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

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

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

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

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

VL - 22 IS - 1 ER - TY - JOUR T1 - Immunotherapy in nonsmall-cell lung cancer: current status and future prospects for liquid biopsy. JF - Cancer Immunol Immunother Y1 - 2021 A1 - Brozos-Vázquez, Elena María A1 - Díaz-Peña, Roberto A1 - García-González, Jorge A1 - León-Mateos, Luis A1 - Mondelo-Macía, Patricia A1 - Peña-Chilet, Maria A1 - López-López, Rafael KW - Animals KW - Biomarkers, Tumor KW - Carcinoma, Non-Small-Cell Lung KW - Cell-Free Nucleic Acids KW - Exosomes KW - Humans KW - Immunotherapy KW - Liquid Biopsy KW - Lung Neoplasms AB -

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

VL - 70 IS - 5 ER - TY - JOUR T1 - Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. JF - Genes (Basel) Y1 - 2020 A1 - León, Carlos A1 - Garcia-Garcia, Francisco A1 - Llames, Sara A1 - García-Pérez, Eva A1 - Carretero, Marta A1 - Arriba, María Del Carmen A1 - Dopazo, Joaquin A1 - Del Rio, Marcela A1 - Escamez, Maria José A1 - Martínez-Santamaría, Lucía KW - Animals KW - Diabetes Mellitus, Experimental KW - Gene Expression Profiling KW - Gene Expression Regulation KW - Gene ontology KW - Humans KW - Metabolic Networks and Pathways KW - Mice KW - Mice, Nude KW - Microarray Analysis KW - Molecular Sequence Annotation KW - Principal Component Analysis KW - Signal Transduction KW - Skin KW - Skin Transplantation KW - Skin Ulcer KW - Streptozocin KW - Tissue Engineering KW - Transcriptome KW - Transplantation, Heterologous KW - Wound Healing AB -

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

VL - 12 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/33396192?dopt=Abstract ER - TY - JOUR T1 - Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome. JF - Bioinformatics Y1 - 2020 A1 - Casimiro-Soriguer, C S A1 - Rigual, M M A1 - Brokate-Llanos, A M A1 - Muñoz, M J A1 - Garzón, A A1 - Pérez-Pulido, A J A1 - Jimenez, J KW - Animals KW - Caenorhabditis elegans KW - Computational Biology KW - Genome KW - Open Reading Frames KW - Software AB -

MOTIVATION: Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance.

RESULTS: AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes.

AVAILABILITY AND IMPLEMENTATION: AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

VL - 36 IS - 19 U1 - https://www.ncbi.nlm.nih.gov/pubmed/32614398?dopt=Abstract ER - TY - JOUR T1 - The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid. JF - Microb Genom Y1 - 2018 A1 - Rodríguez Hernáez, Javier A1 - Cerón Cucchi, Maria Esperanza A1 - Cravero, Silvio A1 - Martinez, Maria Carolina A1 - Gonzalez, Sergio A1 - Puebla, Andrea A1 - Dopazo, Joaquin A1 - Farber, Marisa A1 - Paniego, Norma A1 - Rivarola, Máximo KW - Animals KW - Butyrivibrio fibrisolvens KW - Cattle KW - Genome, Bacterial KW - Genomics KW - Humans KW - Milk KW - Rumen KW - Sequence Analysis, DNA AB -

Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.

VL - 4 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/30216146?dopt=Abstract ER - TY - JOUR T1 - LRH-1 agonism favours an immune-islet dialogue which protects against diabetes mellitus. JF - Nat Commun Y1 - 2018 A1 - Cobo-Vuilleumier, Nadia A1 - Lorenzo, Petra I A1 - Rodríguez, Noelia García A1 - Herrera Gómez, Irene de Gracia A1 - Fuente-Martin, Esther A1 - López-Noriega, Livia A1 - Mellado-Gil, José Manuel A1 - Romero-Zerbo, Silvana-Yanina A1 - Baquié, Mathurin A1 - Lachaud, Christian Claude A1 - Stifter, Katja A1 - Perdomo, German A1 - Bugliani, Marco A1 - De Tata, Vincenzo A1 - Bosco, Domenico A1 - Parnaud, Geraldine A1 - Pozo, David A1 - Hmadcha, Abdelkrim A1 - Florido, Javier P A1 - Toscano, Miguel G A1 - de Haan, Peter A1 - Schoonjans, Kristina A1 - Sánchez Palazón, Luis A1 - Marchetti, Piero A1 - Schirmbeck, Reinhold A1 - Martín-Montalvo, Alejandro A1 - Meda, Paolo A1 - Soria, Bernat A1 - Bermúdez-Silva, Francisco-Javier A1 - St-Onge, Luc A1 - Gauthier, Benoit R KW - Animals KW - Apoptosis KW - Cell Communication KW - Cell Survival KW - Diabetes Mellitus, Experimental KW - Diabetes Mellitus, Type 2 KW - Female KW - Gene Expression Regulation KW - Humans KW - Hypoglycemic Agents KW - Immunity, Innate KW - insulin KW - Insulin-Secreting Cells KW - Islets of Langerhans KW - Islets of Langerhans Transplantation KW - Macrophages KW - Male KW - Mice KW - Mice, Inbred C57BL KW - Phenalenes KW - Receptors, Cytoplasmic and Nuclear KW - Streptozocin KW - T-Lymphocytes, Regulatory KW - Transplantation, Heterologous AB -

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

VL - 9 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/29662071?dopt=Abstract ER - TY - JOUR T1 - ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. JF - BMC Bioinformatics Y1 - 2017 A1 - Gonzalez, Sergio A1 - Clavijo, Bernardo A1 - Rivarola, Máximo A1 - Moreno, Patricio A1 - Fernandez, Paula A1 - Dopazo, Joaquin A1 - Paniego, Norma KW - Animals KW - Databases, Genetic KW - Gene Expression Profiling KW - High-Throughput Nucleotide Sequencing KW - Internet KW - Sequence Analysis, RNA KW - Transcriptome KW - User-Computer Interface AB -

BACKGROUND: In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species.

