOUR T1 - Therapeutic targets for olive pollen allergy defined by gene markers modulated by Ole e 1-derived peptides. JF - Molecular immunology Y1 - 2015 A1 - Calzada, David A1 - Aguerri, Miriam A1 - Baos, Selene A1 - Montaner, David A1 - Mata, Manuel A1 - Joaquín Dopazo A1 - Quiralte, Joaquín A1 - Florido, Fernando A1 - Lahoz, Carlos A1 - Cárdaba, Blanca AB - Two regions of Ole e 1, the major olive-pollen allergen, have been characterized as T-cell epitopes, one as immunodominant region (aa91-130) and the other, as mainly recognized by non-allergic subjects (aa10-31). This report tries to characterize the specific relevance of these epitopes in the allergic response to olive pollen by analyzing the secreted cytokines and the gene expression profiles induced after specific stimulation of peripheral blood mononuclear cells (PBMCs). PBMCs from olive pollen-allergic and non-allergic control subjects were stimulated with olive-pollen extract and Ole e 1 dodecapeptides containing relevant T-cell epitopes. Levels of cytokines were measured in cellular supernatants and gene expression was determined by microarrays, on the RNAs extracted from PBMCs. One hundred eighty-nine differential genes (fold change >2 or <-2, P<0.05) were validated by qRT-PCR in a large population. It was not possible to define a pattern of response according the overall cytokine results but interesting differences were observed, mainly in the regulatory cytokines. Principal component (PCA) gene-expression analysis defined clusters that correlated with the experimental conditions in the group of allergic subjects. Gene expression and functional analyses revealed differential genes and pathways among the experimental conditions. A set of 51 genes (many essential to T-cell tolerance and homeostasis) correlated with the response to aa10-31 of Ole e 1. In conclusion, two peptides derived from Ole e 1 could regulate the immune response in allergic patients, by gene-expression modification of several regulation-related genes. These results open new research ways to the regulation of allergy by Oleaceae family members. VL - 64 UR - http://www.sciencedirect.com/science/article/pii/S0161589014003356 ER - TY - JOUR T1 - Whole Exome Sequencing Reveals ZNF408 as a New Gene Associated With Autosomal Recessive Retinitis Pigmentosa with Vitreal Alterations. JF - Human molecular genetics Y1 - 2015 A1 - Avila-Fernandez, Almudena A1 - Perez-Carro, Raquel A1 - Corton, Marta A1 - Lopez-Molina, Maria Isabel A1 - Campello, Laura A1 - Garanto, Alex A1 - Fernadez-Sanchez, Laura A1 - Duijkers, Lonneke A1 - Lopez-Martinez, Miguel Angel A1 - Riveiro-Alvarez, Rosa A1 - da Silva, Luciana Rodrigues Jacy A1 - Sanchez-Alcudia, Rocío A1 - Martin-Garrido, Esther A1 - Reyes, Noelia A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Garcia-Sandoval, Blanca A1 - Collin, Rob W A1 - Cuenca, Nicolas A1 - Ayuso, Carmen AB - Retinitis Pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype-phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors ten predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina. VL - 24 UR - http://hmg.oxfordjournals.org/content/early/2015/04/16/hmg.ddv140.abstract ER - TY - JOUR T1 - Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. JF - Hum Mol Genet Y1 - 2015 A1 - Avila-Fernandez, Almudena A1 - Perez-Carro, Raquel A1 - Corton, Marta A1 - Lopez-Molina, Maria Isabel A1 - Campello, Laura A1 - Garanto, Alejandro A1 - Fernandez-Sanchez, Laura A1 - Duijkers, Lonneke A1 - Lopez-Martinez, Miguel Angel A1 - Riveiro-Alvarez, Rosa A1 - da Silva, Luciana Rodrigues Jacy A1 - Sanchez-Alcudia, Rocío A1 - Martin-Garrido, Esther A1 - Reyes, Noelia A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Garcia-Sandoval, Blanca A1 - Collin, Rob W J A1 - Cuenca, Nicolas A1 - Ayuso, Carmen KW - Amino Acid Sequence KW - Animals KW - Chlorocebus aethiops KW - Chromosome Mapping KW - COS Cells KW - DNA-Binding Proteins KW - Exome KW - Genome-Wide Association Study KW - High-Throughput Nucleotide Sequencing KW - Homozygote KW - Humans KW - Molecular Sequence Data KW - Mutant Proteins KW - Pedigree KW - Retina KW - Retinal Cone Photoreceptor Cells KW - Retinal Rod Photoreceptor Cells KW - Retinitis pigmentosa KW - Transcription Factors AB -

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype-phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.

VL - 24 IS - 14 U1 - https://www.ncbi.nlm.nih.gov/pubmed/25882705?dopt=Abstract ER - TY - JOUR T1 - The Activation of the Sox2 RR2 Pluripotency Transcriptional Reporter in Human Breast Cancer Cell Lines is Dynamic and Labels Cells with Higher Tumorigenic Potential. JF - Front Oncol Y1 - 2014 A1 - Iglesias, Juan Manuel A1 - Leis, Olatz A1 - Pérez Ruiz, Estíbaliz A1 - Gumuzio Barrie, Juan A1 - Garcia-Garcia, Francisco A1 - Aduriz, Ariane A1 - Beloqui, Izaskun A1 - Hernandez-Garcia, Susana A1 - Lopez-Mato, Maria Paz A1 - Dopazo, Joaquin A1 - Pandiella, Atanasio A1 - Menendez, Javier A A1 - Martin, Angel Garcia AB -

The striking similarity displayed at the mechanistic level between tumorigenesis and the generation of induced pluripotent stem cells and the fact that genes and pathways relevant for embryonic development are reactivated during tumor progression highlights the link between pluripotency and cancer. Based on these observations, we tested whether it is possible to use a pluripotency-associated transcriptional reporter, whose activation is driven by the SRR2 enhancer from the Sox2 gene promoter (named S4+ reporter), to isolate cancer stem cells (CSCs) from breast cancer cell lines. The S4+ pluripotency transcriptional reporter allows the isolation of cells with enhanced tumorigenic potential and its activation was switched on and off in the cell lines studied, reflecting a plastic cellular process. Microarray analysis comparing the populations in which the reporter construct is active versus inactive showed that positive cells expressed higher mRNA levels of cytokines (IL-8, IL-6, TNF) and genes (such as ATF3, SNAI2, and KLF6) previously related with the CSC phenotype in breast cancer.

VL - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/25414831?dopt=Abstract ER - TY - JOUR T1 - Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. JF - Nature communications Y1 - 2014 A1 - Munro, Sarah A A1 - Lund, Steven P A1 - Pine, P Scott A1 - Binder, Hans A1 - Clevert, Djork-Arné A1 - Ana Conesa A1 - Dopazo, Joaquin A1 - Fasold, Mario A1 - Hochreiter, Sepp A1 - Hong, Huixiao A1 - Jafari, Nadereh A1 - Kreil, David P A1 - Labaj, Paweł P A1 - Li, Sheng A1 - Liao, Yang A1 - Lin, Simon M A1 - Meehan, Joseph A1 - Mason, Christopher E A1 - Santoyo-López, Javier A1 - Setterquist, Robert A A1 - Shi, Leming A1 - Shi, Wei A1 - Smyth, Gordon K A1 - Stralis-Pavese, Nancy A1 - Su, Zhenqiang A1 - Tong, Weida A1 - Wang, Charles A1 - Wang, Jian A1 - Xu, Joshua A1 - Ye, Zhan A1 - Yang, Yong A1 - Yu, Ying A1 - Salit, Marc KW - RNA-seq AB - There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here we assess technical performance with a proposed standard ’dashboard’ of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared among 12 laboratories with three different measurement processes demonstrates generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias are also comparable among laboratories for the same measurement process. We observe different biases for measurement processes using different mRNA-enrichment protocols. VL - 5 UR - http://www.nature.com/ncomms/2014/140925/ncomms6125/full/ncomms6125.html ER - TY - JOUR T1 - Combined genetic and high-throughput strategies for molecular diagnosis of inherited retinal dystrophies. JF - PloS one Y1 - 2014 A1 - de Castro-Miró, Marta A1 - Pomares, Esther A1 - Lorés-Motta, Laura A1 - Tonda, Raul A1 - Joaquín Dopazo A1 - Marfany, Gemma A1 - Gonzàlez-Duarte, Roser AB - Most diagnostic laboratories are confronted with the increasing demand for molecular diagnosis from patients and families and the ever-increasing genetic heterogeneity of visual disorders. Concerning Retinal Dystrophies (RD), almost 200 causative genes have been reported to date, and most families carry private mutations. We aimed to approach RD genetic diagnosis using all the available genetic information to prioritize candidates for mutational screening, and then restrict the number of cases to be analyzed by massive sequencing. We constructed and optimized a comprehensive cosegregation RD-chip based on SNP genotyping and haplotype analysis. The RD-chip allows to genotype 768 selected SNPs (closely linked to 100 RD causative genes) in a single cost-, time-effective step. Full diagnosis was attained in 17/36 Spanish pedigrees, yielding 12 new and 12 previously reported mutations in 9 RD genes. The most frequently mutated genes were USH2A and CRB1. Notably, RD3-up to now only associated to Leber Congenital Amaurosis- was identified as causative of Retinitis Pigmentosa. The main assets of the RD-chip are: i) the robustness of the genetic information that underscores the most probable candidates, ii) the invaluable clues in cases of shared haplotypes, which are indicative of a common founder effect, and iii) the detection of extended haplotypes over closely mapping genes, which substantiates cosegregation, although the assumptions in which the genetic analysis is based could exceptionally lead astray. The combination of the genetic approach with whole exome sequencing (WES) greatly increases the diagnosis efficiency, and revealed novel mutations in USH2A and GUCY2D. Overall, the RD-chip diagnosis efficiency ranges from 16% in dominant, to 80% in consanguineous recessive pedigrees, with an average of 47%, well within the upper range of massive sequencing approaches, highlighting the validity of this time- and cost-effective approach whilst high-throughput methodologies become amenable for routine diagnosis in medium sized labs. VL - 9 UR - http://dx.plos.org/10.1371/journal.pone.0088410 ER - TY - JOUR T1 - A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. JF - Nature biotechnology Y1 - 2014 A1 - Su, Z. A1 - Labaj, P.P. A1 - .... A1 - Dopazo, J. A1 - .... A1 - Mason, C.E. A1 - Shi, L KW - NGS KW - RNA-seq KW - SEQC AB - We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. VL - 32 UR - http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2957.html ER - TY - JOUR T1 - Molecular interactions between sugar beet and Polymyxa betae during its life cycle JF - Annals of Applied Biology Y1 - 2014 A1 - N. Desoignies A1 - Carbonell, J. A1 - J.-S. Moreau A1 - A. Conesa A1 - Dopazo, J. A1 - A. Legrève AB - Polymyxa betae is a biotrophic obligate sugar beet parasite that belongs to plasmodiophorids. The infection of sugar beet roots by this parasite is asymptomatic, except when it transmits Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. To date, there has been little work on P. betae–sugar beet molecular interactions, mainly because of the obligate nature of the parasite and also because research on rhizomania has tended to focus on the virus. In this study, we investigated these interactions through differential transcript analysis, using suppressive subtractive hybridization. The analysis included 76 P. betae and 120 sugar beet expressed sequence tags (ESTs). The expression of selected ESTs from both organisms was monitored during the protist life cycle, revealing a potential role of two P. betae proteins, profilin and a Von Willebrand factor domain-containing protein, in the early phase of infection. This study also revealed an over-expression of some sugar beet genes involved in defence, such as those encoding PR proteins, stress resistance proteins or lectins, especially during the plasmodial stage of the P. betae life cycle. In addition to providing new information on the molecular aspects of P. betae–sugar beet interactions, this study also enabled previously unknown ESTs of P. betae to be sequenced, thus enhancing our knowledge of the genome of this protist. VL - 164 UR - http://onlinelibrary.wiley.com/doi/10.1111/aab.12095/abstract ER - TY - JOUR T1 - A New Overgrowth Syndrome is Due to Mutations in RNF125. JF - Human mutation Y1 - 2014 A1 - Tenorio, Jair A1 - Mansilla, Alicia A1 - Valencia, María A1 - Martínez-Glez, Víctor A1 - Romanelli, Valeria A1 - Arias, Pedro A1 - Castrejón, Nerea A1 - Poletta, Fernando A1 - Guillén-Navarro, Encarna A1 - Gordo, Gema A1 - Mansilla, Elena A1 - García-Santiago, Fé A1 - González-Casado, Isabel A1 - Vallespín, Elena A1 - Palomares, María A1 - Mori, María A A1 - Santos-Simarro, Fernando A1 - García-Miñaur, Sixto A1 - Fernández, Luis A1 - Mena, Rocío A1 - Benito-Sanz, Sara A1 - Del Pozo, Angela A1 - Silla, Juan Carlos A1 - Ibañez, Kristina A1 - López-Granados, Eduardo A1 - Martín-Trujillo, Alex A1 - Montaner, David A1 - Heath, Karen E A1 - Campos-Barros, Angel A1 - Joaquín Dopazo A1 - Nevado, Julián A1 - Monk, David A1 - Ruiz-Pérez, Víctor L A1 - Lapunzina, Pablo KW - NGS KW - prioritization KW - Rare Disease AB - Overgrowth syndromes (OGS) are a group of disorders in which all parameters of growth and physical development are above the mean for age and sex. We evaluated a series of 270 families from the Spanish Overgrowth Syndrome Registry with no known overgrowth syndrome. We identified one de novo deletion and three missense mutations in RNF125 in six patients from 4 families with overgrowth, macrocephaly, intellectual disability, mild hydrocephaly, hypoglycaemia and inflammatory diseases resembling Sjögren syndrome. RNF125 encodes an E3 ubiquitin ligase and is a novel gene of OGS. Our studies of the RNF125 pathway point to upregulation of RIG-I-IPS1-MDA5 and/or disruption of the PI3K-AKT and interferon signaling pathways as the putative final effectors. This article is protected by copyright. All rights reserved. VL - 35 UR - http://onlinelibrary.wiley.com/doi/10.1002/humu.22689/abstract ER - TY - JOUR T1 - ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. JF - Bioinformatics Y1 - 2014 A1 - López-Domingo, Francisco J A1 - Florido, Javier P A1 - Rueda, Antonio A1 - Dopazo, Joaquin A1 - Santoyo-López, Javier KW - Exome KW - Genome, Human KW - High-Throughput Nucleotide Sequencing KW - Humans KW - Sequence Analysis, DNA KW - Software AB -

MOTIVATION: Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human genome. The efficiency and the lack of bias in the enrichment process need to be assessed as a quality control step before performing downstream analysis of the sequence data. Tools that can report on the sensitivity, specificity, uniformity and other enrichment-specific features are needed.

RESULTS: We have implemented the next-generation sequencing data Capture Assessment Tool (ngsCAT), a tool that takes the information of the mapped reads and the coordinates of the targeted regions as input files, and generates a report with metrics and figures that allows the evaluation of the efficiency of the enrichment process. The tool can also take as input the information of two samples allowing the comparison of two different experiments.

AVAILABILITY AND IMPLEMENTATION: Documentation and downloads for ngsCAT can be found at http://www.bioinfomgp.org/ngscat.

VL - 30 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24578402?dopt=Abstract ER - TY - JOUR T1 - Programmed cell death activated by Rose Bengal in Arabidopsis thaliana cell suspension cultures requires functional chloroplasts. JF - Journal of experimental botany Y1 - 2014 A1 - Gutiérrez, Jorge A1 - González-Pérez, Sergio A1 - Garcia-Garcia, Francisco A1 - Daly, Cara T A1 - Lorenzo, Oscar A1 - Revuelta, José L A1 - McCabe, Paul F A1 - Arellano, Juan B AB - Light-grown Arabidopsis thaliana cell suspension culture (ACSC) were subjected to mild photooxidative damage with Rose Bengal (RB) with the aim of gaining a better understanding of singlet oxygen-mediated defence responses in plants. Additionally, ACSC were treated with H2O2 at concentrations that induced comparable levels of protein oxidation damage. Under low to medium light conditions, both RB and H2O2 treatments activated transcriptional defence responses and inhibited photosynthetic activity, but they differed in that programmed cell death (PCD) was only observed in cells treated with RB. When dark-grown ACSC were subjected to RB in the light, PCD was suppressed, indicating that the singlet oxygen-mediated signalling pathway in ACSC requires functional chloroplasts. Analysis of up-regulated transcripts in light-grown ACSC, treated with RB in the light, showed that both singlet oxygen-responsive transcripts and transcripts with a key role in hormone-activated PCD (i.e. ethylene and jasmonic acid) were present. A co-regulation analysis proved that ACSC treated with RB exhibited higher correlation with the conditional fluorescence (flu) mutant than with other singlet oxygen-producing mutants or wild-type plants subjected to high light. However, there was no evidence for the up-regulation of EDS1, suggesting that activation of PCD was not associated with the EXECUTER- and EDS1-dependent signalling pathway described in the flu mutant. Indigo Carmine and Methylene Violet, two photosensitizers unable to enter chloroplasts, did not activate transcriptional defence responses in ACSC; however, whether this was due to their location or to their inherently low singlet oxygen quantum efficiencies was not determined. UR - http://jxb.oxfordjournals.org/content/early/2014/04/09/jxb.eru151.long ER - TY - JOUR T1 - Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. JF - Fungal Genet Biol Y1 - 2014 A1 - Larriba, Eduardo A1 - Jaime, María D L A A1 - Carbonell-Caballero, José A1 - Conesa, Ana A1 - Dopazo, Joaquin A1 - Nislow, Corey A1 - Martín-Nieto, José A1 - Lopez-Llorca, Luis Vicente KW - Animals KW - Ascomycota KW - Female KW - Gene Expression Regulation, Fungal KW - Gene ontology KW - Genome, Fungal KW - Hordeum KW - Host-Pathogen Interactions KW - Nematoda KW - Ovum KW - Phylogeny KW - Plant Roots KW - Sequence Analysis, DNA KW - Signal Transduction KW - Transcriptome AB -

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.

VL - 65 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24530791?dopt=Abstract ER - TY - JOUR T1 - Two novel mutations in the BCKDK (branched-chain keto-acid dehydrogenase kinase) gene are responsible for a neurobehavioral deficit in two pediatric unrelated patients. JF - Hum Mutat Y1 - 2014 A1 - García-Cazorla, Angels A1 - Oyarzabal, Alfonso A1 - Fort, Joana A1 - Robles, Concepción A1 - Castejón, Esperanza A1 - Ruiz-Sala, Pedro A1 - Bodoy, Susanna A1 - Merinero, Begoña A1 - Lopez-Sala, Anna A1 - Dopazo, Joaquin A1 - Nunes, Virginia A1 - Ugarte, Magdalena A1 - Artuch, Rafael A1 - Palacín, Manuel A1 - Rodríguez-Pombo, Pilar A1 - Alcaide, Patricia A1 - Navarrete, Rosa A1 - Sanz, Paloma A1 - Font-Llitjós, Mariona A1 - Vilaseca, Ma Antonia A1 - Ormaizabal, Aida A1 - Pristoupilova, Anna A1 - Agulló, Sergi Beltran KW - Amino Acids, Branched-Chain KW - Developmental Disabilities KW - Fibroblasts KW - Humans KW - Male KW - Mutation, Missense KW - Nervous System Diseases KW - Pediatrics KW - Protein Kinases AB -

Inactivating mutations in the BCKDK gene, which codes for the kinase responsible for the negative regulation of the branched-chain α-keto acid dehydrogenase complex (BCKD), have recently been associated with a form of autism in three families. In this work, two novel exonic BCKDK mutations, c.520C>G/p.R174G and c.1166T>C/p.L389P, were identified at the homozygous state in two unrelated children with persistently reduced body fluid levels of branched-chain amino acids (BCAAs), developmental delay, microcephaly, and neurobehavioral abnormalities. Functional analysis of the mutations confirmed the missense character of the c.1166T>C change and showed a splicing defect r.[520c>g;521_543del]/p.R174Gfs1*, for c.520C>G due to the presence of a new donor splice site. Mutation p.L389P showed total loss of kinase activity. Moreover, patient-derived fibroblasts showed undetectable (p.R174Gfs1*) or barely detectable (p.L389P) levels of BCKDK protein and its phosphorylated substrate (phospho-E1α), resulting in increased BCKD activity and the very rapid BCAA catabolism manifested by the patients' clinical phenotype. Based on these results, a protein-rich diet plus oral BCAA supplementation was implemented in the patient homozygous for p.R174Gfs1*. This treatment normalized plasma BCAA levels and improved growth, developmental and behavioral variables. Our results demonstrate that BCKDK mutations can result in neurobehavioral deficits in humans and support the rationale for dietary intervention.

