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

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.

%B Front Immunol %V 14 %P 1282859 %8 2023 %G eng %R 10.3389/fimmu.2023.1282859 %0 Journal Article %J J Transl Med %D 2024 %T The mechanistic functional landscape of retinitis pigmentosa: a machine learning-driven approach to therapeutic target discovery. %A Esteban-Medina, Marina %A Loucera, Carlos %A Rian, Kinza %A Velasco, Sheyla %A Olivares-González, Lorena %A Rodrigo, Regina %A Dopazo, Joaquin %A Peña-Chilet, Maria %K Animals %K Mice %K Retinitis pigmentosa %K Signal Transduction %X

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.

%B J Transl Med %V 22 %P 139 %8 2024 Feb 06 %G eng %N 1 %R 10.1186/s12967-024-04911-7 %0 Journal Article %J Cell Rep %D 2023 %T Defective extracellular matrix remodeling in brown adipose tissue is associated with fibro-inflammation and reduced diet-induced thermogenesis. %A Pellegrinelli, Vanessa %A Figueroa-Juárez, Elizabeth %A Samuelson, Isabella %A U-Din, Mueez %A Rodriguez-Fdez, Sonia %A Virtue, Samuel %A Leggat, Jennifer %A Cubuk, Cankut %A Peirce, Vivian J %A Niemi, Tarja %A Campbell, Mark %A Rodriguez-Cuenca, Sergio %A Dopazo, Joaquin %A Carobbio, Stefania %A Virtanen, Kirsi A %A Vidal-Puig, Antonio %X

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.

%B Cell Rep %V 42 %P 112640 %8 2023 Jun 13 %G eng %N 6 %R 10.1016/j.celrep.2023.112640 %0 Journal Article %J Int J Mol Sci %D 2023 %T 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. %A Perez-Florido, Javier %A Casimiro-Soriguer, Carlos S %A Ortuno, Francisco %A Fernandez-Rueda, Jose L %A Aguado, Andrea %A Lara, María %A Riazzo, Cristina %A Rodriguez-Iglesias, Manuel A %A Camacho-Martinez, Pedro %A Merino-Diaz, Laura %A Pupo-Ledo, Inmaculada %A de Salazar, Adolfo %A Viñuela, Laura %A Fuentes, Ana %A Chueca, Natalia %A García, Federico %A Dopazo, Joaquin %A Lepe, Jose A %X

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.

%B Int J Mol Sci %V 24 %8 2023 Jan 26 %G eng %N 3 %R 10.3390/ijms24032419 %0 Journal Article %J Epidemiol Infect %D 2023 %T Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. %A Chaves-Blanco, Lucía %A de Salazar, Adolfo %A Fuentes, Ana %A Viñuela, Laura %A Perez-Florido, Javier %A Dopazo, Joaquin %A García, Federico %K Alleles %K COVID-19 %K COVID-19 Testing %K Humans %K Real-Time Polymerase Chain Reaction %K SARS-CoV-2 %K Sensitivity and Specificity %X

This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.

%B Epidemiol Infect %V 151 %P e201 %8 2023 Nov 24 %G eng %R 10.1017/S095026882300184X %0 Journal Article %J Med Clin (Barc) %D 2023 %T 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). %A Loucera, Carlos %A Carmona, Rosario %A Bostelmann, Gerrit %A Muñoyerro-Muñiz, Dolores %A Villegas, Román %A Gonzalez-Manzanares, Rafael %A Dopazo, Joaquin %A Anguita, Manuel %X

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.

%B Med Clin (Barc) %8 2023 Nov 20 %G eng %R 10.1016/j.medcli.2023.10.008 %0 Journal Article %J Commun Biol %D 2023 %T Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging. %A Sola-García, Alejandro %A Cáliz-Molina, María Ángeles %A Espadas, Isabel %A Petr, Michael %A Panadero-Morón, Concepción %A González-Morán, Daniel %A Martín-Vázquez, María Eugenia %A Narbona-Pérez, Álvaro Jesús %A López-Noriega, Livia %A Martínez-Corrales, Guillermo %A López-Fernández-Sobrino, Raúl %A Carmona-Marin, Lina M %A Martínez-Force, Enrique %A Yanes, Oscar %A Vinaixa, Maria %A López-López, Daniel %A Reyes, José Carlos %A Dopazo, Joaquin %A Martín, Franz %A Gauthier, Benoit R %A Scheibye-Knudsen, Morten %A Capilla-González, Vivian %A Martín-Montalvo, Alejandro %X

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.

%B Commun Biol %V 6 %P 250 %8 2023 Mar 08 %G eng %N 1 %R 10.1038/s42003-023-04625-4 %0 Journal Article %J Aging Cell %D 2023 %T microRNAs-mediated regulation of insulin signaling in white adipose tissue during aging: Role of caloric restriction. %A Corrales, Patricia %A Martin-Taboada, Marina %A Vivas-García, Yurena %A Torres, Lucia %A Ramirez-Jimenez, Laura %A Lopez, Yamila %A Horrillo, Daniel %A Vila-Bedmar, Rocio %A Barber-Cano, Eloisa %A Izquierdo-Lahuerta, Adriana %A Peña-Chilet, Maria %A Martínez, Carmen %A Dopazo, Joaquin %A Ros, Manuel %A Medina-Gomez, Gema %X

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.

%B Aging Cell %P e13919 %8 2023 Jul 04 %G eng %R 10.1111/acel.13919 %0 Journal Article %J Virol J %D 2023 %T Real-world evidence with a retrospective cohort of 15,968 COVID-19 hospitalized patients suggests 21 new effective treatments. %A Loucera, Carlos %A Carmona, Rosario %A Esteban-Medina, Marina %A Bostelmann, Gerrit %A Muñoyerro-Muñiz, Dolores %A Villegas, Román %A Peña-Chilet, Maria %A Dopazo, Joaquin %X

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.

%B Virol J %V 20 %P 226 %8 2023 Oct 06 %G eng %N 1 %R 10.1186/s12985-023-02195-9 %0 Journal Article %J Viruses %D 2022 %T Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival. %A Loucera, Carlos %A Perez-Florido, Javier %A Casimiro-Soriguer, Carlos S %A Ortuno, Francisco M %A Carmona, Rosario %A Bostelmann, Gerrit %A Martínez-González, L Javier %A Muñoyerro-Muñiz, Dolores %A Villegas, Román %A Rodríguez-Baño, Jesús %A Romero-Gómez, Manuel %A Lorusso, Nicola %A Garcia-León, Javier %A Navarro-Marí, Jose M %A Camacho-Martinez, Pedro %A Merino-Diaz, Laura %A Salazar, Adolfo de %A Viñuela, Laura %A Lepe, Jose A %A García, Federico %A Dopazo, Joaquin %K COVID-19 %K Genome, Viral %K Humans %K mutation %K Pandemics %K Phylogeny %K SARS-CoV-2 %X

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.

%B Viruses %V 14 %8 2022 Aug 27 %G eng %N 9 %R 10.3390/v14091893 %0 Journal Article %J Hum Mol Genet %D 2022 %T Novel genes and sex differences in COVID-19 severity. %A Cruz, Raquel %A Almeida, Silvia Diz-de %A Heredia, Miguel López %A Quintela, Inés %A Ceballos, Francisco C %A Pita, Guillermo %A Lorenzo-Salazar, José M %A González-Montelongo, Rafaela %A Gago-Domínguez, Manuela %A Porras, Marta Sevilla %A Castaño, Jair Antonio Tenorio %A Nevado, Julián %A Aguado, Jose María %A Aguilar, Carlos %A Aguilera-Albesa, Sergio %A Almadana, Virginia %A Almoguera, Berta %A Alvarez, Nuria %A Andreu-Bernabeu, Álvaro %A Arana-Arri, Eunate %A Arango, Celso %A Arranz, María J %A Artiga, Maria-Jesus %A Baptista-Rosas, Raúl C %A Barreda-Sánchez, María %A Belhassen-Garcia, Moncef %A Bezerra, Joao F %A Bezerra, Marcos A C %A Boix-Palop, Lucía %A Brión, Maria %A Brugada, Ramón %A Bustos, Matilde %A Calderón, Enrique J %A Carbonell, Cristina %A Castano, Luis %A Castelao, Jose E %A Conde-Vicente, Rosa %A Cordero-Lorenzana, M Lourdes %A Cortes-Sanchez, Jose L %A Corton, Marta %A Darnaude, M Teresa %A De Martino-Rodríguez, Alba %A Campo-Pérez, Victor %A Bustamante, Aranzazu Diaz %A Domínguez-Garrido, Elena %A Luchessi, André D %A Eirós, Rocío %A Sanabria, Gladys Mercedes Estigarribia %A Fariñas, María Carmen %A Fernández-Robelo, Uxía %A Fernández-Rodríguez, Amanda %A Fernández-Villa, Tania %A Gil-Fournier, Belén %A Gómez-Arrue, Javier %A Álvarez, Beatriz González %A Quirós, Fernan Gonzalez Bernaldo %A González-Peñas, Javier %A Gutiérrez-Bautista, Juan F %A Herrero, María José %A Herrero-Gonzalez, Antonio %A Jimenez-Sousa, María A %A Lattig, María Claudia %A Borja, Anabel Liger %A Lopez-Rodriguez, Rosario %A Mancebo, Esther %A Martín-López, Caridad %A Martín, Vicente %A Martinez-Nieto, Oscar %A Martinez-Lopez, Iciar %A Martinez-Resendez, Michel F %A Martinez-Perez, Ángel %A Mazzeu, Juliana A %A Macías, Eleuterio Merayo %A Minguez, Pablo %A Cuerda, Victor Moreno %A Silbiger, Vivian N %A Oliveira, Silviene F %A Ortega-Paino, Eva %A Parellada, Mara %A Paz-Artal, Estela %A Santos, Ney P C %A Pérez-Matute, Patricia %A Perez, Patricia %A Pérez-Tomás, M Elena %A Perucho, Teresa %A Pinsach-Abuin, Mel Lina %A Pompa-Mera, Ericka N %A Porras-Hurtado, Gloria L %A Pujol, Aurora %A León, Soraya Ramiro %A Resino, Salvador %A Fernandes, Marianne R %A Rodríguez-Ruiz, Emilio %A Rodriguez-Artalejo, Fernando %A Rodriguez-Garcia, José A %A Ruiz-Cabello, Francisco %A Ruiz-Hornillos, Javier %A Ryan, Pablo %A Soria, José Manuel %A Souto, Juan Carlos %A Tamayo, Eduardo %A Tamayo-Velasco, Alvaro %A Taracido-Fernandez, Juan Carlos %A Teper, Alejandro %A Torres-Tobar, Lilian %A Urioste, Miguel %A Valencia-Ramos, Juan %A Yáñez, Zuleima %A Zarate, Ruth %A Nakanishi, Tomoko %A Pigazzini, Sara %A Degenhardt, Frauke %A Butler-Laporte, Guillaume %A Maya-Miles, Douglas %A Bujanda, Luis %A Bouysran, Youssef %A Palom, Adriana %A Ellinghaus, David %A Martínez-Bueno, Manuel %A Rolker, Selina %A Amitrano, Sara %A Roade, Luisa %A Fava, Francesca %A Spinner, Christoph D %A Prati, Daniele %A Bernardo, David %A García, Federico %A Darcis, Gilles %A Fernández-Cadenas, Israel %A Holter, Jan Cato %A Banales, Jesus M %A Frithiof, Robert %A Duga, Stefano %A Asselta, Rosanna %A Pereira, Alexandre C %A Romero-Gómez, Manuel %A Nafría-Jiménez, Beatriz %A Hov, Johannes R %A Migeotte, Isabelle %A Renieri, Alessandra %A Planas, Anna M %A Ludwig, Kerstin U %A Buti, Maria %A Rahmouni, Souad %A Alarcón-Riquelme, Marta E %A Schulte, Eva C %A Franke, Andre %A Karlsen, Tom H %A Valenti, Luca %A Zeberg, Hugo %A Richards, Brent %A Ganna, Andrea %A Boada, Mercè %A Rojas, Itziar %A Ruiz, Agustín %A Sánchez, Pascual %A Real, Luis Miguel %A Guillén-Navarro, Encarna %A Ayuso, Carmen %A González-Neira, Anna %A Riancho, José A %A Rojas-Martinez, Augusto %A Flores, Carlos %A Lapunzina, Pablo %A Carracedo, Ángel %X

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.

%B Hum Mol Genet %8 2022 Jun 16 %G eng %R 10.1093/hmg/ddac132 %0 Journal Article %J Antioxidants (Basel) %D 2022 %T An SPM-Enriched Marine Oil Supplement Shifted Microglia Polarization toward M2, Ameliorating Retinal Degeneration in Mice. %A Olivares-González, Lorena %A Velasco, Sheyla %A Gallego, Idoia %A Esteban-Medina, Marina %A Puras, Gustavo %A Loucera, Carlos %A Martínez-Romero, Alicia %A Peña-Chilet, Maria %A Pedraz, José Luis %A Rodrigo, Regina %X

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.

%B Antioxidants (Basel) %V 12 %8 2022 Dec 30 %G eng %N 1 %R 10.3390/antiox12010098 %0 Journal Article %J BMC Bioinformatics %D 2021 %T A comprehensive database for integrated analysis of omics data in autoimmune diseases. %A Martorell-Marugán, Jordi %A López-Domínguez, Raúl %A García-Moreno, Adrián %A Toro-Domínguez, Daniel %A Villatoro-García, Juan Antonio %A Barturen, Guillermo %A Martín-Gómez, Adoración %A Troule, Kevin %A Gómez-López, Gonzalo %A Al-Shahrour, Fátima %A González-Rumayor, Víctor %A Peña-Chilet, Maria %A Dopazo, Joaquin %A Saez-Rodriguez, Julio %A Alarcón-Riquelme, Marta E %A Carmona-Sáez, Pedro %K Autoimmune Diseases %K Computational Biology %K Databases, Factual %K Humans %X

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.

%B BMC Bioinformatics %V 22 %P 343 %8 2021 Jun 24 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34167460?dopt=Abstract %R 10.1186/s12859-021-04268-4 %0 Journal Article %J Mol Syst Biol %D 2021 %T COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. %A Ostaszewski, Marek %A Niarakis, Anna %A Mazein, Alexander %A Kuperstein, Inna %A Phair, Robert %A Orta-Resendiz, Aurelio %A Singh, Vidisha %A Aghamiri, Sara Sadat %A Acencio, Marcio Luis %A Glaab, Enrico %A Ruepp, Andreas %A Fobo, Gisela %A Montrone, Corinna %A Brauner, Barbara %A Frishman, Goar %A Monraz Gómez, Luis Cristóbal %A Somers, Julia %A Hoch, Matti %A Kumar Gupta, Shailendra %A Scheel, Julia %A Borlinghaus, Hanna %A Czauderna, Tobias %A Schreiber, Falk %A Montagud, Arnau %A Ponce de Leon, Miguel %A Funahashi, Akira %A Hiki, Yusuke %A Hiroi, Noriko %A Yamada, Takahiro G %A Dräger, Andreas %A Renz, Alina %A Naveez, Muhammad %A Bocskei, Zsolt %A Messina, Francesco %A Börnigen, Daniela %A Fergusson, Liam %A Conti, Marta %A Rameil, Marius %A Nakonecnij, Vanessa %A Vanhoefer, Jakob %A Schmiester, Leonard %A Wang, Muying %A Ackerman, Emily E %A Shoemaker, Jason E %A Zucker, Jeremy %A Oxford, Kristie %A Teuton, Jeremy %A Kocakaya, Ebru %A Summak, Gökçe Yağmur %A Hanspers, Kristina %A Kutmon, Martina %A Coort, Susan %A Eijssen, Lars %A Ehrhart, Friederike %A Rex, Devasahayam Arokia Balaya %A Slenter, Denise %A Martens, Marvin %A Pham, Nhung %A Haw, Robin %A Jassal, Bijay %A Matthews, Lisa %A Orlic-Milacic, Marija %A Senff Ribeiro, Andrea %A Rothfels, Karen %A Shamovsky, Veronica %A Stephan, Ralf %A Sevilla, Cristoffer %A Varusai, Thawfeek %A Ravel, Jean-Marie %A Fraser, Rupsha %A Ortseifen, Vera %A Marchesi, Silvia %A Gawron, Piotr %A Smula, Ewa %A Heirendt, Laurent %A Satagopam, Venkata %A Wu, Guanming %A Riutta, Anders %A Golebiewski, Martin %A Owen, Stuart %A Goble, Carole %A Hu, Xiaoming %A Overall, Rupert W %A Maier, Dieter %A Bauch, Angela %A Gyori, Benjamin M %A Bachman, John A %A Vega, Carlos %A Grouès, Valentin %A Vazquez, Miguel %A Porras, Pablo %A Licata, Luana %A Iannuccelli, Marta %A Sacco, Francesca %A Nesterova, Anastasia %A Yuryev, Anton %A de Waard, Anita %A Turei, Denes %A Luna, Augustin %A Babur, Ozgun %A Soliman, Sylvain %A Valdeolivas, Alberto %A Esteban-Medina, Marina %A Peña-Chilet, Maria %A Rian, Kinza %A Helikar, Tomáš %A Puniya, Bhanwar Lal %A Modos, Dezso %A Treveil, Agatha %A Olbei, Marton %A De Meulder, Bertrand %A Ballereau, Stephane %A Dugourd, Aurélien %A Naldi, Aurélien %A Noël, Vincent %A Calzone, Laurence %A Sander, Chris %A Demir, Emek %A Korcsmaros, Tamas %A Freeman, Tom C %A Augé, Franck %A Beckmann, Jacques S %A Hasenauer, Jan %A Wolkenhauer, Olaf %A Wilighagen, Egon L %A Pico, Alexander R %A Evelo, Chris T %A Gillespie, Marc E %A Stein, Lincoln D %A Hermjakob, Henning %A D'Eustachio, Peter %A Saez-Rodriguez, Julio %A Dopazo, Joaquin %A Valencia, Alfonso %A Kitano, Hiroaki %A Barillot, Emmanuel %A Auffray, Charles %A Balling, Rudi %A Schneider, Reinhard %K Antiviral Agents %K Computational Biology %K Computer Graphics %K COVID-19 %K Cytokines %K Data Mining %K Databases, Factual %K Gene Expression Regulation %K Host Microbial Interactions %K Humans %K Immunity, Cellular %K Immunity, Humoral %K Immunity, Innate %K Lymphocytes %K Metabolic Networks and Pathways %K Myeloid Cells %K Protein Interaction Mapping %K SARS-CoV-2 %K Signal Transduction %K Software %K Transcription Factors %K Viral Proteins %X

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.

%B Mol Syst Biol %V 17 %P e10387 %8 2021 10 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/34664389?dopt=Abstract %R 10.15252/msb.202110387 %0 Journal Article %J Mol Oncol %D 2021 %T A DNA damage repair gene-associated signature predicts responses of patients with advanced soft-tissue sarcoma to treatment with trabectedin. %A Moura, David S %A Peña-Chilet, Maria %A Cordero Varela, Juan Antonio %A Alvarez-Alegret, Ramiro %A Agra-Pujol, Carolina %A Izquierdo, Francisco %A Ramos, Rafael %A Ortega-Medina, Luis %A Martin-Davila, Francisco %A Castilla-Ramirez, Carolina %A Hernandez-Leon, Carmen Nieves %A Romagosa, Cleofe %A Vaz Salgado, Maria Angeles %A Lavernia, Javier %A Bagué, Silvia %A Mayodormo-Aranda, Empar %A Vicioso, Luis %A Hernández Barceló, Jose Emilio %A Rubio-Casadevall, Jordi %A de Juan, Ana %A Fiaño-Valverde, Maria Concepcion %A Hindi, Nadia %A Lopez-Alvarez, Maria %A Lacerenza, Serena %A Dopazo, Joaquin %A Gutierrez, Antonio %A Alvarez, Rosa %A Valverde, Claudia %A Martinez-Trufero, Javier %A Martin-Broto, Javier %X

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.

%B Mol Oncol %V 15 %P 3691-3705 %8 2021 12 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/33983674?dopt=Abstract %R 10.1002/1878-0261.12996 %0 Journal Article %J Clinical Epigenetics %D 2021 %T Genome-wide analysis of DNA methylation in Hirschsprung enteric precursor cells: unraveling the epigenetic landscape of enteric nervous system developmentAbstractBackgroundResultsConclusionsGraphic abstract %A Villalba-Benito, Leticia %A López-López, Daniel %A Torroglosa, Ana %A Casimiro-Soriguer, Carlos S. %A Luzón-Toro, Berta %A Fernández, Raquel María %A Moya-Jiménez, María José %A Antiňolo, Guillermo %A Dopazo, Joaquin %A Borrego, Salud %B Clinical Epigenetics %V 13 %8 Jan-12-2021 %G eng %U http://link.springer.com/article/10.1186/s13148-021-01040-6/fulltext.html %N 1 %! Clin Epigenet %R 10.1186/s13148-021-01040-6 %0 Journal Article %J Cancers (Basel) %D 2021 %T Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development. %A Millán-Esteban, David %A Peña-Chilet, Maria %A García-Casado, Zaida %A Manrique-Silva, Esperanza %A Requena, Celia %A Bañuls, José %A Lopez-Guerrero, Jose Antonio %A Rodríguez-Hernández, Aranzazu %A Traves, Víctor %A Dopazo, Joaquin %A Virós, Amaya %A Kumar, Rajiv %A Nagore, Eduardo %X

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.

%B Cancers (Basel) %V 13 %8 2021 Oct 18 %G eng %N 20 %R 10.3390/cancers13205219 %0 Journal Article %J Front Mol Neurosci %D 2021 %T Presenilin-1 Mutations Are a Cause of Primary Lateral Sclerosis-Like Syndrome. %A Vázquez-Costa, Juan Francisco %A Payá-Montes, María %A Martínez-Molina, Marina %A Jaijo, Teresa %A Szymanski, Jazek %A Mazón, Miguel %A Sopena-Novales, Pablo %A Pérez-Tur, Jordi %A Sevilla, Teresa %X

Background and Purpose: Primary lateral sclerosis (PLS) is a progressive upper motor neuron (UMN) disorder. It is debated whether PLS is part of the amyotrophic lateral sclerosis (ALS) spectrum, or a syndrome encompassing different neurodegenerative diseases. Recently, new diagnostic criteria for PLS have been proposed. We describe four patients of two pedigrees, meeting definite PLS criteria and harboring two different mutations in presenilin 1 ().