RESULTS: We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results.

CONCLUSIONS: ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .

VL - 18 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/28222698?dopt=Abstract ER - TY - JOUR T1 - Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types. JF - Cereb Cortex Y1 - 2017 A1 - Gil-Ibañez, Pilar A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Bernal, Juan A1 - Morte, Beatriz KW - Animals KW - Astrocytes KW - Cells, Cultured KW - Cerebral Cortex KW - Fluorescent Antibody Technique KW - Gene Expression Profiling KW - Mice, 129 Strain KW - Mice, Inbred BALB C KW - Mice, Inbred C57BL KW - Neurons KW - Piperazines KW - Transcriptome KW - Triiodothyronine AB -

Thyroid hormones, thyroxine, and triiodothyronine (T3) are crucial for cerebral cortex development acting through regulation of gene expression. To define the transcriptional program under T3 regulation, we have performed RNA-Seq of T3-treated and untreated primary mouse cerebrocortical cells. The expression of 1145 genes or 7.7% of expressed genes was changed upon T3 addition, of which 371 responded to T3 in the presence of cycloheximide indicating direct transcriptional regulation. The results were compared with available transcriptomic datasets of defined cellular types. In this way, we could identify targets of T3 within genes enriched in astrocytes and neurons, in specific layers including the subplate, and in specific neurons such as prepronociceptin, cholecystokinin, or cortistatin neurons. The subplate and the prepronociceptin neurons appear as potentially major targets of T3 action. T3 upregulates mostly genes related to cell membrane events, such as G-protein signaling, neurotransmission, and ion transport and downregulates genes involved in nuclear events associated with the M phase of cell cycle, such as chromosome organization and segregation. Remarkably, the transcriptomic changes induced by T3 sustain the transition from fetal to adult patterns of gene expression. The results allow defining in molecular terms the elusive role of thyroid hormones on neocortical development.

VL - 27 IS - 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26534908?dopt=Abstract ER - TY - JOUR T1 - Reference genome assessment from a population scale perspective: an accurate profile of variability and noise. JF - Bioinformatics Y1 - 2017 A1 - Carbonell-Caballero, José A1 - Amadoz, Alicia A1 - Alonso, Roberto A1 - Hidalgo, Marta R A1 - Cubuk, Cankut A1 - Conesa, David A1 - López-Quílez, Antonio A1 - Dopazo, Joaquin KW - Animals KW - Genetic Variation KW - Genome KW - Genomics KW - Genotype KW - Humans KW - Models, Statistical KW - Quality Control KW - Reproducibility of Results KW - Software AB -

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

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

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

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

Supplementary information: Supplementary data are available at Bioinformatics online.

VL - 33 UR - https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx482 IS - 22 U1 - https://www.ncbi.nlm.nih.gov/pubmed/28961772?dopt=Abstract ER - TY - JOUR T1 - Dysfunctional mitochondrial fission impairs cell reprogramming. JF - Cell Cycle Y1 - 2016 A1 - Prieto, Javier A1 - León, Marian A1 - Ponsoda, Xavier A1 - Garcia-Garcia, Francisco A1 - Bort, Roque A1 - Serna, Eva A1 - Barneo-Muñoz, Manuela A1 - Palau, Francesc A1 - Dopazo, Joaquin A1 - López-García, Carlos A1 - Torres, Josema KW - Animals KW - Cell Cycle Checkpoints KW - Cellular Reprogramming KW - DNA Damage KW - G2 Phase KW - Gene Knockdown Techniques KW - Mice KW - Mitochondrial Dynamics KW - Mitosis KW - Nerve Tissue Proteins KW - Pluripotent Stem Cells KW - Transcription Factors AB -

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

VL - 15 IS - 23 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27753531?dopt=Abstract ER - TY - JOUR T1 - Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa. JF - Sci Rep Y1 - 2016 A1 - Corton, M A1 - Avila-Fernández, A A1 - Campello, L A1 - Sánchez, M A1 - Benavides, B A1 - López-Molina, M I A1 - Fernández-Sánchez, L A1 - Sánchez-Alcudia, R A1 - da Silva, L R J A1 - Reyes, N A1 - Martín-Garrido, E A1 - Zurita, O A1 - Fernández-San José, P A1 - Pérez-Carro, R A1 - García-García, F A1 - Dopazo, J A1 - García-Sandoval, B A1 - Cuenca, N A1 - Ayuso, C KW - Aged KW - Animals KW - Co-Repressor Proteins KW - Codon, Nonsense KW - Cohort Studies KW - Comparative Genomic Hybridization KW - Consanguinity KW - DNA Mutational Analysis KW - Exome KW - Eye Proteins KW - Female KW - Gene Expression Regulation KW - Genes, Recessive KW - Homeodomain Proteins KW - Homozygote KW - Humans KW - Male KW - Mice KW - Middle Aged KW - Polymorphism, Single Nucleotide KW - Protein Interaction Mapping KW - Retina KW - Retinal Dystrophies KW - Retinal Rod Photoreceptor Cells KW - Retinitis pigmentosa KW - Spain KW - Trans-Activators KW - Transcription Factors AB -