VL - 35 IS - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24449431?dopt=Abstract ER - TY - JOUR T1 - Two Novel Mutations in the BCKDK Gene (Branched-Chain Keto-Acid Dehydrogenase Kinase) are Responsible of a Neurobehavioral Deficit in two Pediatric Unrelated Patients. JF - Human mutation Y1 - 2014 A1 - García-Cazorla, Angels A1 - Oyarzabal, Alfonso A1 - Fort, Joana A1 - Robles, Concepción A1 - Castejón, Esperanza A1 - Ruiz-Sala, Pedro A1 - Bodoy, Susanna A1 - Merinero, Begoña A1 - Lopez-Sala, Anna A1 - Joaquín Dopazo A1 - Nunes, Virginia A1 - Ugarte, Magdalena A1 - Artuch, Rafael A1 - Palacín, Manuel A1 - Rodríguez-Pombo, Pilar AB - Inactivating mutations in the BCKDK gene, which codes for the kinase responsible for the negative regulation of the branched-chain keto-acid dehydrogenase complex (BCKD), have recently been associated with a form of autism in three families. In this work, two novel exonic BCKDK mutations, c.520C>G/p.R174G and c.1166T>C/p.L389P, were identified at the homozygous state in two unrelated children with persistently reduced body fluid levels of branched-chain amino acids (BCAAs), developmental delay, microcephaly and neurobehavioral abnormalities. Functional analysis of the mutations confirmed the missense character of the c.1166T>C change and showed a splicing defect r.[520c>g;521_543del]/p.R174Gfs1*, for c.520C>G due to the presence of a new donor splice site. Mutation p.L389P showed total loss of kinase activity. Moreover, patient-derived fibroblasts showed undetectable (p.R174Gfs1*) or barely detectable (p.L389P) levels of BCKDK protein and its phosphorylated substrate (phospho-E1α), resulting in increased BCKD activity and the very rapid BCAA catabolism manifested by the patients’ clinical phenotype. Based on these results, a protein-rich diet plus oral BCAA supplementation was implemented in the patient homozygous for p.R174Gfs1*. This treatment normalized plasma BCAA levels and improved growth, developmental and behavioral variables. Our results demonstrate that BCKDK mutations can result in neurobehavioral deficits in humans and support the rationale for dietary intervention. This article is protected by copyright. All rights reserved. VL - 35 UR - http://onlinelibrary.wiley.com/doi/10.1002/humu.22513/abstract ER - TY - JOUR T1 - Differential gene-expression analysis defines a molecular pattern related to olive pollen allergy. JF - J Biol Regul Homeost Agents Y1 - 2013 A1 - Aguerri, M A1 - Calzada, D A1 - Montaner, D A1 - Mata, M A1 - Florido, F A1 - Quiralte, J A1 - Dopazo, J A1 - Lahoz, C A1 - Cardaba, B KW - Adult KW - Female KW - Gene Expression Profiling KW - Humans KW - Male KW - Middle Aged KW - Olea KW - Principal Component Analysis KW - Rhinitis, Allergic, Seasonal AB -

Analysis of gene-expression profiles by microarrays is useful for characterization of candidate genes, key regulatory networks, and to define phenotypes or molecular signatures which improve the diagnosis and/or classification of the allergic processes. We have used this approach in the study of olive pollen response in order to find differential molecular markers among responders and non-responders to this allergenic source. Five clinical groups, non-allergic, asymptomatic, allergic but not to olive pollen, untreated-olive-pollen allergic patients and olive-pollen allergic patients (under specific-immunotherapy), were assessed during and outside pollen seasons. Whole-genome gene expression analysis was performed in RNAs extracted from PBMCs. After assessment of data quality and principal components analysis (PCA), differential gene-expression, by multiple testing and, functional analyses by KEGG, for pathways and Gene-Ontology for biological processes were performed. Relevance was defined by fold change and corrected P values (less than 0.05). The most differential genes were validated by qRT-PCR in a larger set of individuals. Interestingly, gene-expression profiling obtained by PCA clearly showed five clusters of samples that correlated with the five clinical groups. Furthermore, differential gene expression and functional analyses revealed differential genes and pathways in the five clinical groups. The 93 most significant genes found were validated, and one set of 35 genes was able to discriminate profiles of olive pollen response. Our results, in addition to providing new information on allergic response, define a possible molecular signature for olive pollen allergy which could be useful for the diagnosis and treatment of this and other sensitizations.

VL - 27 IS - 2 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23830385?dopt=Abstract ER - TY - JOUR T1 - Grape antioxidant dietary fiber (GADF) inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. JF - Carcinogenesis Y1 - 2013 A1 - Sánchez-Tena, Susana A1 - Lizarraga, Daneida A1 - Miranda, Anibal A1 - Vinardell, Maria Pilar A1 - Garcia-Garcia, Francisco A1 - Joaquín Dopazo A1 - Torres, Josep Lluís A1 - Saura-Calixto, Fulgencio A1 - Capellà, Gabriel A1 - Cascante, Marta AB - Epidemiological and experimental studies suggest that fiber and phenolic compounds might have a protective effect on the development of colon cancer in humans. Accordingly, we assessed the chemopreventive efficacy and associated mechanisms of action of a lyophilized red grape pomace containing proanthocyanidin-rich dietary fiber (Grape Antioxidant Dietary Fiber, GADF) on spontaneous intestinal tumorigenesis in the Apc(Min/+) mouse model. Mice were fed a standard diet (control group) or a 1% (w/w) GADF-supplemented diet (GADF group) for 6 weeks. GADF supplementation greatly reduced intestinal tumorigenesis, significantly decreasing the total number of polyps by 76%. Moreover, size distribution analysis showed a considerable reduction in all polyp size categories [diameter <1 mm (65%), 1-2 mm (67%) and >2 mm (87%)]. In terms of polyp formation in the proximal, middle and distal portions of the small intestine a decrease of 76%, 81% and 73% was observed respectively. Putative molecular mechanisms underlying the inhibition of intestinal tumorigenesis were investigated by comparison of microarray expression profiles of GADF-treated and non-treated mice. We observed that the effects of GADF are mainly associated with the induction of a G1 cell cycle arrest and the downregulation of genes related to the immune response and inflammation. Our findings show for the first time the efficacy and associated mechanisms of action of GADF against intestinal tumorigenesis in Apc(Min/+) mice, suggesting its potential for the prevention of colorectal cancer. UR - http://carcin.oxfordjournals.org/content/early/2013/04/23/carcin.bgt140.abstract ER - TY - JOUR T1 - Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. JF - Carcinogenesis Y1 - 2013 A1 - Sánchez-Tena, Susana A1 - Lizarraga, Daneida A1 - Miranda, Anibal A1 - Vinardell, Maria P A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Torres, Josep L A1 - Saura-Calixto, Fulgencio A1 - Capellà, Gabriel A1 - Cascante, Marta KW - Animals KW - Antioxidants KW - Body Weight KW - Carcinogenesis KW - Cell Cycle KW - Cell Cycle Checkpoints KW - Colorectal Neoplasms KW - Dietary Fiber KW - Dietary Supplements KW - Down-Regulation KW - G1 Phase KW - Inflammation KW - Intestinal Polyposis KW - Intestinal Polyps KW - Intestine, Small KW - Male KW - Mice KW - Transcriptome KW - Vitis AB -

Epidemiological and experimental studies suggest that fiber and phenolic compounds might have a protective effect on the development of colon cancer in humans. Accordingly, we assessed the chemopreventive efficacy and associated mechanisms of action of a lyophilized red grape pomace containing proanthocyanidin (PA)-rich dietary fiber [grape antioxidant dietary fiber (GADF)] on spontaneous intestinal tumorigenesis in the Apc(Min/+) mouse model. Mice were fed a standard diet (control group) or a 1% (w/w) GADF-supplemented diet (GADF group) for 6 weeks. GADF supplementation greatly reduced intestinal tumorigenesis, significantly decreasing the total number of polyps by 76%. Moreover, size distribution analysis showed a considerable reduction in all polyp size categories [diameter <1mm (65%), 1-2mm (67%) and >2mm (87%)]. In terms of polyp formation in the proximal, middle and distal portions of the small intestine, a decrease of 76, 81 and 73% was observed, respectively. Putative molecular mechanisms underlying the inhibition of intestinal tumorigenesis were investigated by comparison of microarray expression profiles of GADF-treated and non-treated mice. We observed that the effects of GADF are mainly associated with the induction of a G1 cell cycle arrest and the downregulation of genes related to the immune response and inflammation. Our findings show for the first time the efficacy and associated mechanisms of action of GADF against intestinal tumorigenesis in Apc(Min/+) mice, suggesting its potential for the prevention of colorectal cancer.

VL - 34 IS - 8 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23615403?dopt=Abstract ER - TY - JOUR T1 - Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin JF - PLoS ONE Y1 - 2013 A1 - Manuel Iglesias, Juan A1 - Beloqui, Izaskun A1 - Garcia-Garcia, Francisco A1 - Leis, Olatz A1 - Vazquez-Martin, Alejandro A1 - Eguiara, Arrate A1 - Cufi, Silvia A1 - Pavon, Andres A1 - Menendez, Javier A. A1 - Dopazo, Joaquin A1 - Martin, Angel G. AB -

Tumors are heterogeneous at the cellular level where the ability to maintain tumor growth resides in discrete cell populations. Floating sphere-forming assays are broadly used to test stem cell activity in tissues, tumors and cell lines. Spheroids are originated from a small population of cells with stem cell features able to grow in suspension culture and behaving as tumorigenic in mice. We tested the ability of eleven common breast cancer cell lines representing the major breast cancer subtypes to grow as mammospheres, measuring the ability to maintain cell viability upon serial non-adherent passage. Only MCF7, T47D, BT474, MDA-MB-436 and JIMT1 were successfully propagated as long-term mammosphere cultures, measured as the increase in the number of viable cells upon serial non-adherent passages. Other cell lines tested (SKBR3, MDA-MB-231, MDA-MB-468 and MDA-MB-435) formed cell clumps that can be disaggregated mechanically, but cell viability drops dramatically on their second passage. HCC1937 and HCC1569 cells formed typical mammospheres, although they could not be propagated as long-term mammosphere cultures. All the sphere forming lines but MDA-MB-436 express E-cadherin on their surface. Knock down of E-cadherin expression in MCF-7 cells abrogated its ability to grow as mammospheres, while re-expression of E-cadherin in SKBR3 cells allow them to form mammospheres. Therefore, the mammosphere assay is suitable to reveal stem like features in breast cancer cell lines that express E-cadherin.

PB - Public Library of Science VL - 8 UR - http://dx.doi.org/10.1371%2Fjournal.pone.0077281 ER - TY - JOUR T1 - Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin. JF - PLoS One Y1 - 2013 A1 - Manuel Iglesias, Juan A1 - Beloqui, Izaskun A1 - Garcia-Garcia, Francisco A1 - Leis, Olatz A1 - Vazquez-Martin, Alejandro A1 - Eguiara, Arrate A1 - Cufi, Silvia A1 - Pavon, Andres A1 - Menendez, Javier A A1 - Dopazo, Joaquin A1 - Martin, Angel G KW - Breast Neoplasms KW - Cadherins KW - Cell Line, Tumor KW - Cell Proliferation KW - Cluster Analysis KW - Female KW - gene expression KW - Gene Expression Profiling KW - Gene Expression Regulation, Neoplastic KW - Gene Knockdown Techniques KW - Humans KW - MCF-7 Cells KW - Neoplastic Stem Cells KW - Spheroids, Cellular KW - Tumor Cells, Cultured AB -

Tumors are heterogeneous at the cellular level where the ability to maintain tumor growth resides in discrete cell populations. Floating sphere-forming assays are broadly used to test stem cell activity in tissues, tumors and cell lines. Spheroids are originated from a small population of cells with stem cell features able to grow in suspension culture and behaving as tumorigenic in mice. We tested the ability of eleven common breast cancer cell lines representing the major breast cancer subtypes to grow as mammospheres, measuring the ability to maintain cell viability upon serial non-adherent passage. Only MCF7, T47D, BT474, MDA-MB-436 and JIMT1 were successfully propagated as long-term mammosphere cultures, measured as the increase in the number of viable cells upon serial non-adherent passages. Other cell lines tested (SKBR3, MDA-MB-231, MDA-MB-468 and MDA-MB-435) formed cell clumps that can be disaggregated mechanically, but cell viability drops dramatically on their second passage. HCC1937 and HCC1569 cells formed typical mammospheres, although they could not be propagated as long-term mammosphere cultures. All the sphere forming lines but MDA-MB-436 express E-cadherin on their surface. Knock down of E-cadherin expression in MCF-7 cells abrogated its ability to grow as mammospheres, while re-expression of E-cadherin in SKBR3 cells allow them to form mammospheres. Therefore, the mammosphere assay is suitable to reveal stem like features in breast cancer cell lines that express E-cadherin.

VL - 8 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24124614?dopt=Abstract ER - TY - JOUR T1 - Maslinic Acid-Enriched Diet Decreases Intestinal Tumorigenesis in Apc(Min/+) Mice through Transcriptomic and Metabolomic Reprogramming. JF - PloS one Y1 - 2013 A1 - Sánchez-Tena, Susana A1 - Reyes-Zurita, Fernando J A1 - Díaz-Moralli, Santiago A1 - Vinardell, Maria Pilar A1 - Reed, Michelle A1 - Garcia-Garcia, Francisco A1 - Joaquín Dopazo A1 - Lupiáñez, José A A1 - Günther, Ulrich A1 - Cascante, Marta AB - Chemoprevention is a pragmatic approach to reduce the risk of colorectal cancer, one of the leading causes of cancer-related death in western countries. In this regard, maslinic acid (MA), a pentacyclic triterpene extracted from wax-like coatings of olives, is known to inhibit proliferation and induce apoptosis in colon cancer cell lines without affecting normal intestinal cells. The present study evaluated the chemopreventive efficacy and associated mechanisms of maslinic acid treatment on spontaneous intestinal tumorigenesis in Apc(Min/+) mice. Twenty-two mice were randomized into 2 groups: control group and MA group, fed with a maslinic acid-supplemented diet for six weeks. MA treatment reduced total intestinal polyp formation by 45% (P<0.01). Putative molecular mechanisms associated with suppressing intestinal polyposis in Apc(Min/+) mice were investigated by comparing microarray expression profiles of MA-treated and control mice and by analyzing the serum metabolic profile using NMR techniques. The different expression phenotype induced by MA suggested that it exerts its chemopreventive action mainly by inhibiting cell-survival signaling and inflammation. These changes eventually induce G1-phase cell cycle arrest and apoptosis. Moreover, the metabolic changes induced by MA treatment were associated with a protective profile against intestinal tumorigenesis. These results show the efficacy and underlying mechanisms of MA against intestinal tumor development in the Apc(Min/+) mice model, suggesting its chemopreventive potential against colorectal cancer. VL - 8 ER - TY - JOUR T1 - Novel genes detected by transcriptional profiling from whole-blood cells in patients with early onset of acute coronary syndrome. JF - Clin Chim Acta Y1 - 2013 A1 - Silbiger, Vivian N A1 - Luchessi, André D A1 - Hirata, Rosário D C A1 - Lima-Neto, Lídio G A1 - Cavichioli, Débora A1 - Carracedo, Ángel A1 - Brión, Maria A1 - Dopazo, Joaquin A1 - Garcia-Garcia, Francisco A1 - Dos Santos, Elizabete S A1 - Ramos, Rui F A1 - Sampaio, Marcelo F A1 - Armaganijan, Dikran A1 - Sousa, Amanda G M R A1 - Hirata, Mario H KW - Acute Coronary Syndrome KW - Acute-Phase Proteins KW - Adult KW - biomarkers KW - Blood Cells KW - Early Diagnosis KW - gene expression KW - Gene Expression Profiling KW - Humans KW - Male KW - Middle Aged KW - Oligonucleotide Array Sequence Analysis KW - RNA, Messenger KW - Transcriptome AB -

BACKGROUND: Genome-wide expression analysis using microarrays has been used as a research strategy to discovery new biomarkers and candidate genes for a number of diseases. We aim to find new biomarkers for the prediction of acute coronary syndrome (ACS) with a differentially expressed mRNA profiling approach using whole genomic expression analysis in a peripheral blood cell model from patients with early ACS.

METHODS AND RESULTS: This study was carried out in two phases. On phase 1 a restricted clinical criteria (ACS-Ph1, n=9 and CG-Ph1, n=6) was used in order to select potential mRNA biomarkers candidates. A subsequent phase 2 study was performed using selected phase 1 markers analyzed by RT-qPCR using a larger and independent casuistic (ACS-Ph2, n=74 and CG-Ph2, n=41). A total of 549 genes were found to be differentially expressed in the first 48 h after the ACS-Ph1. Technical and biological validation further confirmed that ALOX15, AREG, BCL2A1, BCL2L1, CA1, COX7B, ECHDC3, IL18R1, IRS2, KCNE1, MMP9, MYL4 and TREML4, are differentially expressed in both phases of this study.

CONCLUSIONS: Transcriptomic analysis by microarray technology demonstrated differential expression during a 48 h time course suggesting a potential use of some of these genes as biomarkers for very early stages of ACS, as well as for monitoring early cardiac ischemic recovery.