Methods: Patients underwent neurological and neuropsychological examination, MRI, 18F-fluorodeoxyglucose positron emission tomography (FDG-PET), amyloid-related biomarkers, and next-generation sequencing (NGS) testing.

Results: Four patients, aged 25-45 years old, presented with a progressive UMN syndrome meeting clinical criteria of definite PLS. Cognitive symptoms and signs were mild or absent during the first year of the disease but appeared or progressed later in the disease course. Brain MRI showed microbleeds in two siblings, but iron-related hypointensities in the motor cortex were absent. Brain FDG-PET showed variable areas of hypometabolism, including the motor cortex and frontotemporal lobes. Amyloid deposition was confirmed with either cerebrospinal fluid (CSF) or imaging biomarkers. Two heterozygous likely pathogenic mutations in (p.Pro88Leu and p.Leu166Pro) were found in the NGS testing.

Conclusion: Clinically defined PLS is a syndrome encompassing different neurodegenerative diseases. The NGS testing should be part of the diagnostic workup in patients with PLS, at least in those with red flags, such as early-onset, cognitive impairment, and/or family history of neurodegenerative diseases.

%B Front Mol Neurosci %V 14 %P 721047 %8 2021 %G eng %R 10.3389/fnmol.2021.721047 %0 Journal Article %J Sci Rep %D 2021 %T Real world evidence of calcifediol or vitamin D prescription and mortality rate of COVID-19 in a retrospective cohort of hospitalized Andalusian patients. %A Loucera, Carlos %A Peña-Chilet, Maria %A Esteban-Medina, Marina %A Muñoyerro-Muñiz, Dolores %A Villegas, Román %A López-Miranda, José %A Rodríguez-Baño, Jesús %A Túnez, Isaac %A Bouillon, Roger %A Dopazo, Joaquin %A Quesada Gomez, Jose Manuel %K Calcifediol %K COVID-19 %K Female %K Humans %K Kaplan-Meier Estimate %K Male %K Retrospective Studies %K Spain %K Survival Analysis %K Vitamin D %X

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.

%B Sci Rep %V 11 %P 23380 %8 2021 12 03 %G eng %N 1 %R 10.1038/s41598-021-02701-5 %0 Journal Article %J Nat Med %D 2021 %T Reporting guidelines for human microbiome research: the STORMS checklist. %A Mirzayi, Chloe %A Renson, Audrey %A Zohra, Fatima %A Elsafoury, Shaimaa %A Geistlinger, Ludwig %A Kasselman, Lora J %A Eckenrode, Kelly %A van de Wijgert, Janneke %A Loughman, Amy %A Marques, Francine Z %A MacIntyre, David A %A Arumugam, Manimozhiyan %A Azhar, Rimsha %A Beghini, Francesco %A Bergstrom, Kirk %A Bhatt, Ami %A Bisanz, Jordan E %A Braun, Jonathan %A Bravo, Hector Corrada %A Buck, Gregory A %A Bushman, Frederic %A Casero, David %A Clarke, Gerard %A Collado, Maria Carmen %A Cotter, Paul D %A Cryan, John F %A Demmer, Ryan T %A Devkota, Suzanne %A Elinav, Eran %A Escobar, Juan S %A Fettweis, Jennifer %A Finn, Robert D %A Fodor, Anthony A %A Forslund, Sofia %A Franke, Andre %A Furlanello, Cesare %A Gilbert, Jack %A Grice, Elizabeth %A Haibe-Kains, Benjamin %A Handley, Scott %A Herd, Pamela %A Holmes, Susan %A Jacobs, Jonathan P %A Karstens, Lisa %A Knight, Rob %A Knights, Dan %A Koren, Omry %A Kwon, Douglas S %A Langille, Morgan %A Lindsay, Brianna %A McGovern, Dermot %A McHardy, Alice C %A McWeeney, Shannon %A Mueller, Noel T %A Nezi, Luigi %A Olm, Matthew %A Palm, Noah %A Pasolli, Edoardo %A Raes, Jeroen %A Redinbo, Matthew R %A Rühlemann, Malte %A Balfour Sartor, R %A Schloss, Patrick D %A Schriml, Lynn %A Segal, Eran %A Shardell, Michelle %A Sharpton, Thomas %A Smirnova, Ekaterina %A Sokol, Harry %A Sonnenburg, Justin L %A Srinivasan, Sujatha %A Thingholm, Louise B %A Turnbaugh, Peter J %A Upadhyay, Vaibhav %A Walls, Ramona L %A Wilmes, Paul %A Yamada, Takuji %A Zeller, Georg %A Zhang, Mingyu %A Zhao, Ni %A Zhao, Liping %A Bao, Wenjun %A Culhane, Aedin %A Devanarayan, Viswanath %A Dopazo, Joaquin %A Fan, Xiaohui %A Fischer, Matthias %A Jones, Wendell %A Kusko, Rebecca %A Mason, Christopher E %A Mercer, Tim R %A Sansone, Susanna-Assunta %A Scherer, Andreas %A Shi, Leming %A Thakkar, Shraddha %A Tong, Weida %A Wolfinger, Russ %A Hunter, Christopher %A Segata, Nicola %A Huttenhower, Curtis %A Dowd, Jennifer B %A Jones, Heidi E %A Waldron, Levi %K Computational Biology %K Dysbiosis %K Humans %K Microbiota %K Observational Studies as Topic %K Research Design %K Translational Science, Biomedical %X

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.

%B Nat Med %V 27 %P 1885-1892 %8 2021 11 %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/34789871?dopt=Abstract %R 10.1038/s41591-021-01552-x %0 Journal Article %J Genes %D 2021 %T Schuurs–Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review %A Tenorio-Castaño, Jair %A Morte, Beatriz %A Nevado, Julián %A Martínez-Glez, Víctor %A Santos-Simarro, Fernando %A García-Miñaur, Sixto %A Palomares-Bralo, María %A Pacio-Míguez, Marta %A Gómez, Beatriz %A Arias, Pedro %A Alcochea, Alba %A Carrión, Juan %A Arias, Patricia %A Almoguera, Berta %A López-Grondona, Fermina %A Lorda-Sanchez, Isabel %A Galán-Gómez, Enrique %A Valenzuela, Irene %A Méndez Perez, María %A Cuscó, Ivón %A Barros, Francisco %A Pié, Juan %A Ramos, Sergio %A Ramos, Feliciano %A Kuechler, Alma %A Tizzano, Eduardo %A Ayuso, Carmen %A Kaiser, Frank %A Pérez-Jurado, Luis %A Carracedo, Ángel %A Lapunzina, Pablo %B Genes %V 12 %P 738 %8 Jan-05-2021 %G eng %U https://www.mdpi.com/2073-4425/12/5/738https://www.mdpi.com/2073-4425/12/5/738/pdf %N 5 %! Genes %R 10.3390/genes12050738 %0 Journal Article %J Mol Med %D 2021 %T Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism. %A Méndez-Salazar, Eder Orlando %A Vázquez-Mellado, Janitzia %A Casimiro-Soriguer, Carlos S %A Dopazo, Joaquin %A Cubuk, Cankut %A Zamudio-Cuevas, Yessica %A Francisco-Balderas, Adriana %A Martínez-Flores, Karina %A Fernández-Torres, Javier %A Lozada-Pérez, Carlos %A Pineda, Carlos %A Sánchez-González, Austreberto %A Silveira, Luis H %A Burguete-García, Ana I %A Orbe-Orihuela, Citlalli %A Lagunas-Martínez, Alfredo %A Vazquez-Gomez, Alonso %A López-Reyes, Alberto %A Palacios-González, Berenice %A Martínez-Nava, Gabriela Angélica %K Biodiversity %K Computational Biology %K Dysbiosis %K Gastrointestinal Microbiome %K Gout %K Humans %K Metagenome %K metagenomics %K Protein Interaction Mapping %K Protein Interaction Maps %K Uric Acid %X

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.

%B Mol Med %V 27 %P 50 %8 2021 05 24 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34030623?dopt=Abstract %R 10.1186/s10020-021-00311-5 %0 Journal Article %J Sci Data %D 2020 %T COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. %A Ostaszewski, Marek %A Mazein, Alexander %A Gillespie, Marc E %A Kuperstein, Inna %A Niarakis, Anna %A Hermjakob, Henning %A Pico, Alexander R %A Willighagen, Egon L %A Evelo, Chris T %A Hasenauer, Jan %A Schreiber, Falk %A Dräger, Andreas %A Demir, Emek %A Wolkenhauer, Olaf %A Furlong, Laura I %A Barillot, Emmanuel %A Dopazo, Joaquin %A Orta-Resendiz, Aurelio %A Messina, Francesco %A Valencia, Alfonso %A Funahashi, Akira %A Kitano, Hiroaki %A Auffray, Charles %A Balling, Rudi %A Schneider, Reinhard %K Betacoronavirus %K Computational Biology %K Coronavirus Infections %K COVID-19 %K Databases, Factual %K Host Microbial Interactions %K Host-Pathogen Interactions %K Humans %K International Cooperation %K Models, Biological %K Pandemics %K Pneumonia, Viral %K SARS-CoV-2 %B Sci Data %V 7 %P 136 %8 2020 05 05 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32371892?dopt=Abstract %R 10.1038/s41597-020-0477-8 %0 Journal Article %J F1000Res %D 2020 %T The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. %A Salgado, David %A Armean, Irina M %A Baudis, Michael %A Beltran, Sergi %A Capella-Gutíerrez, Salvador %A Carvalho-Silva, Denise %A Dominguez Del Angel, Victoria %A Dopazo, Joaquin %A Furlong, Laura I %A Gao, Bo %A Garcia, Leyla %A Gerloff, Dietlind %A Gut, Ivo %A Gyenesei, Attila %A Habermann, Nina %A Hancock, John M %A Hanauer, Marc %A Hovig, Eivind %A Johansson, Lennart F %A Keane, Thomas %A Korbel, Jan %A Lauer, Katharina B %A Laurie, Steve %A Leskošek, Brane %A Lloyd, David %A Marqués-Bonet, Tomás %A Mei, Hailiang %A Monostory, Katalin %A Piñero, Janet %A Poterlowicz, Krzysztof %A Rath, Ana %A Samarakoon, Pubudu %A Sanz, Ferran %A Saunders, Gary %A Sie, Daoud %A Swertz, Morris A %A Tsukanov, Kirill %A Valencia, Alfonso %A Vidak, Marko %A Yenyxe González, Cristina %A Ylstra, Bauke %A Béroud, Christophe %K Computational Biology %K DNA Copy Number Variations %K High-Throughput Nucleotide Sequencing %K Humans %X

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.

%B F1000Res %V 9 %8 2020 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34367618?dopt=Abstract %& 1229 %R 10.12688/f1000research.24887.1 %0 Journal Article %J iScience %D 2020 %T Immune Cell Associations with Cancer Risk. %A Palomero, Luis %A Galván-Femenía, Ivan %A de Cid, Rafael %A Espín, Roderic %A Barnes, Daniel R %A Blommaert, Eline %A Gil-Gil, Miguel %A Falo, Catalina %A Stradella, Agostina %A Ouchi, Dan %A Roso-Llorach, Albert %A Violan, Concepció %A Peña-Chilet, Maria %A Dopazo, Joaquin %A Extremera, Ana Isabel %A García-Valero, Mar %A Herranz, Carmen %A Mateo, Francesca %A Mereu, Elisabetta %A Beesley, Jonathan %A Chenevix-Trench, Georgia %A Roux, Cecilia %A Mak, Tak %A Brunet, Joan %A Hakem, Razq %A Gorrini, Chiara %A Antoniou, Antonis C %A Lázaro, Conxi %A Pujana, Miquel Angel %X

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.

%B iScience %V 23 %P 101296 %8 2020 Jul 24 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/32622267?dopt=Abstract %R 10.1016/j.isci.2020.101296 %0 Journal Article %J Gac Sanit %D 2020 %T [Impact assessment on data protection in research projects]. %A García-León, Francisco Javier %A Villegas-Portero, Román %A Goicoechea-Salazar, Juan Antonio %A Muñoyerro-Muñiz, Dolores %A Dopazo, Joaquin %K Computer Security %K Humans %X

Recent changes in European regulations for personal data protection still allow the use of health data for research purposes, but they have set the Impact Assessment on Data Protection as an instrument for reflection and risk analysis in the process of data processing. The publication of a guide for facilitates this impact assessment, although it is not directly applicable to research projects. Experience in a specific project is detailed, showing how the context of the treatment becomes relevant with respect to the data characteristics. Carrying out an impact assessment is an opportunity to ensure compliance with the principles of data protection in an increasingly complex environment with greater ethical challenges.

%B Gac Sanit %V 34 %P 521-523 %8 2020 Sep - Oct %G spa %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/31980148?dopt=Abstract %R 10.1016/j.gaceta.2019.10.006 %0 Journal Article %J J Immunother Cancer %D 2020 %T Nivolumab and sunitinib combination in advanced soft tissue sarcomas: a multicenter, single-arm, phase Ib/II trial. %A Martin-Broto, Javier %A Hindi, Nadia %A Grignani, Giovanni %A Martinez-Trufero, Javier %A Redondo, Andres %A Valverde, Claudia %A Stacchiotti, Silvia %A Lopez-Pousa, Antonio %A D'Ambrosio, Lorenzo %A Gutierrez, Antonio %A Perez-Vega, Herminia %A Encinas-Tobajas, Victor %A de Alava, Enrique %A Collini, Paola %A Peña-Chilet, Maria %A Dopazo, Joaquin %A Carrasco-Garcia, Irene %A Lopez-Alvarez, Maria %A Moura, David S %A Lopez-Martin, Jose A %K Adult %K Aged %K Antineoplastic Agents, Immunological %K Female %K Humans %K Male %K Middle Aged %K Nivolumab %K Sarcoma %K Sunitinib %K Young Adult %X

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.

%B J Immunother Cancer %V 8 %8 2020 11 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/33203665?dopt=Abstract %R 10.1136/jitc-2020-001561 %0 Journal Article %J J Med Genet %D 2020 %T Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. %A Bogliolo, Massimo %A Pujol, Roser %A Aza-Carmona, Miriam %A Muñoz-Subirana, Núria %A Rodriguez-Santiago, Benjamin %A Casado, José Antonio %A Rio, Paula %A Bauser, Christopher %A Reina-Castillón, Judith %A Lopez-Sanchez, Marcos %A Gonzalez-Quereda, Lidia %A Gallano, Pia %A Catalá, Albert %A Ruiz-Llobet, Ana %A Badell, Isabel %A Diaz-Heredia, Cristina %A Hladun, Raquel %A Senent, Leonort %A Argiles, Bienvenida %A Bergua Burgues, Juan Miguel %A Bañez, Fatima %A Arrizabalaga, Beatriz %A López Almaraz, Ricardo %A Lopez, Monica %A Figuera, Ángela %A Molinés, Antonio %A Pérez de Soto, Inmaculada %A Hernando, Inés %A Muñoz, Juan Antonio %A Del Rosario Marin, Maria %A Balmaña, Judith %A Stjepanovic, Neda %A Carrasco, Estela %A Cuesta, Isabel %A Cosuelo, José Miguel %A Regueiro, Alexandra %A Moraleda Jimenez, José %A Galera-Miñarro, Ana Maria %A Rosiñol, Laura %A Carrió, Anna %A Beléndez-Bieler, Cristina %A Escudero Soto, Antonio %A Cela, Elena %A de la Mata, Gregorio %A Fernández-Delgado, Rafael %A Garcia-Pardos, Maria Carmen %A Sáez-Villaverde, Raquel %A Barragaño, Marta %A Portugal, Raquel %A Lendinez, Francisco %A Hernadez, Ines %A Vagace, José Manue %A Tapia, Maria %A Nieto, José %A Garcia, Marta %A Gonzalez, Macarena %A Vicho, Cristina %A Galvez, Eva %A Valiente, Alberto %A Antelo, Maria Luisa %A Ancliff, Phil %A García, Francisco %A Dopazo, Joaquin %A Sevilla, Julian %A Paprotka, Tobias %A Pérez-Jurado, Luis Alberto %A Bueren, Juan %A Surralles, Jordi %K Cell Line %K DNA Copy Number Variations %K DNA Repair %K DNA-Binding Proteins %K Fanconi Anemia %K Fanconi Anemia Complementation Group A Protein %K Female %K Gene Knockout Techniques %K Genetic Predisposition to Disease %K Humans %K Male %K Mutation, Missense %K Polymorphism, Single Nucleotide %K whole exome sequencing %X

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.

%B J Med Genet %V 57 %P 258-268 %8 2020 04 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/31586946?dopt=Abstract %R 10.1136/jmedgenet-2019-106249 %0 Journal Article %J IEEE J Biomed Health Inform %D 2020 %T Towards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets. %A Galvez, Juan M %A Castillo-Secilla, Daniel %A Herrera, Luis J %A Valenzuela, Olga %A Caba, Octavio %A Prados, Jose C %A Ortuno, Francisco M %A Rojas, Ignacio %K Biomarkers, Tumor %K Computational Biology %K Diagnosis, Computer-Assisted %K Gene Expression Profiling %K Humans %K Machine Learning %K RNA-seq %K Skin Neoplasms %X

Many clinical studies have revealed the high biological similarities existing among different skin pathological states. These similarities create difficulties in the efficient diagnosis of skin cancer, and encourage to study and design new intelligent clinical decision support systems. In this sense, gene expression analysis can help find differentially expressed genes (DEGs) simultaneously discerning multiple skin pathological states in a single test. The integration of multiple heterogeneous transcriptomic datasets requires different pipeline stages to be properly designed: from suitable batch merging and efficient biomarker selection to automated classification assessment. This article presents a novel approach addressing all these technical issues, with the intention of providing new sights about skin cancer diagnosis. Although new future efforts will have to be made in the search for better biomarkers recognizing specific skin pathological states, our study found a panel of 8 highly relevant multiclass DEGs for discerning up to 10 skin pathological states: 2 healthy skin conditions a priori, 2 cataloged precancerous skin diseases and 6 cancerous skin states. Their power of diagnosis over new samples was widely tested by previously well-trained classification models. Robust performance metrics such as overall and mean multiclass F1-score outperformed recognition rates of 94% and 80%, respectively. Clinicians should give special attention to highlighted multiclass DEGs that have high gene expression changes present among them, and understand their biological relationship to different skin pathological states.

%B IEEE J Biomed Health Inform %V 24 %P 2119-2130 %8 2020 07 %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/31871000?dopt=Abstract %R 10.1109/JBHI.2019.2953978 %0 Journal Article %J Nat Commun %D 2019 %T Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. %A Menden, Michael P %A Wang, Dennis %A Mason, Mike J %A Szalai, Bence %A Bulusu, Krishna C %A Guan, Yuanfang %A Yu, Thomas %A Kang, Jaewoo %A Jeon, Minji %A Wolfinger, Russ %A Nguyen, Tin %A Zaslavskiy, Mikhail %A Jang, In Sock %A Ghazoui, Zara %A Ahsen, Mehmet Eren %A Vogel, Robert %A Neto, Elias Chaibub %A Norman, Thea %A Tang, Eric K Y %A Garnett, Mathew J %A Veroli, Giovanni Y Di %A Fawell, Stephen %A Stolovitzky, Gustavo %A Guinney, Justin %A Dry, Jonathan R %A Saez-Rodriguez, Julio %K ADAM17 Protein %K Antineoplastic Combined Chemotherapy Protocols %K Benchmarking %K Biomarkers, Tumor %K Cell Line, Tumor %K Computational Biology %K Datasets as Topic %K Drug Antagonism %K Drug Resistance, Neoplasm %K Drug Synergism %K Genomics %K Humans %K Molecular Targeted Therapy %K mutation %K Neoplasms %K pharmacogenetics %K Phosphatidylinositol 3-Kinases %K Phosphoinositide-3 Kinase Inhibitors %K Treatment Outcome %X

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.

%B Nat Commun %V 10 %P 2674 %8 2019 06 17 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/31209238?dopt=Abstract %R 10.1038/s41467-019-09799-2 %0 Journal Article %J Brief Bioinform %D 2019 %T Precision medicine needs pioneering clinical bioinformaticians. %A Gómez-López, Gonzalo %A Dopazo, Joaquin %A Cigudosa, Juan C %A Valencia, Alfonso %A Al-Shahrour, Fátima %K Cohort Studies %K Computational Biology %K Humans %K Precision Medicine %X

Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which in conjunction can lead to effective therapies. From such a scenario emerges the need for a new professional profile, an expert bioinformatician with training in clinical areas who can make sense of multi-omics data to improve therapeutic interventions in patients, and the design of optimized basket trials. In this review, we first describe the main policies and international initiatives that focus on precision medicine. Secondly, we review the currently ongoing clinical trials in precision medicine, introducing the concept of 'precision bioinformatics', and we describe current pioneering bioinformatics efforts aimed at implementing tools and computational infrastructures for precision medicine in health institutions around the world. Thirdly, we discuss the challenges related to the clinical training of bioinformaticians, and the urgent need for computational specialists capable of assimilating medical terminologies and protocols to address real clinical questions. We also propose some skills required to carry out common tasks in clinical bioinformatics and some tips for emergent groups. Finally, we explore the future perspectives and the challenges faced by precision medicine bioinformatics.