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

VL - 6 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27734943?dopt=Abstract ER - TY - JOUR T1 - Mutations in the MORC2 gene cause axonal Charcot-Marie-Tooth disease. JF - Brain Y1 - 2016 A1 - Sevilla, Teresa A1 - Lupo, Vincenzo A1 - Martínez-Rubio, Dolores A1 - Sancho, Paula A1 - Sivera, Rafael A1 - Chumillas, María J A1 - García-Romero, Mar A1 - Pascual-Pascual, Samuel I A1 - Muelas, Nuria A1 - Dopazo, Joaquin A1 - Vílchez, Juan J A1 - Palau, Francesc A1 - Espinós, Carmen KW - Adult KW - Aged KW - Animals KW - Axons KW - Charcot-Marie-Tooth Disease KW - Female KW - gene expression KW - Humans KW - Infant KW - Male KW - Mice KW - Middle Aged KW - mutation KW - Pedigree KW - Phenotype KW - Sciatic Nerve KW - Sural Nerve KW - Transcription Factors KW - Young Adult AB -

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

VL - 139 IS - Pt 1 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26497905?dopt=Abstract ER - TY - JOUR T1 - Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. JF - Hum Genet Y1 - 2016 A1 - Lucariello, Mario A1 - Vidal, Enrique A1 - Vidal, Silvia A1 - Saez, Mauricio A1 - Roa, Laura A1 - Huertas, Dori A1 - Pineda, Mercè A1 - Dalfó, Esther A1 - Dopazo, Joaquin A1 - Jurado, Paola A1 - Armstrong, Judith A1 - Esteller, Manel KW - Adolescent KW - Adult KW - Animals KW - Caenorhabditis elegans KW - Carrier Proteins KW - Cell Cycle Proteins KW - Child KW - Child, Preschool KW - DNA Mutational Analysis KW - Exome KW - Female KW - Forkhead Transcription Factors KW - Genetic Variation KW - High-Throughput Nucleotide Sequencing KW - Humans KW - Methyl-CpG-Binding Protein 2 KW - mutation KW - Nerve Tissue Proteins KW - Protein Serine-Threonine Kinases KW - Receptors, Nicotinic KW - Rett Syndrome AB -

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

VL - 135 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/27541642?dopt=Abstract ER - TY - JOUR T1 - A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. JF - PLoS Comput Biol Y1 - 2015 A1 - Porta-Pardo, Eduard A1 - García-Alonso, Luz A1 - Hrabe, Thomas A1 - Dopazo, Joaquin A1 - Godzik, Adam KW - Animals KW - Base Sequence KW - Biomarkers, Tumor KW - Catalogs as Topic KW - Chromosome Mapping KW - Computer Simulation KW - DNA Mutational Analysis KW - Genetic Predisposition to Disease KW - Humans KW - Models, Genetic KW - Molecular Sequence Data KW - mutation KW - Neoplasm Proteins KW - Neoplasms KW - Polymorphism, Single Nucleotide KW - Protein Interaction Mapping KW - Signal Transduction AB -

Despite their importance in maintaining the integrity of all cellular pathways, the role of mutations on protein-protein interaction (PPI) interfaces as cancer drivers has not been systematically studied. Here we analyzed the mutation patterns of the PPI interfaces from 10,028 proteins in a pan-cancer cohort of 5,989 tumors from 23 projects of The Cancer Genome Atlas (TCGA) to find interfaces enriched in somatic missense mutations. To that end we use e-Driver, an algorithm to analyze the mutation distribution of specific protein functional regions. We identified 103 PPI interfaces enriched in somatic cancer mutations. 32 of these interfaces are found in proteins coded by known cancer driver genes. The remaining 71 interfaces are found in proteins that have not been previously identified as cancer drivers even that, in most cases, there is an extensive literature suggesting they play an important role in cancer. Finally, we integrate these findings with clinical information to show how tumors apparently driven by the same gene have different behaviors, including patient outcomes, depending on which specific interfaces are mutated.

VL - 11 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/26485003?dopt=Abstract ER - TY - JOUR T1 - Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations. JF - Hum Mol Genet Y1 - 2015 A1 - Avila-Fernandez, Almudena A1 - Perez-Carro, Raquel A1 - Corton, Marta A1 - Lopez-Molina, Maria Isabel A1 - Campello, Laura A1 - Garanto, Alejandro A1 - Fernandez-Sanchez, Laura A1 - Duijkers, Lonneke A1 - Lopez-Martinez, Miguel Angel A1 - Riveiro-Alvarez, Rosa A1 - da Silva, Luciana Rodrigues Jacy A1 - Sanchez-Alcudia, Rocío A1 - Martin-Garrido, Esther A1 - Reyes, Noelia A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Garcia-Sandoval, Blanca A1 - Collin, Rob W J A1 - Cuenca, Nicolas A1 - Ayuso, Carmen KW - Amino Acid Sequence KW - Animals KW - Chlorocebus aethiops KW - Chromosome Mapping KW - COS Cells KW - DNA-Binding Proteins KW - Exome KW - Genome-Wide Association Study KW - High-Throughput Nucleotide Sequencing KW - Homozygote KW - Humans KW - Molecular Sequence Data KW - Mutant Proteins KW - Pedigree KW - Retina KW - Retinal Cone Photoreceptor Cells KW - Retinal Rod Photoreceptor Cells KW - Retinitis pigmentosa KW - Transcription Factors AB -

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

VL - 24 IS - 14 U1 - https://www.ncbi.nlm.nih.gov/pubmed/25882705?dopt=Abstract ER - TY - JOUR T1 - Permanent cardiac sarcomere changes in a rabbit model of intrauterine growth restriction. JF - PLoS One Y1 - 2014 A1 - Torre, Iratxe A1 - González-Tendero, Anna A1 - García-Cañadilla, Patricia A1 - Crispi, Fátima A1 - Garcia-Garcia, Francisco A1 - Bijnens, Bart A1 - Iruretagoyena, Igor A1 - Dopazo, Joaquin A1 - Amat-Roldán, Ivan A1 - Gratacós, Eduard KW - Animals KW - biomarkers KW - Blood Pressure KW - Body Weight KW - Disease Models, Animal KW - Echocardiography KW - Female KW - Fetal Growth Retardation KW - Fetal Heart KW - Fetus KW - Gene Expression Profiling KW - Organ Size KW - Placenta KW - Pregnancy KW - Rabbits KW - Sarcomeres AB -

BACKGROUND: Intrauterine growth restriction (IUGR) induces fetal cardiac remodelling and dysfunction, which persists postnatally and may explain the link between low birth weight and increased cardiovascular mortality in adulthood. However, the cellular and molecular bases for these changes are still not well understood. We tested the hypothesis that IUGR is associated with structural and functional gene expression changes in the fetal sarcomere cytoarchitecture, which remain present in adulthood.