VL - 421 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23535507?dopt=Abstract ER - TY - JOUR T1 - Novel genes detected by transcriptional profiling from whole-blood cells in patients with early onset of acute coronary syndrome: Transcriptional profiling of acute coronary syndrome. JF - Clinica chimica acta; international journal of clinical chemistry Y1 - 2013 A1 - Silbiger, Vivian N A1 - Luchessi, André D A1 - Hirata, Rosário D C A1 - Lima-Neto, Lídio G A1 - Cavichioli, Débora A1 - Carracedo, Ángel A1 - Brión, Maria A1 - Joaquín Dopazo A1 - Garcia-Garcia, Francisco A1 - Dos Santos, Elizabete S A1 - Ramos, Rui F A1 - Sampaio, Marcelo F A1 - Armaganijan, Dikran A1 - Sousa, Amanda G M R A1 - Hirata, Mario H AB - {BACKGROUND: Genome-wide expression analysis using microarrays has been used as a research strategy to discovery new biomarkers and candidate genes for a number of diseases. We aim to find new biomarkers for the prediction of acute coronary syndrome (ACS) with a differentially expressed mRNA profiling approach using whole genomic expression analysis in a peripheral blood cell model from patients with early ACS. METHODS AND RESULTS: This study was carried out in two phases. On phase 1 a restricted clinical criteria (ACS-Ph1 ER - TY - JOUR T1 - Pathways systematically associated to Hirschsprung’s disease. JF - Orphanet journal of rare diseases Y1 - 2013 A1 - Fernández, Raquel M A1 - Bleda, Marta A1 - Luzón-Toro, Berta A1 - García-Alonso, Luz A1 - Arnold, Stacey A1 - Sribudiani, Yunia A1 - Besmond, Claude A1 - Lantieri, Francesca A1 - Doan, Betty A1 - Ceccherini, Isabella A1 - Lyonnet, Stanislas A1 - Hofstra, Robert Mw A1 - Chakravarti, Aravinda A1 - Antiňolo, Guillermo A1 - Joaquín Dopazo A1 - Borrego, Salud KW - GWAS KW - Hirschprung KW - network analysis KW - Pathway Based Analysis AB - Despite it has been reported that several loci are involved in Hirschsprung’s disease, the molecular basis of the disease remains yet essentially unknown. The study of collective properties of modules of functionally-related genes provides an efficient and sensitive statistical framework that can overcome sample size limitations in the study of rare diseases. Here, we present the extension of a previous study of a Spanish series of HSCR trios to an international cohort of 162 HSCR trios to validate the generality of the underlying functional basis of the Hirschsprung’s disease mechanisms previously found. The Pathway-Based Analysis (PBA) confirms a strong association of gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other processes related to the disease. In addition, network analysis recovers sub-networks significantly associated to the disease, which contain genes related to the same functionalities, thus providing an independent validation of these findings. The functional profiles of association obtained for patients populations from different countries were compared to each other. While gene associations were different at each series, the main functional associations were identical in all the five populations. These observations would also explain the reported low reproducibility of associations of individual disease genes across populations. VL - 8 UR - http://www.ojrd.com/content/8/1/187/abstract ER - TY - JOUR T1 - Pathways systematically associated to Hirschsprung's disease. JF - Orphanet J Rare Dis Y1 - 2013 A1 - Fernández, Raquel M A1 - Bleda, Marta A1 - Luzón-Toro, Berta A1 - García-Alonso, Luz A1 - Arnold, Stacey A1 - Sribudiani, Yunia A1 - Besmond, Claude A1 - Lantieri, Francesca A1 - Doan, Betty A1 - Ceccherini, Isabella A1 - Lyonnet, Stanislas A1 - Hofstra, Robert Mw A1 - Chakravarti, Aravinda A1 - Antiňolo, Guillermo A1 - Dopazo, Joaquin A1 - Borrego, Salud KW - Female KW - Genetic Predisposition to Disease KW - Genotype KW - Hirschsprung Disease KW - Humans KW - Male KW - Polymorphism, Single Nucleotide AB -

Despite it has been reported that several loci are involved in Hirschsprung's disease, the molecular basis of the disease remains yet essentially unknown. The study of collective properties of modules of functionally-related genes provides an efficient and sensitive statistical framework that can overcome sample size limitations in the study of rare diseases. Here, we present the extension of a previous study of a Spanish series of HSCR trios to an international cohort of 162 HSCR trios to validate the generality of the underlying functional basis of the Hirschsprung's disease mechanisms previously found. The Pathway-Based Analysis (PBA) confirms a strong association of gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other processes related to the disease. In addition, network analysis recovers sub-networks significantly associated to the disease, which contain genes related to the same functionalities, thus providing an independent validation of these findings. The functional profiles of association obtained for patients populations from different countries were compared to each other. While gene associations were different at each series, the main functional associations were identical in all the five populations. These observations would also explain the reported low reproducibility of associations of individual disease genes across populations.

VL - 8 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24289864?dopt=Abstract ER - TY - JOUR T1 - Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. JF - Molecular vision Y1 - 2013 A1 - Méndez-Vidal, Cristina A1 - González-del Pozo, María A1 - Vela-Boza, Alicia A1 - Santoyo-López, Javier A1 - López-Domingo, Francisco J A1 - Vázquez-Marouschek, Carmen A1 - Dopazo, Joaquin A1 - Borrego, Salud A1 - Antiňolo, Guillermo AB - PURPOSE: Retinitis pigmentosa (RP) is an inherited retinal dystrophy characterized by extreme genetic and clinical heterogeneity. Thus, the diagnosis is not always easily performed due to phenotypic and genetic overlap. Current clinical practices have focused on the systematic evaluation of a set of known genes for each phenotype, but this approach may fail in patients with inaccurate diagnosis or infrequent genetic cause. In the present study, we investigated the genetic cause of autosomal recessive RP (arRP) in a Spanish family in which the causal mutation has not yet been identified with primer extension technology and resequencing. METHODS: We designed a whole-exome sequencing (WES)-based approach using NimbleGen SeqCap EZ Exome V3 sample preparation kit and the SOLiD 5500×l next-generation sequencing platform. We sequenced the exomes of both unaffected parents and two affected siblings. Exome analysis resulted in the identification of 43,204 variants in the index patient. All variants passing filter criteria were validated with Sanger sequencing to confirm familial segregation and absence in the control population. In silico prediction tools were used to determine mutational impact on protein function and the structure of the identified variants. RESULTS: Novel Usher syndrome type 2A (USH2A) compound heterozygous mutations, c.4325T>C (p.F1442S) and c.15188T>G (p.L5063R), located in exons 20 and 70, respectively, were identified as probable causative mutations for RP in this family. Family segregation of the variants showed the presence of both mutations in all affected members and in two siblings who were apparently asymptomatic at the time of family ascertainment. Clinical reassessment confirmed the diagnosis of RP in these patients. CONCLUSIONS: Using WES, we identified two heterozygous novel mutations in USH2A as the most likely disease-causing variants in a Spanish family diagnosed with arRP in which the cause of the disease had not yet been identified with commonly used techniques. Our data reinforce the clinical role of WES in the molecular diagnosis of highly heterogeneous genetic diseases where conventional genetic approaches have previously failed in achieving a proper diagnosis. VL - 19 UR - http://www.molvis.org/molvis/v19/2187/ ER - TY - JOUR T1 - Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. JF - Evolutionary bioinformatics online Y1 - 2012 A1 - Lavagnino, Nicolás A1 - Serra, François A1 - Arbiza, Leonardo A1 - Dopazo, Hernán A1 - Hasson, Esteban AB - Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved. VL - 8 UR - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273929/?tool=pubmed ER - TY - JOUR T1 - Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. JF - Orphanet J Rare Dis Y1 - 2012 A1 - Fernández, Raquel Ma A1 - Bleda, Marta A1 - Núñez-Torres, Rocío A1 - Medina, Ignacio A1 - Luzón-Toro, Berta A1 - García-Alonso, Luz A1 - Torroglosa, Ana A1 - Marbà, Martina A1 - Enguix-Riego, Ma Valle A1 - Montaner, David A1 - Antiňolo, Guillermo A1 - Dopazo, Joaquin A1 - Borrego, Salud KW - Female KW - Genetic Predisposition to Disease KW - Genome-Wide Association Study KW - Genotype KW - Hirschsprung Disease KW - Humans KW - Male AB -

Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a pathway-based analysis (PBA) has been initially conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung's disease. Candidate genes have been further validated in an independent population of 106 trios. The study revealed a strong association of 11 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes. Among the preselected candidates, a total of 4 loci, RASGEF1A, IQGAP2, DLC1 and CHRNA7, related to signal transduction and migration processes, were found to be significantly associated to HSCR. Network analysis also confirms their involvement in the network of already known disease genes. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases.

VL - 7 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23270508?dopt=Abstract ER - TY - JOUR T1 - Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung’s disease. JF - Orphanet journal of rare diseases Y1 - 2012 A1 - Fernández, Raquel Ma A1 - Bleda, Marta A1 - Núñez-Torres, Rocío A1 - Medina, Ignacio A1 - Luzón-Toro, Berta A1 - García-Alonso, Luz A1 - Torroglosa, Ana A1 - Marbà, Martina A1 - Enguix-Riego, Ma Valle A1 - Montaner, David A1 - Antiňolo, Guillermo A1 - Joaquín Dopazo A1 - Borrego, Salud AB - ABSTRACT: Finding gene associations in rare diseases is frequently hampered by the reduced numbers of patients accessible. Conventional gene-based association tests rely on the availability of large cohorts, which constitutes a serious limitation for its application in this scenario. To overcome this problem we have used here a combined strategy in which a pathway-based analysis (PBA) has been initially conducted to prioritize candidate genes in a Spanish cohort of 53 trios of short-segment Hirschsprung’s disease. Candidate genes have been further validated in an independent population of 106 trios. The study revealed a strong association of 11 gene ontology (GO) modules related to signal transduction and its regulation, enteric nervous system (ENS) formation and other HSCR-related processes. Among the preselected candidates, a total of 4 loci, RASGEF1A, IQGAP2, DLC1 and CHRNA7, related to signal transduction and migration processes, were found to be significantly associated to HSCR. Network analysis also confirms their involvement in the network of already known disease genes. This approach, based on the study of functionally-related gene sets, requires of lower sample sizes and opens new opportunities for the study of rare diseases. VL - 7 UR - http://www.ojrd.com/content/7/1/103/abstract ER - TY - JOUR T1 - Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. JF - BMC genomics Y1 - 2012 A1 - Jaime, María D L A A1 - Lopez-Llorca, Luis Vicente A1 - Ana Conesa A1 - Lee, Anna Y A1 - Proctor, Michael A1 - Heisler, Lawrence E A1 - Gebbia, Marinella A1 - Giaever, Guri A1 - Westwood, J Timothy A1 - Nislow, Corey AB - BACKGROUND: Chitosan oligosaccharide (COS), a deacetylated derivative of chitin, is an abundant, and renewable natural polymer. COS has higher antimicrobial properties than chitosan and is presumed to act by disrupting/permeabilizing the cell membranes of bacteria, yeast and fungi. COS is relatively non-toxic to mammals. By identifying the molecular and genetic targets of COS, we hope to gain a better understanding of the antifungal mode of action of COS. RESULTS: Three different chemogenomic fitness assays, haploinsufficiency (HIP), homozygous deletion (HOP), and multicopy suppression (MSP) profiling were combined with a transcriptomic analysis to gain insight in to the mode of action and mechanisms of resistance to chitosan oligosaccharides. The fitness assays identified 39 yeast deletion strains sensitive to COS and 21 suppressors of COS sensitivity. The genes identified are involved in processes such as RNA biology (transcription, translation and regulatory mechanisms), membrane functions (e.g. signalling, transport and targeting), membrane structural components, cell division, and proteasome processes. The transcriptomes of control wild type and 5 suppressor strains overexpressing ARL1, BCK2, ERG24, MSG5, or RBA50, were analyzed in the presence and absence of COS. Some of the up-regulated transcripts in the suppressor overexpressing strains exposed to COS included genes involved in transcription, cell cycle, stress response and the Ras signal transduction pathway. Down-regulated transcripts included those encoding protein folding components and respiratory chain proteins. The COS-induced transcriptional response is distinct from previously described environmental stress responses (i.e. thermal, salt, osmotic and oxidative stress) and pre-treatment with these well characterized environmental stressors provided little or any resistance to COS. CONCLUSIONS: Overexpression of the ARL1 gene, a member of the Ras superfamily that regulates membrane trafficking, provides protection against COS-induced cell membrane permeability and damage. We found that the ARL1 COS-resistant over-expression strain was as sensitive to Amphotericin B, Fluconazole and Terbinafine as the wild type cells and that when COS and Fluconazole are used in combination they act in a synergistic fashion. The gene targets of COS identified in this study indicate that COS’s mechanism of action is different from other commonly studied fungicides that target membranes, suggesting that COS may be an effective fungicide for drug-resistant fungal pathogens. VL - 13 ER - TY - JOUR T1 - IL1β induces mesenchymal stem cells migration and leucocyte chemotaxis through NF-κB. JF - Stem Cell Rev Rep Y1 - 2012 A1 - Carrero, Rubén A1 - Cerrada, Inmaculada A1 - Lledó, Elisa A1 - Dopazo, Joaquin A1 - Garcia-Garcia, Francisco A1 - Rubio, Mari-Paz A1 - Trigueros, César A1 - Dorronsoro, Akaitz A1 - Ruiz-Sauri, Amparo A1 - Montero, José Anastasio A1 - Sepúlveda, Pilar KW - Cell Adhesion KW - Cell Movement KW - Cell Proliferation KW - Chemokines KW - Chemotaxis, Leukocyte KW - Collagen KW - Fibronectins KW - Gene Expression Profiling KW - Gene Knockdown Techniques KW - HEK293 Cells KW - Humans KW - I-kappa B Kinase KW - Inflammation Mediators KW - Intercellular Signaling Peptides and Proteins KW - Interleukin-1beta KW - Laminin KW - Leukocytes KW - Mesenchymal Stem Cells KW - NF-kappa B KW - Oligonucleotide Array Sequence Analysis KW - RNA Interference KW - Signal Transduction AB -

Mesenchymal stem cells are often transplanted into inflammatory environments where they are able to survive and modulate host immune responses through a poorly understood mechanism. In this paper we analyzed the responses of MSC to IL-1β: a representative inflammatory mediator. Microarray analysis of MSC treated with IL-1β revealed that this cytokine activateds a set of genes related to biological processes such as cell survival, cell migration, cell adhesion, chemokine production, induction of angiogenesis and modulation of the immune response. Further more detailed analysis by real-time PCR and functional assays revealed that IL-1β mainly increaseds the production of chemokines such as CCL5, CCL20, CXCL1, CXCL3, CXCL5, CXCL6, CXCL10, CXCL11 and CX(3)CL1, interleukins IL-6, IL-8, IL23A, IL32, Toll-like receptors TLR2, TLR4, CLDN1, metalloproteins MMP1 and MMP3, growth factors CSF2 and TNF-α, together with adhesion molecules ICAM1 and ICAM4. Functional analysis of MSC proliferation, migration and adhesion to extracellular matrix components revealed that IL-1β did not affect proliferation but also served to induce the secretion of trophic factors and adhesion to ECM components such as collagen and laminin. IL-1β treatment enhanced the ability of MSC to recruit monocytes and granulocytes in vitro. Blockade of NF-κβ transcription factor activation with IκB kinase beta (IKKβ) shRNA impaired MSC migration, adhesion and leucocyte recruitment, induced by IL-1β demonstrating that NF-κB pathway is an important downstream regulator of these responses. These findings are relevant to understanding the biological responses of MSC to inflammatory environments.

VL - 8 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22467443?dopt=Abstract ER - TY - JOUR T1 - The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. JF - FASEB J Y1 - 2012 A1 - Koziol, Agnieszka A1 - Gonzalo, Pilar A1 - Mota, Alba A1 - Pollán, Angela A1 - Lorenzo, Cristina A1 - Colomé, Nuria A1 - Montaner, David A1 - Dopazo, Joaquin A1 - Arribas, Joaquín A1 - Canals, Francesc A1 - Arroyo, Alicia G KW - Animals KW - Blotting, Western KW - Combinatorial Chemistry Techniques KW - Computational Biology KW - Endothelial Cells KW - Gene Expression Regulation, Enzymologic KW - Inflammation KW - Matrix Metalloproteinase 14 KW - Mice KW - Protein Array Analysis KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA Interference KW - RNA, Small Interfering KW - Transcriptome KW - Tumor Necrosis Factor-alpha AB -

The mechanism by which proteolytic events translate into biological responses is not well understood. To explore the link of pericellular proteolysis to events relevant to capillary sprouting within the inflammatory context, we aimed at the identification of the collection of substrates of the protease MT1-MMP in endothelial tip cells induced by inflammatory stimuli. We applied quantitative proteomics to endothelial cells (ECs) derived from wild-type and MT1-MMP-null mice to identify the substrate repertoire of this protease in TNF-α-activated ECs. Bioinformatics analysis revealed a combinatorial MT1-MMP proteolytic program, in which combined rather than single substrate processing would determine biological decisions by activated ECs, including chemotaxis, cell motility and adhesion, and vasculature development. MT1-MMP-deficient ECs inefficiently processed several of these substrates (TSP1, CYR61, NID1, and SEM3C), validating the model. This novel concept of MT1-MMP-driven combinatorial proteolysis in angiogenesis might be extendable to proteolytic actions in other cellular contexts.

VL - 26 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22859368?dopt=Abstract ER - TY - JOUR T1 - Select your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. JF - International journal of data mining and bioinformatics Y1 - 2012 A1 - Lorente-Galdos, Belén A1 - Medina, Ignacio A1 - Morcillo-Suarez, Carlos A1 - Heredia, Txema A1 - Carreño-Torres, Angel A1 - Sangrós, Ricardo A1 - Alegre, Josep A1 - Pita, Guillermo A1 - Vellalta, Gemma A1 - Malats, Nuria A1 - Pisano, David G A1 - Joaquín Dopazo A1 - Navarro, Arcadi AB - Association studies are the choice approach in the discovery of the genomic basis of complex traits. To carry out such analysis, researchers frequently need to (1) select optimally informative sets of Single Nucleotide Polymorphisms (SNPs) in candidate regions and (2) annotate the results of associations found by means of genome-wide SNP arrays. These are complex tasks, since many criteria have to be considered, including the SNPs’ functional properties, technological information and haplotype frequencies in given populations. SYSNPs implements algorithms that allow for efficient and simultaneous consideration of all the relevant criteria to obtain sets of SNPs that properly cover arbitrarily large lists of genes or genomic regions. Complementarily, SYSNPs allows for comprehensive functional annotation of SNPs linked to any given marker SNP. SYSNPs dramatically reduces the effort needed for SNP selection from days of searching various databases to a few minutes using a simple browser. VL - 6 UR - http://inderscience.metapress.com/content/f76740x8071u513n/ ER - TY - JOUR T1 - Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin. JF - PloS one Y1 - 2012 A1 - Oppert, Brenda A1 - Dowd, Scot E A1 - Bouffard, Pascal A1 - Li, Lewyn A1 - Ana Conesa A1 - Lorenzen, Marcé D A1 - Toutges, Michelle A1 - Marshall, Jeremy A1 - Huestis, Diana L A1 - Fabrick, Jeff A1 - Oppert, Cris A1 - Jurat-Fuentes, Juan Luis KW - Administration KW - Animals KW - Bacterial Proteins KW - Base Sequence KW - Biosynthetic Pathways KW - Complementary KW - DNA KW - Endotoxins KW - Energy Metabolism KW - Gene Expression Profiling KW - Hemolysin Proteins KW - Larva KW - Microarray Analysis KW - Molecular Sequence Data KW - Oral KW - Sequence Analysis KW - Tenebrio KW - Time Factors KW - Transcriptome AB - Bacillus thuringiensis (Bt) crystal (Cry) proteins are effective against a select number of insect pests, but improvements are needed to increase efficacy and decrease time to mortality for coleopteran pests. To gain insight into the Bt intoxication process in Coleoptera, we performed RNA-Seq on cDNA generated from the guts of Tenebrio molitor larvae that consumed either a control diet or a diet containing Cry3Aa protoxin. Approximately 134,090 and 124,287 sequence reads from the control and Cry3Aa-treated groups were assembled into 1,318 and 1,140 contigs, respectively. Enrichment analyses indicated that functions associated with mitochondrial respiration, signalling, maintenance of cell structure, membrane integrity, protein recycling/synthesis, and glycosyl hydrolases were significantly increased in Cry3Aa-treated larvae, whereas functions associated with many metabolic processes were reduced, especially glycolysis, tricarboxylic acid cycle, and fatty acid synthesis. Microarray analysis was used to evaluate temporal changes in gene expression after 6, 12 or 24 h of Cry3Aa exposure. Overall, microarray analysis indicated that transcripts related to allergens, chitin-binding proteins, glycosyl hydrolases, and tubulins were induced, and those related to immunity and metabolism were repressed in Cry3Aa-intoxicated larvae. The 24 h microarray data validated most of the RNA-Seq data. Of the three intoxication intervals, larvae demonstrated more differential expression of transcripts after 12 h exposure to Cry3Aa. Gene expression examined by three different methods in control vs. Cry3Aa-treated larvae at the 24 h time point indicated that transcripts encoding proteins with chitin-binding domain 3 were the most differentially expressed in Cry3Aa-intoxicated larvae. Overall, the data suggest that T. molitor larvae mount a complex response to Cry3Aa during the initial 24 h of intoxication. Data from this study represent the largest genetic sequence dataset for T. molitor to date. Furthermore, the methods in this study are useful for comparative analyses in organisms lacking a sequenced genome. VL - 7 ER - TY - JOUR T1 - Discovery of an ebolavirus-like filovirus in europe. JF - PLoS pathogens Y1 - 2011 A1 - Negredo, Ana A1 - Palacios, Gustavo A1 - Vázquez-Morón, Sonia A1 - González, Félix A1 - Dopazo, Hernán A1 - Molero, Francisca A1 - Juste, Javier A1 - Quetglas, Juan A1 - Savji, Nazir A1 - de la Cruz Martínez, Maria A1 - Herrera, Jesus Enrique A1 - Pizarro, Manuel A1 - Hutchison, Stephen K A1 - Echevarría, Juan E A1 - Lipkin, W Ian A1 - Tenorio, Antonio AB -

Filoviruses, amongst the most lethal of primate pathogens, have only been reported as natural infections in sub-Saharan Africa and the Philippines. Infections of bats with the ebolaviruses and marburgviruses do not appear to be associated with disease. Here we report identification in dead insectivorous bats of a genetically distinct filovirus, provisionally named Lloviu virus, after the site of detection, Cueva del Lloviu, in Spain.