%B Brief Bioinform %V 20 %P 752-766 %8 2019 05 21 %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/29077790?dopt=Abstract %R 10.1093/bib/bbx144 %0 Journal Article %J Nature Communications %D 2018 %T A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection %A Fourati, Slim %A Talla, Aarthi %A Mahmoudian, Mehrad %A Burkhart, Joshua G. %A Klén, Riku %A Henao, Ricardo %A Yu, Thomas %A Aydın, Zafer %A Yeung, Ka Yee %A Ahsen, Mehmet Eren %A Almugbel, Reem %A Jahandideh, Samad %A Liang, Xiao %A Nordling, Torbjörn E. M. %A Shiga, Motoki %A Stanescu, Ana %A Vogel, Robert %A Pandey, Gaurav %A Chiu, Christopher %A McClain, Micah T. %A Woods, Christopher W. %A Ginsburg, Geoffrey S. %A Elo, Laura L. %A Tsalik, Ephraim L. %A Mangravite, Lara M. %A Sieberts, Solveig K. %B Nature Communications %V 9 %8 Jan-12-2018 %G eng %U 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 %N 1 %! Nat Commun %R 10.1038/s41467-018-06735-8 %0 Journal Article %J Sci Rep %D 2018 %T Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade. %A López, M %A Rueda, A %A Florido, J P %A Blasco, L %A Fernández-García, L %A Trastoy, R %A Fernández-Cuenca, F %A Martínez-Martínez, L %A Vila, J %A Pascual, A %A Bou, G %A Tomas, M %K Acinetobacter baumannii %K Acinetobacter Infections %K Bacteriophages %K Cross Infection %K Humans %K Plasmids %K Quorum Sensing %K Retrospective Studies %X

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.

%B Sci Rep %V 8 %P 2523 %8 2018 02 06 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/29410443?dopt=Abstract %R 10.1038/s41598-018-20847-7 %0 Journal Article %J Oncotarget %D 2017 %T Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis. %A Puig-Butille, Joan Anton %A Gimenez-Xavier, Pol %A Visconti, Alessia %A Nsengimana, Jérémie %A Garcia-Garcia, Francisco %A Tell-Marti, Gemma %A Escamez, Maria José %A Newton-Bishop, Julia %A Bataille, Veronique %A Del Rio, Marcela %A Dopazo, Joaquin %A Falchi, Mario %A Puig, Susana %K Adult %K Coculture Techniques %K Computational Biology %K gene expression %K Genetic Predisposition to Disease %K Genomics %K Hair Color %K Humans %K Keratinocytes %K Melanocytes %K Middle Aged %K Phenotype %K Receptor, Melanocortin, Type 1 %X

The MC1R gene plays a crucial role in pigmentation synthesis. Loss-of-function MC1R variants, which impair protein function, are associated with red hair color (RHC) phenotype and increased skin cancer risk. Cultured cutaneous cells bearing loss-of-function MC1R variants show a distinct gene expression profile compared to wild-type MC1R cultured cutaneous cells. We analysed the gene signature associated with RHC co-cultured melanocytes and keratinocytes by Protein-Protein interaction (PPI) network analysis to identify genes related with non-functional MC1R variants. From two detected networks, we selected 23 nodes as hub genes based on topological parameters. Differential expression of hub genes was then evaluated in healthy skin biopsies from RHC and black hair color (BHC) individuals. We also compared gene expression in melanoma tumors from individuals with RHC versus BHC. Gene expression in normal skin from RHC cutaneous cells showed dysregulation in 8 out of 23 hub genes (CLN3, ATG10, WIPI2, SNX2, GABARAPL2, YWHA, PCNA and GBAS). Hub genes did not differ between melanoma tumors in RHC versus BHC individuals. The study suggests that healthy skin cells from RHC individuals present a constitutive genomic deregulation associated with the red hair phenotype and identify novel genes involved in melanocyte biology.

%B Oncotarget %V 8 %P 11589-11599 %8 2017 Feb 14 %G eng %U http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=14140&path%5B%5D=45094 %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/28030792?dopt=Abstract %R 10.18632/oncotarget.14140 %0 Journal Article %J Hum Mutat %D 2017 %T Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation. %A Matalonga, Leslie %A Bravo, Miren %A Serra-Peinado, Carla %A García-Pelegrí, Elisabeth %A Ugarteburu, Olatz %A Vidal, Silvia %A Llambrich, Maria %A Quintana, Ester %A Fuster-Jorge, Pedro %A Gonzalez-Bravo, Maria Nieves %A Beltran, Sergi %A Dopazo, Joaquin %A Garcia-Garcia, Francisco %A Foulquier, François %A Matthijs, Gert %A Mills, Philippa %A Ribes, Antonia %A Egea, Gustavo %A Briones, Paz %A Tort, Frederic %A Girós, Marisa %K Abnormalities, Multiple %K Alleles %K Amino Acid Substitution %K Brain %K Congenital Disorders of Glycosylation %K Genotype %K Humans %K Magnetic Resonance Imaging %K Male %K mutation %K Phenotype %K Vesicular Transport Proteins %K Whole Genome Sequencing %X

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.

%B Hum Mutat %V 38 %P 148-151 %8 2017 02 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/27862579?dopt=Abstract %R 10.1002/humu.23145 %0 Journal Article %J Genome Biology %D 2017 %T Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes %A Gui, Hongsheng %A Schriemer, Duco %A Cheng, William W. %A Chauhan, Rajendra K. %A Antiňolo, Guillermo %A Berrios, Courtney %A Bleda, Marta %A Brooks, Alice S. %A Brouwer, Rutger W. W. %A Burns, Alan J. %A Cherny, Stacey S. %A Dopazo, Joaquin %A Eggen, Bart J. L. %A Griseri, Paola %A Jalloh, Binta %A Le, Thuy-Linh %A Lui, Vincent C. H. %A Luzón-Toro, Berta %A Matera, Ivana %A Ngan, Elly S. W. %A Pelet, Anna %A Ruiz-Ferrer, Macarena %A Sham, Pak C. %A Shepherd, Iain T. %A So, Man-Ting %A Sribudiani, Yunia %A Tang, Clara S. M. %A van den Hout, Mirjam C. G. N. %A van der Linde, Herma C. %A van Ham, Tjakko J. %A van IJcken, Wilfred F. J. %A Verheij, Joke B. G. M. %A Amiel, Jeanne %A Borrego, Salud %A Ceccherini, Isabella %A Chakravarti, Aravinda %A Lyonnet, Stanislas %A Tam, Paul K. H. %A Garcia-Barceló, Maria-Mercè %A Hofstra, Robert M. W. %B Genome Biology %V 18 %8 Jan-12-2017 %G eng %U http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1174-6http://link.springer.com/content/pdf/10.1186/s13059-017-1174-6.pdf %N 1 %! Genome Biol %R 10.1186/s13059-017-1174-6 %0 Journal Article %J Genome biology %D 2017 %T Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. %A Gui, Hongsheng %A Schriemer, Duco %A Cheng, William W %A Chauhan, Rajendra K %A Antiňolo, Guillermo %A Berrios, Courtney %A Bleda, Marta %A Brooks, Alice S %A Brouwer, Rutger W W %A Burns, Alan J %A Cherny, Stacey S %A Dopazo, Joaquin %A Eggen, Bart J L %A Griseri, Paola %A Jalloh, Binta %A Le, Thuy-Linh %A Lui, Vincent C H %A Luzón-Toro, Berta %A Matera, Ivana %A Ngan, Elly S W %A Pelet, Anna %A Ruiz-Ferrer, Macarena %A Sham, Pak C %A Shepherd, Iain T %A So, Man-Ting %A Sribudiani, Yunia %A Tang, Clara S M %A van den Hout, Mirjam C G N %A van der Linde, Herma C %A van Ham, Tjakko J %A van IJcken, Wilfred F J %A Verheij, Joke B G M %A Amiel, Jeanne %A Borrego, Salud %A Ceccherini, Isabella %A Chakravarti, Aravinda %A Lyonnet, Stanislas %A Tam, Paul K H %A Garcia-Barceló, Maria-Mercè %A Hofstra, Robert Mw %K Hirschprung %K Rare Disease %K WES %X 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. %B Genome biology %V 18 %P 48 %8 2017 Mar 08 %G eng %U http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1174-6 %R 10.1186/s13059-017-1174-6 %0 Journal Article %J Molecular biology and evolution %D 2016 %T 267 Spanish exomes reveal population-specific differences in disease-related genetic variation. %A Joaquín Dopazo %A Amadoz, Alicia %A Bleda, Marta %A García-Alonso, Luz %A Alemán, Alejandro %A Garcia-Garcia, Francisco %A Rodriguez, Juan A %A Daub, Josephine T %A Muntané, Gerard %A Antonio Rueda %A Vela-Boza, Alicia %A López-Domingo, Francisco J %A Florido, Javier P %A Arce, Pablo %A Ruiz-Ferrer, Macarena %A Méndez-Vidal, Cristina %A Arnold, Todd E %A Spleiss, Olivia %A Alvarez-Tejado, Miguel %A Navarro, Arcadi %A Bhattacharya, Shomi S %A Borrego, Salud %A Santoyo-López, Javier %A Antiňolo, Guillermo %K disease %K NGS %K polymorphisms %K Population genomics %K prioritization %K SNP %X 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. %B Molecular biology and evolution %8 2016 Jan 13 %G eng %U https://mbe.oxfordjournals.org/content/early/2016/02/17/molbev.msw005.full %R 10.1093/molbev/msw005 %0 Journal Article %J The Journal of molecular diagnostics : JMD %D 2016 %T Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy. %A Lupo, Vincenzo %A Garcia-Garcia, Francisco %A Sancho, Paula %A Tello, Cristina %A García-Romero, Mar %A Villarreal, Liliana %A Alberti, Antonia %A Sivera, Rafael %A Joaquín Dopazo %A Pascual-Pascual, Samuel I %A Márquez-Infante, Celedonio %A Casasnovas, Carlos %A Sevilla, Teresa %A Espinós, Carmen %K Charcot-Marie-Tooth %K CMT %K Diagnostic %K NGS %K Panels %K rare diseases %K Targeted resequencing %X 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. %B The Journal of molecular diagnostics : JMD %8 2016 Jan 2 %G eng %U http://www.sciencedirect.com/science/article/pii/S1525157815002615 %R 10.1016/j.jmoldx.2015.10.005 %0 Journal Article %J Stress (Amsterdam, Netherlands) %D 2016 %T Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice. %A Sanghez, Valentina %A Cubuk, Cankut %A Sebastián-Leon, Patricia %A Carobbio, Stefania %A Dopazo, Joaquin %A Vidal-Puig, Antonio %A Bartolomucci, Alessandro %K Adipose tissue %K insulin %K IRS1 %K IRS2 %K metabolic syndrome %K obesity %K pathway analysis %X Chronic stress has been associated with obesity, glucose intolerance, and insulin resistance. We developed a model of chronic psychosocial stress (CPS) in which subordinate mice are vulnerable to obesity and the metabolic-like syndrome while dominant mice exhibit a healthy metabolic phenotype. Here we tested the hypothesis that the metabolic difference between subordinate and dominant mice is associated with changes in functional pathways relevant for insulin sensitivity, glucose and lipid homeostasis. Male mice were exposed to CPS for four weeks and fed either a standard diet or a high-fat diet (HFD). We first measured, by real-time PCR candidate genes, in the liver, skeletal muscle, and the perigonadal white adipose tissue (pWAT). Subsequently, we used a probabilistic analysis approach to analyze different ways in which signals can be transmitted across the pathways in each tissue. Results showed that subordinate mice displayed a drastic downregulation of the insulin pathway in liver and muscle, indicative of insulin resistance, already on standard diet. Conversely, pWAT showed molecular changes suggestive of facilitated fat deposition in an otherwise insulin-sensitive tissue. The molecular changes in subordinate mice fed a standard diet were greater compared to HFD-fed controls. Finally, dominant mice maintained a substantially normal metabolic and molecular phenotype even when fed a HFD. Overall, our data demonstrate that subordination stress is a potent stimulus for the downregulation of the insulin signaling pathway in liver and muscle and a major risk factor for the development of obesity, insulin resistance, and type 2 diabetes mellitus. %B Stress (Amsterdam, Netherlands) %P 1-11 %8 2016 Mar 7 %G eng %U http://www.tandfonline.com/doi/abs/10.3109/10253890.2016.1151491?journalCode=ists20 %R 10.3109/10253890.2016.1151491 %0 Journal Article %J Nature Communications %D 2016 %T Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq) %A Lagarde, Julien %A Uszczynska-Ratajczak, Barbara %A Santoyo-López, Javier %A Gonzalez, Jose Manuel %A Tapanari, Electra %A Mudge, Jonathan M. %A Steward, Charles A. %A Wilming, Laurens %A Tanzer, Andrea %A Howald, Cédric %A Chrast, Jacqueline %A Vela-Boza, Alicia %A Rueda, Antonio %A Lopez-Domingo, Francisco J. %A Dopazo, Joaquin %A Reymond, Alexandre %A Guigó, Roderic %A Harrow, Jennifer %B Nature Communications %V 7 %8 Jan-11-2016 %G eng %U http://www.nature.com/articles/ncomms12339http://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339 %N 1 %! Nat Commun %R 10.1038/ncomms12339 %0 Journal Article %J Nature communications %D 2016 %T Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). %A Lagarde, Julien %A Uszczynska-Ratajczak, Barbara %A Santoyo-López, Javier %A Gonzalez, Jose Manuel %A Tapanari, Electra %A Mudge, Jonathan M %A Steward, Charles A %A Wilming, Laurens %A Tanzer, Andrea %A Howald, Cédric %A Chrast, Jacqueline %A Vela-Boza, Alicia %A Antonio Rueda %A López-Domingo, Francisco J %A Dopazo, Joaquin %A Reymond, Alexandre %A Guigó, Roderic %A Harrow, Jennifer %X 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. %B Nature communications %V 7 %P 12339 %8 2016 %G eng %U http://www.nature.com/articles/ncomms12339 %R 10.1038/ncomms12339 %0 Journal Article %J Transl Psychiatry %D 2016 %T Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns. %A Sanchez-Mut, J V %A Heyn, H %A Vidal, E %A Moran, S %A Sayols, S %A Delgado-Morales, R %A Schultz, M D %A Ansoleaga, B %A Garcia-Esparcia, P %A Pons-Espinal, M %A de Lagran, M M %A Dopazo, J %A Rabano, A %A Avila, J %A Dierssen, M %A Lott, I %A Ferrer, I %A Ecker, J R %A Esteller, M %K Adult %K Aged %K Aged, 80 and over %K DNA Methylation %K Epigenomics %K Female %K Humans %K Male %K Middle Aged %K neurodegenerative diseases %K Prefrontal Cortex %K Tissue Array Analysis %X

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.

%B Transl Psychiatry %V 6 %P e718 %8 2016 Jan 19 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26784972?dopt=Abstract %R 10.1038/tp.2015.214 %0 Journal Article %J PLoS One %D 2016 %T The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. %A Ibáñez, Mariam %A Carbonell-Caballero, José %A García-Alonso, Luz %A Such, Esperanza %A Jiménez-Almazán, Jorge %A Vidal, Enrique %A Barragán, Eva %A López-Pavía, María %A LLop, Marta %A Martín, Iván %A Gómez-Seguí, Inés %A Montesinos, Pau %A Sanz, Miguel A %A Dopazo, Joaquin %A Cervera, José %K Exome %K Gene Regulatory Networks %K Genome, Human %K Humans %K INDEL Mutation %K Leukemia, Promyelocytic, Acute %K mutation %K Mutation Rate %K Polymorphism, Single Nucleotide %K Reproducibility of Results %X

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.

%B PLoS One %V 11 %P e0148346 %8 2016 %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/26886259?dopt=Abstract %R 10.1371/journal.pone.0148346 %0 Journal Article %J Brain %D 2016 %T Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease. %A Sevilla, Teresa %A Lupo, Vincenzo %A Martínez-Rubio, Dolores %A Sancho, Paula %A Sivera, Rafael %A Chumillas, María J %A García-Romero, Mar %A Pascual-Pascual, Samuel I %A Muelas, Nuria %A Dopazo, Joaquin %A Vílchez, Juan J %A Palau, Francesc %A Espinós, Carmen %K Adult %K Aged %K Animals %K Axons %K Charcot-Marie-Tooth Disease %K Female %K gene expression %K Humans %K Infant %K Male %K Mice %K Middle Aged %K mutation %K Pedigree %K Phenotype %K Sciatic Nerve %K Sural Nerve %K Transcription Factors %K Young Adult %X

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.

%B Brain %V 139 %P 62-72 %8 2016 Jan %G eng %N Pt 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26497905?dopt=Abstract %R 10.1093/brain/awv311 %0 Journal Article %J Am J Med Genet A %D 2016 %T Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes. %A Urreizti, Roser %A Roca-Ayats, Neus %A Trepat, Judith %A Garcia-Garcia, Francisco %A Alemán, Alejandro %A Orteschi, Daniela %A Marangi, Giuseppe %A Neri, Giovanni %A Opitz, John M %A Dopazo, Joaquin %A Cormand, Bru %A Vilageliu, Lluïsa %A Balcells, Susana %A Grinberg, Daniel %K Adolescent %K Antigens, CD %K Child %K Child, Preschool %K Craniosynostoses %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Intellectual Disability %K Male %K mutation %K Pedigree %K Phenotype %K Prognosis %K Repressor Proteins %X

Opitz C trigonocephaly (or Opitz C syndrome, OTCS) and Bohring-Opitz syndrome (BOS or C-like syndrome) are two rare genetic disorders with phenotypic overlap. The genetic causes of these diseases are not understood. However, two genes have been associated with OTCS or BOS with dominantly inherited de novo mutations. Whereas CD96 has been related to OTCS (one case) and to BOS (one case), ASXL1 has been related to BOS only (several cases). In this study we analyze CD96 and ASXL1 in a group of 11 affected individuals, including 2 sibs, 10 of them were diagnosed with OTCS, and one had a BOS phenotype. Exome sequences were available on six patients with OTCS and three parent pairs. Thus, we could analyze the CD96 and ASXL1 sequences in these patients bioinformatically. Sanger sequencing of all exons of CD96 and ASXL1 was carried out in the remaining patients. Detailed scrutiny of the sequences and assessment of variants allowed us to exclude putative pathogenic and private mutations in all but one of the patients. In this patient (with BOS) we identified a de novo mutation in ASXL1 (c.2100dupT). By nature and location within the gene, this mutation resembles those previously described in other BOS patients and we conclude that it may be responsible for the condition. Our results indicate that in 10 of 11, the disease (OTCS or BOS) cannot be explained by small changes in CD96 or ASXL1. However, the cohort is too small to make generalizations about the genetic etiology of these diseases.

%B Am J Med Genet A %V 170A %P 24-31 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26768331?dopt=Abstract %R 10.1002/ajmg.a.37418 %0 Journal Article %J Mol Metab %D 2016 %T Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis. %A Razzoli, Maria %A Frontini, Andrea %A Gurney, Allison %A Mondini, Eleonora %A Cubuk, Cankut %A Katz, Liora S %A Cero, Cheryl %A Bolan, Patrick J %A Dopazo, Joaquin %A Vidal-Puig, Antonio %A Cinti, Saverio %A Bartolomucci, Alessandro %X

BACKGROUND: Stress-associated conditions such as psychoemotional reactivity and depression have been paradoxically linked to either weight gain or weight loss. This bi-directional effect of stress is not understood at the functional level. Here we tested the hypothesis that pre-stress level of adaptive thermogenesis and brown adipose tissue (BAT) functions explain the vulnerability or resilience to stress-induced obesity.

METHODS: We used wt and triple β1,β2,β3-Adrenergic Receptors knockout (β-less) mice exposed to a model of chronic subordination stress (CSS) at either room temperature (22 °C) or murine thermoneutrality (30 °C). A combined behavioral, physiological, molecular, and immunohistochemical analysis was conducted to determine stress-induced modulation of energy balance and BAT structure and function. Immortalized brown adipocytes were used for in vitro assays.

RESULTS: Departing from our initial observation that βARs are dispensable for cold-induced BAT browning, we demonstrated that under physiological conditions promoting low adaptive thermogenesis and BAT activity (e.g. thermoneutrality or genetic deletion of the βARs), exposure to CSS acted as a stimulus for BAT activation and thermogenesis, resulting in resistance to diet-induced obesity despite the presence of hyperphagia. Conversely, in wt mice acclimatized to room temperature, and therefore characterized by sustained BAT function, exposure to CSS increased vulnerability to obesity. Exposure to CSS enhanced the sympathetic innervation of BAT in wt acclimatized to thermoneutrality and in β-less mice. Despite increased sympathetic innervation suggesting adrenergic-mediated browning, norepinephrine did not promote browning in βARs knockout brown adipocytes, which led us to identify an alternative sympathetic/brown adipocytes purinergic pathway in the BAT. This pathway is downregulated under conditions of low adaptive thermogenesis requirements, is induced by stress, and elicits activation of UCP1 in wt and β-less brown adipocytes. Importantly, this purinergic pathway is conserved in human BAT.

CONCLUSION: Our findings demonstrate that thermogenesis and BAT function are determinant of the resilience or vulnerability to stress-induced obesity. Our data support a model in which adrenergic and purinergic pathways exert complementary/synergistic functions in BAT, thus suggesting an alternative to βARs agonists for the activation of human BAT.

%B Mol Metab %V 5 %P 19-33 %8 2016 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/26844204?dopt=Abstract %R 10.1016/j.molmet.2015.10.005 %0 Journal Article %J Hum Genet %D 2016 %T Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. %A Lucariello, Mario %A Vidal, Enrique %A Vidal, Silvia %A Saez, Mauricio %A Roa, Laura %A Huertas, Dori %A Pineda, Mercè %A Dalfó, Esther %A Dopazo, Joaquin %A Jurado, Paola %A Armstrong, Judith %A Esteller, Manel %K Adolescent %K Adult %K Animals %K Caenorhabditis elegans %K Carrier Proteins %K Cell Cycle Proteins %K Child %K Child, Preschool %K DNA Mutational Analysis %K Exome %K Female %K Forkhead Transcription Factors %K Genetic Variation %K High-Throughput Nucleotide Sequencing %K Humans %K Methyl-CpG-Binding Protein 2 %K mutation %K Nerve Tissue Proteins %K Protein Serine-Threonine Kinases %K Receptors, Nicotinic %K Rett Syndrome %X

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.