METHODS AND RESULTS: IUGR was induced in New Zealand pregnant rabbits by selective ligation of the utero-placental vessels. Fetal echocardiography demonstrated more globular hearts and signs of cardiac dysfunction in IUGR. Second harmonic generation microscopy (SHGM) showed shorter sarcomere length and shorter A-band and thick-thin filament interaction lengths, that were already present in utero and persisted at 70 postnatal days (adulthood). Sarcomeric M-band (GO: 0031430) functional term was over-represented in IUGR fetal hearts.

CONCLUSION: The results suggest that IUGR induces cardiac dysfunction and permanent changes on the sarcomere.

VL - 9 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/25402351?dopt=Abstract ER - TY - JOUR T1 - Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. JF - Fungal Genet Biol Y1 - 2014 A1 - Larriba, Eduardo A1 - Jaime, María D L A A1 - Carbonell-Caballero, José A1 - Conesa, Ana A1 - Dopazo, Joaquin A1 - Nislow, Corey A1 - Martín-Nieto, José A1 - Lopez-Llorca, Luis Vicente KW - Animals KW - Ascomycota KW - Female KW - Gene Expression Regulation, Fungal KW - Gene ontology KW - Genome, Fungal KW - Hordeum KW - Host-Pathogen Interactions KW - Nematoda KW - Ovum KW - Phylogeny KW - Plant Roots KW - Sequence Analysis, DNA KW - Signal Transduction KW - Transcriptome AB -

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

VL - 65 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24530791?dopt=Abstract ER - TY - JOUR T1 - Grape antioxidant dietary fiber inhibits intestinal polyposis in ApcMin/+ mice: relation to cell cycle and immune response. JF - Carcinogenesis Y1 - 2013 A1 - Sánchez-Tena, Susana A1 - Lizarraga, Daneida A1 - Miranda, Anibal A1 - Vinardell, Maria P A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Torres, Josep L A1 - Saura-Calixto, Fulgencio A1 - Capellà, Gabriel A1 - Cascante, Marta KW - Animals KW - Antioxidants KW - Body Weight KW - Carcinogenesis KW - Cell Cycle KW - Cell Cycle Checkpoints KW - Colorectal Neoplasms KW - Dietary Fiber KW - Dietary Supplements KW - Down-Regulation KW - G1 Phase KW - Inflammation KW - Intestinal Polyposis KW - Intestinal Polyps KW - Intestine, Small KW - Male KW - Mice KW - Transcriptome KW - Vitis AB -

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

VL - 34 IS - 8 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23615403?dopt=Abstract ER - TY - JOUR T1 - Inferring the functional effect of gene expression changes in signaling pathways. JF - Nucleic Acids Res Y1 - 2013 A1 - Sebastián-Leon, Patricia A1 - Carbonell, José A1 - Salavert, Francisco A1 - Sánchez, Rubén A1 - Medina, Ignacio A1 - Dopazo, Joaquin KW - Animals KW - Humans KW - Internet KW - Mice KW - Models, Statistical KW - Receptors, Cell Surface KW - Signal Transduction KW - Software KW - Transcriptome AB -

Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few methods aimed to identify the signaling circuits, within a pathway, associated to the biological problem studied exist and none of them provide a convenient graphical web interface. We present PATHiWAYS, a web-based signaling pathway visualization system that infers changes in signaling that affect cell functionality from the measurements of gene expression values in typical expression microarray case-control experiments. A simple probabilistic model of the pathway is used to estimate the probabilities for signal transmission from any receptor to any final effector molecule (taking into account the pathway topology) using for this the individual probabilities of gene product presence/absence inferred from gene expression values. Significant changes in these probabilities allow linking different cell functionalities triggered by the pathway to the biological problem studied. PATHiWAYS is available at: http://pathiways.babelomics.org/.

VL - 41 IS - Web Server issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/23748960?dopt=Abstract ER - TY - JOUR T1 - Intrauterine growth restriction is associated with cardiac ultrastructural and gene expression changes related to the energetic metabolism in a rabbit model. JF - Am J Physiol Heart Circ Physiol Y1 - 2013 A1 - González-Tendero, Anna A1 - Torre, Iratxe A1 - García-Cañadilla, Patricia A1 - Crispi, Fátima A1 - Garcia-Garcia, Francisco A1 - Dopazo, Joaquin A1 - Bijnens, Bart A1 - Gratacós, Eduard KW - Animals KW - Disease Models, Animal KW - Energy Metabolism KW - Female KW - Fetal Growth Retardation KW - gene expression KW - Mitochondria KW - Myocardium KW - Oxidative Phosphorylation KW - Placenta KW - Pregnancy KW - Rabbits AB -

Intrauterine growth restriction (IUGR) affects 7-10% of pregnancies and is associated with cardiovascular remodeling and dysfunction, which persists into adulthood. The underlying subcellular remodeling and cardiovascular programming events are still poorly documented. Cardiac muscle is central in the fetal adaptive mechanism to IUGR given its high energetic demands. The energetic homeostasis depends on the correct interaction of several molecular pathways and the adequate arrangement of intracellular energetic units (ICEUs), where mitochondria interact with the contractile machinery and the main cardiac ATPases to enable a quick and efficient energy transfer. We studied subcellular cardiac adaptations to IUGR in an experimental rabbit model. We evaluated the ultrastructure of ICEUs with transmission electron microscopy and observed an altered spatial arrangement in IUGR, with significant increases in cytosolic space between mitochondria and myofilaments. A global decrease of mitochondrial density was also observed. In addition, we conducted a global gene expression profile by advanced bioinformatics tools to assess the expression of genes involved in the cardiomyocyte energetic metabolism and identified four gene modules with a coordinated over-representation in IUGR: oxygen homeostasis (GO: 0032364), mitochondrial respiratory chain complex I (GO:0005747), oxidative phosphorylation (GO: 0006119), and NADH dehydrogenase activity (GO:0003954). These findings might contribute to changes in energetic homeostasis in IUGR. The potential persistence and role of these changes in long-term cardiovascular programming deserves further investigation.