VL - 7 ER - TY - JOUR T1 - Does singlet oxygen activate cell death in Arabidopsis cell suspension cultures? Analysis of the early transcriptional defence responses to high light stress. JF - Plant signaling & behavior Y1 - 2011 A1 - Gutiérrez, Jorge A1 - González-Pérez, Sergio A1 - Garcia-Garcia, Francisco A1 - Lorenzo, Oscar A1 - Arellano, Juan B AB -

Can Arabidopsis cell suspension cultures (ACSC) provide a useful working model to investigate genetically-controlled defence responses with signalling cascades starting in chloroplasts? In order to provide a convincing answer, we analysed the early transcriptional profile of Arabidopsis cells at high light (HL). The results showed that ACSC respond to HL in a manner that resembles the singlet oxygen ( ( 1) O 2)-mediated defence responses described for the conditional fluorescent (flu) mutant of Arabidopsis thaliana. The flu mutant is characterized by the accumulation of free protochlorophyllide (Pchlide) in plastids when put into darkness and the subsequent production of ( 1) O 2 when the light is on. In ACSC, ( 1) O 2 is produced in chloroplasts at HL when excess excitation energy flows into photosystem II (PSII). Other reactive oxygen species are also produced in ACSC at HL, but to a lesser extent. When the HL stress ceases, ACSC recovers the initial rate of oxygen evolution and cell growth continues. We can conclude that chloroplasts of ACSC are both photosynthetically active and capable of initiating ( 1) O 2-mediated signalling cascades that activate a broad range of genetically-controlled defence responses. The up-regulation of transcripts associated with the biosynthesis and signalling pathways of OPDA (12-oxophytodienoic acid) and ethylene (ET) suggests that the activated defence responses at HL are governed by these two hormones. In contrast to the flu mutant, the ( 1) O 2-mediated defence responses were independent of the up-regulation of EDS1 (enhanced disease susceptibility) required for the accumulation of salicylic acid (SA) and genetically-controlled cell death. 

VL - 6 ER - TY - JOUR T1 - Early transcriptional defence responses in Arabidopsis cell suspension culture under high light conditions. JF - Plant physiology Y1 - 2011 A1 - González-Pérez, Sergio A1 - Gutiérrez, Jorge A1 - Garcia-Garcia, Francisco A1 - Osuna, Daniel A1 - Joaquín Dopazo A1 - Lorenzo, Oscar A1 - Revuelta, José L A1 - Arellano, Juan B AB -

The early transcriptional defence responses and ROS production in Arabidopsis cell suspension culture (ACSC), containing functional chloroplasts, were examined at high light (HL). The transcriptional analysis revealed that most of the ROS markers identified among the 449 transcripts with significant differential expression were transcripts specifically up-regulated by singlet oxygen (1O2). On the contrary, minimal correlation was established with transcripts specifically up-regulated by superoxide radical (O2•) or hydrogen peroxide (H2O2). The transcriptional analysis was supported by fluorescence microscopy experiments. The incubation of ACSC with the 1O2 sensor green reagent and 2’,7’-dichlorofluorescein diacetate showed that the 30-min-HL-treated cultures emitted fluorescence that corresponded with the production of 1O2, but not of H2O2. Furthermore, the in vivo photodamage of the D1 protein of photosystem II (PSII) indicated that the photogeneration of 1O2 took place within the PSII reaction centre. Functional enrichment analyses identified transcripts that are key components of the ROS signalling transduction pathway in plants as well as others encoding transcription factors that regulate both ROS scavenging and water deficit stress. A meta-analysis examining the transcriptional profiles of mutants and hormone treatments in Arabidopsis showed a high correlation between ACSC at HL and the flu mutant family of Arabidopsis, a producer of 1O2 in plastids. Intriguingly, a high correlation was also observed with aba1 and max4, two mutants with defects in the biosynthesis pathways of two key (apo)carotenoid-derived plant hormones (i.e. ABA and strigolactones, respectively). ACSC has proven to be a valuable system for studying early transcriptional responses to HL stress.

VL - 156 UR - http://www.plantphysiol.org/content/early/2011/04/29/pp.111.177766.short?keytype=ref&ijkey=ph5B6J2khjnqwzN ER - TY - JOUR T1 - Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. JF - Plant Physiol Y1 - 2011 A1 - González-Pérez, Sergio A1 - Gutiérrez, Jorge A1 - Garcia-Garcia, Francisco A1 - Osuna, Daniel A1 - Dopazo, Joaquin A1 - Lorenzo, Oscar A1 - Revuelta, José L A1 - Arellano, Juan B KW - Arabidopsis KW - Blotting, Western KW - Cell Culture Techniques KW - Cells, Cultured KW - Chloroplasts KW - Cluster Analysis KW - Gene Expression Profiling KW - Gene Expression Regulation, Plant KW - Hydrogen Peroxide KW - Light KW - mutation KW - Oligonucleotide Array Sequence Analysis KW - Photosystem II Protein Complex KW - Plant Growth Regulators KW - Reproducibility of Results KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA, Messenger KW - Signal Transduction KW - Stress, Physiological KW - Transcription, Genetic AB -

The early transcriptional defense responses and reactive oxygen species (ROS) production in Arabidopsis (Arabidopsis thaliana) cell suspension culture (ACSC), containing functional chloroplasts, were examined at high light (HL). The transcriptional analysis revealed that most of the ROS markers identified among the 449 transcripts with significant differential expression were transcripts specifically up-regulated by singlet oxygen ((1)O(2)). On the contrary, minimal correlation was established with transcripts specifically up-regulated by superoxide radical or hydrogen peroxide. The transcriptional analysis was supported by fluorescence microscopy experiments. The incubation of ACSC with the (1)O(2) sensor green reagent and 2',7'-dichlorofluorescein diacetate showed that the 30-min-HL-treated cultures emitted fluorescence that corresponded with the production of (1)O(2) but not of hydrogen peroxide. Furthermore, the in vivo photodamage of the D1 protein of photosystem II indicated that the photogeneration of (1)O(2) took place within the photosystem II reaction center. Functional enrichment analyses identified transcripts that are key components of the ROS signaling transduction pathway in plants as well as others encoding transcription factors that regulate both ROS scavenging and water deficit stress. A meta-analysis examining the transcriptional profiles of mutants and hormone treatments in Arabidopsis showed a high correlation between ACSC at HL and the fluorescent mutant family of Arabidopsis, a producer of (1)O(2) in plastids. Intriguingly, a high correlation was also observed with ABA deficient1 and more axillary growth4, two mutants with defects in the biosynthesis pathways of two key (apo)carotenoid-derived plant hormones (i.e. abscisic acid and strigolactones, respectively). ACSC has proven to be a valuable system for studying early transcriptional responses to HL stress.

VL - 156 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21531897?dopt=Abstract ER - TY - JOUR T1 - Histone modifications and expression of DAM6 gene in peach are modulated during bud dormancy release in a cultivar-dependent manner. JF - The New phytologist Y1 - 2011 A1 - Leida, Carmen A1 - Ana Conesa A1 - Llácer, Gerardo A1 - Badenes, María Luisa A1 - Ríos, Gabino AB -

• Bud dormancy release in many woody perennial plants responds to the seasonal accumulation of chilling stimulus. MADS-box transcription factors encoded by DORMANCY ASSOCIATED MADS-box (DAM) genes in peach (Prunus persica) are implicated in this pathway, but other regulatory factors remain to be identified. In addition, the regulation of DAM gene expression is not well known at the molecular level. • A microarray hybridization approach was performed to identify genes whose expression correlates with the bud dormancy-related behaviour in 10 different peach cultivars. Histone modifications in DAM6 gene were investigated by chromatin immunoprecipitation in two different cultivars. • The expression of DAM4-DAM6 and several genes related to abscisic acid and drought stress response correlated with the dormancy behaviour of peach cultivars. The trimethylation of histone H3 at K27 in the DAM6 promoter, coding region and the second large intron was preceded by a decrease in acetylated H3 and trimethylated H3K4 in the region of translation start, coinciding with repression of DAM6 during dormancy release. • Analysis of chromatin modifications reinforced the role of epigenetic mechanisms in DAM6 regulation and bud dormancy release, and highlighted common features with the vernalization process in Arabidopsis thaliana and cereals.

ER - TY - JOUR T1 - Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. JF - Hum Mol Genet Y1 - 2011 A1 - Yung, Sun A1 - Ledran, Maria A1 - Moreno-Gimeno, Inmaculada A1 - Conesa, Ana A1 - Montaner, David A1 - Dopazo, Joaquin A1 - Dimmick, Ian A1 - Slater, Nicholas J A1 - Marenah, Lamin A1 - Real, Pedro J A1 - Paraskevopoulou, Iliana A1 - Bisbal, Viviana A1 - Burks, Deborah A1 - Santibanez-Koref, Mauro A1 - Moreno, Ruben A1 - Mountford, Joanne A1 - Menendez, Pablo A1 - Armstrong, Lyle A1 - Lako, Majlinda KW - Acute Disease KW - Anemia, Hemolytic KW - Animals KW - Basic Helix-Loop-Helix Transcription Factors KW - Cell Differentiation KW - Cell Line KW - Cell Lineage KW - Cluster Analysis KW - Embryonic Stem Cells KW - Erythroid Cells KW - Flow Cytometry KW - Gene Expression Profiling KW - Hematopoietic Stem Cells KW - Humans KW - Mice KW - Myeloid Cells KW - Paracrine Communication KW - Proto-Oncogene Proteins KW - Reverse Transcriptase Polymerase Chain Reaction KW - rho GTP-Binding Proteins KW - Signal Transduction KW - Stem Cell Transplantation KW - T-Cell Acute Lymphocytic Leukemia Protein 1 KW - Transcriptome AB -

Understanding the transcriptional cues that direct differentiation of human embryonic stem cells (hESCs) and human-induced pluripotent stem cells to defined and functional cell types is essential for future clinical applications. In this study, we have compared transcriptional profiles of haematopoietic progenitors derived from hESCs at various developmental stages of a feeder- and serum-free differentiation method and show that the largest transcriptional changes occur during the first 4 days of differentiation. Data mining on the basis of molecular function revealed Rho-GTPase signalling as a key regulator of differentiation. Inhibition of this pathway resulted in a significant reduction in the numbers of emerging haematopoietic progenitors throughout the differentiation window, thereby uncovering a previously unappreciated role for Rho-GTPase signalling during human haematopoietic development. Our analysis indicated that SCL was the 11th most upregulated transcript during the first 4 days of the hESC differentiation process. Overexpression of SCL in hESCs promoted differentiation to meso-endodermal lineages, the emergence of haematopoietic and erythro-megakaryocytic progenitors and accelerated erythroid differentiation. Importantly, intrasplenic transplantation of SCL-overexpressing hESC-derived haematopoietic cells enhanced recovery from induced acute anaemia without significant cell engraftment, suggesting a paracrine-mediated effect.

VL - 20 IS - 24 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21937587?dopt=Abstract ER - TY - JOUR T1 - Modeling human endometrial decidualization from the interaction between proteome and secretome. JF - The Journal of clinical endocrinology and metabolism Y1 - 2011 A1 - Garrido-Gomez, Tamara A1 - Dominguez, Francisco A1 - Lopez, Juan Antonio A1 - Camafeita, Emilio A1 - Quiñonero, Alicia A1 - Martinez-Conejero, Jose Antonio A1 - Pellicer, Antonio A1 - Ana Conesa A1 - Simon, Carlos AB -

Decidualization of the human endometrium, which involves morphological and biochemical modifications of the endometrial stromal cells (ESCs), is a prerequisite for adequate trophoblast invasion and placenta formation.

VL - 96 ER - TY - JOUR T1 - Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing. JF - BMC genomics Y1 - 2011 A1 - Durban, Jordi A1 - Juárez, Paula A1 - Angulo, Yamileth A1 - Lomonte, Bruno A1 - Flores-Diaz, Marietta A1 - Alape-Girón, Alberto A1 - Sasa, Mahmood A1 - Sanz, Libia A1 - Gutiérrez, José M A1 - Joaquín Dopazo A1 - Ana Conesa A1 - Calvete, Juan J AB -

A long term research goal of venomics, of applied importance for improving current antivenom therapy, but also for drug discovery, is to understand the pharmacological potential of venoms. Individually or combined, proteomic and transcriptomic studies have demonstrated their feasibility to explore in depth the molecular diversity of venoms. In the absence of genome sequence, transcriptomes represent also valuable searchable databases for proteomic projects.

VL - 12 ER - TY - JOUR T1 - Recent human evolution has shaped geographical differences in susceptibility to disease. JF - BMC genomics Y1 - 2011 A1 - Marigorta, Urko M A1 - Lao, Oscar A1 - Casals, Ferran A1 - Calafell, Francesc A1 - Morcillo-Suarez, Carlos A1 - Faria, Rui A1 - Bosch, Elena A1 - Serra, François A1 - Bertranpetit, Jaume A1 - Dopazo, Hernán A1 - Navarro, Arcadi AB -

Searching for associations between genetic variants and complex diseases has been a very active area of research for over two decades. More than 51,000 potential associations have been studied and published, a figure that keeps increasing, especially with the recent explosion of array-based Genome-Wide Association Studies. Even if the number of true associations described so far is high, many of the putative risk variants detected so far have failed to be consistently replicated and are widely considered false positives. Here, we focus on the world-wide patterns of replicability of published association studies.

VL - 12 ER - TY - JOUR T1 - Sexual selection halts the relaxation of protamine 2 among rodents. JF - PloS one Y1 - 2011 A1 - Lüke, Lena A1 - Vicens, Alberto A1 - Serra, François A1 - Luque-Larena, Juan Jose A1 - Dopazo, Hernán A1 - Roldan, Eduardo R S A1 - Gomendio, Montserrat AB - Sexual selection has been proposed as the driving force promoting the rapid evolutionary changes observed in some reproductive genes including protamines. We test this hypothesis in a group of rodents which show marked differences in the intensity of sexual selection. Levels of sperm competition were not associated with the evolutionary rates of protamine 1 but, contrary to expectations, were negatively related to the evolutionary rate of cleaved- and mature-protamine 2. Since both domains were found to be under relaxation, our findings reveal an unforeseen role of sexual selection: to halt the degree of degeneration that proteins within families may experience due to functional redundancy. The degree of relaxation of protamine 2 in this group of rodents is such that in some species it has become dysfunctional and it is not expressed in mature spermatozoa. In contrast, protamine 1 is functionally conserved but shows directed positive selection on specific sites which are functionally relevant such as DNA-anchoring domains and phosphorylation sites. We conclude that in rodents protamine 2 is under relaxation and that sexual selection removes deleterious mutations among species with high levels of sperm competition to maintain the protein functional and the spermatozoa competitive. VL - 6 UR - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029247 ER - TY - JOUR T1 - SUS1 introns are required for efficient mRNA nuclear export in yeast. JF - Nucleic acids research Y1 - 2011 A1 - Cuenca-Bono, Bernardo A1 - García-Molinero, Varinia A1 - Pascual-García, Pau A1 - Dopazo, Hernán A1 - Llopis, Ana A1 - Vilardell, Josep A1 - Rodríguez-Navarro, Susana AB -

Efficient coupling between mRNA synthesis and export is essential for gene expression. Sus1/ENY2, a component of the SAGA and TREX-2 complexes, is involved in both transcription and mRNA export. While most yeast genes lack introns, we previously reported that yeast SUS1 bears two. Here we show that this feature is evolutionarily conserved and critical for Sus1 function. We determine that while SUS1 splicing is inefficient, it responds to cellular conditions, and intronic mutations either promoting or blocking splicing lead to defects in mRNA export and cell growth. Consistent with this, we find that an intron-less SUS1 only partially rescues sus1Δ phenotypes. Remarkably, splicing of each SUS1 intron is also affected by the presence of the other and by SUS1 exonic sequences. Moreover, by following SUS1 RNA and protein levels we establish that nonsense-mediated decay (NMD) pathway and the splicing factor Mud2 both play a role in SUS1 expression. Our data (and those of the accompanying work by Hossain et al.) provide evidence of the involvement of splicing, translation, and decay in the regulation of early events in mRNP biogenesis; and imply the additional requirement for a balance in splicing isoforms from a single gene.

VL - 39 ER - TY - JOUR T1 - The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. JF - Nature structural & molecular biology Y1 - 2011 A1 - Baù, Davide A1 - Sanyal, Amartya A1 - Lajoie, Bryan R A1 - Capriotti, Emidio A1 - Byron, Meg A1 - Lawrence, Jeanne B A1 - Dekker, Job A1 - Marti-Renom, Marc A AB -

We developed a general approach that combines chromosome conformation capture carbon copy (5C) with the Integrated Modeling Platform (IMP) to generate high-resolution three-dimensional models of chromatin at the megabase scale. We applied this approach to the ENm008 domain on human chromosome 16, containing the α-globin locus, which is expressed in K562 cells and silenced in lymphoblastoid cells (GM12878). The models accurately reproduce the known looping interactions between the α-globin genes and their distal regulatory elements. Further, we find using our approach that the domain folds into a single globular conformation in GM12878 cells, whereas two globules are formed in K562 cells. The central cores of these globules are enriched for transcribed genes, whereas nontranscribed chromatin is more peripheral. We propose that globule formation represents a higher-order folding state related to clustering of transcribed genes around shared transcription machineries, as previously observed by microscopy.