%B Hum Genet %V 135 %P 1343-1354 %8 2016 12 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/27541642?dopt=Abstract %R 10.1007/s00439-016-1721-3 %0 Journal Article %J Hearing research %D 2015 %T Comparative gene expression study of the vestibular organ of the Igf1 deficient mouse using whole-transcript arrays. %A Rodríguez-de la Rosa, Lourdes %A Sánchez-Calderón, Hortensia %A Contreras, Julio %A Murillo-Cuesta, Silvia %A Falagan, Sandra %A Avendaño, Carlos %A Joaquín Dopazo %A Varela-Nieto, Isabel %A Milo, Marta %X The auditory and vestibular organs form the inner ear and have a common developmental origin. Insulin like growth factor 1 (IGF-1) has a central role in the development of the cochlea and maintenance of hearing. Its deficiency causes sensorineural hearing loss in man and mice. During chicken early development, IGF-1 modulates neurogenesis of the cochleovestibular ganglion but no further studies have been conducted to explore the potential role of IGF-1 in the vestibular system. In this study we have compared the whole transcriptome of the vestibular organ from wild type and Igf1(-/-) mice at different developmental and postnatal times. RNA was prepared from E18.5, P15 and P90 vestibular organs of Igf1(-/-) and Igf1(+/+) mice and the transcriptome analysed in triplicates using Affymetrix® Mouse Gene 1.1 ST Array Plates. These plates are whole-transcript arrays that include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA), with a coverage of over 28 thousand coding transcripts and over 7 thousands non-coding transcripts. Given the complexity of the data we used two different methods VSN-RMA and mmBGX to analyse and compare the data. This is to better evaluate the number of false positives and to quantify uncertainty of low signals. We identified a number of differentially expressed genes that we described using functional analysis and validated using RT-qPCR. The morphology of the vestibular organ did not show differences between genotypes and no evident alterations were observed in the vestibular sensory areas of the null mice. However, well-defined cellular alterations were found in the vestibular neurons with respect their number and size. Although these mice did not show a dramatic vestibular phenotype, we conducted a functional analysis on differentially expressed genes between genotypes and across time. This was with the aim to identify new pathways that are involved in the development of the vestibular organ as well as pathways that maybe affected by the lack of IGF-1 and be associated to the morphological changes of the vestibular neurons that we observed in the Igf1(-/-) mice. %B Hearing research %8 2015 Sep 1 %G eng %U http://www.sciencedirect.com/science/article/pii/S0378595515001835 %R 10.1016/j.heares.2015.08.016 %0 Journal Article %J Eur J Neurol %D 2015 %T The EGR2 gene is involved in axonal Charcot-Marie-Tooth disease. %A Sevilla, T %A Sivera, R %A Martínez-Rubio, D %A Lupo, V %A Chumillas, M J %A Calpena, E %A Dopazo, J %A Vílchez, J J %A Palau, F %A Espinós, C %K Adult %K Aged %K Aged, 80 and over %K Axons %K Charcot-Marie-Tooth Disease %K Early Growth Response Protein 2 %K Exome %K Female %K Humans %K Male %K Middle Aged %K mutation %K Pedigree %K Phenotype %K Severity of Illness Index %K Young Adult %X

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.

%B Eur J Neurol %V 22 %P 1548-55 %8 2015 Dec %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/26204789?dopt=Abstract %R 10.1111/ene.12782 %0 Journal Article %J Eur J Oral Sci %D 2015 %T Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate. %A Fonseca, Renata F %A de Carvalho, Flávia M %A Poletta, Fernando A %A Montaner, David %A Dopazo, Joaquin %A Mereb, Juan C %A Moreira, Miguel A M %A Seuanez, Hector N %A Vieira, Alexandre R %A Castilla, Eduardo E %A Orioli, Iêda M %X

The etiology of cleft lip with or without cleft palate (CL±P) is complex and heterogeneous, and multiple genetic and environmental factors are involved. Some candidate genes reported to be associated with oral clefts are located on the X chromosome. At least three genes causing X-linked syndromes [midline 1 (MID1), oral-facial-digital syndrome 1 (OFD1), and dystrophin (DMD)] were previously found to be associated with isolated CL±P. We attempted to confirm the role of X-linked genes in the etiology of isolated CL±P in a South American population through a family-based genome-wide scan. We studied 27 affected children and their mothers, from 26 families, in a Patagonian population with a high prevalence of CL±P. We conducted an exploratory analysis of the X chromosome to identify candidate regions associated with CL±P. Four genomic segments were identified, two of which showed a statistically significant association with CL±P. One is an 11-kb region of Xp21.1 containing the DMD gene, and the other is an intergenic region (8.7 kb; Xp11.4). Our results are consistent with recent data on the involvement of the DMD gene in the etiology of CL±P. The MID1 and OFD1 genes were not included in the four potential CL±P-associated X-chromosome genomic segments.

%B Eur J Oral Sci %V 123 %P 381-384 %8 2015 Oct %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26331285?dopt=Abstract %R 10.1111/eos.12212 %0 Journal Article %J Sci Rep %D 2015 %T Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. %A Amadoz, Alicia %A Sebastián-Leon, Patricia %A Vidal, Enrique %A Salavert, Francisco %A Dopazo, Joaquin %K Algorithms %K Antineoplastic Agents %K biomarkers %K Cell Line, Tumor %K Cell Survival %K gene expression %K Humans %K Lethal Dose 50 %K Neoplasms %K Phosphorylation %K Proteins %K Signal Transduction %X

Many complex traits, as drug response, are associated with changes in biological pathways rather than being caused by single gene alterations. Here, a predictive framework is presented in which gene expression data are recoded into activity statuses of signal transduction circuits (sub-pathways within signaling pathways that connect receptor proteins to final effector proteins that trigger cell actions). Such activity values are used as features by a prediction algorithm which can efficiently predict a continuous variable such as the IC50 value. The main advantage of this prediction method is that the features selected by the predictor, the signaling circuits, are themselves rich-informative, mechanism-based biomarkers which provide insight into or drug molecular mechanisms of action (MoA).

%B Sci Rep %V 5 %P 18494 %8 2015 Dec 18 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26678097?dopt=Abstract %R 10.1038/srep18494 %0 Journal Article %J Cancer research %D 2014 %T A Comprehensive DNA Methylation Profile of Epithelial-to-Mesenchymal Transition. %A Carmona, F Javier %A Davalos, Veronica %A Vidal, Enrique %A Gomez, Antonio %A Heyn, Holger %A Hashimoto, Yutaka %A Vizoso, Miguel %A Martinez-Cardus, Anna %A Sayols, Sergi %A Ferreira, Humberto %A Sanchez-Mut, Jose %A Moran, Sebastian %A Margeli, Mireia %A Castella, Eva %A Berdasco, Maria %A Stefansson, Olafur Andri %A Eyfjord, Jorunn E %A Gonzalez-Suarez, Eva %A Dopazo, Joaquin %A Orozco, Modesto %A Gut, Ivo %A Esteller, Manel %K Methyl-Seq %K Methylomics %K Next Generation Sequencing %X Epithelial-to-mesenchymal transition (EMT) is a plastic process in which fully differentiated epithelial cells are converted into poorly differentiated, migratory and invasive mesenchymal cells and it has been related to the metastasis potential of tumors. This is a reversible process and cells can also eventually undergo mesenchymal-to-epithelial transition (MET). The existence of a dynamic EMT process suggests the involvement of epigenetic shifts in the phenotype. Herein, we obtained the DNA methylomes at single-base resolution of MDCK cells undergoing epithelial-to-mesenchymal transition (EMT) and translated the identified differentially methylated regions (DMRs) to human breast cancer cells undergoing a gain of migratory and invasive capabilities associated with the EMT phenotype. We noticed dynamic and reversible changes of DNA methylation, both on promoter sequences and gene-bodies in association with transcription regulation of EMT-related genes. Most importantly, the identified DNA methylation markers of EMT were present in primary mammary tumors in association with the epithelial or the mesenchymal phenotype of the studied breast cancer samples. %B Cancer research %V 74 %P 5608–19 %8 2014 Aug 8 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/25106427 %R 10.1158/0008-5472.CAN-13-3659 %0 Journal Article %J Molecular Genetics & Genomic Medicine %D 2014 %T Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet–Biedl family %A González-del Pozo, María %A Méndez-Vidal, Cristina %A Santoyo-López, Javier %A Vela-Boza, Alicia %A Nereida Bravo-Gil %A Antonio Rueda %A García-Alonso, Luz %A Vázquez-Marouschek, Carmen %A Joaquín Dopazo %A Borrego, Salud %A Antiňolo, Guillermo %X Bardet–Biedl syndrome (BBS) is a model ciliopathy characterized by a wide range of clinical variability. The heterogeneity of this condition is reflected in the number of underlying gene defects and the epistatic interactions between the proteins encoded. BBS is generally inherited in an autosomal recessive trait. However, in some families, mutations across different loci interact to modulate the expressivity of the phenotype. In order to investigate the magnitude of epistasis in one BBS family with remarkable intrafamilial phenotypic variability, we designed an exome sequencing–based approach using SOLID 5500xl platform. This strategy allowed the reliable detection of the primary causal mutations in our family consisting of two novel compound heterozygous mutations in McKusick–Kaufman syndrome (MKKS) gene (p.D90G and p.V396F). Additionally, exome sequencing enabled the detection of one novel heterozygous NPHP4 variant which is predicted to activate a cryptic acceptor splice site and is only present in the most severely affected patient. Here, we provide an exome sequencing analysis of a BBS family and show the potential utility of this tool, in combination with network analysis, to detect disease-causing mutations and second-site modifiers. Our data demonstrate how next-generation sequencing (NGS) can facilitate the dissection of epistatic phenomena, and shed light on the genetic basis of phenotypic variability. %B Molecular Genetics & Genomic Medicine %V 2 %P 124-133 %G eng %U http://onlinelibrary.wiley.com/doi/10.1002/mgg3.50/full %R 10.1002/mgg3.50 %0 Journal Article %J Mol Genet Genomic Med %D 2014 %T Deciphering intrafamilial phenotypic variability by exome sequencing in a Bardet-Biedl family. %A González-del Pozo, María %A Méndez-Vidal, Cristina %A Santoyo-López, Javier %A Vela-Boza, Alicia %A Bravo-Gil, Nereida %A Rueda, Antonio %A García-Alonso, Luz %A Vázquez-Marouschek, Carmen %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %X

Bardet-Biedl syndrome (BBS) is a model ciliopathy characterized by a wide range of clinical variability. The heterogeneity of this condition is reflected in the number of underlying gene defects and the epistatic interactions between the proteins encoded. BBS is generally inherited in an autosomal recessive trait. However, in some families, mutations across different loci interact to modulate the expressivity of the phenotype. In order to investigate the magnitude of epistasis in one BBS family with remarkable intrafamilial phenotypic variability, we designed an exome sequencing-based approach using SOLID 5500xl platform. This strategy allowed the reliable detection of the primary causal mutations in our family consisting of two novel compound heterozygous mutations in McKusick-Kaufman syndrome (MKKS) gene (p.D90G and p.V396F). Additionally, exome sequencing enabled the detection of one novel heterozygous NPHP4 variant which is predicted to activate a cryptic acceptor splice site and is only present in the most severely affected patient. Here, we provide an exome sequencing analysis of a BBS family and show the potential utility of this tool, in combination with network analysis, to detect disease-causing mutations and second-site modifiers. Our data demonstrate how next-generation sequencing (NGS) can facilitate the dissection of epistatic phenomena, and shed light on the genetic basis of phenotypic variability.

%B Mol Genet Genomic Med %V 2 %P 124-33 %8 2014 Mar %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/24689075?dopt=Abstract %R 10.1002/mgg3.50 %0 Journal Article %J PLoS One %D 2014 %T Exome sequencing reveals novel and recurrent mutations with clinical significance in inherited retinal dystrophies. %A González-del Pozo, María %A Méndez-Vidal, Cristina %A Bravo-Gil, Nereida %A Vela-Boza, Alicia %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %K Adolescent %K Adult %K Amino Acid Sequence %K Base Sequence %K Child %K Chromosome Segregation %K DNA Mutational Analysis %K Exome %K Family %K Female %K Humans %K Inheritance Patterns %K Male %K Middle Aged %K Molecular Sequence Data %K mutation %K Pedigree %K Retinal Dystrophies %K Rhodopsin %X

This study aimed to identify the underlying molecular genetic cause in four Spanish families clinically diagnosed of Retinitis Pigmentosa (RP), comprising one autosomal dominant RP (adRP), two autosomal recessive RP (arRP) and one with two possible modes of inheritance: arRP or X-Linked RP (XLRP). We performed whole exome sequencing (WES) using NimbleGen SeqCap EZ Exome V3 sample preparation kit and SOLID 5500xl platform. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation and the absence in local control population. This strategy allowed the detection of: (i) one novel heterozygous splice-site deletion in RHO, c.937-2_944del, (ii) one rare homozygous mutation in C2orf71, c.1795T>C; p.Cys599Arg, not previously associated with the disease, (iii) two heterozygous null mutations in ABCA4, c.2041C>T; p.R681* and c.6088C>T; p.R2030*, and (iv) one mutation, c.2405-2406delAG; p.Glu802Glyfs*31 in the ORF15 of RPGR. The molecular findings for RHO and C2orf71 confirmed the initial diagnosis of adRP and arRP, respectively, while patients with the two ABCA4 mutations, both previously associated with Stargardt disease, presented symptoms of RP with early macular involvement. Finally, the X-Linked inheritance was confirmed for the family with the RPGR mutation. This latter finding allowed the inclusion of carrier sisters in our preimplantational genetic diagnosis program.

%B PLoS One %V 9 %P e116176 %8 2014 %G eng %N 12 %1 https://www.ncbi.nlm.nih.gov/pubmed/25544989?dopt=Abstract %R 10.1371/journal.pone.0116176 %0 Journal Article %J Human mutation %D 2014 %T A New Overgrowth Syndrome is Due to Mutations in RNF125. %A Tenorio, Jair %A Mansilla, Alicia %A Valencia, María %A Martínez-Glez, Víctor %A Romanelli, Valeria %A Arias, Pedro %A Castrejón, Nerea %A Poletta, Fernando %A Guillén-Navarro, Encarna %A Gordo, Gema %A Mansilla, Elena %A García-Santiago, Fé %A González-Casado, Isabel %A Vallespín, Elena %A Palomares, María %A Mori, María A %A Santos-Simarro, Fernando %A García-Miñaur, Sixto %A Fernández, Luis %A Mena, Rocío %A Benito-Sanz, Sara %A Del Pozo, Angela %A Silla, Juan Carlos %A Ibañez, Kristina %A López-Granados, Eduardo %A Martín-Trujillo, Alex %A Montaner, David %A Heath, Karen E %A Campos-Barros, Angel %A Joaquín Dopazo %A Nevado, Julián %A Monk, David %A Ruiz-Pérez, Víctor L %A Lapunzina, Pablo %K NGS %K prioritization %K Rare Disease %X 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. %B Human mutation %V 35 %P 1436–1441 %8 2014 Sep 5 %G eng %U http://onlinelibrary.wiley.com/doi/10.1002/humu.22689/abstract %R 10.1002/humu.22689 %0 Journal Article %J BMC Genet %D 2014 %T Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree. %A Méndez-Vidal, Cristina %A Bravo-Gil, Nereida %A González-del Pozo, María %A Vela-Boza, Alicia %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %K Bardet-Biedl Syndrome %K Base Sequence %K Case-Control Studies %K DNA Mutational Analysis %K Eye Proteins %K Genes, Recessive %K Genetic Association Studies %K Humans %K Microsatellite Repeats %K Microtubule-Associated Proteins %K Mutation, Missense %K Pedigree %K Phenotype %K Retina %K Retinitis pigmentosa %X

BACKGROUND: Molecular diagnosis of Inherited Retinal Dystrophies (IRD) has long been challenging due to the extensive clinical and genetic heterogeneity present in this group of disorders. Here, we describe the clinical application of an integrated next-generation sequencing approach to determine the underlying genetic defects in a Spanish family with a provisional clinical diagnosis of autosomal recessive Retinitis Pigmentosa (arRP).

RESULTS: Exome sequencing of the index patient resulted in the identification of the homozygous BBS1 p.M390R mutation. Sanger sequencing of additional members of the family showed lack of co-segregation of the p.M390R variant in some individuals. Clinical reanalysis indicated co-ocurrence of two different phenotypes in the same family: Bardet-Biedl syndrome in the individual harboring the BBS1 mutation and non-syndromic arRP in extended family members. To identify possible causative mutations underlying arRP, we conducted disease-targeted gene sequencing using a panel of 26 IRD genes. The in-house custom panel was validated using 18 DNA samples known to harbor mutations in relevant genes. All variants were redetected, indicating a high mutation detection rate. This approach allowed the identification of two novel heterozygous null mutations in RP1 (c.4582_4585delATCA; p.I1528Vfs*10 and c.5962dupA; p.I1988Nfs*3) which co-segregated with the disease in arRP patients. Additionally, a mutational screening in 96 patients of our cohort with genetically unresolved IRD revealed the presence of the c.5962dupA mutation in one unrelated family.

CONCLUSIONS: The combination of molecular findings for RP1 and BBS1 genes through exome and gene panel sequencing enabled us to explain the co-existence of two different retinal phenotypes in a family. The identification of two novel variants in RP1 suggests that the use of panels containing the prevalent genes of a particular population, together with an optimized data analysis pipeline, is an efficient and cost-effective approach that can be reliably implemented into the routine diagnostic process of diverse inherited retinal disorders. Moreover, the identification of these novel variants in two unrelated families supports the relatively high prevalence of RP1 mutations in Spanish population and the role of private mutations for commonly mutated genes, while extending the mutational spectrum of RP1.

%B BMC Genet %V 15 %P 143 %8 2014 Dec 14 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/25494902?dopt=Abstract %R 10.1186/s12863-014-0143-2 %0 Journal Article %J Mol Syst Biol %D 2014 %T The role of the interactome in the maintenance of deleterious variability in human populations. %A García-Alonso, Luz %A Jiménez-Almazán, Jorge %A Carbonell-Caballero, José %A Vela-Boza, Alicia %A Santoyo-López, Javier %A Antiňolo, Guillermo %A Dopazo, Joaquin %K Alleles %K Exome %K Gene Library %K Genetic Variation %K Genetics, Population %K Genome, Human %K Genomics %K Humans %K Models, Genetic %K mutation %K Phenotype %K Protein Conformation %K Protein Interaction Maps %K Sequence Analysis, DNA %K Whites %X

Recent genomic projects have revealed the existence of an unexpectedly large amount of deleterious variability in the human genome. Several hypotheses have been proposed to explain such an apparently high mutational load. However, the mechanisms by which deleterious mutations in some genes cause a pathological effect but are apparently innocuous in other genes remain largely unknown. This study searched for deleterious variants in the 1,000 genomes populations, as well as in a newly sequenced population of 252 healthy Spanish individuals. In addition, variants causative of monogenic diseases and somatic variants from 41 chronic lymphocytic leukaemia patients were analysed. The deleterious variants found were analysed in the context of the interactome to understand the role of network topology in the maintenance of the observed mutational load. Our results suggest that one of the mechanisms whereby the effect of these deleterious variants on the phenotype is suppressed could be related to the configuration of the protein interaction network. Most of the deleterious variants observed in healthy individuals are concentrated in peripheral regions of the interactome, in combinations that preserve their connectivity, and have a marginal effect on interactome integrity. On the contrary, likely pathogenic cancer somatic deleterious variants tend to occur in internal regions of the interactome, often with associated structural consequences. Finally, variants causative of monogenic diseases seem to occupy an intermediate position. Our observations suggest that the real pathological potential of a variant might be more a systems property rather than an intrinsic property of individual proteins.

%B Mol Syst Biol %V 10 %P 752 %8 2014 Sep 26 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/25261458?dopt=Abstract %R 10.15252/msb.20145222 %0 Journal Article %J Hum Mutat %D 2014 %T Two novel mutations in the BCKDK (branched-chain keto-acid dehydrogenase kinase) gene are responsible for a neurobehavioral deficit in two pediatric unrelated patients. %A García-Cazorla, Angels %A Oyarzabal, Alfonso %A Fort, Joana %A Robles, Concepción %A Castejón, Esperanza %A Ruiz-Sala, Pedro %A Bodoy, Susanna %A Merinero, Begoña %A Lopez-Sala, Anna %A Dopazo, Joaquin %A Nunes, Virginia %A Ugarte, Magdalena %A Artuch, Rafael %A Palacín, Manuel %A Rodríguez-Pombo, Pilar %A Alcaide, Patricia %A Navarrete, Rosa %A Sanz, Paloma %A Font-Llitjós, Mariona %A Vilaseca, Ma Antonia %A Ormaizabal, Aida %A Pristoupilova, Anna %A Agulló, Sergi Beltran %K Amino Acids, Branched-Chain %K Developmental Disabilities %K Fibroblasts %K Humans %K Male %K Mutation, Missense %K Nervous System Diseases %K Pediatrics %K Protein Kinases %X

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.