VL - 305 IS - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/24097427?dopt=Abstract ER - TY - JOUR T1 - Diversification of the expanded teleost-specific toll-like receptor family in Atlantic cod, Gadus morhua. JF - BMC Evol Biol Y1 - 2012 A1 - Sundaram, Arvind Y M A1 - Kiron, Viswanath A1 - Dopazo, Joaquin A1 - Fernandes, Jorge M O KW - Amino Acid Sequence KW - Animals KW - Binding Sites KW - Evolution, Molecular KW - Fish Diseases KW - Fish Proteins KW - Gadus morhua KW - Gene Expression Profiling KW - Genetic Variation KW - Gills KW - Head Kidney KW - Host-Pathogen Interactions KW - Models, Molecular KW - Molecular Sequence Data KW - Multigene Family KW - Phylogeny KW - Protein Structure, Tertiary KW - Reverse Transcriptase Polymerase Chain Reaction KW - Selection, Genetic KW - Sequence Analysis, DNA KW - Sequence Homology, Amino Acid KW - Temperature KW - Toll-Like Receptors KW - Vibrio AB -

BACKGROUND: Toll-like receptors (Tlrs) are major molecular pattern recognition receptors of the innate immune system. Atlantic cod (Gadus morhua) is the first vertebrate known to have lost most of the mammalian Tlr orthologues, particularly all bacterial recognising and other cell surface Tlrs. On the other hand, its genome encodes a unique repertoire of teleost-specific Tlrs. The aim of this study was to investigate if these duplicate Tlrs have been retained through adaptive evolution to compensate for the lack of other cell surface Tlrs in the cod genome.

RESULTS: In this study, one tlr21, 12 tlr22 and two tlr23 genes representing the teleost-specific Tlr family have been cloned and characterised in cod. Phylogenetic analysis grouped all tlr22 genes under a single clade, indicating that the multiple cod paralogues have arisen through lineage-specific duplications. All tlrs examined were transcribed in immune-related tissues as well as in stomach, gut and gonads of adult cod and were differentially expressed during early development. These tlrs were also differentially regulated following immune challenge by immersion with Vibrio anguillarum, indicating their role in the immune response. An increase in water temperature from 4 to 12°C was associated with a 5.5-fold down-regulation of tlr22d transcript levels in spleen. Maximum likelihood analysis with different evolution models revealed that tlr22 genes are under positive selection. A total of 24 codons were found to be positively selected, of which 19 are in the ligand binding region of ectodomain.

CONCLUSION: Positive selection pressure coupled with experimental evidence of differential expression strongly support the hypothesis that teleost-specific tlr paralogues in cod are undergoing neofunctionalisation and can recognise bacterial pathogen-associated molecular patterns to compensate for the lack of other cell surface Tlrs.

VL - 12 U1 - https://www.ncbi.nlm.nih.gov/pubmed/23273344?dopt=Abstract ER - TY - JOUR T1 - Extensive translatome remodeling during ER stress response in mammalian cells. JF - PLoS One Y1 - 2012 A1 - Ventoso, Iván A1 - Kochetov, Alex A1 - Montaner, David A1 - Dopazo, Joaquin A1 - Santoyo, Javier KW - Animals KW - Endoplasmic Reticulum Stress KW - Humans KW - Jurkat Cells KW - Mice KW - NIH 3T3 Cells KW - Oligonucleotide Array Sequence Analysis KW - Protein Biosynthesis KW - RNA, Messenger KW - Transcription, Genetic AB -

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.

VL - 7 IS - 5 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22574127?dopt=Abstract ER - TY - JOUR T1 - The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. JF - FASEB J Y1 - 2012 A1 - Koziol, Agnieszka A1 - Gonzalo, Pilar A1 - Mota, Alba A1 - Pollán, Angela A1 - Lorenzo, Cristina A1 - Colomé, Nuria A1 - Montaner, David A1 - Dopazo, Joaquin A1 - Arribas, Joaquín A1 - Canals, Francesc A1 - Arroyo, Alicia G KW - Animals KW - Blotting, Western KW - Combinatorial Chemistry Techniques KW - Computational Biology KW - Endothelial Cells KW - Gene Expression Regulation, Enzymologic KW - Inflammation KW - Matrix Metalloproteinase 14 KW - Mice KW - Protein Array Analysis KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA Interference KW - RNA, Small Interfering KW - Transcriptome KW - Tumor Necrosis Factor-alpha AB -