VL - 18 ER - TY - JOUR T1 - Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. JF - Genome research Y1 - 2010 A1 - Javierre, Biola M A1 - Fernandez, Agustin F A1 - Richter, Julia A1 - Fatima Al-Shahrour A1 - Martin-Subero, J Ignacio A1 - Rodriguez-Ubreva, Javier A1 - Berdasco, Maria A1 - Fraga, Mario F A1 - O’Hanlon, Terrance P A1 - Rider, Lisa G A1 - Jacinto, Filipe V A1 - Lopez-Longo, F Javier A1 - Dopazo, Joaquin A1 - Forn, Marta A1 - Peinado, Miguel A A1 - Carreño, Luis A1 - Sawalha, Amr H A1 - Harley, John B A1 - Siebert, Reiner A1 - Esteller, Manel A1 - Miller, Frederick W A1 - Ballestar, Esteban AB -

Monozygotic (MZ) twins are partially concordant for most complex diseases, including autoimmune disorders. Whereas phenotypic concordance can be used to study heritability, discordance suggests the role of non-genetic factors. In autoimmune diseases, environmentally driven epigenetic changes are thought to contribute to their etiology. Here we report the first high-throughput and candidate sequence analyses of DNA methylation to investigate discordance for autoimmune disease in twins. We used a cohort of MZ twins discordant for three diseases whose clinical signs often overlap: systemic lupus erythematosus (SLE), rheumatoid arthritis, and dermatomyositis. Only MZ twins discordant for SLE featured widespread changes in the DNA methylation status of a significant number of genes. Gene ontology analysis revealed enrichment in categories associated with immune function. Individual analysis confirmed the existence of DNA methylation and expression changes in genes relevant to SLE pathogenesis. These changes occurred in parallel with a global decrease in the 5-methylcytosine content that was concomitantly accompanied with changes in DNA methylation and expression levels of ribosomal RNA genes, although no changes in repetitive sequences were found. Our findings not only identify potentially relevant DNA methylation markers for the clinical characterization of SLE patients but also support the notion that epigenetic changes may be critical in the clinical manifestations of autoimmune disease.

VL - 20 ER - TY - JOUR T1 - DNA methylation epigenotypes in breast cancer molecular subtypes. JF - Breast Cancer Res Y1 - 2010 A1 - Bediaga, Naiara G A1 - Acha-Sagredo, Amelia A1 - Guerra, Isabel A1 - Viguri, Amparo A1 - Albaina, Carmen A1 - Ruiz Diaz, Irune A1 - Rezola, Ricardo A1 - Alberdi, Maria Jesus A1 - Dopazo, Joaquin A1 - Montaner, David A1 - Renobales, Mertxe A1 - Fernandez, Agustin F A1 - Field, John K A1 - Fraga, Mario F A1 - Liloglou, Triantafillos A1 - de Pancorbo, Marian M KW - Aged KW - Breast Neoplasms KW - CpG Islands KW - DNA Methylation KW - Epigenesis, Genetic KW - Female KW - Gene Expression Profiling KW - Genes, p53 KW - Genotype KW - Humans KW - Ki-67 Antigen KW - Middle Aged KW - mutation KW - Neoplasm Grading KW - Oligonucleotide Array Sequence Analysis KW - Receptor, ErbB-2 KW - Tumor Suppressor Protein p53 AB -

INTRODUCTION: Identification of gene expression based breast cancer subtypes is considered as a critical means of prognostication. Genetic mutations along with epigenetic alterations contribute to gene expression changes occurring in breast cancer. So far, these epigenetic contributions to sporadic breast cancer subtypes have not been well characterized, and there is only a limited understanding of the epigenetic mechanisms affected in those particular breast cancer subtypes. The present study was undertaken to dissect the breast cancer methylome and deliver specific epigenotypes associated with particular breast cancer subtypes.

METHODS: Using a microarray approach we analyzed DNA methylation in regulatory regions of 806 cancer related genes in 28 breast cancer paired samples. We subsequently performed substantial technical and biological validation by Pyrosequencing, investigating the top qualifying 19 CpG regions in independent cohorts encompassing 47 basal-like, 44 ERBB2+ overexpressing, 48 luminal A and 48 luminal B paired breast cancer/adjacent tissues. Using all-subset selection method, we identified the most subtype predictive methylation profiles in multivariable logistic regression analysis.

RESULTS: The approach efficiently recognized 15 individual CpG loci differentially methylated in breast cancer tumor subtypes. We further identify novel subtype specific epigenotypes which clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors.

CONCLUSIONS: Our results provide evidence that well defined DNA methylation profiles enables breast cancer subtype prediction and support the utilization of this biomarker for prognostication and therapeutic stratification of patients with breast cancer.

VL - 12 IS - 5 U1 - https://www.ncbi.nlm.nih.gov/pubmed/20920229?dopt=Abstract ER - TY - JOUR T1 - Exploring the link between germline and somatic genetic alterations in breast carcinogenesis. JF - PLoS One Y1 - 2010 A1 - Bonifaci, Núria A1 - Górski, Bohdan A1 - Masojć, Bartlomiej A1 - Wokołorczyk, Dominika A1 - Jakubowska, Anna A1 - Dębniak, Tadeusz A1 - Berenguer, Antoni A1 - Serra Musach, Jordi A1 - Brunet, Joan A1 - Dopazo, Joaquin A1 - Narod, Steven A A1 - Lubiński, Jan A1 - Lázaro, Conxi A1 - Cybulski, Cezary A1 - Pujana, Miguel Angel KW - Adult KW - Bone Morphogenetic Protein Receptors, Type I KW - Breast KW - Breast Neoplasms KW - Calcium-Calmodulin-Dependent Protein Kinases KW - Case-Control Studies KW - Cyclin-Dependent Kinases KW - Disease Progression KW - Estrogen Receptor alpha KW - Female KW - Gene Frequency KW - Genetic Predisposition to Disease KW - Genome-Wide Association Study KW - Genotype KW - Germ-Line Mutation KW - Humans KW - Odds Ratio KW - Poland KW - Polymorphism, Single Nucleotide KW - Protein Serine-Threonine Kinases KW - Protein-Tyrosine Kinases KW - Receptor Protein-Tyrosine Kinases KW - Receptor, EphA3 KW - Receptor, EphA7 KW - Receptor, EphB1 KW - Risk Factors AB -

Recent genome-wide association studies (GWASs) have identified candidate genes contributing to cancer risk through low-penetrance mutations. Many of these genes were unexpected and, intriguingly, included well-known players in carcinogenesis at the somatic level. To assess the hypothesis of a germline-somatic link in carcinogenesis, we evaluated the distribution of somatic gene labels within the ordered results of a breast cancer risk GWAS. This analysis suggested frequent influence on risk of genetic variation in loci encoding for "driver kinases" (i.e., kinases encoded by genes that showed higher somatic mutation rates than expected by chance and, therefore, whose deregulation may contribute to cancer development and/or progression). Assessment of these predictions using a population-based case-control study in Poland replicated the association for rs3732568 in EPHB1 (odds ratio (OR) = 0.79; 95% confidence interval (CI): 0.63-0.98; P(trend) = 0.031). Analyses by early age at diagnosis and by estrogen receptor α (ERα) tumor status indicated potential associations for rs6852678 in CDKL2 (OR = 0.32, 95% CI: 0.10-1.00; P(recessive) = 0.044) and rs10878640 in DYRK2 (OR = 2.39, 95% CI: 1.32-4.30; P(dominant) = 0.003), and for rs12765929, rs9836340, rs4707795 in BMPR1A, EPHA3 and EPHA7, respectively (ERα tumor status P(interaction)<0.05). The identification of three novel candidates as EPH receptor genes might indicate a link between perturbed compartmentalization of early neoplastic lesions and breast cancer risk and progression. Together, these data may lay the foundations for replication in additional populations and could potentially increase our knowledge of the underlying molecular mechanisms of breast carcinogenesis.

VL - 5 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21124932?dopt=Abstract ER - TY - JOUR T1 - Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. JF - The ISME journal Y1 - 2010 A1 - Peña, Arantxa A1 - Teeling, Hanno A1 - Huerta-Cepas, Jaime A1 - Santos, Fernando A1 - Yarza, Pablo A1 - Brito-Echeverría, Jocelyn A1 - Lucio, Marianna A1 - Schmitt-Kopplin, Philippe A1 - Meseguer, Inmaculada A1 - Schenowitz, Chantal A1 - Dossat, Carole A1 - Barbe, Valerie A1 - Joaquín Dopazo A1 - Rosselló-Mora, Ramon A1 - Schüler, Margarete A1 - Glöckner, Frank Oliver A1 - Amann, Rudolf A1 - Gabaldón, Toni A1 - Antón, Josefa AB -

Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.The ISME Journal advance online publication, 18 February 2010; doi:10.1038/ismej.2010.6.

ER - TY - JOUR T1 - Initial genomics of the human nucleolus. JF - PLoS genetics Y1 - 2010 A1 - Németh, Attila A1 - Ana Conesa A1 - Santoyo-López, Javier A1 - Medina, Ignacio A1 - Montaner, David A1 - Péterfia, Bálint A1 - Solovei, Irina A1 - Cremer, Thomas A1 - Dopazo, Joaquin A1 - Längst, Gernot KW - NGS KW - nucleolus AB -

We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD-localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD-specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture.

VL - 6 UR - http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000889 ER - TY - JOUR T1 - The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. JF - Nature biotechnology Y1 - 2010 A1 - Shi, Leming A1 - Campbell, Gregory A1 - Jones, Wendell D A1 - Campagne, Fabien A1 - Wen, Zhining A1 - Walker, Stephen J A1 - Su, Zhenqiang A1 - Chu, Tzu-Ming A1 - Goodsaid, Federico M A1 - Pusztai, Lajos A1 - Shaughnessy, John D A1 - Oberthuer, André A1 - Thomas, Russell S A1 - Paules, Richard S A1 - Fielden, Mark A1 - Barlogie, Bart A1 - Chen, Weijie A1 - Du, Pan A1 - Fischer, Matthias A1 - Furlanello, Cesare A1 - Gallas, Brandon D A1 - Ge, Xijin A1 - Megherbi, Dalila B A1 - Symmans, W Fraser A1 - Wang, May D A1 - Zhang, John A1 - Bitter, Hans A1 - Brors, Benedikt A1 - Bushel, Pierre R A1 - Bylesjo, Max A1 - Chen, Minjun A1 - Cheng, Jie A1 - Cheng, Jing A1 - Chou, Jeff A1 - Davison, Timothy S A1 - Delorenzi, Mauro A1 - Deng, Youping A1 - Devanarayan, Viswanath A1 - Dix, David J A1 - Dopazo, Joaquin A1 - Dorff, Kevin C A1 - Elloumi, Fathi A1 - Fan, Jianqing A1 - Fan, Shicai A1 - Fan, Xiaohui A1 - Fang, Hong A1 - Gonzaludo, Nina A1 - Hess, Kenneth R A1 - Hong, Huixiao A1 - Huan, Jun A1 - Irizarry, Rafael A A1 - Judson, Richard A1 - Juraeva, Dilafruz A1 - Lababidi, Samir A1 - Lambert, Christophe G A1 - Li, Li A1 - Li, Yanen A1 - Li, Zhen A1 - Lin, Simon M A1 - Liu, Guozhen A1 - Lobenhofer, Edward K A1 - Luo, Jun A1 - Luo, Wen A1 - McCall, Matthew N A1 - Nikolsky, Yuri A1 - Pennello, Gene A A1 - Perkins, Roger G A1 - Philip, Reena A1 - Popovici, Vlad A1 - Price, Nathan D A1 - Qian, Feng A1 - Scherer, Andreas A1 - Shi, Tieliu A1 - Shi, Weiwei A1 - Sung, Jaeyun A1 - Thierry-Mieg, Danielle A1 - Thierry-Mieg, Jean A1 - Thodima, Venkata A1 - Trygg, Johan A1 - Vishnuvajjala, Lakshmi A1 - Wang, Sue Jane A1 - Wu, Jianping A1 - Wu, Yichao A1 - Xie, Qian A1 - Yousef, Waleed A A1 - Zhang, Liang A1 - Zhang, Xuegong A1 - Zhong, Sheng A1 - Zhou, Yiming A1 - Zhu, Sheng A1 - Arasappan, Dhivya A1 - Bao, Wenjun A1 - Lucas, Anne Bergstrom A1 - Berthold, Frank A1 - Brennan, Richard J A1 - Buness, Andreas A1 - Catalano, Jennifer G A1 - Chang, Chang A1 - Chen, Rong A1 - Cheng, Yiyu A1 - Cui, Jian A1 - Czika, Wendy A1 - Demichelis, Francesca A1 - Deng, Xutao A1 - Dosymbekov, Damir A1 - Eils, Roland A1 - Feng, Yang A1 - Fostel, Jennifer A1 - Fulmer-Smentek, Stephanie A1 - Fuscoe, James C A1 - Gatto, Laurent A1 - Ge, Weigong A1 - Goldstein, Darlene R A1 - Guo, Li A1 - Halbert, Donald N A1 - Han, Jing A1 - Harris, Stephen C A1 - Hatzis, Christos A1 - Herman, Damir A1 - Huang, Jianping A1 - Jensen, Roderick V A1 - Jiang, Rui A1 - Johnson, Charles D A1 - Jurman, Giuseppe A1 - Kahlert, Yvonne A1 - Khuder, Sadik A A1 - Kohl, Matthias A1 - Li, Jianying A1 - Li, Li A1 - Li, Menglong A1 - Li, Quan-Zhen A1 - Li, Shao A1 - Li, Zhiguang A1 - Liu, Jie A1 - Liu, Ying A1 - Liu, Zhichao A1 - Meng, Lu A1 - Madera, Manuel A1 - Martinez-Murillo, Francisco A1 - Medina, Ignacio A1 - Meehan, Joseph A1 - Miclaus, Kelci A1 - Moffitt, Richard A A1 - Montaner, David A1 - Mukherjee, Piali A1 - Mulligan, George J A1 - Neville, Padraic A1 - Nikolskaya, Tatiana A1 - Ning, Baitang A1 - Page, Grier P A1 - Parker, Joel A1 - Parry, R Mitchell A1 - Peng, Xuejun A1 - Peterson, Ron L A1 - Phan, John H A1 - Quanz, Brian A1 - Ren, Yi A1 - Riccadonna, Samantha A1 - Roter, Alan H A1 - Samuelson, Frank W A1 - Schumacher, Martin M A1 - Shambaugh, Joseph D A1 - Shi, Qiang A1 - Shippy, Richard A1 - Si, Shengzhu A1 - Smalter, Aaron A1 - Sotiriou, Christos A1 - Soukup, Mat A1 - Staedtler, Frank A1 - Steiner, Guido A1 - Stokes, Todd H A1 - Sun, Qinglan A1 - Tan, Pei-Yi A1 - Tang, Rong A1 - Tezak, Zivana A1 - Thorn, Brett A1 - Tsyganova, Marina A1 - Turpaz, Yaron A1 - Vega, Silvia C A1 - Visintainer, Roberto A1 - von Frese, Juergen A1 - Wang, Charles A1 - Wang, Eric A1 - Wang, Junwei A1 - Wang, Wei A1 - Westermann, Frank A1 - Willey, James C A1 - Woods, Matthew A1 - Wu, Shujian A1 - Xiao, Nianqing A1 - Xu, Joshua A1 - Xu, Lei A1 - Yang, Lun A1 - Zeng, Xiao A1 - Zhang, Jialu A1 - Zhang, Li A1 - Zhang, Min A1 - Zhao, Chen A1 - Puri, Raj K A1 - Scherf, Uwe A1 - Tong, Weida A1 - Wolfinger, Russell D AB -

Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent teams analyzed six microarray data sets to generate predictive models for classifying a sample with respect to one of 13 endpoints indicative of lung or liver toxicity in rodents, or of breast cancer, multiple myeloma or neuroblastoma in humans. In total, >30,000 models were built using many combinations of analytical methods. The teams generated predictive models without knowing the biological meaning of some of the endpoints and, to mimic clinical reality, tested the models on data that had not been used for training. We found that model performance depended largely on the endpoint and team proficiency and that different approaches generated models of similar performance. The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis.

VL - 28 UR - http://www.nature.com/nbt/journal/v28/n8/full/nbt.1665.html ER - TY - JOUR T1 - Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa. JF - Hum Mutat Y1 - 2010 A1 - Barragán, Isabel A1 - Borrego, Salud A1 - Pieras, Juan Ignacio A1 - González-del Pozo, María A1 - Santoyo, Javier A1 - Ayuso, Carmen A1 - Baiget, Montserrat A1 - Millán, José M A1 - Mena, Marcela A1 - Abd El-Aziz, Mai M A1 - Audo, Isabelle A1 - Zeitz, Christina A1 - Littink, Karin W A1 - Dopazo, Joaquin A1 - Bhattacharya, Shomi S A1 - Antiňolo, Guillermo KW - Amino Acid Sequence KW - Animals KW - Case-Control Studies KW - DNA Mutational Analysis KW - Drosophila Proteins KW - Evolution, Molecular KW - Eye Proteins KW - Female KW - Genes, Recessive KW - Genetic Variation KW - Humans KW - Male KW - Molecular Sequence Data KW - mutation KW - Pedigree KW - Polymorphism, Single Nucleotide KW - Protein Structure, Tertiary KW - Retinitis pigmentosa KW - Spain KW - Structural Homology, Protein AB -

Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. We have recently identified a new gene(EYS) encoding an ortholog of Drosophila space maker (spam) as a commonly mutated gene in autosomal recessive RP. In the present study, we report the identification of 73 sequence variations in EYS, of which 28 are novel. Of these, 42.9% (12/28) are very likely pathogenic, 17.9% (5/28)are possibly pathogenic, whereas 39.3% (11/28) are SNPs. In addition, we have detected 3 pathogenic changes previously reported in other populations. We are also presenting the characterisation of EYS homologues in different species, and a detailed analysis of the EYS domains, with the identification of an interesting novel feature: a putative coiled-coil domain.Majority of the mutations in the arRP patients have been found within the domain structures of EYS. The minimum observed prevalence of distinct EYS mutations in our group of patients is of 15.9% (15/94), confirming a major involvement of EYS in the pathogenesis of arRP in the Spanish population. Along with the detection of three recurrent mutations in Caucasian population, our hypothesis of EYS being the first prevalent gene in arRP has been reinforced in the present study.

VL - 31 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21069908?dopt=Abstract ER - TY - JOUR T1 - Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups JF - Leuk Lymphoma Y1 - 2009 A1 - Jantus Lewintre, E. A1 - Reinoso Martin, C. A1 - Montaner, D. A1 - Marin, M. A1 - Jose Terol, M. A1 - Farras, R. A1 - Benet, I. A1 - Calvete, J. J. A1 - Dopazo, J. A1 - Garcia-Conde, J. KW - cancer KW - microarray data analysis AB -

B cell chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder with a variable clinical course. Patients with unmutated IgV(H) gene show a shorter progression-free and overall survival than patients with immunoglobulin heavy chain variable regions (IgV(H)) gene mutated. In addition, BCL6 mutations identify a subgroup of patients with high risk of progression. Gene expression was analysed in 36 early-stage patients using high-density microarrays. Around 150 genes differentially expressed were found according to IgV(H) mutations, whereas no difference was found according to BCL6 mutations. Functional profiling methods allowed us to distinguish KEGG and gene ontology terms showing coordinated gene expression changes across subgroups of CLL. We validated a set of differentially expressed genes according to IgV(H) status, scoring them as putative prognostic markers in CLL. Among them, CRY1, LPL, CD82 and DUSP22 are the ones with at least equal or superior performance to ZAP70 which is actually the most used surrogate marker of IgV(H) status.