%B Hum Mutat %V 35 %P 470-7 %8 2014 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/24449431?dopt=Abstract %R 10.1002/humu.22513 %0 Journal Article %J BMC systems biology %D 2014 %T Understanding disease mechanisms with models of signaling pathway activities %A Sebastián-Leon, Patricia %A Vidal, Enrique %A Minguez, Pablo %A Conesa, Ana %A Tarazona, Sonia %A Amadoz, Alicia %A Armero, Carmen %A Salavert Torres, Francisco %A Vidal-Puig, Antonio %A Montaner, David %A Dopazo, Joaquin %B BMC systems biology %V 8 %P 121 %8 10 %G eng %R 10.1186/s12918-014-0121-3 %0 Journal Article %J BMC systems biology %D 2014 %T Understanding disease mechanisms with models of signaling pathway activities. %A Sebastián-Leon, Patricia %A Vidal, Enrique %A Minguez, Pablo %A Ana Conesa %A Sonia Tarazona %A Amadoz, Alicia %A Armero, Carmen %A Salavert, Francisco %A Vidal-Puig, Antonio %A Montaner, David %A Joaquín Dopazo %K Disease mechanism %K pathway %K signalling %K Systems biology %X BackgroundUnderstanding the aspects of the cell functionality that account for disease or drug action mechanisms is one of the main challenges in the analysis of genomic data and is on the basis of the future implementation of precision medicine.ResultsHere we propose a simple probabilistic model in which signaling pathways are separated into elementary sub-pathways or signal transmission circuits (which ultimately trigger cell functions) and then transforms gene expression measurements into probabilities of activation of such signal transmission circuits. Using this model, differential activation of such circuits between biological conditions can be estimated. Thus, circuit activation statuses can be interpreted as biomarkers that discriminate among the compared conditions. This type of mechanism-based biomarkers accounts for cell functional activities and can easily be associated to disease or drug action mechanisms. The accuracy of the proposed model is demonstrated with simulations and real datasets.ConclusionsThe proposed model provides detailed information that enables the interpretation disease mechanisms as a consequence of the complex combinations of altered gene expression values. Moreover, it offers a framework for suggesting possible ways of therapeutic intervention in a pathologically perturbed system. %B BMC systems biology %V 8 %P 121 %8 2014 Oct 25 %G eng %U http://www.biomedcentral.com/1752-0509/8/121/abstract %R 10.1186/s12918-014-0121-3 %0 Journal Article %J PLoS One %D 2013 %T Defining the genomic signature of totipotency and pluripotency during early human development. %A Galan, Amparo %A Diaz-Gimeno, Patricia %A Poo, Maria Eugenia %A Valbuena, Diana %A Sanchez, Eva %A Ruiz, Veronica %A Dopazo, Joaquin %A Montaner, David %A Conesa, Ana %A Simon, Carlos %K Blastocyst Inner Cell Mass %K Blastomeres %K Cell Differentiation %K Embryonic Development %K Embryonic Stem Cells %K Gene Expression Profiling %K Gene Regulatory Networks %K Genome, Human %K Humans %K Molecular Sequence Annotation %K Pluripotent Stem Cells %K Totipotent Stem Cells %X

The genetic mechanisms governing human pre-implantation embryo development and the in vitro counterparts, human embryonic stem cells (hESCs), still remain incomplete. Previous global genome studies demonstrated that totipotent blastomeres from day-3 human embryos and pluripotent inner cell masses (ICMs) from blastocysts, display unique and differing transcriptomes. Nevertheless, comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. To understand early human stages evolution, we developed an undifferentiation network signature (UNS) and applied it to a differential gene expression profile between single blastomeres from day-3 embryos, ICMs and hESCs. This allowed us to establish a unique signature composed of highly interconnected genes characteristic of totipotency (61 genes), in vivo pluripotency (20 genes), and in vitro pluripotency (107 genes), and which are also proprietary according to functional analysis. This systems biology approach has led to an improved understanding of the molecular and signaling processes governing human pre-implantation embryo development, as well as enabling us to comprehend how hESCs might adapt to in vitro culture conditions.

%B PLoS One %V 8 %P e62135 %8 2013 %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/23614026?dopt=Abstract %R 10.1371/journal.pone.0062135 %0 Journal Article %J Mol Genet Metab %D 2013 %T Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria. %A Tort, Frederic %A García-Silva, María Teresa %A Ferrer-Cortès, Xènia %A Navarro-Sastre, Aleix %A Garcia-Villoria, Judith %A Coll, Maria Josep %A Vidal, Enrique %A Jiménez-Almazán, Jorge %A Dopazo, Joaquin %A Briones, Paz %A Elpeleg, Orly %A Ribes, Antonia %K Adolescent %K Adult %K Carboxylic Ester Hydrolases %K Child %K Exome %K Female %K High-Throughput Nucleotide Sequencing %K Humans %K Infant %K Male %K Metabolism, Inborn Errors %K mutation %X

3-Methylglutaconic aciduria (3-MGA-uria) is a heterogeneous group of syndromes characterized by an increased excretion of 3-methylglutaconic and 3-methylglutaric acids. Five types of 3-MGA-uria (I to V) with different clinical presentations have been described. Causative mutations in TAZ, OPA3, DNAJC19, ATP12, ATP5E, and TMEM70 have been identified. After excluding the known genetic causes of 3-MGA-uria we used exome sequencing to investigate a patient with Leigh syndrome and 3-MGA-uria. We identified a homozygous variant in SERAC1 (c.202C>T; p.Arg68*), that generates a premature stop codon at position 68 of SERAC1 protein. Western blot analysis in patient's fibroblasts showed a complete absence of SERAC1 that was consistent with the prediction of a truncated protein and supports the pathogenic role of the mutation. During the course of this project a parallel study identified mutations in SERAC1 as the genetic cause of the disease in 15 patients with MEGDEL syndrome, which was compatible with the clinical and biochemical phenotypes of the patient described here. In addition, our patient developed microcephaly and optic atrophy, two features not previously reported in MEGDEL syndrome. We highlight the usefulness of exome sequencing to reveal the genetic bases of human rare diseases even if only one affected individual is available.

%B Mol Genet Metab %V 110 %P 73-7 %8 2013 Sep-Oct %G eng %N 1-2 %1 https://www.ncbi.nlm.nih.gov/pubmed/23707711?dopt=Abstract %R 10.1016/j.ymgme.2013.04.021 %0 Journal Article %J Carcinogenesis %D 2013 %T Grape antioxidant dietary fiber (GADF) inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. %A Sánchez-Tena, Susana %A Lizarraga, Daneida %A Miranda, Anibal %A Vinardell, Maria Pilar %A Garcia-Garcia, Francisco %A Joaquín Dopazo %A Torres, Josep Lluís %A Saura-Calixto, Fulgencio %A Capellà, Gabriel %A Cascante, Marta %X 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. %B Carcinogenesis %8 2013 Apr 24 %G eng %U http://carcin.oxfordjournals.org/content/early/2013/04/23/carcin.bgt140.abstract %R 10.1093/carcin/bgt140 %0 Journal Article %J Carcinogenesis %D 2013 %T Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. %A Sánchez-Tena, Susana %A Lizarraga, Daneida %A Miranda, Anibal %A Vinardell, Maria P %A Garcia-Garcia, Francisco %A Dopazo, Joaquin %A Torres, Josep L %A Saura-Calixto, Fulgencio %A Capellà, Gabriel %A Cascante, Marta %K Animals %K Antioxidants %K Body Weight %K Carcinogenesis %K Cell Cycle %K Cell Cycle Checkpoints %K Colorectal Neoplasms %K Dietary Fiber %K Dietary Supplements %K Down-Regulation %K G1 Phase %K Inflammation %K Intestinal Polyposis %K Intestinal Polyps %K Intestine, Small %K Male %K Mice %K Transcriptome %K Vitis %X

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.

%B Carcinogenesis %V 34 %P 1881-8 %8 2013 Aug %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/23615403?dopt=Abstract %R 10.1093/carcin/bgt140 %0 Journal Article %J PLoS One %D 2013 %T Mammosphere formation in breast carcinoma cell lines depends upon expression of E-cadherin. %A Manuel Iglesias, Juan %A Beloqui, Izaskun %A Garcia-Garcia, Francisco %A Leis, Olatz %A Vazquez-Martin, Alejandro %A Eguiara, Arrate %A Cufi, Silvia %A Pavon, Andres %A Menendez, Javier A %A Dopazo, Joaquin %A Martin, Angel G %K Breast Neoplasms %K Cadherins %K Cell Line, Tumor %K Cell Proliferation %K Cluster Analysis %K Female %K gene expression %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Gene Knockdown Techniques %K Humans %K MCF-7 Cells %K Neoplastic Stem Cells %K Spheroids, Cellular %K Tumor Cells, Cultured %X

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.

%B PLoS One %V 8 %P e77281 %8 2013 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/24124614?dopt=Abstract %R 10.1371/journal.pone.0077281 %0 Journal Article %J PLoS ONE %D 2013 %T Mammosphere Formation in Breast Carcinoma Cell Lines Depends upon Expression of E-cadherin %A Manuel Iglesias, Juan %A Beloqui, Izaskun %A Garcia-Garcia, Francisco %A Leis, Olatz %A Vazquez-Martin, Alejandro %A Eguiara, Arrate %A Cufi, Silvia %A Pavon, Andres %A Menendez, Javier A. %A Dopazo, Joaquin %A Martin, Angel G. %X

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.

%B PLoS ONE %I Public Library of Science %V 8 %P e77281 - %8 2013/10/04 %G eng %U http://dx.doi.org/10.1371%2Fjournal.pone.0077281 %0 Journal Article %J PloS one %D 2013 %T Maslinic Acid-Enriched Diet Decreases Intestinal Tumorigenesis in Apc(Min/+) Mice through Transcriptomic and Metabolomic Reprogramming. %A Sánchez-Tena, Susana %A Reyes-Zurita, Fernando J %A Díaz-Moralli, Santiago %A Vinardell, Maria Pilar %A Reed, Michelle %A Garcia-Garcia, Francisco %A Joaquín Dopazo %A Lupiáñez, José A %A Günther, Ulrich %A Cascante, Marta %X 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. %B PloS one %V 8 %P e59392 %8 2013 %G eng %R 10.1371/journal.pone.0059392 %0 Journal Article %J Molecular vision %D 2013 %T Whole-exome sequencing identifies novel compound heterozygous mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa. %A Méndez-Vidal, Cristina %A González-del Pozo, María %A Vela-Boza, Alicia %A Santoyo-López, Javier %A López-Domingo, Francisco J %A Vázquez-Marouschek, Carmen %A Dopazo, Joaquin %A Borrego, Salud %A Antiňolo, Guillermo %X 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. %B Molecular vision %V 19 %P 2187-95 %8 2013 %G eng %U http://www.molvis.org/molvis/v19/2187/ %0 Journal Article %J Nucleic Acids Res %D 2012 %T Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. %A García-Alonso, Luz %A Alonso, Roberto %A Vidal, Enrique %A Amadoz, Alicia %A De Maria, Alejandro %A Minguez, Pablo %A Medina, Ignacio %A Dopazo, Joaquin %K Bipolar Disorder %K Fanconi Anemia %K Gene Regulatory Networks %K Genes, Neoplasm %K Genome-Wide Association Study %K Genomics %K Humans %K Protein Interaction Mapping %X

Genomic experiments (e.g. differential gene expression, single-nucleotide polymorphism association) typically produce ranked list of genes. We present a simple but powerful approach which uses protein-protein interaction data to detect sub-networks within such ranked lists of genes or proteins. We performed an exhaustive study of network parameters that allowed us concluding that the average number of components and the average number of nodes per component are the parameters that best discriminate between real and random networks. A novel aspect that increases the efficiency of this strategy in finding sub-networks is that, in addition to direct connections, also connections mediated by intermediate nodes are considered to build up the sub-networks. The possibility of using of such intermediate nodes makes this approach more robust to noise. It also overcomes some limitations intrinsic to experimental designs based on differential expression, in which some nodes are invariant across conditions. The proposed approach can also be used for candidate disease-gene prioritization. Here, we demonstrate the usefulness of the approach by means of several case examples that include a differential expression analysis in Fanconi Anemia, a genome-wide association study of bipolar disorder and a genome-scale study of essentiality in cancer genes. An efficient and easy-to-use web interface (available at http://www.babelomics.org) based on HTML5 technologies is also provided to run the algorithm and represent the network.

%B Nucleic Acids Res %V 40 %P e158 %8 2012 Nov 01 %G eng %N 20 %1 https://www.ncbi.nlm.nih.gov/pubmed/22844098?dopt=Abstract %R 10.1093/nar/gks699 %0 Journal Article %J PLoS One %D 2012 %T Extensive translatome remodeling during ER stress response in mammalian cells. %A Ventoso, Iván %A Kochetov, Alex %A Montaner, David %A Dopazo, Joaquin %A Santoyo, Javier %K Animals %K Endoplasmic Reticulum Stress %K Humans %K Jurkat Cells %K Mice %K NIH 3T3 Cells %K Oligonucleotide Array Sequence Analysis %K Protein Biosynthesis %K RNA, Messenger %K Transcription, Genetic %X

In this work we have described the translatome of two mammalian cell lines, NIH3T3 and Jurkat, by scoring the relative polysome association of ∼10,000 mRNA under normal and ER stress conditions. We have found that translation efficiencies of mRNA correlated poorly with transcript abundance, although a general tendency was observed so that the highest translation efficiencies were found in abundant mRNA. Despite the differences found between mouse (NIH3T3) and human (Jurkat) cells, both cell types share a common translatome composed by ∼800-900 mRNA that encode proteins involved in basic cellular functions. Upon stress, an extensive remodeling in translatomes was observed so that translation of ∼50% of mRNA was inhibited in both cell types, this effect being more dramatic for those mRNA that accounted for most of the cell translation. Interestingly, we found two subsets comprising 1000-1500 mRNA whose translation resisted or was induced by stress. Translation arrest resistant class includes many mRNA encoding aminoacyl tRNA synthetases, ATPases and enzymes involved in DNA replication and stress response such as BiP. This class of mRNA is characterized by high translation rates in both control and stress conditions. Translation inducible class includes mRNA whose translation was relieved after stress, showing a high enrichment in early response transcription factors of bZIP and zinc finger C2H2 classes. Unlike yeast, a general coordination between changes in translation and transcription upon stress (potentiation) was not observed in mammalian cells. Among the different features of mRNA analyzed, we found a relevant association of translation efficiency with the presence of upstream ATG in the 5'UTR and with the length of coding sequence of mRNA, and a looser association with other parameters such as the length and the G+C content of 5'UTR. A model for translatome remodeling during the acute phase of stress response in mammalian cells is proposed.

%B PLoS One %V 7 %P e35915 %8 2012 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/22574127?dopt=Abstract %R 10.1371/journal.pone.0035915 %0 Journal Article %J Genome medicine %D 2012 %T A map of human microRNA variation uncovers unexpectedly high levels of variability. %A Carbonell, José %A Alloza, Eva %A Arce, Pablo %A Borrego, Salud %A Santoyo, Javier %A Ruiz-Ferrer, Macarena %A Medina, Ignacio %A Jiménez-Almazán, Jorge %A Méndez-Vidal, Cristina %A González-del Pozo, María %A Vela, Alicia %A Bhattacharya, Shomi S %A Antiňolo, Guillermo %A Dopazo, Joaquin %K NGS %X ABSTRACT: BACKGROUND: MicroRNAs (miRNAs) are key components of the gene regulatory network in many species. During the past few years, these regulatory elements have been shown to be involved in an increasing number and range of diseases. Consequently, the compilation of a comprehensive map of natural variability in healthy population seems an obvious requirement for future research on miRNA-related pathologies. METHODS: Data on 14 populations from the 1000 Genomes Project were analysed, along with new data extracted from 60 exomes of healthy individuals from a southern Spain population, sequenced in the context of the Medical Genome Project, to derive an accurate map of miRNA variability. RESULTS: Despite the common belief that miRNAs are highly conserved elements, analysis of the sequences of the 1,152 individuals indicated that the observed level of variability is double what was expected. A total of 527 variants were found. Among these, 45 variants affected the recognition region of the corresponding miRNA and were found in 43 different miRNAs, 26 of which are known to be involved in 57 diseases. Different parts of the mature structure of the miRNA were affected to different degrees by variants, which suggests the existence of a selective pressure related to the relative functional impact of the change. Moreover, 41 variants showed a significant deviation from the Hardy-Weinberg equilibrium, which supports the existence of a selective process against some alleles. The average number of variants per individual in miRNAs was 28. CONCLUSIONS: Despite an expectation that miRNAs would be highly conserved genomic elements, our study reports a level of variability comparable to that observed for coding genes. %B Genome medicine %V 4 %P 62 %8 2012 Aug 20 %G eng %U http://genomemedicine.com/content/4/8/62/abstract %R 10.1186/gm363 %0 Journal Article %J International journal of data mining and bioinformatics %D 2012 %T Select your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. %A Lorente-Galdos, Belén %A Medina, Ignacio %A Morcillo-Suarez, Carlos %A Heredia, Txema %A Carreño-Torres, Angel %A Sangrós, Ricardo %A Alegre, Josep %A Pita, Guillermo %A Vellalta, Gemma %A Malats, Nuria %A Pisano, David G %A Joaquín Dopazo %A Navarro, Arcadi %X 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. %B International journal of data mining and bioinformatics %V 6 %P 324-34 %8 2012 %G eng %U http://inderscience.metapress.com/content/f76740x8071u513n/ %0 Journal Article %J Nucleic Acids Res %D 2012 %T SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. %A De Baets, Greet %A Van Durme, Joost %A Reumers, Joke %A Maurer-Stroh, Sebastian %A Vanhee, Peter %A Dopazo, Joaquin %A Schymkowitz, Joost %A Rousseau, Frederic %K Databases, Protein %K Humans %K Internet %K Meta-Analysis as Topic %K Phenotype %K Polymorphism, Single Nucleotide %K Protein Conformation %K Proteins %X

Single nucleotide variants (SNVs) are, together with copy number variation, the primary source of variation in the human genome and are associated with phenotypic variation such as altered response to drug treatment and susceptibility to disease. Linking structural effects of non-synonymous SNVs to functional outcomes is a major issue in structural bioinformatics. The SNPeffect database (http://snpeffect.switchlab.org) uses sequence- and structure-based bioinformatics tools to predict the effect of protein-coding SNVs on the structural phenotype of proteins. It integrates aggregation prediction (TANGO), amyloid prediction (WALTZ), chaperone-binding prediction (LIMBO) and protein stability analysis (FoldX) for structural phenotyping. Additionally, SNPeffect holds information on affected catalytic sites and a number of post-translational modifications. The database contains all known human protein variants from UniProt, but users can now also submit custom protein variants for a SNPeffect analysis, including automated structure modeling. The new meta-analysis application allows plotting correlations between phenotypic features for a user-selected set of variants.

%B Nucleic Acids Res %V 40 %P D935-9 %8 2012 Jan %G eng %N Database issue %1 https://www.ncbi.nlm.nih.gov/pubmed/22075996?dopt=Abstract %R 10.1093/nar/gkr996 %0 Journal Article %J Epigenetics %D 2012 %T Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. %A Heyn, Holger %A Vidal, Enrique %A Sayols, Sergi %A Sanchez-Mut, Jose V %A Moran, Sebastian %A Medina, Ignacio %A Sandoval, Juan %A Simó-Riudalbas, Laia %A Szczesna, Karolina %A Huertas, Dori %A Gatto, Sole %A Matarazzo, Maria R %A Dopazo, Joaquin %A Esteller, Manel %K B-Lymphocytes %K Cell Line, Transformed %K Child, Preschool %K DNA (Cytosine-5-)-Methyltransferases %K DNA Methylation %K Epigenesis, Genetic %K Face %K Female %K Genome, Human %K High-Throughput Nucleotide Sequencing %K Humans %K Immunologic Deficiency Syndromes %K mutation %K Primary Immunodeficiency Diseases %K Sequence Analysis, DNA %K Sulfites %X

The immunodeficiency, centromere instability and facial anomalies (ICF) syndrome is associated to mutations of the DNA methyl-transferase DNMT3B, resulting in a reduction of enzyme activity. Aberrant expression of immune system genes and hypomethylation of pericentromeric regions accompanied by chromosomal instability were determined as alterations driving the disease phenotype. However, so far only technologies capable to analyze single loci were applied to determine epigenetic alterations in ICF patients. In the current study, we performed whole-genome bisulphite sequencing to assess alteration in DNA methylation at base pair resolution. Genome-wide we detected a decrease of methylation level of 42%, with the most profound changes occurring in inactive heterochromatic regions, satellite repeats and transposons. Interestingly, transcriptional active loci and ribosomal RNA repeats escaped global hypomethylation. Despite a genome-wide loss of DNA methylation the epigenetic landscape and crucial regulatory structures were conserved. Remarkably, we revealed a mislocated activity of mutant DNMT3B to H3K4me1 loci resulting in hypermethylation of active promoters. Functionally, we could associate alterations in promoter methylation with the ICF syndrome immunodeficient phenotype by detecting changes in genes related to the B-cell receptor mediated maturation pathway.

%B Epigenetics %V 7 %P 542-50 %8 2012 Jun 01 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/22595875?dopt=Abstract %R 10.4161/epi.20523 %0 Journal Article %J PloS one %D 2011 %T Analysis of normal-tumour tissue interaction in tumours: prediction of prostate cancer features from the molecular profile of adjacent normal cells. %A Trevino, Victor %A Tadesse, Mahlet G %A Vannucci, Marina %A Fatima Al-Shahrour %A Antczak, Philipp %A Durant, Sarah %A Bikfalvi, Andreas %A Dopazo, Joaquin %A Campbell, Moray J %A Falciani, Francesco %X

Statistical modelling, in combination with genome-wide expression profiling techniques, has demonstrated that the molecular state of the tumour is sufficient to infer its pathological state. These studies have been extremely important in diagnostics and have contributed to improving our understanding of tumour biology. However, their importance in in-depth understanding of cancer patho-physiology may be limited since they do not explicitly take into consideration the fundamental role of the tissue microenvironment in specifying tumour physiology. Because of the importance of normal cells in shaping the tissue microenvironment we formulate the hypothesis that molecular components of the profile of normal epithelial cells adjacent the tumour are predictive of tumour physiology. We addressed this hypothesis by developing statistical models that link gene expression profiles representing the molecular state of adjacent normal epithelial cells to tumour features in prostate cancer. Furthermore, network analysis showed that predictive genes are linked to the activity of important secreted factors, which have the potential to influence tumor biology, such as IL1, IGF1, PDGF BB, AGT, and TGFβ.