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

VL - 26 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22859368?dopt=Abstract ER - TY - JOUR T1 - Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin. JF - PloS one Y1 - 2012 A1 - Oppert, Brenda A1 - Dowd, Scot E A1 - Bouffard, Pascal A1 - Li, Lewyn A1 - Ana Conesa A1 - Lorenzen, Marcé D A1 - Toutges, Michelle A1 - Marshall, Jeremy A1 - Huestis, Diana L A1 - Fabrick, Jeff A1 - Oppert, Cris A1 - Jurat-Fuentes, Juan Luis KW - Administration KW - Animals KW - Bacterial Proteins KW - Base Sequence KW - Biosynthetic Pathways KW - Complementary KW - DNA KW - Endotoxins KW - Energy Metabolism KW - Gene Expression Profiling KW - Hemolysin Proteins KW - Larva KW - Microarray Analysis KW - Molecular Sequence Data KW - Oral KW - Sequence Analysis KW - Tenebrio KW - Time Factors KW - Transcriptome AB - Bacillus thuringiensis (Bt) crystal (Cry) proteins are effective against a select number of insect pests, but improvements are needed to increase efficacy and decrease time to mortality for coleopteran pests. To gain insight into the Bt intoxication process in Coleoptera, we performed RNA-Seq on cDNA generated from the guts of Tenebrio molitor larvae that consumed either a control diet or a diet containing Cry3Aa protoxin. Approximately 134,090 and 124,287 sequence reads from the control and Cry3Aa-treated groups were assembled into 1,318 and 1,140 contigs, respectively. Enrichment analyses indicated that functions associated with mitochondrial respiration, signalling, maintenance of cell structure, membrane integrity, protein recycling/synthesis, and glycosyl hydrolases were significantly increased in Cry3Aa-treated larvae, whereas functions associated with many metabolic processes were reduced, especially glycolysis, tricarboxylic acid cycle, and fatty acid synthesis. Microarray analysis was used to evaluate temporal changes in gene expression after 6, 12 or 24 h of Cry3Aa exposure. Overall, microarray analysis indicated that transcripts related to allergens, chitin-binding proteins, glycosyl hydrolases, and tubulins were induced, and those related to immunity and metabolism were repressed in Cry3Aa-intoxicated larvae. The 24 h microarray data validated most of the RNA-Seq data. Of the three intoxication intervals, larvae demonstrated more differential expression of transcripts after 12 h exposure to Cry3Aa. Gene expression examined by three different methods in control vs. Cry3Aa-treated larvae at the 24 h time point indicated that transcripts encoding proteins with chitin-binding domain 3 were the most differentially expressed in Cry3Aa-intoxicated larvae. Overall, the data suggest that T. molitor larvae mount a complex response to Cry3Aa during the initial 24 h of intoxication. Data from this study represent the largest genetic sequence dataset for T. molitor to date. Furthermore, the methods in this study are useful for comparative analyses in organisms lacking a sequenced genome. VL - 7 ER - TY - JOUR T1 - Using GPUs for the exact alignment of short-read genetic sequences by means of the Burrows-Wheeler transform. JF - IEEE/ACM Trans Comput Biol Bioinform Y1 - 2012 A1 - Salavert Torres, Jose A1 - Blanquer Espert, Ignacio A1 - Domínguez, Andrés Tomás A1 - Hernández García, Vicente A1 - Medina Castelló, Ignacio A1 - Tárraga Giménez, Joaquín A1 - Dopazo Blázquez, Joaquín KW - Algorithms KW - Animals KW - Computational Biology KW - Computer Graphics KW - Data Compression KW - Drosophila melanogaster KW - Genes, Insect KW - Image Processing, Computer-Assisted KW - Models, Genetic KW - Sequence Alignment KW - Sequence Analysis, DNA AB -

General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm with state-of-the-art implementations of the same algorithm over standard CPUs, and considering the same conditions in terms of I/O. Excluding disk transfers, the implementation of the algorithm in GPUs shows a speedup larger than 12, when compared to CPU execution. This implementation exploits the parallelism by concurrently searching different sequences on the same reference search tree, maximizing memory locality and ensuring a symmetric access to the data. The paper describes the behavior of the algorithm in GPU, showing a good scalability in the performance, only limited by the size of the GPU inner memory.

VL - 9 IS - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22450827?dopt=Abstract ER - TY - JOUR T1 - Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass. JF - BMC Med Genomics Y1 - 2011 A1 - Vivas, Yurena A1 - Martinez-Garcia, Cristina A1 - Izquierdo, Adriana A1 - Garcia-Garcia, Francisco A1 - Callejas, Sergio A1 - Velasco, Ismael A1 - Campbell, Mark A1 - Ros, Manuel A1 - Dopazo, Ana A1 - Dopazo, Joaquin A1 - Vidal-Puig, Antonio A1 - Medina-Gomez, Gema KW - Animals KW - Cell Proliferation KW - Cell Survival KW - Cholesterol KW - Down-Regulation KW - Female KW - Gene Expression Regulation KW - Gene Knockout Techniques KW - Insulin Resistance KW - Insulin-Secreting Cells KW - Mice KW - obesity KW - Oxidation-Reduction KW - Phosphorylation KW - PPAR gamma KW - Signal Transduction KW - Transcription, Genetic KW - Transforming Growth Factor beta AB -

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.

VL - 4 U1 - https://www.ncbi.nlm.nih.gov/pubmed/22208362?dopt=Abstract ER - TY - JOUR T1 - Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. JF - Brief Bioinform Y1 - 2011 A1 - Huerta-Cepas, Jaime A1 - Dopazo, Joaquin A1 - Huynen, Martijn A A1 - Gabaldón, Toni KW - Animals KW - Conserved Sequence KW - Evolution, Molecular KW - Gene Duplication KW - gene expression KW - Genome KW - Humans KW - Mice KW - Organ Specificity AB -

Gene duplication is one of the main mechanisms by which genomes can acquire novel functions. It has been proposed that the retention of gene duplicates can be associated to processes of tissue expression divergence. These models predict that acquisition of divergent expression patterns should be acquired shortly after the duplication, and that larger divergence in tissue expression would be expected for paralogs, as compared to orthologs of a similar age. Many studies have shown that gene duplicates tend to have divergent expression patterns and that gene family expansions are associated with high levels of tissue specificity. However, the timeframe in which these processes occur have rarely been investigated in detail, particularly in vertebrates, and most analyses do not include direct comparisons of orthologs as a baseline for the expected levels of tissue specificity in absence of duplications. To assess the specific contribution of duplications to expression divergence, we combine here phylogenetic analyses and expression data from human and mouse. In particular, we study differences in spatial expression among human-mouse paralogs, specifically duplicated after the radiation of mammals, and compare them to pairs of orthologs in the same species. Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event.