VL - 50 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19127482 N1 -

Jantus Lewintre, Eloisa Reinoso Martin, Cristina Montaner, David Marin, Miguel Jose Terol, Maria Farras, Rosa Benet, Isabel Calvete, Juan J Dopazo, Joaquin Garcia-Conde, Javier Research Support, Non-U.S. Gov’t England Leukemia & lymphoma Leuk Lymphoma. 2009 Jan;50(1):68-79.

ER - TY - JOUR T1 - Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks JF - Funct Integr Genomics Y1 - 2009 A1 - Brumos, J. A1 - Colmenero-Flores, J. M. A1 - A. Conesa A1 - Izquierdo, P. A1 - Sanchez, G. A1 - Iglesias, D. J. A1 - Lopez-Climent, M. F. A1 - Gomez-Cadenas, A. A1 - Talon, M. AB -

Salinity tolerance in Citrus is strongly related to leaf chloride accumulation. Both chloride homeostasis and specific genetic responses to Cl(-) toxicity are issues scarcely investigated in plants. To discriminate the transcriptomic network related to Cl(-) toxicity and salinity tolerance, we have used two Cl(-) salt treatments (NaCl and KCl) to perform a comparative microarray approach on two Citrus genotypes, the salt-sensitive Carrizo citrange, a poor Cl(-) excluder, and the tolerant Cleopatra mandarin, an efficient Cl(-) excluder. The data indicated that Cl(-) toxicity, rather than Na(+) toxicity and/or the concomitant osmotic perturbation, is the primary factor involved in the molecular responses of citrus plant leaves to salinity. A number of uncharacterized membrane transporter genes, like NRT1-2, were differentially regulated in the tolerant and the sensitive genotypes, suggesting its potential implication in Cl(-) homeostasis. Analyses of enriched functional categories showed that the tolerant rootstock induced wider stress responses in gene expression while repressing central metabolic processes such as photosynthesis and carbon utilization. These features were in agreement with phenotypic changes in the patterns of photosynthesis, transpiration, and stomatal conductance and support the concept that regulation of transpiration and its associated metabolic adjustments configure an adaptive response to salinity that reduces Cl(-) accumulation in the tolerant genotype.

UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19190944 N1 -

Journal article Functional & integrative genomics Funct Integr Genomics. 2009 Feb 4.

ER - TY - JOUR T1 - Modeling and managing experimental data using FuGE. JF - OMICS Y1 - 2009 A1 - Andrew R Jones A1 - Allyson L Lister A1 - Leandro Hermida A1 - Peter Wilkinson A1 - Martin Eisenacher A1 - Khalid Belhajjame A1 - Frank Gibson A1 - Phil Lord A1 - Matthew Pocock A1 - Heiko Rosenfelder A1 - Santoyo-López, Javier A1 - Anil Wipat A1 - Norman W Paton VL - 13 ER - TY - CONF T1 - Peripheral blood cells transcriptome to study new biomarkers for myocardial infarction follow up Y1 - 2009 A1 - Silbiger, Vivian A1 - Luchessi, André A1 - Hirata, Rosario A1 - Carracedo, Ángel A1 - Brión, Maria A1 - Lima Neto, Lidio A1 - P. Pastorelli, C A1 - Dopazo, Joaquin A1 - Montaner, David A1 - Garcia, F A1 - P. Sampaio, M A1 - P. Pereira, M A1 - S. Santos, E A1 - Armaganijan, Dikran A1 - Hirata, Mario ER - TY - CHAP T1 - Protein Interactions for Functional Genomics T2 - Biological Data Mining in Protein Interaction Networks Y1 - 2009 A1 - Minguez, P. A1 - Dopazo, J. ED - Li, Xiao-Li ED - Ng, See-Kiong JF - Biological Data Mining in Protein Interaction Networks PB - Idea Group Inc (IGI) CY - Hershey, USA UR - http://books.google.es/books?id=pNyCy5GsqtkC ER - TY - JOUR T1 - Statistical methods for analysis of high-throughput RNA interference screens JF - Nature Methods Y1 - 2009 A1 - Birmingham, Amanda A1 - Selfors, Laura M A1 - Forster, Thorsten A1 - Wrobel, David A1 - Kennedy, Caleb J A1 - Shanks, Emma A1 - Santoyo-López, Javier A1 - Dunican, Dara J A1 - Long, Aideen A1 - Kelleher, Dermot A1 - Smith, Queta A1 - Beijersbergen, Roderick L A1 - Ghazal, Peter A1 - Shamu, Caroline E KW - gene silencing KW - regulation KW - siRNA PB - Nature Publishing Group VL - 6 SN - 1548-7091 UR - http://dx.doi.org/10.1038/nmeth.1351 N1 -

10.1038/nmeth.1351

ER - TY - CHAP T1 - The core of a minimal gene set: insights from natural reduced genomes T2 - Protocells: Bridging nonliving and living matter Y1 - 2008 A1 - Gabaldón, T. A1 - Gil, R. A1 - Peretó, J. A1 - Latorre, A. A1 - Moya, A. JF - Protocells: Bridging nonliving and living matter PB - The MIT Press CY - USA ER - TY - JOUR T1 - Interoperability with Moby 1.0--it's better than sharing your toothbrush! JF - Brief Bioinform Y1 - 2008 A1 - Wilkinson, Mark D A1 - Senger, Martin A1 - Kawas, Edward A1 - Bruskiewich, Richard A1 - Gouzy, Jerome A1 - Noirot, Celine A1 - Bardou, Philippe A1 - Ng, Ambrose A1 - Haase, Dirk A1 - Saiz, Enrique de Andres A1 - Wang, Dennis A1 - Gibbons, Frank A1 - Gordon, Paul M K A1 - Sensen, Christoph W A1 - Carrasco, Jose Manuel Rodriguez A1 - Fernández, José M A1 - Shen, Lixin A1 - Links, Matthew A1 - Ng, Michael A1 - Opushneva, Nina A1 - Neerincx, Pieter B T A1 - Leunissen, Jack A M A1 - Ernst, Rebecca A1 - Twigger, Simon A1 - Usadel, Bjorn A1 - Good, Benjamin A1 - Wong, Yan A1 - Stein, Lincoln A1 - Crosby, William A1 - Karlsson, Johan A1 - Royo, Romina A1 - Párraga, Iván A1 - Ramírez, Sergio A1 - Gelpi, Josep Lluis A1 - Trelles, Oswaldo A1 - Pisano, David G A1 - Jimenez, Natalia A1 - Kerhornou, Arnaud A1 - Rosset, Roman A1 - Zamacola, Leire A1 - Tárraga, Joaquín A1 - Huerta-Cepas, Jaime A1 - Carazo, Jose María A1 - Dopazo, Joaquin A1 - Guigó, Roderic A1 - Navarro, Arcadi A1 - Orozco, Modesto A1 - Valencia, Alfonso A1 - Claros, M Gonzalo A1 - Pérez, Antonio J A1 - Aldana, Jose A1 - Rojano, M Mar A1 - Fernandez-Santa Cruz, Raul A1 - Navas, Ismael A1 - Schiltz, Gary A1 - Farmer, Andrew A1 - Gessler, Damian A1 - Schoof, Heiko A1 - Groscurth, Andreas KW - Computational Biology KW - Database Management Systems KW - Databases, Factual KW - Information Storage and Retrieval KW - Internet KW - Programming Languages KW - Systems Integration AB -

The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.

VL - 9 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/18238804?dopt=Abstract ER - TY - JOUR T1 - Interoperability with Moby 1.0–it’s better than sharing your toothbrush! JF - Brief Bioinform Y1 - 2008 A1 - Wilkinson, M. D. A1 - Senger, M. A1 - Kawas, E. A1 - Bruskiewich, R. A1 - Gouzy, J. A1 - Noirot, C. A1 - Bardou, P. A1 - Ng, A. A1 - Haase, D. A1 - Saiz Ede, A. A1 - Wang, D. A1 - Gibbons, F. A1 - Gordon, P. M. A1 - Sensen, C. W. A1 - Carrasco, J. M. A1 - Fernandez, J. M. A1 - Shen, L. A1 - Links, M. A1 - Ng, M. A1 - Opushneva, N. A1 - Neerincx, P. B. A1 - Leunissen, J. A. A1 - Ernst, R. A1 - Twigger, S. A1 - Usadel, B. A1 - Good, B. A1 - Wong, Y. A1 - Stein, L. A1 - Crosby, W. A1 - Karlsson, J. A1 - Royo, R. A1 - Parraga, I. A1 - Ramirez, S. A1 - Gelpi, J. L. A1 - Trelles, O. A1 - Pisano, D. G. A1 - Jimenez, N. A1 - Kerhornou, A. A1 - Rosset, R. A1 - Zamacola, L. A1 - Tarraga, J. A1 - Huerta-Cepas, J. A1 - Carazo, J. M. A1 - Dopazo, J. A1 - R. Guigo A1 - Navarro, A. A1 - Orozco, M. A1 - Valencia, A. A1 - Claros, M. G. A1 - Perez, A. J. A1 - Aldana, J. A1 - Rojano, M. M. A1 - Fernandez-Santa Cruz, R. A1 - Navas, I. A1 - Schiltz, G. A1 - Farmer, A. A1 - Gessler, D. A1 - Schoof, H. A1 - Groscurth, A. KW - Computational Biology/*methods *Database Management Systems *Databases KW - Factual Information Storage and Retrieval/*methods *Internet *Programming Languages Systems Integration AB -

The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.

VL - 9 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18238804 N1 -

BioMoby Consortium Wilkinson, Mark D Senger, Martin Kawas, Edward Bruskiewich, Richard Gouzy, Jerome Noirot, Celine Bardou, Philippe Ng, Ambrose Haase, Dirk Saiz, Enrique de Andres Wang, Dennis Gibbons, Frank Gordon, Paul M K Sensen, Christoph W Carrasco, Jose Manuel Rodriguez Fernandez, Jose M Shen, Lixin Links, Matthew Ng, Michael Opushneva, Nina Neerincx, Pieter B T Leunissen, Jack A M Ernst, Rebecca Twigger, Simon Usadel, Bjorn Good, Benjamin Wong, Yan Stein, Lincoln Crosby, William Karlsson, Johan Royo, Romina Parraga, Ivan Ramirez, Sergio Gelpi, Josep Lluis Trelles, Oswaldo Pisano, David G Jimenez, Natalia Kerhornou, Arnaud Rosset, Roman Zamacola, Leire Tarraga, Joaquin Huerta-Cepas, Jaime Carazo, Jose Maria Dopazo, Joaquin Guigo, Roderic Navarro, Arcadi Orozco, Modesto Valencia, Alfonso Claros, M Gonzalo Perez, Antonio J Aldana, Jose Rojano, M Mar Fernandez-Santa Cruz, Raul Navas, Ismael Schiltz, Gary Farmer, Andrew Gessler, Damian Schoof, Heiko Groscurth, Andreas Research Support, Non-U.S. Gov’t Review England Briefings in bioinformatics Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31.

ER - TY - JOUR T1 - Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information JF - Oncogene Y1 - 2008 A1 - Montero-Conde, C. A1 - Martin-Campos, J. M. A1 - Lerma, E. A1 - Gimenez, G. A1 - Martinez-Guitarte, J. L. A1 - Combalia, N. A1 - Montaner, D. A1 - Matias-Guiu, X. A1 - Dopazo, J. A1 - de Leiva, A. A1 - M. Robledo A1 - Mauricio, D. KW - Adenoma/genetics/metabolism/pathology Adolescent Adult Aged Carcinoma/genetics/metabolism/pathology Carcinoma KW - Biological/*genetics/metabolism KW - Neoplasm/genetics/metabolism Reverse Transcriptase Polymerase Chain Reaction Signal Transduction Thyroid Neoplasms/classification/*genetics/metabolism Tumor Markers KW - Neoplastic Humans Male Middle Aged *Oligonucleotide Array Sequence Analysis Prognosis RNA KW - Papillary/genetics/metabolism/pathology Cell Differentiation Female *Gene Expression Profiling *Gene Expression Regulation AB -

Undifferentiated and poorly differentiated thyroid tumors are responsible for more than half of thyroid cancer patient deaths in spite of their low incidence. Conventional treatments do not obtain substantial benefits, and the lack of alternative approaches limits patient survival. Additionally, the absence of prognostic markers for well-differentiated tumors complicates patient-specific treatments and favors the progression of recurrent forms. In order to recognize the molecular basis involved in tumor dedifferentiation and identify potential markers for thyroid cancer prognosis prediction, we analysed the expression profile of 44 thyroid primary tumors with different degrees of dedifferentiation and aggressiveness using cDNA microarrays. Transcriptome comparison of dedifferentiated and well-differentiated thyroid tumors identified 1031 genes with >2-fold difference in absolute values and false discovery rate of <0.15. According to known molecular interaction and reaction networks, the products of these genes were mainly clustered in the MAPkinase signaling pathway, the TGF-beta signaling pathway, focal adhesion and cell motility, activation of actin polymerization and cell cycle. An exhaustive search in several databases allowed us to identify various members of the matrix metalloproteinase, melanoma antigen A and collagen gene families within the upregulated gene set. We also identified a prognosis classifier comprising just 30 transcripts with an overall accuracy of 95%. These findings may clarify the molecular mechanisms involved in thyroid tumor dedifferentiation and provide a potential prognosis predictor as well as targets for new therapies.

VL - 27 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17873908 N1 -

Montero-Conde, C Martin-Campos, J M Lerma, E Gimenez, G Martinez-Guitarte, J L Combalia, N Montaner, D Matias-Guiu, X Dopazo, J de Leiva, A Robledo, M Mauricio, D Research Support, Non-U.S. Gov’t England Oncogene Oncogene. 2008 Mar 6;27(11):1554-61. Epub 2007 Sep 17.

ER - TY - JOUR T1 - Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information. JF - Oncogene Y1 - 2008 A1 - Montero-Conde, C A1 - Martín-Campos, J M A1 - Lerma, E A1 - Gimenez, G A1 - Martínez-Guitarte, J L A1 - Combalía, N A1 - Montaner, D A1 - Matías-Guiu, X A1 - Dopazo, J A1 - de Leiva, A A1 - Robledo, M A1 - Mauricio, D KW - Adenoma KW - Adolescent KW - Adult KW - Aged KW - Biomarkers, Tumor KW - Carcinoma KW - Carcinoma, Papillary KW - Cell Differentiation KW - Female KW - Gene Expression Profiling KW - Gene Expression Regulation, Neoplastic KW - Humans KW - Male KW - Middle Aged KW - Oligonucleotide Array Sequence Analysis KW - Prognosis KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA, Neoplasm KW - Signal Transduction KW - Thyroid Neoplasms AB -

Undifferentiated and poorly differentiated thyroid tumors are responsible for more than half of thyroid cancer patient deaths in spite of their low incidence. Conventional treatments do not obtain substantial benefits, and the lack of alternative approaches limits patient survival. Additionally, the absence of prognostic markers for well-differentiated tumors complicates patient-specific treatments and favors the progression of recurrent forms. In order to recognize the molecular basis involved in tumor dedifferentiation and identify potential markers for thyroid cancer prognosis prediction, we analysed the expression profile of 44 thyroid primary tumors with different degrees of dedifferentiation and aggressiveness using cDNA microarrays. Transcriptome comparison of dedifferentiated and well-differentiated thyroid tumors identified 1031 genes with >2-fold difference in absolute values and false discovery rate of <0.15. According to known molecular interaction and reaction networks, the products of these genes were mainly clustered in the MAPkinase signaling pathway, the TGF-beta signaling pathway, focal adhesion and cell motility, activation of actin polymerization and cell cycle. An exhaustive search in several databases allowed us to identify various members of the matrix metalloproteinase, melanoma antigen A and collagen gene families within the upregulated gene set. We also identified a prognosis classifier comprising just 30 transcripts with an overall accuracy of 95%. These findings may clarify the molecular mechanisms involved in thyroid tumor dedifferentiation and provide a potential prognosis predictor as well as targets for new therapies.

VL - 27 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/17873908?dopt=Abstract ER - TY - JOUR T1 - SNP and haplotype mapping for genetic analysis in the rat JF - Nat Genet Y1 - 2008 A1 - K. Saar A1 - A. Beck A1 - M. T. Bihoreau A1 - E. Birney A1 - D. Brocklebank A1 - Y. Chen A1 - E. Cuppen A1 - S. Demonchy A1 - Dopazo, J. A1 - P. Flicek A1 - M. Foglio A1 - A. Fujiyama A1 - I. G. Gut A1 - D. Gauguier A1 - R. Guigo A1 - V. Guryev A1 - M. Heinig A1 - O. Hummel A1 - N. Jahn A1 - S. Klages A1 - V. Kren A1 - M. Kube A1 - H. Kuhl A1 - Kuramoto, T. A1 - Kuroki, Y. A1 - Lechner, D. A1 - Lee, Y. A. A1 - Lopez-Bigas, N. A1 - Lathrop, G. M. A1 - Mashimo, T. A1 - Medina, Ignacio A1 - Mott, R. A1 - Patone, G. A1 - Perrier-Cornet, J. A. A1 - Platzer, M. A1 - Pravenec, M. A1 - Reinhardt, R. A1 - Sakaki, Y. A1 - Schilhabel, M. A1 - Schulz, H. A1 - Serikawa, T. A1 - Shikhagaie, M. A1 - Tatsumoto, S. A1 - Taudien, S. A1 - Toyoda, A. A1 - Voigt, B. A1 - Zelenika, D. A1 - Zimdahl, H. A1 - Hubner, N. KW - Animals Chromosome Mapping *Databases KW - Genetic KW - Genetic Genome *Haplotypes Linkage Disequilibrium Phylogeny *Polymorphism KW - Inbred Strains/*genetics Recombination KW - Single Nucleotide *Quantitative Trait Loci Rats/*genetics Rats AB -

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

VL - 40 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18443594 N1 -

STAR Consortium Saar, Kathrin Beck, Alfred Bihoreau, Marie-Therese Birney, Ewan Brocklebank, Denise Chen, Yuan Cuppen, Edwin Demonchy, Stephanie Dopazo, Joaquin Flicek, Paul Foglio, Mario Fujiyama, Asao Gut, Ivo G Gauguier, Dominique Guigo, Roderic Guryev, Victor Heinig, Matthias Hummel, Oliver Jahn, Niels Klages, Sven Kren, Vladimir Kube, Michael Kuhl, Heiner Kuramoto, Takashi Kuroki, Yoko Lechner, Doris Lee, Young-Ae Lopez-Bigas, Nuria Lathrop, G Mark Mashimo, Tomoji Medina, Ignacio Mott, Richard Patone, Giannino Perrier-Cornet, Jeanne-Antide Platzer, Matthias Pravenec, Michal Reinhardt, Richard Sakaki, Yoshiyuki Schilhabel, Markus Schulz, Herbert Serikawa, Tadao Shikhagaie, Medya Tatsumoto, Shouji Taudien, Stefan Toyoda, Atsushi Voigt, Birger Zelenika, Diana Zimdahl, Heike Hubner, Norbert 057733/Z/99/A/Wellcome Trust/United Kingdom 066780/Z/01/Z/Wellcome Trust/United Kingdom Research Support, Non-U.S. Gov’t Technical Report United States Nature genetics Nat Genet. 2008 May;40(5):560-6.