%B PloS one %V 6 %P e16492 %8 2011 %G eng %0 Journal Article %J Diabetes %D 2011 %T Differential Lipid Partitioning Between Adipocytes and Tissue Macrophages Modulates Macrophage Lipotoxicity and M2/M1 Polarization in Obese Mice. %A Prieur, Xavier %A Mok, Crystal Y L %A Velagapudi, Vidya R %A Núñez, Vanessa %A Fuentes, Lucía %A Montaner, David %A Ishikawa, Ko %A Camacho, Alberto %A Barbarroja, Nuria %A O’Rahilly, Stephen %A Sethi, Jaswinder %A Dopazo, Joaquin %A Oresic, Matej %A Ricote, Mercedes %A Vidal-Puig, Antonio %X

OBJECTIVE Obesity-associated insulin resistance is characterized by a state of chronic, low-grade inflammation that is associated with the accumulation of M1 proinflammatory macrophages in adipose tissue. Although different evidence explains the mechanisms linking the expansion of adipose tissue and adipose tissue macrophage (ATM) polarization, in the current study we investigated the concept of lipid-induced toxicity as the pathogenic link that could explain the trigger of this response. RESEARCH DESIGN AND METHODS We addressed this question using isolated ATMs and adipocytes from genetic and diet-induced murine models of obesity. Through transcriptomic and lipidomic analysis, we created a model integrating transcript and lipid species networks simultaneously occurring in adipocytes and ATMs and their reversibility by thiazolidinedione treatment. RESULTS We show that polarization of ATMs is associated with lipid accumulation and the consequent formation of foam cell-like cells in adipose tissue. Our study reveals that early stages of adipose tissue expansion are characterized by M2-polarized ATMs and that progressive lipid accumulation within ATMs heralds the M1 polarization, a macrophage phenotype associated with severe obesity and insulin resistance. Furthermore, rosiglitazone treatment, which promotes redistribution of lipids toward adipocytes and extends the M2 ATM polarization state, prevents the lipid alterations associated with M1 ATM polarization. CONCLUSIONS Our data indicate that the M1 ATM polarization in obesity might be a macrophage-specific manifestation of a more general lipotoxic pathogenic mechanism. This indicates that strategies to optimize fat deposition and repartitioning toward adipocytes might improve insulin sensitivity by preventing ATM lipotoxicity and M1 polarization.

%B Diabetes %V 60 %P 797-809 %8 2011 Jan 24 %G eng %0 Journal Article %J PLoS pathogens %D 2011 %T Discovery of an ebolavirus-like filovirus in europe. %A Negredo, Ana %A Palacios, Gustavo %A Vázquez-Morón, Sonia %A González, Félix %A Dopazo, Hernán %A Molero, Francisca %A Juste, Javier %A Quetglas, Juan %A Savji, Nazir %A de la Cruz Martínez, Maria %A Herrera, Jesus Enrique %A Pizarro, Manuel %A Hutchison, Stephen K %A Echevarría, Juan E %A Lipkin, W Ian %A Tenorio, Antonio %X

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.

%B PLoS pathogens %V 7 %P e1002304 %8 2011 Oct %G eng %0 Journal Article %J BMC Med Genomics %D 2011 %T Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. %A Vivas, Yurena %A Martinez-Garcia, Cristina %A Izquierdo, Adriana %A Garcia-Garcia, Francisco %A Callejas, Sergio %A Velasco, Ismael %A Campbell, Mark %A Ros, Manuel %A Dopazo, Ana %A Dopazo, Joaquin %A Vidal-Puig, Antonio %A Medina-Gomez, Gema %K Animals %K Cell Proliferation %K Cell Survival %K Cholesterol %K Down-Regulation %K Female %K Gene Expression Regulation %K Gene Knockout Techniques %K Insulin Resistance %K Insulin-Secreting Cells %K Mice %K obesity %K Oxidation-Reduction %K Phosphorylation %K PPAR gamma %K Signal Transduction %K Transcription, Genetic %K Transforming Growth Factor beta %X

BACKGROUND: The progression towards type 2 diabetes depends on the allostatic response of pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a plastic tissue able to expand or regress in response to the requirements imposed by physiological and pathophysiological states associated to insulin resistance such as pregnancy, obesity or ageing, but the mechanisms mediating beta cell mass expansion in these scenarios are not well defined. We have recently shown that ob/ob mice with genetic ablation of PPARγ2, a mouse model known as the POKO mouse failed to expand its beta cell mass. This phenotype contrasted with the appropriate expansion of the beta cell mass observed in their obese littermate ob/ob mice. Thus, comparison of these models islets particularly at early ages could provide some new insights on early PPARγ dependent transcriptional responses involved in the process of beta cell mass expansion

RESULTS: Here we have investigated PPARγ dependent transcriptional responses occurring during the early stages of beta cell adaptation to insulin resistance in wild type, ob/ob, PPARγ2 KO and POKO mice. We have identified genes known to regulate both the rate of proliferation and the survival signals of beta cells. Moreover we have also identified new pathways induced in ob/ob islets that remained unchanged in POKO islets, suggesting an important role for PPARγ in maintenance/activation of mechanisms essential for the continued function of the beta cell.

CONCLUSIONS: Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with the activation of an immune response that fails to occur in POKO islets. We have also indentified other PPARγ dependent differentially regulated pathways including cholesterol biosynthesis, apoptosis through TGF-β signaling and decreased oxidative phosphorylation.

%B BMC Med Genomics %V 4 %P 86 %8 2011 Dec 30 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/22208362?dopt=Abstract %R 10.1186/1755-8794-4-86 %0 Journal Article %J PloS one %D 2011 %T Sexual selection halts the relaxation of protamine 2 among rodents. %A Lüke, Lena %A Vicens, Alberto %A Serra, François %A Luque-Larena, Juan Jose %A Dopazo, Hernán %A Roldan, Eduardo R S %A Gomendio, Montserrat %X 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. %B PloS one %V 6 %P e29247 %8 2011 %G eng %U http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029247 %R 10.1371/journal.pone.0029247 %0 Journal Article %J Nucleic acids research %D 2011 %T SUS1 introns are required for efficient mRNA nuclear export in yeast. %A Cuenca-Bono, Bernardo %A García-Molinero, Varinia %A Pascual-García, Pau %A Dopazo, Hernán %A Llopis, Ana %A Vilardell, Josep %A Rodríguez-Navarro, Susana %X

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.

%B Nucleic acids research %V 39 %P 8599-611 %8 2011 Oct 1 %G eng %0 Journal Article %J Breast Cancer Res %D 2010 %T DNA methylation epigenotypes in breast cancer molecular subtypes. %A Bediaga, Naiara G %A Acha-Sagredo, Amelia %A Guerra, Isabel %A Viguri, Amparo %A Albaina, Carmen %A Ruiz Diaz, Irune %A Rezola, Ricardo %A Alberdi, Maria Jesus %A Dopazo, Joaquin %A Montaner, David %A Renobales, Mertxe %A Fernandez, Agustin F %A Field, John K %A Fraga, Mario F %A Liloglou, Triantafillos %A de Pancorbo, Marian M %K Aged %K Breast Neoplasms %K CpG Islands %K DNA Methylation %K Epigenesis, Genetic %K Female %K Gene Expression Profiling %K Genes, p53 %K Genotype %K Humans %K Ki-67 Antigen %K Middle Aged %K mutation %K Neoplasm Grading %K Oligonucleotide Array Sequence Analysis %K Receptor, ErbB-2 %K Tumor Suppressor Protein p53 %X

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.

%B Breast Cancer Res %V 12 %P R77 %8 2010 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/20920229?dopt=Abstract %R 10.1186/bcr2721 %0 Journal Article %J PLoS One %D 2010 %T Functional genomics of 5- to 8-cell stage human embryos by blastomere single-cell cDNA analysis. %A Galan, Amparo %A Montaner, David %A Póo, M Eugenia %A Valbuena, Diana %A Ruiz, Veronica %A Aguilar, Cristóbal %A Dopazo, Joaquin %A Simon, Carlos %K Blastomeres %K DNA, Complementary %K Gene Expression Profiling %K Genomics %K Humans %K Oligonucleotide Array Sequence Analysis %X

Blastomere fate and embryonic genome activation (EGA) during human embryonic development are unsolved areas of high scientific and clinical interest. Forty-nine blastomeres from 5- to 8-cell human embryos have been investigated following an efficient single-cell cDNA amplification protocol to provide a template for high-density microarray analysis. The previously described markers, characteristic of Inner Cell Mass (ICM) (n = 120), stemness (n = 190) and Trophectoderm (TE) (n = 45), were analyzed, and a housekeeping pattern of 46 genes was established. All the human blastomeres from the 5- to 8-cell stage embryo displayed a common gene expression pattern corresponding to ICM markers (e.g., DDX3, FOXD3, LEFTY1, MYC, NANOG, POU5F1), stemness (e.g., POU5F1, DNMT3B, GABRB3, SOX2, ZFP42, TERT), and TE markers (e.g., GATA6, EOMES, CDX2, LHCGR). The EGA profile was also investigated between the 5-6- and 8-cell stage embryos, and compared to the blastocyst stage. Known genes (n = 92) such as depleted maternal transcripts (e.g., CCNA1, CCNB1, DPPA2) and embryo-specific activation (e.g., POU5F1, CDH1, DPPA4), as well as novel genes, were confirmed. In summary, the global single-cell cDNA amplification microarray analysis of the 5- to 8-cell stage human embryos reveals that blastomere fate is not committed to ICM or TE. Finally, new EGA features in human embryogenesis are presented.

%B PLoS One %V 5 %P e13615 %8 2010 Oct 26 %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/21049019?dopt=Abstract %R 10.1371/journal.pone.0013615 %0 Journal Article %J Nature biotechnology %D 2010 %T The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. %A Shi, Leming %A Campbell, Gregory %A Jones, Wendell D %A Campagne, Fabien %A Wen, Zhining %A Walker, Stephen J %A Su, Zhenqiang %A Chu, Tzu-Ming %A Goodsaid, Federico M %A Pusztai, Lajos %A Shaughnessy, John D %A Oberthuer, André %A Thomas, Russell S %A Paules, Richard S %A Fielden, Mark %A Barlogie, Bart %A Chen, Weijie %A Du, Pan %A Fischer, Matthias %A Furlanello, Cesare %A Gallas, Brandon D %A Ge, Xijin %A Megherbi, Dalila B %A Symmans, W Fraser %A Wang, May D %A Zhang, John %A Bitter, Hans %A Brors, Benedikt %A Bushel, Pierre R %A Bylesjo, Max %A Chen, Minjun %A Cheng, Jie %A Cheng, Jing %A Chou, Jeff %A Davison, Timothy S %A Delorenzi, Mauro %A Deng, Youping %A Devanarayan, Viswanath %A Dix, David J %A Dopazo, Joaquin %A Dorff, Kevin C %A Elloumi, Fathi %A Fan, Jianqing %A Fan, Shicai %A Fan, Xiaohui %A Fang, Hong %A Gonzaludo, Nina %A Hess, Kenneth R %A Hong, Huixiao %A Huan, Jun %A Irizarry, Rafael A %A Judson, Richard %A Juraeva, Dilafruz %A Lababidi, Samir %A Lambert, Christophe G %A Li, Li %A Li, Yanen %A Li, Zhen %A Lin, Simon M %A Liu, Guozhen %A Lobenhofer, Edward K %A Luo, Jun %A Luo, Wen %A McCall, Matthew N %A Nikolsky, Yuri %A Pennello, Gene A %A Perkins, Roger G %A Philip, Reena %A Popovici, Vlad %A Price, Nathan D %A Qian, Feng %A Scherer, Andreas %A Shi, Tieliu %A Shi, Weiwei %A Sung, Jaeyun %A Thierry-Mieg, Danielle %A Thierry-Mieg, Jean %A Thodima, Venkata %A Trygg, Johan %A Vishnuvajjala, Lakshmi %A Wang, Sue Jane %A Wu, Jianping %A Wu, Yichao %A Xie, Qian %A Yousef, Waleed A %A Zhang, Liang %A Zhang, Xuegong %A Zhong, Sheng %A Zhou, Yiming %A Zhu, Sheng %A Arasappan, Dhivya %A Bao, Wenjun %A Lucas, Anne Bergstrom %A Berthold, Frank %A Brennan, Richard J %A Buness, Andreas %A Catalano, Jennifer G %A Chang, Chang %A Chen, Rong %A Cheng, Yiyu %A Cui, Jian %A Czika, Wendy %A Demichelis, Francesca %A Deng, Xutao %A Dosymbekov, Damir %A Eils, Roland %A Feng, Yang %A Fostel, Jennifer %A Fulmer-Smentek, Stephanie %A Fuscoe, James C %A Gatto, Laurent %A Ge, Weigong %A Goldstein, Darlene R %A Guo, Li %A Halbert, Donald N %A Han, Jing %A Harris, Stephen C %A Hatzis, Christos %A Herman, Damir %A Huang, Jianping %A Jensen, Roderick V %A Jiang, Rui %A Johnson, Charles D %A Jurman, Giuseppe %A Kahlert, Yvonne %A Khuder, Sadik A %A Kohl, Matthias %A Li, Jianying %A Li, Li %A Li, Menglong %A Li, Quan-Zhen %A Li, Shao %A Li, Zhiguang %A Liu, Jie %A Liu, Ying %A Liu, Zhichao %A Meng, Lu %A Madera, Manuel %A Martinez-Murillo, Francisco %A Medina, Ignacio %A Meehan, Joseph %A Miclaus, Kelci %A Moffitt, Richard A %A Montaner, David %A Mukherjee, Piali %A Mulligan, George J %A Neville, Padraic %A Nikolskaya, Tatiana %A Ning, Baitang %A Page, Grier P %A Parker, Joel %A Parry, R Mitchell %A Peng, Xuejun %A Peterson, Ron L %A Phan, John H %A Quanz, Brian %A Ren, Yi %A Riccadonna, Samantha %A Roter, Alan H %A Samuelson, Frank W %A Schumacher, Martin M %A Shambaugh, Joseph D %A Shi, Qiang %A Shippy, Richard %A Si, Shengzhu %A Smalter, Aaron %A Sotiriou, Christos %A Soukup, Mat %A Staedtler, Frank %A Steiner, Guido %A Stokes, Todd H %A Sun, Qinglan %A Tan, Pei-Yi %A Tang, Rong %A Tezak, Zivana %A Thorn, Brett %A Tsyganova, Marina %A Turpaz, Yaron %A Vega, Silvia C %A Visintainer, Roberto %A von Frese, Juergen %A Wang, Charles %A Wang, Eric %A Wang, Junwei %A Wang, Wei %A Westermann, Frank %A Willey, James C %A Woods, Matthew %A Wu, Shujian %A Xiao, Nianqing %A Xu, Joshua %A Xu, Lei %A Yang, Lun %A Zeng, Xiao %A Zhang, Jialu %A Zhang, Li %A Zhang, Min %A Zhao, Chen %A Puri, Raj K %A Scherf, Uwe %A Tong, Weida %A Wolfinger, Russell D %X

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.

%B Nature biotechnology %V 28 %P 827-38 %8 2010 Aug %G eng %U http://www.nature.com/nbt/journal/v28/n8/full/nbt.1665.html %0 Journal Article %J Leuk Lymphoma %D 2009 %T Functional signatures identified in B-cell non-Hodgkin lymphoma profiles. %A Aggarwal, Mohit %A Sánchez-Beato, Margarita %A Gómez-López, Gonzalo %A Al-Shahrour, Fátima %A Martínez, Nerea %A Rodríguez, Antonia %A Ruiz-Ballesteros, Elena %A Camacho, Francisca I %A Pérez-Rosado, Alberto %A de la Cueva, Paloma %A Artiga, María J %A Pisano, David G %A Kimby, Eva %A Dopazo, Joaquin %A Villuendas, Raquel %A Piris, Miguel A %K Adult %K Cluster Analysis %K Gene Expression Profiling %K Gene Expression Regulation, Leukemic %K Genetic Heterogeneity %K Humans %K Lymphoma, B-Cell %K Neoplasm Proteins %K Oligonucleotide Array Sequence Analysis %K RNA, Messenger %K RNA, Neoplasm %K Transcription, Genetic %X

Gene-expression profiling in B-cell lymphomas has provided crucial data on specific lymphoma types, which can contribute to the identification of essential lymphoma survival genes and pathways. In this study, the gene-expression profiling data of all major B-cell lymphoma types were analyzed by unsupervised clustering. The transcriptome classification so obtained, was explored using gene set enrichment analysis generating a heatmap for B-cell lymphoma that identifies common lymphoma survival mechanisms and potential therapeutic targets, recognizing sets of coregulated genes and functional pathways expressed in different lymphoma types. Some of the most relevant signatures (stroma, cell cycle, B-cell receptor (BCR)) are shared by multiple lymphoma types or subclasses. A specific attention was paid to the analysis of BCR and coregulated pathways, defining molecular heterogeneity within multiple B-cell lymphoma types.

%B Leuk Lymphoma %V 50 %P 1699-708 %8 2009 Oct %G eng %N 10 %1 https://www.ncbi.nlm.nih.gov/pubmed/19863341?dopt=Abstract %R 10.1080/10428190903189035 %0 Journal Article %J BMC Res Notes %D 2009 %T Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. %A Johan H van Heerden %A Ana Conesa %A Dan J Stein %A Montaner, David %A Vivienne Russell %A Nicola Illing %B BMC Res Notes %V 2 %P 195 %G eng %0 Journal Article %J J Biomed Inform %D 2008 %T CLEAR-test: combining inference for differential expression and variability in microarray data analysis %A Valls, J. %A Grau, M. %A Sole, X. %A Hernandez, P. %A Montaner, D. %A Dopazo, J. %A Peinado, M. A. %A Capella, G. %A Moreno, V. %A Pujana, M. A. %K *Algorithms Artificial Intelligence *Data Interpretation %K Statistical Gene Expression Profiling/*methods Gene Expression Regulation/*physiology Oligonucleotide Array Sequence Analysis/*methods Proteome/*metabolism Signal Transduction/*physiology %X

A common goal of microarray experiments is to detect genes that are differentially expressed under distinct experimental conditions. Several statistical tests have been proposed to determine whether the observed changes in gene expression are significant. The t-test assigns a score to each gene on the basis of changes in its expression relative to its estimated variability, in such a way that genes with a higher score (in absolute values) are more likely to be significant. Most variants of the t-test use the complete set of genes to influence the variance estimate for each single gene. However, no inference is made in terms of the variability itself. Here, we highlight the problem of low observed variances in the t-test, when genes with relatively small changes are declared differentially expressed. Alternatively, the z-test could be used although, unlike the t-test, it can declare differentially expressed genes with high observed variances. To overcome this, we propose to combine the z-test, which focuses on large changes, with a chi(2) test to evaluate variability. We call this procedure CLEAR-test and we provide a combined p-value that offers a compromise between both aspects. Analysis of three publicly available microarray datasets reveals the greater performance of the CLEAR-test relative to the t-test and alternative methods. Finally, empirical and simulated data analyses demonstrate the greater reproducibility and statistical power of the CLEAR-test and z-test with respect to current alternative methods. In addition, the CLEAR-test improves the z-test by capturing reproducible genes with high variability.

%B J Biomed Inform %V 41 %P 33-45 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597009 %0 Journal Article %J Nucleic Acids Res %D 2008 %T GEPAS, a web-based tool for microarray data analysis and interpretation. %A Tárraga, Joaquín %A Medina, Ignacio %A Carbonell, José %A Huerta-Cepas, Jaime %A Minguez, Pablo %A Alloza, Eva %A Al-Shahrour, Fátima %A Vegas-Azcárate, Susana %A Goetz, Stefan %A Escobar, Pablo %A Garcia-Garcia, Francisco %A Conesa, Ana %A Montaner, David %A Dopazo, Joaquin %K Computer Graphics %K Dose-Response Relationship, Drug %K Gene Expression Profiling %K Internet %K Kinetics %K Oligonucleotide Array Sequence Analysis %K Software %X

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

%B Nucleic Acids Res %V 36 %P W308-14 %8 2008 Jul 01 %G eng %N Web Server issue %1 https://www.ncbi.nlm.nih.gov/pubmed/18508806?dopt=Abstract %R 10.1093/nar/gkn303 %0 Journal Article %J Nucleic Acids Res %D 2008 %T GEPAS, a web-based tool for microarray data analysis and interpretation %A Tarraga, J. %A Medina, Ignacio %A Carbonell, J. %A Huerta-Cepas, J. %A Minguez, P. %A Alloza, E. %A Fatima Al-Shahrour %A Vegas-Azcarate, S. %A Goetz, S. %A Escobar, P. %A Garcia-Garcia, F. %A A. Conesa %A Montaner, D. %A Dopazo, J. %K gepas %K microarray data analysis %X

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

%B Nucleic Acids Res %V 36 %P W308-14 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806 %0 Journal Article %J Brief Bioinform %D 2008 %T Interoperability with Moby 1.0--it's better than sharing your toothbrush! %A Wilkinson, Mark D %A Senger, Martin %A Kawas, Edward %A Bruskiewich, Richard %A Gouzy, Jerome %A Noirot, Celine %A Bardou, Philippe %A Ng, Ambrose %A Haase, Dirk %A Saiz, Enrique de Andres %A Wang, Dennis %A Gibbons, Frank %A Gordon, Paul M K %A Sensen, Christoph W %A Carrasco, Jose Manuel Rodriguez %A Fernández, José M %A Shen, Lixin %A Links, Matthew %A Ng, Michael %A Opushneva, Nina %A Neerincx, Pieter B T %A Leunissen, Jack A M %A Ernst, Rebecca %A Twigger, Simon %A Usadel, Bjorn %A Good, Benjamin %A Wong, Yan %A Stein, Lincoln %A Crosby, William %A Karlsson, Johan %A Royo, Romina %A Párraga, Iván %A Ramírez, Sergio %A Gelpi, Josep Lluis %A Trelles, Oswaldo %A Pisano, David G %A Jimenez, Natalia %A Kerhornou, Arnaud %A Rosset, Roman %A Zamacola, Leire %A Tárraga, Joaquín %A Huerta-Cepas, Jaime %A Carazo, Jose María %A Dopazo, Joaquin %A Guigó, Roderic %A Navarro, Arcadi %A Orozco, Modesto %A Valencia, Alfonso %A Claros, M Gonzalo %A Pérez, Antonio J %A Aldana, Jose %A Rojano, M Mar %A Fernandez-Santa Cruz, Raul %A Navas, Ismael %A Schiltz, Gary %A Farmer, Andrew %A Gessler, Damian %A Schoof, Heiko %A Groscurth, Andreas %K Computational Biology %K Database Management Systems %K Databases, Factual %K Information Storage and Retrieval %K Internet %K Programming Languages %K Systems Integration %X

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/.