VL - 12 IS - 5 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21515902?dopt=Abstract ER - TY - JOUR T1 - Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells. JF - Hum Mol Genet Y1 - 2011 A1 - Yung, Sun A1 - Ledran, Maria A1 - Moreno-Gimeno, Inmaculada A1 - Conesa, Ana A1 - Montaner, David A1 - Dopazo, Joaquin A1 - Dimmick, Ian A1 - Slater, Nicholas J A1 - Marenah, Lamin A1 - Real, Pedro J A1 - Paraskevopoulou, Iliana A1 - Bisbal, Viviana A1 - Burks, Deborah A1 - Santibanez-Koref, Mauro A1 - Moreno, Ruben A1 - Mountford, Joanne A1 - Menendez, Pablo A1 - Armstrong, Lyle A1 - Lako, Majlinda KW - Acute Disease KW - Anemia, Hemolytic KW - Animals KW - Basic Helix-Loop-Helix Transcription Factors KW - Cell Differentiation KW - Cell Line KW - Cell Lineage KW - Cluster Analysis KW - Embryonic Stem Cells KW - Erythroid Cells KW - Flow Cytometry KW - Gene Expression Profiling KW - Hematopoietic Stem Cells KW - Humans KW - Mice KW - Myeloid Cells KW - Paracrine Communication KW - Proto-Oncogene Proteins KW - Reverse Transcriptase Polymerase Chain Reaction KW - rho GTP-Binding Proteins KW - Signal Transduction KW - Stem Cell Transplantation KW - T-Cell Acute Lymphocytic Leukemia Protein 1 KW - Transcriptome AB -

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

VL - 20 IS - 24 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21937587?dopt=Abstract ER - TY - JOUR T1 - Natural selection on functional modules, a genome-wide analysis. JF - PLoS Comput Biol Y1 - 2011 A1 - Serra, François A1 - Arbiza, Leonardo A1 - Dopazo, Joaquin A1 - Dopazo, Hernán KW - Animals KW - Databases, Genetic KW - Drosophila KW - Genome, Insect KW - Genome-Wide Association Study KW - Genomics KW - Mammals KW - Phylogeny KW - Selection, Genetic KW - Sequence Analysis, DNA AB -

Classically, the functional consequences of natural selection over genomes have been analyzed as the compound effects of individual genes. The current paradigm for large-scale analysis of adaptation is based on the observed significant deviations of rates of individual genes from neutral evolutionary expectation. This approach, which assumed independence among genes, has not been able to identify biological functions significantly enriched in positively selected genes in individual species. Alternatively, pooling related species has enhanced the search for signatures of selection. However, grouping signatures does not allow testing for adaptive differences between species. Here we introduce the Gene-Set Selection Analysis (GSSA), a new genome-wide approach to test for evidences of natural selection on functional modules. GSSA is able to detect lineage specific evolutionary rate changes in a notable number of functional modules. For example, in nine mammal and Drosophilae genomes GSSA identifies hundreds of functional modules with significant associations to high and low rates of evolution. Many of the detected functional modules with high evolutionary rates have been previously identified as biological functions under positive selection. Notably, GSSA identifies conserved functional modules with many positively selected genes, which questions whether they are exclusively selected for fitting genomes to environmental changes. Our results agree with previous studies suggesting that adaptation requires positive selection, but not every mutation under positive selection contributes to the adaptive dynamical process of the evolution of species.

VL - 7 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21390268?dopt=Abstract ER - TY - JOUR T1 - Hypoxia promotes efficient differentiation of human embryonic stem cells to functional endothelium. JF - Stem Cells Y1 - 2010 A1 - Prado-Lopez, Sonia A1 - Conesa, Ana A1 - Armiñán, Ana A1 - Martínez-Losa, Magdalena A1 - Escobedo-Lucea, Carmen A1 - Gandia, Carolina A1 - Tarazona, Sonia A1 - Melguizo, Dario A1 - Blesa, David A1 - Montaner, David A1 - Sanz-González, Silvia A1 - Sepúlveda, Pilar A1 - Götz, Stefan A1 - O'Connor, José Enrique A1 - Moreno, Ruben A1 - Dopazo, Joaquin A1 - Burks, Deborah J A1 - Stojkovic, Miodrag KW - Angiopoietin-1 KW - Animals KW - biomarkers KW - Cell Culture Techniques KW - Cell Differentiation KW - Cell Hypoxia KW - Cell Transplantation KW - Cells, Cultured KW - Down-Regulation KW - Embryonic Stem Cells KW - Endothelial Cells KW - Gene Expression Profiling KW - Gene Expression Regulation KW - Humans KW - Male KW - Myocardial Infarction KW - Neovascularization, Physiologic KW - Oxygen KW - Pluripotent Stem Cells KW - Rats KW - Rats, Nude KW - Vascular Endothelial Growth Factor A AB -

Early development of mammalian embryos occurs in an environment of relative hypoxia. Nevertheless, human embryonic stem cells (hESC), which are derived from the inner cell mass of blastocyst, are routinely cultured under the same atmospheric conditions (21% O(2)) as somatic cells. We hypothesized that O(2) levels modulate gene expression and differentiation potential of hESC, and thus, we performed gene profiling of hESC maintained under normoxic or hypoxic (1% or 5% O(2)) conditions. Our analysis revealed that hypoxia downregulates expression of pluripotency markers in hESC but increases significantly the expression of genes associated with angio- and vasculogenesis including vascular endothelial growth factor and angiopoitein-like proteins. Consequently, we were able to efficiently differentiate hESC to functional endothelial cells (EC) by varying O(2) levels; after 24 hours at 5% O(2), more than 50% of cells were CD34+. Transplantation of resulting endothelial-like cells improved both systolic function and fractional shortening in a rodent model of myocardial infarction. Moreover, analysis of the infarcted zone revealed that transplanted EC reduced the area of fibrous scar tissue by 50%. Thus, use of hypoxic conditions to specify the endothelial lineage suggests a novel strategy for cellular therapies aimed at repair of damaged vasculature in pathologies such as cerebral ischemia and myocardial infarction.