ER - TY - JOUR T1 - SNP and haplotype mapping for genetic analysis in the rat. JF - Nat Genet Y1 - 2008 A1 - Saar, Kathrin A1 - Beck, Alfred A1 - Bihoreau, Marie-Thérèse A1 - Birney, Ewan A1 - Brocklebank, Denise A1 - Chen, Yuan A1 - Cuppen, Edwin A1 - Demonchy, Stephanie A1 - Dopazo, Joaquin A1 - Flicek, Paul A1 - Foglio, Mario A1 - Fujiyama, Asao A1 - Gut, Ivo G A1 - Gauguier, Dominique A1 - Guigó, Roderic A1 - Guryev, Victor A1 - Heinig, Matthias A1 - Hummel, Oliver A1 - Jahn, Niels A1 - Klages, Sven A1 - Kren, Vladimir A1 - Kube, Michael A1 - Kuhl, Heiner A1 - Kuramoto, Takashi A1 - Kuroki, Yoko A1 - Lechner, Doris A1 - Lee, Young-Ae A1 - Lopez-Bigas, Nuria A1 - Lathrop, G Mark A1 - Mashimo, Tomoji A1 - Medina, Ignacio A1 - Mott, Richard A1 - Patone, Giannino A1 - Perrier-Cornet, Jeanne-Antide A1 - Platzer, Matthias A1 - Pravenec, Michal A1 - Reinhardt, Richard A1 - Sakaki, Yoshiyuki A1 - Schilhabel, Markus A1 - Schulz, Herbert A1 - Serikawa, Tadao A1 - Shikhagaie, Medya A1 - Tatsumoto, Shouji A1 - Taudien, Stefan A1 - Toyoda, Atsushi A1 - Voigt, Birger A1 - Zelenika, Diana A1 - Zimdahl, Heike A1 - Hubner, Norbert KW - Animals KW - Chromosome Mapping KW - Databases, Genetic KW - Genome KW - Haplotypes KW - Linkage Disequilibrium KW - Phylogeny KW - Polymorphism, Single Nucleotide KW - Quantitative Trait Loci KW - Rats KW - Rats, Inbred Strains KW - Recombination, Genetic AB -

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

VL - 40 IS - 5 U1 - https://www.ncbi.nlm.nih.gov/pubmed/18443594?dopt=Abstract ER - TY - JOUR T1 - Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush JF - Mol Vis Y1 - 2008 A1 - Agudo, M. A1 - Perez-Marin, M. C. A1 - Lonngren, U. A1 - Sobrado, P. A1 - A. Conesa A1 - Canovas, I. A1 - Salinas-Navarro, M. A1 - Miralles-Imperial, J. A1 - Hallbook, F. A1 - Vidal-Sanz, M. KW - Animals Cell Death Cluster Analysis Female *Gene Expression Profiling Gene Expression Regulation *Nerve Crush Optic Nerve/*metabolism/*pathology Optic Nerve Injuries/*genetics Rats Rats KW - Sprague-Dawley Reproducibility of Results Retina/*metabolism/*pathology Time Factors AB - PURPOSE: A time-course analysis of gene regulation in the adult rat retina after intraorbital nerve crush (IONC) and intraorbital nerve transection (IONT). METHODS: RNA was extracted from adult rat retinas undergoing either IONT or IONC at increasing times post-lesion. Affymetrix RAE230.2 arrays were hybridized and analyzed. Statistically regulated genes were annotated and functionally clustered. Arrays were validated by means of quantative reverse transcription polymerase chain reaction (qRT-PCR) on ten regulated genes at two times post-lesion. Western blotting and immunohistofluorescence for four pro-apoptotic proteins were performed on naive and injured retinas. Finally, custom signaling maps for IONT- and IONC-induced death response were generated (MetaCore, Genego Inc.). RESULTS: Here we show that over time, 3,219 sequences were regulated after IONT and 1,996 after IONC. Out of the total of regulated sequences, 1,078 were commonly regulated by both injuries. Interestingly, while IONT mainly triggers a gene upregulation-sustained over time, IONC causes a transitory downregulation. Functional clustering identified the regulation of high interest biologic processes, most importantly cell death wherein apoptosis was the most significant cluster. Ten death-related genes upregulated by both injuries were used for array validation by means of qRT-PCR. In addition, western blotting and immunohistofluorescence of total and active Caspase 3 (Casp3), tumor necrosis factor receptor type 1 associated death domain (TRADD), tumor necrosis factor receptor superfamily member 1a (TNFR1a), and c-fos were performed to confirm their protein regulation and expression pattern in naive and injured retinas. These analyses demonstrated that for these genes, protein regulation followed transcriptional regulation and that these pro-apoptotic proteins were expressed by retinal ganglion cells (RGCs). MetaCore-based death-signaling maps show that several apoptotic cascades were regulated in the retina following optic nerve injury and highlight the similarities and differences between IONT and IONC in cell death profiling. CONCLUSIONS: This comprehensive time course retinal transcriptome study comparing IONT and IONC lesions provides a unique valuable tool to understand the molecular mechanisms underlying optic nerve injury and to design neuroprotective protocols. VL - 14 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18552980 N1 - Agudo, Marta Perez-Marin, Maria Cruz Lonngren, Ulrika Sobrado, Paloma Conesa, Ana Canovas, Isabel Salinas-Navarro, Manuel Miralles-Imperial, Jaime Hallbook, Finn Vidal-Sanz, Manuel Research Support, Non-U.S. Gov’t United States Molecular vision Mol Vis. 2008 Jun 3;14:1050-63. ER - TY - JOUR T1 - Transcriptional profiling of mRNA expression in the mouse distal colon JF - Gastroenterology Y1 - 2008 A1 - Hoogerwerf, W. A. A1 - Sinha, M. A1 - A. Conesa A1 - Luxon, B. A. A1 - Shahinian, V. B. A1 - Cornelissen, G. A1 - Halberg, F. A1 - Bostwick, J. A1 - Timm, J. A1 - Cassone, V. M. KW - Animals Blotting KW - Genetic KW - Inbred C57BL Microarray Analysis Proteins/*genetics/metabolism RNA KW - Messenger/biosynthesis/*genetics Reverse Transcriptase Polymerase Chain Reaction *Transcription KW - Western Cell Proliferation Circadian Rhythm/*genetics Colon/cytology/*metabolism Male Mice Mice AB - BACKGROUND & AIMS: Intestinal epithelial cells and the myenteric plexus of the mouse gastrointestinal tract contain a circadian clock-based intrinsic time-keeping system. Because disruption of the biological clock has been associated with increased susceptibility to colon cancer and gastrointestinal symptoms, we aimed to identify rhythmically expressed genes in the mouse distal colon. METHODS: Microarray analysis was used to identify genes that were rhythmically expressed over a 24-hour light/dark cycle. The transcripts were then classified according to expression pattern, function, and association with physiologic and pathophysiologic processes of the colon. RESULTS: A circadian gene expression pattern was detected in approximately 3.7% of distal colonic genes. A large percentage of these genes were involved in cell signaling, differentiation, and proliferation and cell death. Of all the rhythmically expressed genes in the mouse colon, approximately 7% (64/906) have been associated with colorectal cancer formation (eg, B-cell leukemia/lymphoma-2 [Bcl2]) and 1.8% (18/906) with various colonic functions such as motility and secretion (eg, vasoactive intestinal polypeptide, cystic fibrosis transmembrane conductance regulator). CONCLUSIONS: A subset of genes in the murine colon follows a rhythmic expression pattern. These findings may have significant implications for colonic physiology and pathophysiology. VL - 135 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18848557 N1 - Hoogerwerf, Willemijntje A Sinha, Mala Conesa, Ana Luxon, Bruce A Shahinian, Vahakn B Cornelissen, Germaine Halberg, Franz Bostwick, Jonathon Timm, John Cassone, Vincent M R21 DK074477-01A1/DK/NIDDK NIH HHS/United States Comparative Study Research Support, N.I.H., Extramural United States Gastroenterology Gastroenterology. 2008 Dec;135(6):2019-29. Epub 2008 Sep 3. ER - TY - JOUR T1 - Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole JF - Food Chem Toxicol Y1 - 2008 A1 - Stierum, R. A1 - A. Conesa A1 - Heijne, W. A1 - Ommen, B. A1 - Junker, K. A1 - Scott, M. P. A1 - Price, R. J. A1 - Meredith, C. A1 - Lake, B. G. A1 - Groten, J. KW - Animals Aryl Hydrocarbon Hydroxylases/metabolism Body Weight/drug effects Butylated Hydroxytoluene/toxicity Curcumin/toxicity Cytochrome P-450 CYP1A2/metabolism Cytochrome P-450 CYP2B1/metabolism DNA KW - Complementary/biosynthesis/genetics Data Interpretation KW - Sprague-Dawley Reverse Transcriptase Polymerase Chain Reaction Steroid Hydroxylases/metabolism Thiabendazole/toxicity KW - Statistical *Diet Food Additives/*toxicity Gene Expression/drug effects *Gene Expression Profiling Glutathione Transferase/metabolism Liver/*drug effects Male Organ Size/drug effects Oxidation-Reduction Palmitoyl Coenzyme A/metabolism Propyl Gallate/toxi AB - Transcriptomics was performed to gain insight into mechanisms of food additives butylated hydroxytoluene (BHT), curcumin (CC), propyl gallate (PG), and thiabendazole (TB), additives for which interactions in the liver can not be excluded. Additives were administered in diets for 28 days to Sprague-Dawley rats and cDNA microarray experiments were performed on hepatic RNA. BHT induced changes in the expression of 10 genes, including phase I (CYP2B1/2; CYP3A9; CYP2C6) and phase II metabolism (GST mu2). The CYP2B1/2 and GST expression findings were confirmed by real time RT-PCR, western blotting, and increased GST activity towards DCNB. CC altered the expression of 12 genes. Three out of these were related to peroxisomes (phytanoyl-CoA dioxygenase, enoyl-CoA hydratase; CYP4A3). Increased cyanide insensitive palmitoyl-CoA oxidation was observed, suggesting that CC is a weak peroxisome proliferator. TB changed the expression of 12 genes, including CYP1A2. In line, CYP1A2 protein expression was increased. The expression level of five genes, associated with p53 was found to change upon TB treatment, including p53 itself, GADD45alpha, DN-7, protein kinase C beta and serum albumin. These array experiments led to the novel finding that TB is capable of inducing p53 at the protein level, at least at the highest dose levels employed above the current NOAEL. The expression of eight genes changed upon PG administration. This study shows the value of gene expression profiling in food toxicology in terms of generating novel hypotheses on the mechanisms of action of food additives in relation to pathology. VL - 46 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18539377 N1 - Stierum, Rob Conesa, Ana Heijne, Wilbert Ommen, Ben van Junker, Karin Scott, Mary P Price, Roger J Meredith, Clive Lake, Brian G Groten, John Research Support, Non-U.S. Gov’t England Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association Food Chem Toxicol. 2008 Aug;46(8):2616-28. Epub 2008 Apr 25. ER - TY - JOUR T1 - Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance JF - BMC Genomics Y1 - 2007 A1 - Terol, J. A1 - A. Conesa A1 - Colmenero, J. M. A1 - Cercos, M. A1 - Tadeo, F. A1 - Agusti, J. A1 - Alos, E. A1 - Andres, F. A1 - Soler, G. A1 - Brumos, J. A1 - Iglesias, D. J. A1 - Gotz, S. A1 - Legaz, F. A1 - Argout, X. A1 - Courtois, B. A1 - Ollitrault, P. A1 - Dossat, C. A1 - Wincker, P. A1 - Morillon, R. A1 - Talon, M. KW - Acclimatization/*genetics Amino Acid Motifs Citrus/*genetics Cluster Analysis Expressed Sequence Tags Fruit/genetics Gene Duplication *Gene Expression Regulation KW - Plant Gene Library Genes KW - Plant Genomics Molecular Sequence Data Multigene Family Phylogeny *Salts/adverse effects AB - BACKGROUND: Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. RESULTS: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis x Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of 13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains CONCLUSION: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays. VL - 8 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17254327 N1 - Terol, Javier Conesa, Ana Colmenero, Jose M Cercos, Manuel Tadeo, Francisco Agusti, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talon, Manuel Comparative Study Research Support, Non-U.S. Gov’t England BMC genomics BMC Genomics. 2007 Jan 25;8:31. ER - TY - JOUR T1 - Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma JF - Cancer Res Y1 - 2007 A1 - Ruiz-Llorente, S. A1 - Montero-Conde, C. A1 - Milne, R. L. A1 - Moya, C. M. A1 - Cebrian, A. A1 - Leton, R. A1 - Cascon, A. A1 - Mercadillo, F. A1 - Landa, I. A1 - Borrego, S. A1 - Perez de Nanclares, G. A1 - Alvarez-Escola, C. A1 - Diaz-Perez, J. A. A1 - Carracedo, A. A1 - Urioste, M. A1 - Gonzalez-Neira, A. A1 - Benitez, J. A1 - Santisteban, P. A1 - Dopazo, J. A1 - Ponder, B. A. A1 - M. Robledo KW - 80 and over Carcinoma KW - Adolescent Adult Aged Aged KW - Genetic KW - Genetic Proto-Oncogene Proteins c-ret/*genetics/metabolism Signal Transduction Thyroid Neoplasms/*genetics/metabolism Transcription KW - Medullary/*genetics/metabolism Case-Control Studies Cyclin-Dependent Kinase Inhibitor p15/biosynthesis/genetics Female Genetic Predisposition to Disease Germ-Line Mutation Haplotypes Humans Male Middle Aged Penetrance Polymorphism KW - Single Nucleotide Promoter Regions AB - To date, few association studies have been done to better understand the genetic basis for the development of sporadic medullary thyroid carcinoma (sMTC). To identify additional low-penetrance genes, we have done a two-stage case-control study in two European populations using high-throughput genotyping. We selected 417 single nucleotide polymorphisms (SNP) belonging to 69 genes either related to RET signaling pathway/functions or involved in key processes for cancer development. TagSNPs and functional variants were included where possible. These SNPs were initially studied in the largest known series of sMTC cases (n = 266) and controls (n = 422), all of Spanish origin. In stage II, an independent British series of 155 sMTC patients and 531 controls was included to validate the previous results. Associations were assessed by an exhaustive analysis of individual SNPs but also considering gene- and linkage disequilibrium-based haplotypes. This strategy allowed us to identify seven low-penetrance genes, six of them (STAT1, AURKA, BCL2, CDKN2B, CDK6, and COMT) consistently associated with sMTC risk in the two case-control series and a seventh (HRAS) with individual SNPs and haplotypes associated with sMTC in the Spanish data set. The potential role of CDKN2B was confirmed by a functional assay showing a role of a SNP (rs7044859) in the promoter region in altering the binding of the transcription factor HNF1. These results highlight the utility of association studies using homogeneous series of cases for better understanding complex diseases. VL - 67 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17909067 N1 - Ruiz-Llorente, Sergio Montero-Conde, Cristina Milne, Roger L Moya, Christian M Cebrian, Arancha Leton, Rocio Cascon, Alberto Mercadillo, Fatima Landa, Inigo Borrego, Salud Perez de Nanclares, Guiomar Alvarez-Escola, Cristina Diaz-Perez, Jose Angel Carracedo, Angel Urioste, Miguel Gonzalez-Neira, Anna Benitez, Javier Santisteban, Pilar Dopazo, Joaquin Ponder, Bruce A Robledo, Mercedes Medullary Thyroid Carcinoma Clinical Group Research Support, Non-U.S. Gov’t United States Cancer research Cancer Res. 2007 Oct 1;67(19):9561-7. ER - TY - JOUR T1 - Spatial differentiation in the vegetative mycelium of Aspergillus niger JF - Eukaryot Cell Y1 - 2007 A1 - Levin, A. M. A1 - de Vries, R. P. A1 - A. Conesa A1 - de Bekker, C. A1 - Talon, M. A1 - Menke, H. H. A1 - van Peij, N. N. A1 - Wosten, H. A. KW - Aspergillus niger/*metabolism Cell Wall/metabolism Fungal Proteins/metabolism *Gene Expression Regulation KW - Biological Mycelium/*metabolism Oligonucleotide Array Sequence Analysis RNA KW - Fungal Genes KW - Fungal Genome KW - Fungal Glucans/chemistry Maltose/chemistry Models KW - Fungal Time Factors Trans-Activators/metabolism Xylose/chemistry AB - Fungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium. VL - 6 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17951513 N1 - Levin, Ana M de Vries, Ronald P Conesa, Ana de Bekker, Charissa Talon, Manuel Menke, Hildegard H van Peij, Noel N M E Wosten, Han A B Research Support, Non-U.S. Gov’t United States Eukaryotic cell Eukaryot Cell. 2007 Dec;6(12):2311-22. Epub 2007 Oct 19. ER - TY - JOUR T1 - Structural analyses of a hypothetical minimal metabolism JF - Philos Trans R Soc Lond B Biol Sci Y1 - 2007 A1 - Gabaldón, T. A1 - Peretó, J. A1 - Montero, F. A1 - Gil, R. A1 - Latorre, A. A1 - Moya, A. KW - *Cell Physiological Phenomena Cells/*metabolism Cluster Analysis *Computer Simulation *Metabolic Networks and Pathways *Models KW - Biological Models KW - Statistical AB - By integrating data from comparative genomics and large-scale deletion studies, we previously proposed a minimal gene set comprising 206 protein-coding genes. To evaluate the consistency of the metabolism encoded by such a minimal genome, we have carried out a series of computational analyses. Firstly, the topology of the minimal metabolism was compared with that of the reconstructed networks from natural bacterial genomes. Secondly, the robustness of the metabolic network was evaluated by simulated mutagenesis and, finally, the stoichiometric consistency was assessed by automatically deriving the steady-state solutions from the reaction set. The results indicated that the proposed minimal metabolism presents stoichiometric consistency and that it is organized as a complex power-law network with topological parameters falling within the expected range for a natural metabolism of its size. The robustness analyses revealed that most random mutations do not alter the topology of the network significantly, but do cause significant damage by preventing the synthesis of several compounds or compromising the stoichiometric consistency of the metabolism. The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed. VL - 362 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17510022 N1 - Gabaldon, Toni Pereto, Juli Montero, Francisco Gil, Rosario Latorre, Amparo Moya, Andres Research Support, Non-U.S. Gov’t England Philosophical transactions of the Royal Society of London. Series B, Biological sciences Philos Trans R Soc Lond B Biol Sci. 2007 Oct 29;362(1486):1751-62. ER - TY - JOUR T1 - Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma JF - Haematologica Y1 - 2006 A1 - Largo, C. A1 - Alvarez, S. A1 - Saez, B. A1 - Blesa, D. A1 - Martin-Subero, J. I. A1 - Gonzalez-Garcia, I. A1 - Brieva, J. A. A1 - Dopazo, J. A1 - Siebert, R. A1 - Calasanz, M. J. A1 - Cigudosa, J. C. KW - B-Cell KW - Caspases Cell Line KW - Human *Gene Amplification Gene Dosage Gene Expression Profiling *Gene Expression Regulation KW - Marginal Zone/genetics Multiple Myeloma/*genetics Neoplasm Proteins/genetics Proto-Oncogene Proteins c-bcl-2/genetics KW - Neoplasm Humans Immunoglobulin Heavy Chains/genetics Lymphoma KW - Neoplastic Gene Rearrangement *Genes KW - Tumor *Chromosomes AB - BACKGROUND AND OBJECTIVES: Multiple myeloma (MM) is a malignancy characterized by clonal expansion of plasma cells. In 50% of the cases, the neoplastic transformation begins with a chromosomal translocation that juxtaposes the IGH gene locus to an oncogene. Gene copy number changes are also frequent in MM but less characterized than in other neoplasias. We aimed to characterize genes that are amplified and overexpressed in human myeloma cell lines (HMCL) to provide putative molecular targets for MM therapy. DESIGN AND METHODS: Nine HMCL were characterized by fluorescent in situ hybridization, comparative genomic hybridization (CGH) and cDNA microarrays for gene expression profiling and copy number changes. RESULTS: After defining the IGH-translocations present in the cell lines, we conducted expression-profiling analysis. Supervised analysis identified 166 genes with significantly different expression among the cell lines harboring MMSET/FGFR3 (4p16), MAF (16q) and CCND1 (11q13) rearrangements. Array-CGH was then performed. Five chromosomes recurrently affected by gains/amplifications in primary samples and cell lines were analyzed in detail. Sixty amplified and overexpressed genes were found and 25 (42%) of them were only overexpressed when amplified; moreover, six showed a significant association between overexpression and gain/amplification. We also found co-amplification and overexpression for genes located within the same amplicons, such as MALT1 and BCL2. INTERPRETATION AND CONCLUSIONS: Parallel analysis of gene copy numbers and expression levels by cDNA microarray in MM allowed efficient identification of genes whose expression levels are elevated because of increased copy number. This is the first time that MALT1 and BCL2 have been shown to be overexpressed and amplified in MM. VL - 91 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16461302 N1 - Largo, Cristina Alvarez, Sara Saez, Borja Blesa, David Martin-Subero, Jose I Gonzalez-Garcia, Ines Brieva, Jose A Dopazo, Joaquin Siebert, Reiner Calasanz, Maria J Cigudosa, Juan C Research Support, Non-U.S. Gov’t Italy Haematologica Haematologica. 2006 Feb;91(2):184-91. ER - TY - JOUR T1 - The C-type lectin fold as an evolutionary solution for massive sequence variation JF - Nat Struct Mol Biol Y1 - 2005 A1 - McMahon, S. A. A1 - Miller, J. L. A1 - Lawton, J. A. A1 - Kerkow, D. E. A1 - Hodes, A. A1 - M. A. Marti-Renom A1 - Doulatov, S. A1 - Narayanan, E. A1 - Sali, A. A1 - Miller, J. F. A1 - Ghosh, P. KW - Amino Acid Sequence Bacterial Outer Membrane Proteins/*chemistry Bacteriophages/*metabolism Bordetella/*virology Evolution KW - Bordetella/*chemistry KW - C-Type/*chemistry Molecular Sequence Data Protein Conformation Protein Folding Viral Proteins/*chemistry/*genetics Virulence Factors KW - Molecular Genetic Variation Genome KW - Viral Lectins AB - Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements. VL - 12 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16170324 N1 - McMahon, Stephen A Miller, Jason L Lawton, Jeffrey A Kerkow, Donald E Hodes, Asher Marti-Renom, Marc A Doulatov, Sergei Narayanan, Eswar Sali, Andrej Miller, Jeff F Ghosh, Partho F31AI061840/AI/NIAID NIH HHS/United States F32AI49695/AI/NIAID NIH HHS/United States T32GM008326/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. United States Nature structural & molecular biology Nat Struct Mol Biol. 2005 Oct;12(10):886-92. Epub 2005 Sep 18. ER - TY - JOUR T1 - Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies JF - Plant Mol Biol Y1 - 2005 A1 - J. Forment A1 - J. Gadea A1 - Huerta, L. A1 - Abizanda, L. A1 - Agusti, J. A1 - Alamar, S. A1 - Alos, E. A1 - Andres, F. A1 - Arribas, R. A1 - Beltran, J. P. A1 - Berbel, A. A1 - Blazquez, M. A. A1 - Brumos, J. A1 - Canas, L. A. A1 - Cercos, M. A1 - Colmenero-Flores, J. M. A1 - A. Conesa A1 - Estables, B. A1 - Gandia, M. A1 - Garcia-Martinez, J. L. A1 - Gimeno, J. A1 - Gisbert, A. A1 - Gomez, G. A1 - Gonzalez-Candelas, L. A1 - Granell, A. A1 - Guerri, J. A1 - Lafuente, M. T. A1 - Madueno, F. A1 - Marcos, J. F. A1 - Marques, M. C. A1 - Martinez, F. A1 - Martinez-Godoy, M. A. A1 - Miralles, S. A1 - Moreno, P. A1 - Navarro, L. A1 - Pallas, V. A1 - Perez-Amador, M. A. A1 - Perez-Valle, J. A1 - Pons, C. A1 - Rodrigo, I. A1 - Rodriguez, P. L. A1 - Royo, C. A1 - Serrano, R. A1 - Soler, G. A1 - Tadeo, F. A1 - Talon, M. A1 - Terol, J. A1 - Trenor, M. A1 - Vaello, L. A1 - Vicente, O. A1 - Vidal, Ch A1 - Zacarias, L. A1 - Conejero, V. KW - Citrus/*genetics DNA KW - Complementary/chemistry/genetics *Expressed Sequence Tags Gene Expression Profiling Gene Library *Genome KW - DNA KW - Plant Genomics/*methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis/*methods RNA KW - Plant/genetics/metabolism Reproducibility of Results Sequence Analysis AB - A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis. VL - 57 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128 N1 - Forment, J Gadea, J Huerta, L Abizanda, L Agusti, J Alamar, S Alos, E Andres, F Arribas, R Beltran, J P Berbel, A Blazquez, M A Brumos, J Canas, L A Cercos, M Colmenero-Flores, J M Conesa, A Estables, B Gandia, M Garcia-Martinez, J L Gimeno, J Gisbert, A Gomez, G Gonzalez-Candelas, L Granell, A Guerri, J Lafuente, M T Madueno, F Marcos, J F Marques, M C Martinez, F Martinez-Godoy, M A Miralles, S Moreno, P Navarro, L Pallas, V Perez-Amador, M A Perez-Valle, J Pons, C Rodrigo, I Rodriguez, P L Royo, C Serrano, R Soler, G Tadeo, F Talon, M Terol, J Trenor, M Vaello, L Vicente, O Vidal, Ch Zacarias, L Conejero, V Comparative Study Research Support, U.S. Gov’t, Non-P.H.S. Netherlands Plant molecular biology Plant Mol Biol. 2005 Feb;57(3):375-91. ER - TY - JOUR T1 - A novel candidate region linked to development of both pheochromocytoma and head/neck paraganglioma JF - Genes Chromosomes Cancer Y1 - 2005 A1 - Cascon, A. A1 - Ruiz-Llorente, S. A1 - Rodriguez-Perales, S. A1 - Honrado, E. A1 - Martinez-Ramirez, A. A1 - Leton, R. A1 - Montero-Conde, C. A1 - Benitez, J. A1 - Dopazo, J. A1 - Cigudosa, J. C. A1 - M. Robledo KW - 80 and over Child Chromosomes KW - Adolescent Adrenal Gland Neoplasms/*genetics Adult Aged Aged KW - Biological/*genetics KW - Human KW - Pair 1/genetics Chromosomes KW - Pair 11/genetics Chromosomes KW - Pair 3/genetics Chromosomes KW - Pair 8/genetics Female Gene Deletion Head and Neck Neoplasms/*genetics Humans Male Middle Aged Nucleic Acid Hybridization Paraganglioma/*genetics Pheochromocytoma/*genetics Tumor Markers AB - Although the histologic distinction between pheochromocytomas and head and neck paragangliomas is clear, little is known about the genetic differences between them. To date, various sets of genes have been found to be involved in inherited susceptibility to developing both tumor types, but the genes involved in sporadic pathogenesis are still unknown. To define new candidate regions, we performed CGH analysis on 29 pheochromocytomas and on 24 paragangliomas mainly of head and neck origin (20 of 24), which allowed us to differentiate between the two tumor types. Loss of 3q was significantly more frequent in pheochromocytomas, and loss of 1q appeared only in paragangliomas. We also found gain of 11q13 to be a significantly frequent alteration in malignant cases of both types. In addition, recurrent loss of 8p22-23 was found in 62% of pheochromocytomas (including all malignant cases) versus in 33% of paragangliomas, suggesting that this region contains candidate genes involved in the pathogenesis of this abnormality. Using FISH analysis on tissue microarrays, we confirmed genomic deletion of this region in 55% of pheochromocytomas compared to 12% of paragangliomas. Loss of 8p22-23 appears to be an important event in the sporadic development of these tumors, and additional molecular studies are necessary to identify candidate genes in this chromosomal region. VL - 42 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15609347 N1 - Cascon, Alberto Ruiz-Llorente, Sergio Rodriguez-Perales, Sandra Honrado, Emiliano Martinez-Ramirez, Angel Leton, Rocio Montero-Conde, Cristina Benitez, Javier Dopazo, Joaquin Cigudosa, Juan C Robledo, Mercedes Research Support, Non-U.S. Gov’t United States Genes, chromosomes & cancer Genes Chromosomes Cancer. 2005 Mar;42(3):260-8. ER - TY - JOUR T1 - Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers JF - Breast Cancer Res Treat Y1 - 2005 A1 - Palacios, J. A1 - Honrado, E. A1 - Osorio, A. A1 - Cazorla, A. A1 - Sarrio, D. A1 - Barroso, A. A1 - Rodriguez, S. A1 - Cigudosa, J. C. A1 - Diez, O. A1 - Alonso, C. A1 - Lerma, E. A1 - Dopazo, J. A1 - Rivas, C. A1 - Benitez, J. KW - Adult Apoptosis Breast Neoplasms/*genetics/*pathology Cell Cycle Proteins Cluster Analysis Female *Genes KW - Biological/genetics/metabolism KW - BRCA1 *Genes KW - BRCA2 Humans Immunohistochemistry In Situ Hybridization KW - Fluorescence Phenotype Spain *Tissue Array Analysis *Tumor Markers AB - Familial breast cancers that are associated with BRCA1 or BRCA2 germline mutations differ in both their morphological and immunohistochemical characteristics. To further characterize the molecular difference between genotypes, the authors evaluated the expression of 37 immunohistochemical markers in a tissue microarray (TMA) containing cores from 20 BRCA1, 14 BRCA2, and 59 sporadic age-matched breast carcinomas. Markers analyzed included, amog others, common markers in breast cancer, such as hormone receptors, p53 and HER2, along with 15 molecules involved in cell cycle regulation, such as cyclins, cyclin dependent kinases (CDK) and CDK inhibitors (CDKI), apoptosis markers, such as BCL2 and active caspase 3, and two basal/myoepithelial markers (CK 5/6 and P-cadherin). In addition, we analyzed the amplification of CCND1, CCNE, HER2 and MYC by FISH.Unsupervised cluster data analysis of both hereditary and sporadic cases using the complete set of immunohistochemical markers demonstrated that most BRCA1-associated carcinomas grouped in a branch of ER-, HER2-negative tumors that expressed basal cell markers and/or p53 and had higher expression of activated caspase 3. The cell cycle proteins associated with these tumors were E2F6, cyclins A, B1 and E, SKP2 and Topo IIalpha. In contrast, most BRCA2-associated carcinomas grouped in a branch composed by ER/PR/BCL2-positive tumors with a higher expression of the cell cycle proteins cyclin D1, cyclin D3, p27, p16, p21, CDK4, CDK2 and CDK1. In conclusion, our study in hereditary breast cancer tumors analyzing 37 immunohistochemical markers, define the molecular differences between BRCA1 and BRCA2 tumors with respect to hormonal receptors, cell cycle, apoptosis and basal cell markers. VL - 90 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15770521 N1 - Palacios, Jose Honrado, Emiliano Osorio, Ana Cazorla, Alicia Sarrio, David Barroso, Alicia Rodriguez, Sandra Cigudosa, Juan C Diez, Orland Alonso, Carmen Lerma, Enrique Dopazo, Joaquin Rivas, Carmen Benitez, Javier Research Support, Non-U.S. Gov’t Netherlands Breast cancer research and treatment Breast Cancer Res Treat. 2005 Mar;90(1):5-14. ER - TY - JOUR T1 - Expression profiling of T-cell lymphomas differentiates peripheral and lymphoblastic lymphomas and defines survival related genes. JF - Clinical cancer research : an official journal of the American Association for Cancer Research Y1 - 2004 A1 - Martinez-Delgado, Beatriz A1 - Meléndez, Barbara A1 - Cuadros, Marta A1 - Alvarez, Javier A1 - Castrillo, Jose Maria A1 - Ruiz De La Parte, Ana A1 - Mollejo, Manuela A1 - Bellas, Carmen A1 - Diaz, Ramon A1 - Lombardía, Luis A1 - Fatima Al-Shahrour A1 - Domínguez, Orlando A1 - Cascon, Alberto A1 - Robledo, Mercedes A1 - Rivas, Carmen A1 - Benitez, Javier AB -