%B Brief Bioinform %V 9 %P 220-31 %8 2008 May %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/18238804?dopt=Abstract %R 10.1093/bib/bbn003 %0 Journal Article %J Brief Bioinform %D 2008 %T Interoperability with Moby 1.0–it’s better than sharing your toothbrush! %A Wilkinson, M. D. %A Senger, M. %A Kawas, E. %A Bruskiewich, R. %A Gouzy, J. %A Noirot, C. %A Bardou, P. %A Ng, A. %A Haase, D. %A Saiz Ede, A. %A Wang, D. %A Gibbons, F. %A Gordon, P. M. %A Sensen, C. W. %A Carrasco, J. M. %A Fernandez, J. M. %A Shen, L. %A Links, M. %A Ng, M. %A Opushneva, N. %A Neerincx, P. B. %A Leunissen, J. A. %A Ernst, R. %A Twigger, S. %A Usadel, B. %A Good, B. %A Wong, Y. %A Stein, L. %A Crosby, W. %A Karlsson, J. %A Royo, R. %A Parraga, I. %A Ramirez, S. %A Gelpi, J. L. %A Trelles, O. %A Pisano, D. G. %A Jimenez, N. %A Kerhornou, A. %A Rosset, R. %A Zamacola, L. %A Tarraga, J. %A Huerta-Cepas, J. %A Carazo, J. M. %A Dopazo, J. %A R. Guigo %A Navarro, A. %A Orozco, M. %A Valencia, A. %A Claros, M. G. %A Perez, A. J. %A Aldana, J. %A Rojano, M. M. %A Fernandez-Santa Cruz, R. %A Navas, I. %A Schiltz, G. %A Farmer, A. %A Gessler, D. %A Schoof, H. %A Groscurth, A. %K Computational Biology/*methods *Database Management Systems *Databases %K Factual Information Storage and Retrieval/*methods *Internet *Programming Languages Systems Integration %X

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/.

%B Brief Bioinform %V 9 %P 220-31 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18238804 %0 Journal Article %J Nucleic Acids Res %D 2008 %T Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases %A Reumers, J. %A L. Conde %A Medina, Ignacio %A Maurer-Stroh, S. %A Van Durme, J. %A Dopazo, J. %A Rousseau, F. %A Schymkowitz, J. %K Amino Acid Substitution Animals *Databases %K Genetic Genetic Diseases %K Inborn/genetics HSP70 Heat-Shock Proteins/metabolism Humans Internet Mice MicroRNAs/metabolism *Mutation *Polymorphism %K Single Nucleotide Proteins/chemistry/genetics RNA Splice Sites Rats Transcription Factors/metabolism %X

Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments. The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations. In addition, SNPeffect now contains predictions of Tango2: an improved aggregation detector, and Waltz: a novel predictor of amyloid-forming sequences, as well as improved predictors for regions that are recognized by the Hsp70 family of chaperones. The new PupaSuite version incorporates predictions for SNPs in silencers and miRNAs including their targets, as well as additional methods for predicting SNPs in TFBSs and splice sites. Also predictions for mouse and rat genomes have been added. In addition, a PupaSuite web service has been developed to enable data access, programmatically. The combined database holds annotations for 4,965,073 regulatory as well as 133,505 coding human SNPs and 14,935 disease mutations, and phenotypic descriptions of 43,797 human proteins and is accessible via http://snpeffect.vib.be and http://pupasuite.bioinfo.cipf.es/.

%B Nucleic Acids Res %V 36 %P D825-9 %G eng %U http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D825 %0 Journal Article %J Nucleic Acids Res %D 2008 %T Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. %A Reumers, Joke %A Conde, Lucia %A Medina, Ignacio %A Maurer-Stroh, Sebastian %A Van Durme, Joost %A Dopazo, Joaquin %A Rousseau, Frederic %A Schymkowitz, Joost %K Amino Acid Substitution %K Animals %K Databases, Genetic %K Genetic Diseases, Inborn %K HSP70 Heat-Shock Proteins %K Humans %K Internet %K Mice %K MicroRNAs %K mutation %K Polymorphism, Single Nucleotide %K Proteins %K Rats %K RNA Splice Sites %K Transcription Factors %X

Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutation and polymorphism is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments. The SNPeffect and PupaSuite databases are now synchronized to deliver annotations for both non-coding and coding SNP, as well as annotations for the SwissProt set of human disease mutations. In addition, SNPeffect now contains predictions of Tango2: an improved aggregation detector, and Waltz: a novel predictor of amyloid-forming sequences, as well as improved predictors for regions that are recognized by the Hsp70 family of chaperones. The new PupaSuite version incorporates predictions for SNPs in silencers and miRNAs including their targets, as well as additional methods for predicting SNPs in TFBSs and splice sites. Also predictions for mouse and rat genomes have been added. In addition, a PupaSuite web service has been developed to enable data access, programmatically. The combined database holds annotations for 4,965,073 regulatory as well as 133,505 coding human SNPs and 14,935 disease mutations, and phenotypic descriptions of 43,797 human proteins and is accessible via http://snpeffect.vib.be and http://pupasuite.bioinfo.cipf.es/.

%B Nucleic Acids Res %V 36 %P D825-9 %8 2008 Jan %G eng %N Database issue %1 https://www.ncbi.nlm.nih.gov/pubmed/18086700?dopt=Abstract %R 10.1093/nar/gkm979 %0 Journal Article %J Nat Genet %D 2008 %T SNP and haplotype mapping for genetic analysis in the rat. %A Saar, Kathrin %A Beck, Alfred %A Bihoreau, Marie-Thérèse %A Birney, Ewan %A Brocklebank, Denise %A Chen, Yuan %A Cuppen, Edwin %A Demonchy, Stephanie %A Dopazo, Joaquin %A Flicek, Paul %A Foglio, Mario %A Fujiyama, Asao %A Gut, Ivo G %A Gauguier, Dominique %A Guigó, Roderic %A Guryev, Victor %A Heinig, Matthias %A Hummel, Oliver %A Jahn, Niels %A Klages, Sven %A Kren, Vladimir %A Kube, Michael %A Kuhl, Heiner %A Kuramoto, Takashi %A Kuroki, Yoko %A Lechner, Doris %A Lee, Young-Ae %A Lopez-Bigas, Nuria %A Lathrop, G Mark %A Mashimo, Tomoji %A Medina, Ignacio %A Mott, Richard %A Patone, Giannino %A Perrier-Cornet, Jeanne-Antide %A Platzer, Matthias %A Pravenec, Michal %A Reinhardt, Richard %A Sakaki, Yoshiyuki %A Schilhabel, Markus %A Schulz, Herbert %A Serikawa, Tadao %A Shikhagaie, Medya %A Tatsumoto, Shouji %A Taudien, Stefan %A Toyoda, Atsushi %A Voigt, Birger %A Zelenika, Diana %A Zimdahl, Heike %A Hubner, Norbert %K Animals %K Chromosome Mapping %K Databases, Genetic %K Genome %K Haplotypes %K Linkage Disequilibrium %K Phylogeny %K Polymorphism, Single Nucleotide %K Quantitative Trait Loci %K Rats %K Rats, Inbred Strains %K Recombination, Genetic %X

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.

%B Nat Genet %V 40 %P 560-6 %8 2008 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/18443594?dopt=Abstract %R 10.1038/ng.124 %0 Journal Article %J Nat Genet %D 2008 %T SNP and haplotype mapping for genetic analysis in the rat %A K. Saar %A A. Beck %A M. T. Bihoreau %A E. Birney %A D. Brocklebank %A Y. Chen %A E. Cuppen %A S. Demonchy %A Dopazo, J. %A P. Flicek %A M. Foglio %A A. Fujiyama %A I. G. Gut %A D. Gauguier %A R. Guigo %A V. Guryev %A M. Heinig %A O. Hummel %A N. Jahn %A S. Klages %A V. Kren %A M. Kube %A H. Kuhl %A Kuramoto, T. %A Kuroki, Y. %A Lechner, D. %A Lee, Y. A. %A Lopez-Bigas, N. %A Lathrop, G. M. %A Mashimo, T. %A Medina, Ignacio %A Mott, R. %A Patone, G. %A Perrier-Cornet, J. A. %A Platzer, M. %A Pravenec, M. %A Reinhardt, R. %A Sakaki, Y. %A Schilhabel, M. %A Schulz, H. %A Serikawa, T. %A Shikhagaie, M. %A Tatsumoto, S. %A Taudien, S. %A Toyoda, A. %A Voigt, B. %A Zelenika, D. %A Zimdahl, H. %A Hubner, N. %K Animals Chromosome Mapping *Databases %K Genetic %K Genetic Genome *Haplotypes Linkage Disequilibrium Phylogeny *Polymorphism %K Inbred Strains/*genetics Recombination %K Single Nucleotide *Quantitative Trait Loci Rats/*genetics Rats %X

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.

%B Nat Genet %V 40 %P 560-6 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18443594 %0 Journal Article %J Mol Vis %D 2008 %T Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush %A Agudo, M. %A Perez-Marin, M. C. %A Lonngren, U. %A Sobrado, P. %A A. Conesa %A Canovas, I. %A Salinas-Navarro, M. %A Miralles-Imperial, J. %A Hallbook, F. %A Vidal-Sanz, M. %K Animals Cell Death Cluster Analysis Female *Gene Expression Profiling Gene Expression Regulation *Nerve Crush Optic Nerve/*metabolism/*pathology Optic Nerve Injuries/*genetics Rats Rats %K Sprague-Dawley Reproducibility of Results Retina/*metabolism/*pathology Time Factors %X 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. %B Mol Vis %V 14 %P 1050-63 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18552980 %0 Journal Article %J BMC Genomics %D 2007 %T Evidence for systems-level molecular mechanisms of tumorigenesis. %A Hernández, Pilar %A Huerta-Cepas, Jaime %A Montaner, David %A Al-Shahrour, Fátima %A Valls, Joan %A Gómez, Laia %A Capellà, Gabriel %A Dopazo, Joaquin %A Pujana, Miguel Angel %K Cell Transformation, Neoplastic %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Humans %K Male %K Models, Biological %K Models, Genetic %K Models, Statistical %K Neoplasm Proteins %K Neoplasms %K Prostatic Neoplasms %K Protein Interaction Mapping %K RNA, Messenger %K Signal Transduction %K Systems biology %X

BACKGROUND: Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth.

RESULTS: Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis.

CONCLUSION: Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

%B BMC Genomics %V 8 %P 185 %8 2007 Jun 20 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/17584915?dopt=Abstract %R 10.1186/1471-2164-8-185 %0 Journal Article %J BMC Genomics %D 2007 %T Evidence for systems-level molecular mechanisms of tumorigenesis %A Hernandez, P. %A Huerta-Cepas, J. %A Montaner, D. %A Fatima Al-Shahrour %A Valls, J. %A Gomez, L. %A Capella, G. %A Dopazo, J. %A Pujana, M. A. %K *Cell Transformation %K Biological Models %K Genetic Models %K Messenger/metabolism Signal Transduction Systems Biology %K Neoplastic *Gene Expression Profiling *Gene Expression Regulation %K Neoplastic Humans Male Models %K Statistical Neoplasm Proteins/*physiology Neoplasms/etiology/*genetics Prostatic Neoplasms/genetics Protein Interaction Mapping RNA %X BACKGROUND: Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. RESULTS: Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. CONCLUSION: Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins. %B BMC Genomics %V 8 %P 185 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17584915 %0 Journal Article %J BMC Genomics %D 2007 %T Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences %A Rico, D. %A Vaquerizas, J. M. %A H. Dopazo %A Bosca, L. %K Animals Base Sequence Conserved Sequence Enhancer Elements %K Genetic *Evolution %K Genetic Response Elements Species Specificity %K Molecular Humans Inflammation/metabolism Interferon-gamma/metabolism Mice NF-kappa B/metabolism Nitric Oxide Synthase Type II/*genetics *Promoter Regions %X BACKGROUND: The majority of the genes involved in the inflammatory response are highly conserved in mammals. These genes are not significantly expressed under normal conditions and are mainly regulated at the transcription and prost-transcriptional level. Transcription from the promoters of these genes is very dependent on NF-kappaB activation, which integrates the response to diverse extracellular stresses. However, in spite of the high conservation of the pattern of promoter regulation in kappaB-regulated genes, there is inter-species diversity in some genes. One example is nitric oxide synthase 2 (NOS-2), which exhibits a species-specific pattern of expression in response to infection or pro-inflammatory challenge. RESULTS: We have conducted a comparative genomic analysis of NOS-2 with different bioinformatic approaches. This analysis shows that in the NOS-2 gene promoter the position and the evolutionary divergence of some conserved regions are different in rodents and non-rodent mammals, and in particular in primates. Two not previously described distal regions in rodents that are similar to the unique upstream region responsible of the NF-kappaB activation of NOS-2 in humans are fragmented and translocated to different locations in the rodent promoters. The rodent sequences moreover lack the functional kappaB sites and IFN-gamma response sites present in the homologous human, rhesus monkey and chimpanzee regions. The absence of kappaB binding in these regions was confirmed by electrophoretic mobility shift assays. CONCLUSION: The data presented reveal divergence between rodents and other mammals in the location and functionality of conserved regions of the NOS-2 promoter containing NF-kappaB and IFN-gamma response elements. %B BMC Genomics %V 8 %P 271 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17686182 %0 Book Section %B Microarray Technology Through Applications %D 2007 %T Microarray Technology in Agricultural Research %A A. Conesa %A J. Forment %A J. Gadea %A van Dijk, J. %K babelomics %B Microarray Technology Through Applications %I F. Falciani. Publisher: Taylor and Francis Group %P 173-209 %G eng %0 Journal Article %J Eukaryot Cell %D 2007 %T Spatial differentiation in the vegetative mycelium of Aspergillus niger %A Levin, A. M. %A de Vries, R. P. %A A. Conesa %A de Bekker, C. %A Talon, M. %A Menke, H. H. %A van Peij, N. N. %A Wosten, H. A. %K Aspergillus niger/*metabolism Cell Wall/metabolism Fungal Proteins/metabolism *Gene Expression Regulation %K Biological Mycelium/*metabolism Oligonucleotide Array Sequence Analysis RNA %K Fungal Genes %K Fungal Genome %K Fungal Glucans/chemistry Maltose/chemistry Models %K Fungal Time Factors Trans-Activators/metabolism Xylose/chemistry %X 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. %B Eukaryot Cell %V 6 %P 2311-22 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17951513 %0 Journal Article %J Nucleic Acids Res %D 2006 %T BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments %A Fatima Al-Shahrour %A Minguez, P. %A Tarraga, J. %A Montaner, D. %A Alloza, E. %A Vaquerizas, J. M. %A L. Conde %A Blaschke, C. %A Vera, J. %A Dopazo, J. %K babelomics %K functional profiling %X

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.

%B Nucleic Acids Res %V 34 %P W472-6 %G eng %U http://nar.oxfordjournals.org/content/34/suppl_2/W472.long %0 Journal Article %J BMC Genomics %D 2006 %T Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions %A Goni, J. R. %A Vaquerizas, J. M. %A Dopazo, J. %A Orozco, M. %K Animals Base Sequence Computational Biology DNA/chemistry/*genetics/*metabolism Genome %K Genetic/genetics Regulatory Sequences %K Human/genetics Humans Mice Nucleic Acid Conformation Nucleotides/genetics Oligonucleotides/chemistry/*genetics/*metabolism Promoter Regions %K Nucleic Acid/*genetics Transcription Factors/metabolism %X BACKGROUND: DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions. RESULTS: Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome. CONCLUSION: Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separators" between protein-recognition sites in the promoter region. %B BMC Genomics %V 7 %P 63 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16566817 %0 Journal Article %J Nucleic Acids Res %D 2006 %T Next station in microarray data analysis: GEPAS %A Montaner, D. %A Tarraga, J. %A Huerta-Cepas, J. %A Burguet, J. %A Vaquerizas, J. M. %A L. Conde %A Minguez, P. %A Vera, J. %A Mukherjee, S. %A Valls, J. %A Pujana, M. A. %A Alloza, E. %A Herrero, J. %A Fatima Al-Shahrour %A Dopazo, J. %K gepas %K microarray data analysis %X

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

%B Nucleic Acids Res %V 34 %P W486-91 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845056 %0 Journal Article %J Biol Direct %D 2006 %T Origin and evolution of the peroxisomal proteome %A Gabaldón, T. %A B. Snel %A van Zimmeren, F. %A Hemrika, W. %A Tabak, H. %A M. A. Huynen %X BACKGROUND: Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes. RESULTS : Our results show that most peroxisomal proteins (39-58%) are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13-18%), consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway. CONCLUSION: Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum. REVIEWERS: This article was reviewed by Arcady Mushegian, Gaspar Jekely and John Logsdon. OPEN PEER REVIEW: Reviewed by Arcady Mushegian, Gaspar Jekely and John Logsdon. For the full reviews, please go to the Reviewers’ comments section. %B Biol Direct %V 1 %P 8 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16556314 %0 Journal Article %J Nucleic Acids Res %D 2006 %T PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes %A L. Conde %A Vaquerizas, J. M. %A H. Dopazo %A Arbiza, L. %A Reumers, J. %A Rousseau, F. %A Schymkowitz, J. %A Dopazo, J. %K Algorithms Computer Graphics Databases %K Molecular Genotype Haplotypes Internet Linkage Disequilibrium *Polymorphism %K Nucleic Acid Evolution %K Single Nucleotide *Software User-Computer Interface %X

We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user’s data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupasnp.org.

%B Nucleic Acids Res %V 34 %P W621-5 %G eng %U http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621 %0 Journal Article %J Nature %D 2005 %T An anaerobic mitochondrion that produces hydrogen %A Boxma, B. %A de Graaf, R. M. %A van der Staay, G. W. %A van Alen, T. A. %A Ricard, G. %A Gabaldón, T. %A van Hoek, A. H. %A Moon-van der Staay, S. Y. %A Koopman, W. J. %A van Hellemond, J. J. %A Tielens, A. G. %A Friedrich, T. %A Veenhuis, M. %A M. A. Huynen %A Hackstein, J. H. %K *Anaerobiosis Animals Ciliophora/*cytology/genetics/*metabolism/ultrastructure Cockroaches/parasitology DNA %K Mitochondrial/genetics Electron Transport Electron Transport Complex I/antagonists & inhibitors/metabolism Genome Glucose/metabolism Hydrogen/*metabolism Mitochondria/enzymology/genetics/*metabolism/ultrastructure Molecular Sequence Data Open Reading Fra %X Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product–biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes. %B Nature %V 434 %P 74-9 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15744302 %0 Journal Article %J Nucleic Acids Res %D 2005 %T BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments %A Fatima Al-Shahrour %A Minguez, P. %A Vaquerizas, J. M. %A L. Conde %A Dopazo, J. %K babelomics %K functional profiling %X

We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22,000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at http://www.babelomics.org.

%B Nucleic Acids Res %V 33 %P W460-4 %G eng %U http://nar.oxfordjournals.org/content/33/suppl_2/W460.long %0 Journal Article %J Plant Mol Biol %D 2005 %T Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies %A J. Forment %A J. Gadea %A Huerta, L. %A Abizanda, L. %A Agusti, J. %A Alamar, S. %A Alos, E. %A Andres, F. %A Arribas, R. %A Beltran, J. P. %A Berbel, A. %A Blazquez, M. A. %A Brumos, J. %A Canas, L. A. %A Cercos, M. %A Colmenero-Flores, J. M. %A A. Conesa %A Estables, B. %A Gandia, M. %A Garcia-Martinez, J. L. %A Gimeno, J. %A Gisbert, A. %A Gomez, G. %A Gonzalez-Candelas, L. %A Granell, A. %A Guerri, J. %A Lafuente, M. T. %A Madueno, F. %A Marcos, J. F. %A Marques, M. C. %A Martinez, F. %A Martinez-Godoy, M. A. %A Miralles, S. %A Moreno, P. %A Navarro, L. %A Pallas, V. %A Perez-Amador, M. A. %A Perez-Valle, J. %A Pons, C. %A Rodrigo, I. %A Rodriguez, P. L. %A Royo, C. %A Serrano, R. %A Soler, G. %A Tadeo, F. %A Talon, M. %A Terol, J. %A Trenor, M. %A Vaello, L. %A Vicente, O. %A Vidal, Ch %A Zacarias, L. %A Conejero, V. %K Citrus/*genetics DNA %K Complementary/chemistry/genetics *Expressed Sequence Tags Gene Expression Profiling Gene Library *Genome %K DNA %K Plant Genomics/*methods Molecular Sequence Data Oligonucleotide Array Sequence Analysis/*methods RNA %K Plant/genetics/metabolism Reproducibility of Results Sequence Analysis %X 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. %B Plant Mol Biol %V 57 %P 375-91 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128 %0 Journal Article %J Nucleic Acids Res %D 2005 %T GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data %A Vaquerizas, J. M. %A L. Conde %A Yankilevich, P. %A Cabezon, A. %A Minguez, P. %A Diaz-Uriarte, R. %A Fatima Al-Shahrour %A Herrero, J. %A Dopazo, J. %K gepas %K microarray data analysis %X

The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76,000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

%B Nucleic Acids Res %V 33 %P W616-20 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980548 %0 Journal Article %J Nucleic Acids Res %D 2005 %T HCAD, closing the gap between breakpoints and genes %A Hoffmann, R. %A Dopazo, J. %A Cigudosa, J. C. %A Valencia, A. %K *Chromosome Breakage Chromosome Disorders/diagnosis/*genetics *Databases %K Genetic Genes *Genetic Predisposition to Disease Humans PubMed Systems Integration %X Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information system that mines the scientific literature and generates textual and comprehensive information on all human breakpoints. We show that the statistical analysis of this textual information and its combination with genomic data can identify genes directly involved in DNA rearrangements. The Human Chromosome Aberration Database (HCAD) is publicly accessible at http://www.pdg.cnb.uam.es/UniPub/HCAD/. %B Nucleic Acids Res %V 33 %P D511-3 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15608250 %0 Journal Article %J Bioinformatics %D 2005 %T Highly specific and accurate selection of siRNAs for high-throughput functional assays %A J. Santoyo %A Vaquerizas, J. M. %A Dopazo, J. %K *Algorithms Base Sequence *Gene Silencing Molecular Sequence Data RNA %K RNA/*methods *Software *User-Computer Interface %K Small Interfering/*genetics Sequence Alignment/*methods Sequence Analysis %X MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es. %B Bioinformatics %V 21 %P 1376-82 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15591357 %0 Journal Article %J Clin Cancer Res %D 2005 %T A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation %A Alvarez, S. %A Diaz-Uriarte, R. %A Osorio, A. %A Barroso, A. %A Melchor, L. %A Paz, M. F. %A Honrado, E. %A Rodriguez, R. %A Urioste, M. %A Valle, L. %A Diez, O. %A Cigudosa, J. C. %A Dopazo, J. %A Esteller, M. %A Benitez, J. %K BRCA1 Protein/*genetics BRCA2 Protein/*genetics Breast Neoplasms/*genetics/pathology Chromosomes %K Genetic/*genetics %K Human %K Human Humans Male Mutation Nucleic Acid Hybridization/methods Promoter Regions %K Pair 12/genetics Chromosomes %K Pair 15/genetics Chromosomes %K Pair 18/genetics Chromosomes %K Pair 2/genetics Chromosomes %K Pair 8/genetics *DNA Methylation Female Genome %X The genetic changes underlying in the development and progression of familial breast cancer are poorly understood. To identify a somatic genetic signature of tumor progression for each familial group, BRCA1, BRCA2, and non-BRCA1/BRCA2 (BRCAX) tumors, by high-resolution comparative genomic hybridization, we have analyzed 77 tumors previously characterized for BRCA1 and BRCA2 germ line mutations. Based on a combination of the somatic genetic changes observed at the six most different chromosomal regions and the status of the estrogen receptor, we developed using random forests a molecular classifier, which assigns to a given tumor a probability to belong either to the BRCA1 or to the BRCA2 class. Because 76.5% (26 of 34) of the BRCAX cases were classified with our predictor to the BRCA1 class with a probability of >50%, we analyzed the BRCA1 promoter region for aberrant methylation in all the BRCAX cases. We found that 15 of the 34 BRCAX analyzed tumors had hypermethylation of the BRCA1 gene. When we considered the predictor, we observed that all the cases with this epigenetic event were assigned to the BRCA1 class with a probability of >50%. Interestingly, 84.6% of the cases (11 of 13) assigned to the BRCA1 class with a probability >80% had an aberrant methylation of the BRCA1 promoter. This fact suggests that somatic BRCA1 inactivation could modify the profile of tumor progression in most of the BRCAX cases. %B Clin Cancer Res %V 11 %P 1146-53 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15709182 %0 Journal Article %J Nucleic Acids Res %D 2005 %T PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes %A L. Conde %A Vaquerizas, J. M. %A Ferrer-Costa, C. %A de la Cruz, X. %A Orozco, M. %A Dopazo, J. %K Computer Graphics Genes *Genetic Predisposition to Disease Genotype Internet Phenotype *Polymorphism %K Single Nucleotide *Software User-Computer Interface %X We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org. %B Nucleic Acids Res %V 33 %P W501-5 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980522 %0 Book Section %B Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya %D 2005 %T Salinibacter ruber: genomics and biogeography %A Antón, J %A Peña, A %A Valens, M %A Santos, F %A Glöckner, F.O %A Bauer, M %A Dopazo, J. %A Herrero, J. %A Rosselló-Mora, R %A Amann, R %B Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya %I Nina Gunde-Cimerman, Ana Plemenitas, and Aharon Oren. Kluwer Academic Publishers %C Dordrecht, Netherlands %V 9 %P 257-266 %G eng %0 Journal Article %J Bioinformatics %D 2004 %T DNMAD: web-based diagnosis and normalization for microarray data %A Vaquerizas, J. M. %A Dopazo, J. %A Diaz-Uriarte, R. %K Algorithms Database Management Systems Gene Expression Profiling/*methods/standards Information Storage and Retrieval/*methods *Internet Oligonucleotide Array Sequence Analysis/*methods/standards Sequence Alignment/methods Sequence Analysis %K DNA/*methods *Software *User-Computer Interface %X SUMMARY: We present a web server for Diagnosis and Normalization of MicroArray Data (DNMAD). DNMAD includes several common data transformations such as spatial and global robust local regression or multiple slide normalization, and allows for detecting several kinds of errors that result from the manipulation and the image analysis of the arrays. This tool offers a user-friendly interface, and is completely integrated within the Gene Expression Pattern Analysis Suite (GEPAS). AVAILABILITY: The tool is accessible on-line at http://dnmad.bioinfo.cnio.es. %B Bioinformatics %V 20 %P 3656-8 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15247094 %0 Journal Article %J Nucleic Acids Res %D 2004 %T New challenges in gene expression data analysis and the extended GEPAS %A Herrero, J. %A Vaquerizas, J. M. %A Fatima Al-Shahrour %A L. Conde %A A. Mateos %A Diaz-Uriarte, J. S. %A Dopazo, J. %K gepas %K microarray data analysis %X

Since the first papers published in the late nineties, including, for the first time, a comprehensive analysis of microarray data, the number of questions that have been addressed through this technique have both increased and diversified. Initially, interest focussed on genes coexpressing across sets of experimental conditions, implying, essentially, the use of clustering techniques. Recently, however, interest has focussed more on finding genes differentially expressed among distinct classes of experiments, or correlated to diverse clinical outcomes, as well as in building predictors. In addition to this, the availability of accurate genomic data and the recent implementation of CGH arrays has made mapping expression and genomic data on the chromosomes possible. There is also a clear demand for methods that allow the automatic transfer of biological information to the results of microarray experiments. Different initiatives, such as the Gene Ontology (GO) consortium, pathways databases, protein functional motifs, etc., provide curated annotations for genes. Whereas many resources on the web focus mainly on clustering methods, GEPAS has evolved to cope with the aforementioned new challenges that have recently arisen in the field of microarray data analysis. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://gepas.bioinfo.cnio.es.

%B Nucleic Acids Res %V 32 %P W485-91 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215434 %0 Journal Article %J EMBO Rep %D 2004 %T Perceptions about postdocs %A Vella, F. %A Mietchen, D. %A Gabaldón, T. %K Europe *Fellowships and Scholarships *Research Personnel %B EMBO Rep %V 5 %P 1104 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15577920 %0 Journal Article %J Nucleic Acids Res %D 2004 %T PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level %A L. Conde %A Vaquerizas, J. M. %A J. Santoyo %A Fatima Al-Shahrour %A Ruiz-Llorente, S. %A M. Robledo %A Dopazo, J. %K Amino Acid Substitution Binding Sites Humans Internet Phenotype *Polymorphism %K Genetic %K Single Nucleotide RNA Splicing *Software Transcription Factors/metabolism *Transcription %X We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es. %B Nucleic Acids Res %V 32 %P W242-8 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15215388 %0 Journal Article %J Nucleic Acids Res %D 2003 %T EVA: Evaluation of protein structure prediction servers %A Koh, I. Y. %A Eyrich, V. A. %A M. A. Marti-Renom %A Przybylski, D. %A Madhusudhan, M. S. %A Eswar, N. %A Grana, O. %A Pazos, F. %A Valencia, A. %A Sali, A. %A Rost, B. %K Automation Databases %K Protein %K Protein Internet *Protein Conformation Protein Folding Protein Structure %K Protein Structural Homology %K Secondary Proteins/chemistry Reproducibility of Results *Sequence Analysis %X EVA (http://cubic.bioc.columbia.edu/eva/) is a web server for evaluation of the accuracy of automated protein structure prediction methods. The evaluation is updated automatically each week, to cope with the large number of existing prediction servers and the constant changes in the prediction methods. EVA currently assesses servers for secondary structure prediction, contact prediction, comparative protein structure modelling and threading/fold recognition. Every day, sequences of newly available protein structures in the Protein Data Bank (PDB) are sent to the servers and their predictions are collected. The predictions are then compared to the experimental structures once a week; the results are published on the EVA web pages. Over time, EVA has accumulated prediction results for a large number of proteins, ranging from hundreds to thousands, depending on the prediction method. This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods. %B Nucleic Acids Res %V 31 %P 3311-5 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824315 %0 Journal Article %J Nucleic Acids Res %D 2003 %T GEPAS: A web-based resource for microarray gene expression data analysis %A Herrero, J. %A Fatima Al-Shahrour %A Diaz-Uriarte, R. %A A. Mateos %A Vaquerizas, J. M. %A J. Santoyo %A Dopazo, J. %K gepas %K microarray data analysis %X

We present a web-based pipeline for microarray gene expression profile analysis, GEPAS, which stands for Gene Expression Profile Analysis Suite (http://gepas.bioinfo.cnio.es). GEPAS is composed of different interconnected modules which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering (which include some of the most popular methods as well as home made algorithms) and several tests for differential gene expression among different classes, continuous variables or survival analysis. A multiple purpose tool for data mining, based on Gene Ontology, is also linked to the tools, which constitutes a very convenient way of analysing clustering results. On-line tutorials are available from our main web server (http://bioinfo.cnio.es).

%B Nucleic Acids Res %V 31 %P 3461-7 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824345 %0 Journal Article %J J Biotechnol %D 2002 %T Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction %A J. Tamames %A Clark, D. %A Herrero, J. %A Dopazo, J. %A Blaschke, C. %A Fernandez, J. M. %A Oliveros, J. C. %A Valencia, A. %K Abstracting and Indexing as Topic/methods *Cluster Analysis *Database Management Systems Databases %K Computer-Assisted/methods Information Storage and Retrieval/*methods Internet Medline National Library of Medicine (U.S.) Oligonucleotide Array Sequence Analysis/*methods United States %K Genetic Gene Expression Gene Expression Profiling/*methods Image Processing %X Expression arrays facilitate the monitoring of changes in the expression patterns of large collections of genes. The analysis of expression array data has become a computationally-intensive task that requires the development of bioinformatics technology for a number of key stages in the process, such as image analysis, database storage, gene clustering and information extraction. Here, we review the current trends in each of these areas, with particular emphasis on the development of the related technology being carried out within our groups. %B J Biotechnol %V 98 %P 269-83 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12141992 %0 Journal Article %J Appl Environ Microbiol %D 2002 %T Calnexin overexpression increases manganese peroxidase production in Aspergillus niger %A A. Conesa %A Jeenes, D. %A Archer, D. B. %A van den Hondel, C. A. %A Punt, P. J. %K Aspergillus niger/*enzymology/genetics Calcium-Binding Proteins/*metabolism Calnexin Culture Media *Fungal Proteins HSP70 Heat-Shock Proteins/metabolism Heme/metabolism Peroxidases/*biosynthesis/genetics Phanerochaete/enzymology/genetics Transformation %K Genetic %X Heme-containing peroxidases from white rot basidiomycetes, in contrast to most proteins of fungal origin, are poorly produced in industrial filamentous fungal strains. Factors limiting peroxidase production are believed to operate at the posttranslational level. In particular, insufficient availability of the prosthetic group which is required for peroxidase biosynthesis has been proposed to be an important bottleneck. In this work, we analyzed the role of two components of the secretion pathway, the chaperones calnexin and binding protein (BiP), in the production of a fungal peroxidase. Expression of the Phanerochaete chrysosporium manganese peroxidase (MnP) in Aspergillus niger resulted in an increase in the expression level of the clxA and bipA genes. In a heme-supplemented medium, where MnP was shown to be overproduced to higher levels, induction of clxA and bipA was also higher. Overexpression of these two chaperones in an MnP-producing strain was analyzed for its effect on MnP production. Whereas bipA overexpression seriously reduced MnP production, overexpression of calnexin resulted in a four- to fivefold increase in the extracellular MnP levels. However, when additional heme was provided in the culture medium, calnexin overexpression had no synergistic effect on MnP production. The possible function of these two chaperones in MnP maturation and production is discussed. %B Appl Environ Microbiol %V 68 %P 846-51 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11823227 %0 Journal Article %J Trends Biotechnol %D 2002 %T Filamentous fungi as cell factories for heterologous protein production %A Punt, P. J. %A van Biezen, N. %A A. Conesa %A Albers, A. %A Mangnus, J. %A van den Hondel, C. %K Fermentation/genetics/physiology Fungi/*genetics/*metabolism Humans Interleukin-6/analysis/*biosynthesis/genetics Peroxidases/analysis/*biosynthesis/genetics Protein Conformation Recombinant Proteins/analysis/*biosynthesis/genetics %X Filamentous fungi have been used as sources of metabolites and enzymes for centuries. For about two decades, molecular genetic tools have enabled us to use these organisms to express extra copies of both endogenous and exogenous genes. This review of current practice reveals that molecular tools have enabled several new developments. But it has been process development that has driven the final breakthrough to achieving commercially relevant quantities of protein. Recent research into gene expression in filamentous fungi has explored their wealth of genetic diversity with a view to exploiting them as expression hosts and as a source of new genes. Inevitably, the progress in the ’genomics’ technology will further develop high-throughput technologies for these organisms. %B Trends Biotechnol %V 20 %P 200-6 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11943375 %0 Journal Article %J J Biotechnol %D 2002 %T Fungal peroxidases: molecular aspects and applications %A A. Conesa %A Punt, P. J. %A van den Hondel, C. A. %K Amino Acid Sequence Binding Sites Biotechnology Catalysis Fungi/*enzymology Molecular Sequence Data Peroxidases/chemistry/*genetics/metabolism Recombinant Proteins Sequence Homology Substrate Specificity %X Peroxidases are oxidoreductases that utilize hydrogen peroxide to catalyze oxidative reactions. A large number of peroxidases have been identified in fungal species and are being characterized at the molecular level. In this manuscript we review the current knowledge on the molecular aspects of this type of enzymes. We present an overview of the research efforts undertaken in deciphering the structural basis of the catalytic properties of fungal peroxidases and discuss molecular genetics and protein homology aspects of this enzyme class. Finally, we summarize the potential biotechnological applications of these enzymes and evaluate recent advances on their expression in heterologous systems for production purposes. %B J Biotechnol %V 93 %P 143-58 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11738721 %0 Journal Article %J Am J Pathol %D 2002 %T Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma %A Tracey, L. %A Villuendas, R. %A Ortiz, P. %A Dopazo, A. %A Spiteri, I. %A Lombardia, L. %A Rodriguez-Peralto, J. L. %A Fernandez-Herrera, J. %A Hernandez, A. %A Fraga, J. %A Dominguez, O. %A Herrero, J. %A Alonso, M. A. %A Dopazo, J. %A Piris, M. A. %K Antineoplastic Agents/*pharmacology/therapeutic use Carrier Proteins/biosynthesis/genetics DNA-Binding Proteins/biosynthesis/genetics Drug Resistance %K Biological Oligonucleotide Array Sequence Analysis RNA %K Cultured %K Cutaneous/diagnosis/drug therapy/*genetics/metabolism *Membrane Glycoproteins Models %K Interleukin-1 Reproducibility of Results STAT1 Transcription Factor STAT3 Transcription Factor Trans-Activators/biosynthesis/genetics Tumor Cells %K Neoplasm Gene Expression Profiling *Gene Expression Regulation %K Neoplasm/biosynthesis *Receptors %K Neoplastic Humans Interferon-alpha/*pharmacology/therapeutic use Kinetics Lymphoma %K T-Cell %X 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. %B Am J Pathol %V 161 %P 1825-37 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12414529 %0 Journal Article %J J Immunol %D 2002 %T Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies %A Iverson, G. M. %A Reddel, S. %A Victoria, E. J. %A Cockerill, K. A. %A Wang, Y. X. %A M. A. Marti-Renom %A Sali, A. %A Marquis, D. M. %A Krilis, S. A. %A Linnik, M. D. %K Amino Acid Substitution/genetics Antibodies %K Antibody/genetics Binding %K Antiphospholipid/blood/*metabolism Antibodies %K Competitive/genetics/immunology Enzyme-Linked Immunosorbent Assay/methods Epitopes/analysis/*immunology/metabolism Glycine/genetics Glycoproteins/biosynthesis/*genetics/*immunology/isolation & purification/metabolism Humans Models %K Molecular Peptide Fragments/genetics/immunology/isolation & purification/metabolism *Point Mutation Protein Structure %K Monoclonal/blood/metabolism Antiphospholipid Syndrome/immunology Arginine/genetics *Binding Sites %K Tertiary/genetics Recombinant Proteins/biosynthesis/immunology/isolation & purification/metabolism Static Electricity beta 2-Glycoprotein I %X 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. %B J Immunol %V 169 %P 7097-103 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12471146 %0 Journal Article %J FEBS Lett %D 2001 %T C-terminal propeptide of the Caldariomyces fumago chloroperoxidase: an intramolecular chaperone? %A A. Conesa %A Weelink, G. %A van den Hondel, C. A. %A Punt, P. J. %K Amino Acid Sequence Ascomycota/*enzymology/genetics Aspergillus niger/genetics Base Sequence Chloride Peroxidase/biosynthesis/*chemistry/genetics DNA Primers/genetics Enzyme Precursors/biosynthesis/chemistry/genetics Gene Expression Molecular Chaperones/b %X The Caldariomyces fumago chloroperoxidase (CPO) is synthesised as a 372-aa precursor which undergoes two proteolytic processing events: removal of a 21-aa N-terminal signal peptide and of a 52-aa C-terminal propeptide. The Aspergillus niger expression system developed for CPO was used to get insight into the function of this C-terminal propeptide. A. niger transformants expressing a CPO protein from which the C-terminal propeptide was deleted failed in producing any extracellular CPO activity, although the CPO polypeptide was synthesised. Expression of the full-length gene in an A. niger strain lacking the KEX2-like protease PclA also resulted in the production of CPO cross-reactive material into the culture medium, but no CPO activity. Based on these results, a function of the C-terminal propeptide in CPO maturation is indicated. %B FEBS Lett %V 503 %P 117-20 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11513866 %0 Journal Article %J Bioinformatics %D 2001 %T EVA: continuous automatic evaluation of protein structure prediction servers %A Eyrich, V. A. %A M. A. Marti-Renom %A Przybylski, D. %A Madhusudhan, M. S. %A Fiser, A. %A Pazos, F. %A Valencia, A. %A Sali, A. %A Rost, B. %K Automation Internet *Protein Conformation Proteins/*analysis *Software %X Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu %B Bioinformatics %V 17 %P 1242-3 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11751240 %0 Journal Article %J J Biol Chem %D 2001 %T Expression of the Caldariomyces fumago chloroperoxidase in Aspergillus niger and characterization of the recombinant enzyme %A A. Conesa %A van De Velde, F. %A van Rantwijk, F. %A Sheldon, R. A. %A van den Hondel, C. A. %A Punt, P. J. %K Aspergillus niger/enzymology/genetics Catalysis Chloride Peroxidase/biosynthesis/*genetics Fungal Proteins/biosynthesis/*genetics Recombinant Proteins/biosynthesis/genetics Substrate Specificity %X The Caldariomyces fumago chloroperoxidase was successfully expressed in Aspergillus niger. The recombinant enzyme was produced in the culture medium as an active protein and could be purified by a three-step purification procedure. The catalytic behavior of recombinant chloroperoxidase (rCPO) was studied and compared with that of native CPO. The specific chlorination activity (47 units/nmol) of rCPO and its pH optimum (pH 2.75) were very similar to those of native CPO. rCPO catalyzes the oxidation of various substrates in comparable yields and selectivities to native CPO. Indole was oxidized to 2-oxindole with 99% selectivity and thioanisole to the corresponding R-sulfoxide (enantiomeric excess >98%). Incorporation of (18)O from labeled H(2)18O(2) into the oxidized products was 100% in both cases. %B J Biol Chem %V 276 %P 17635-40 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11278701 %0 Journal Article %J Bioinformatics %D 2001 %T A hierarchical unsupervised growing neural network for clustering gene expression patterns %A Herrero, J. %A Valencia, A. %A Dopazo, J. %K *Algorithms Automatic Data Processing *Gene Expression Profiling *Neural Networks (Computer) *Oligonucleotide Array Sequence Analysis %X MOTIVATION: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226-233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network. RESULTS: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters. Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and that a computable measure of similarity between data items can be used. AVAILABILITY: A server running the program can be found at: http://bioinfo.cnio.es/sotarray. %B Bioinformatics %V 17 %P 126-36 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11238068 %0 Journal Article %J Fungal Genet Biol %D 2001 %T The secretion pathway in filamentous fungi: a biotechnological view %A A. Conesa %A Punt, P. J. %A van Luijk, N. %A van den Hondel, C. A. %K Animals Biotechnology/*methods Fungal Proteins/*genetics/*metabolism Fungi/*genetics/*metabolism Humans Recombinant Proteins/metabolism %X The high capacity of the secretion machinery of filamentous fungi has been widely exploited for the production of homologous and heterologous proteins; however, our knowledge of the fungal secretion pathway is still at an early stage. Most of the knowledge comes from models developed in yeast and higher eukaryotes, which have served as reference for the studies on fungal species. In this review we compile the data accumulated in recent years on the molecular basis of fungal secretion, emphasizing the relevance of these data for the biotechnological use of the fungal cell and indicating how this information has been applied in attempts to create improved production strains. We also present recent emerging approaches that promise to provide answers to fundamental questions on the molecular genetics of the fungal secretory pathway. %B Fungal Genet Biol %V 33 %P 155-71 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11495573