PURPOSE: T-Cell lymphomas constitute heterogeneous and aggressive tumors in which pathogenic alterations remain largely unknown. Expression profiling has demonstrated to be a useful tool for molecular classification of tumors. EXPERIMENTAL DESIGN: Using DNA microarrays (CNIO-OncoChip) containing 6386 cancer-related genes, we established the expression profiling of T-cell lymphomas and compared them to normal lymphocytes and lymph nodes. RESULTS: We found significant differences between the peripheral and lymphoblastic T-cell lymphomas, which include a deregulation of nuclear factor-kappaB signaling pathway. We also identify differentially expressed genes between peripheral T-cell lymphoma tumors and normal T lymphocytes or reactive lymph nodes, which could represent candidate tumor markers of these lymphomas. Additionally, a close relationship between genes associated to survival and those that differentiate among the stages of disease and responses to therapy was found. CONCLUSIONS: Our results reflect the value of gene expression profiling to gain insight about the molecular alterations involved in the pathogenesis of T-cell lymphomas.

VL - 10 UR - http://clincancerres.aacrjournals.org/content/10/15/4971.long ER - TY - JOUR T1 - Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma JF - Am J Pathol Y1 - 2002 A1 - Tracey, L. A1 - Villuendas, R. A1 - Ortiz, P. A1 - Dopazo, A. A1 - Spiteri, I. A1 - Lombardia, L. A1 - Rodriguez-Peralto, J. L. A1 - Fernandez-Herrera, J. A1 - Hernandez, A. A1 - Fraga, J. A1 - Dominguez, O. A1 - Herrero, J. A1 - Alonso, M. A. A1 - Dopazo, J. A1 - Piris, M. A. KW - Antineoplastic Agents/*pharmacology/therapeutic use Carrier Proteins/biosynthesis/genetics DNA-Binding Proteins/biosynthesis/genetics Drug Resistance KW - Biological Oligonucleotide Array Sequence Analysis RNA KW - Cultured KW - Cutaneous/diagnosis/drug therapy/*genetics/metabolism *Membrane Glycoproteins Models KW - Interleukin-1 Reproducibility of Results STAT1 Transcription Factor STAT3 Transcription Factor Trans-Activators/biosynthesis/genetics Tumor Cells KW - Neoplasm Gene Expression Profiling *Gene Expression Regulation KW - Neoplasm/biosynthesis *Receptors KW - Neoplastic Humans Interferon-alpha/*pharmacology/therapeutic use Kinetics Lymphoma KW - T-Cell AB - Interferon-alpha therapy has been shown to be active in the treatment of mycosis fungoides although the individual response to this therapy is unpredictable and dependent on essentially unknown factors. In an effort to better understand the molecular mechanisms of interferon-alpha resistance we have developed an interferon-alpha resistant variant from a sensitive cutaneous T-cell lymphoma cell line. We have performed expression analysis to detect genes differentially expressed between both variants using a cDNA microarray including 6386 cancer-implicated genes. The experiments showed that resistance to interferon-alpha is consistently associated with changes in the expression of a set of 39 genes, involved in signal transduction, apoptosis, transcription regulation, and cell growth. Additional studies performed confirm that STAT1 and STAT3 expression and interferon-alpha induction and activation are not altered between both variants. The gene MAL, highly overexpressed by resistant cells, was also found to be expressed by tumoral cells in a series of cutaneous T-cell lymphoma patients treated with interferon-alpha and/or photochemotherapy. MAL expression was associated with longer time to complete remission. Time-course experiments of the sensitive and resistant cells showed a differential expression of a subset of genes involved in interferon-response (1 to 4 hours), cell growth and apoptosis (24 to 48 hours.), and signal transduction. VL - 161 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12414529 N1 - Tracey, Lorraine Villuendas, Raquel Ortiz, Pablo Dopazo, Ana Spiteri, Inmaculada Lombardia, Luis Rodriguez-Peralto, Jose L Fernandez-Herrera, Jesus Hernandez, Almudena Fraga, Javier Dominguez, Orlando Herrero, Javier Alonso, Miguel A Dopazo, Joaquin Piris, Miguel A Research Support, Non-U.S. Gov’t United States The American journal of pathology Am J Pathol. 2002 Nov;161(5):1825-37. ER - TY - BOOK T1 - Methods of Microarray Data Analysis IISupervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles Y1 - 2002 A1 - Mateos, Alvaro A1 - Herrero, Javier A1 - Tamames, Javier A1 - Dopazo, Joaquin ED - Lin, Simon M. ED - Johnson, Kimberly F. PB - Kluwer Academic Publishers CY - Boston UR - http://www.springerlink.com/index/10.1007/b112982http://link.springer.com/10.1007/0-306-47598-7_7http://www.springerlink.com/index/pdf/10.1007/0-306-47598-7_7 ER - TY - JOUR T1 - Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies JF - J Immunol Y1 - 2002 A1 - Iverson, G. M. A1 - Reddel, S. A1 - Victoria, E. J. A1 - Cockerill, K. A. A1 - Wang, Y. X. A1 - M. A. Marti-Renom A1 - Sali, A. A1 - Marquis, D. M. A1 - Krilis, S. A. A1 - Linnik, M. D. KW - Amino Acid Substitution/genetics Antibodies KW - Antibody/genetics Binding KW - Antiphospholipid/blood/*metabolism Antibodies KW - Competitive/genetics/immunology Enzyme-Linked Immunosorbent Assay/methods Epitopes/analysis/*immunology/metabolism Glycine/genetics Glycoproteins/biosynthesis/*genetics/*immunology/isolation & purification/metabolism Humans Models KW - Molecular Peptide Fragments/genetics/immunology/isolation & purification/metabolism *Point Mutation Protein Structure KW - Monoclonal/blood/metabolism Antiphospholipid Syndrome/immunology Arginine/genetics *Binding Sites KW - Tertiary/genetics Recombinant Proteins/biosynthesis/immunology/isolation & purification/metabolism Static Electricity beta 2-Glycoprotein I AB - Autoantibodies against beta(2)-glycoprotein I (beta(2)GPI) appear to be a critical feature of the antiphospholipid syndrome (APS). As determined using domain deletion mutants, human autoantibodies bind to the first of five domains present in beta(2)GPI. In this study the fine detail of the domain I epitope has been examined using 10 selected mutants of whole beta(2)GPI containing single point mutations in the first domain. The binding to beta(2)GPI was significantly affected by a number of single point mutations in domain I, particularly by mutations in the region of aa 40-43. Molecular modeling predicted these mutations to affect the surface shape and electrostatic charge of a facet of domain I. Mutation K19E also had an effect, albeit one less severe and involving fewer patients. Similar results were obtained in two different laboratories using affinity-purified anti-beta(2)GPI in a competitive inhibition ELISA and with whole serum in a direct binding ELISA. This study confirms that anti-beta(2)GPI autoantibodies bind to domain I, and that the charged surface patch defined by residues 40-43 contributes to a dominant target epitope. VL - 169 UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146 N1 - Iverson, G Michael Reddel, Stephen Victoria, Edward J Cockerill, Keith A Wang, Ying-Xia Marti-Renom, Marc A Sali, Andrej Marquis, David M Krilis, Steven A Linnik, Matthew D GM54762/GM/NIGMS NIH HHS/United States Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. United States Journal of immunology (Baltimore, Md. : 1950) J Immunol. 2002 Dec 15;169(12):7097-103. ER -