VL - 28 IS - 3 U1 - https://www.ncbi.nlm.nih.gov/pubmed/20049902?dopt=Abstract ER - TY - JOUR T1 - Mutation spectrum of EYS in Spanish patients with autosomal recessive retinitis pigmentosa. JF - Hum Mutat Y1 - 2010 A1 - Barragán, Isabel A1 - Borrego, Salud A1 - Pieras, Juan Ignacio A1 - González-del Pozo, María A1 - Santoyo, Javier A1 - Ayuso, Carmen A1 - Baiget, Montserrat A1 - Millán, José M A1 - Mena, Marcela A1 - Abd El-Aziz, Mai M A1 - Audo, Isabelle A1 - Zeitz, Christina A1 - Littink, Karin W A1 - Dopazo, Joaquin A1 - Bhattacharya, Shomi S A1 - Antiňolo, Guillermo KW - Amino Acid Sequence KW - Animals KW - Case-Control Studies KW - DNA Mutational Analysis KW - Drosophila Proteins KW - Evolution, Molecular KW - Eye Proteins KW - Female KW - Genes, Recessive KW - Genetic Variation KW - Humans KW - Male KW - Molecular Sequence Data KW - mutation KW - Pedigree KW - Polymorphism, Single Nucleotide KW - Protein Structure, Tertiary KW - Retinitis pigmentosa KW - Spain KW - Structural Homology, Protein AB -

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

VL - 31 IS - 11 U1 - https://www.ncbi.nlm.nih.gov/pubmed/21069908?dopt=Abstract ER - TY - JOUR T1 - Expression and microarrays. JF - Methods Mol Biol Y1 - 2008 A1 - Dopazo, Joaquin A1 - Al-Shahrour, Fátima KW - Animals KW - Computational Biology KW - gene expression KW - Gene Expression Profiling KW - Humans KW - Oligonucleotide Array Sequence Analysis AB -

High throughput methodologies have increased by several orders of magnitude the amount of experimental microarray data available. Nevertheless, translating these data into useful biological knowledge remains a challenge. There is a risk of perceiving these methodologies as mere factories that produce never-ending quantities of data if a proper biological interpretation is not provided. Methods of interpreting these data are continuously evolving. Typically, a simple two-step approach has been used, in which genes of interest are first selected based on thresholds for the experimental values, and then enrichment in biologically relevant terms in the annotations of these genes is analyzed in a second step. For various reasons, such methods are quite poor in terms of performance and new procedures inspired by systems biology that directly address sets of functionally related genes are currently under development.

VL - 453 U1 - https://www.ncbi.nlm.nih.gov/pubmed/18712307?dopt=Abstract ER - TY - JOUR T1 - High-throughput functional annotation and data mining with the Blast2GO suite. JF - Nucleic Acids Res Y1 - 2008 A1 - Götz, Stefan A1 - García-Gómez, Juan Miguel A1 - Terol, Javier A1 - Williams, Tim D A1 - Nagaraj, Shivashankar H A1 - Nueda, Maria José A1 - Robles, Montserrat A1 - Talon, Manuel A1 - Dopazo, Joaquin A1 - Conesa, Ana KW - Animals KW - Computational Biology KW - Computer Graphics KW - Databases, Genetic KW - Expressed Sequence Tags KW - Genes KW - Genomics KW - Sequence Analysis, DNA KW - Sequence Analysis, Protein KW - Software KW - Vocabulary, Controlled AB -

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

VL - 36 IS - 10 U1 - https://www.ncbi.nlm.nih.gov/pubmed/18445632?dopt=Abstract ER - TY - JOUR T1 - Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. JF - Nucleic Acids Res Y1 - 2008 A1 - Reumers, Joke A1 - Conde, Lucia A1 - Medina, Ignacio A1 - Maurer-Stroh, Sebastian A1 - Van Durme, Joost A1 - Dopazo, Joaquin A1 - Rousseau, Frederic A1 - Schymkowitz, Joost KW - Amino Acid Substitution KW - Animals KW - Databases, Genetic KW - Genetic Diseases, Inborn KW - HSP70 Heat-Shock Proteins KW - Humans KW - Internet KW - Mice KW - MicroRNAs KW - mutation KW - Polymorphism, Single Nucleotide KW - Proteins KW - Rats KW - RNA Splice Sites KW - Transcription Factors AB -

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/.

VL - 36 IS - Database issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/18086700?dopt=Abstract ER - TY - JOUR T1 - SNP and haplotype mapping for genetic analysis in the rat. JF - Nat Genet Y1 - 2008 A1 - Saar, Kathrin A1 - Beck, Alfred A1 - Bihoreau, Marie-Thérèse A1 - Birney, Ewan A1 - Brocklebank, Denise A1 - Chen, Yuan A1 - Cuppen, Edwin A1 - Demonchy, Stephanie A1 - Dopazo, Joaquin A1 - Flicek, Paul A1 - Foglio, Mario A1 - Fujiyama, Asao A1 - Gut, Ivo G A1 - Gauguier, Dominique A1 - Guigó, Roderic A1 - Guryev, Victor A1 - Heinig, Matthias A1 - Hummel, Oliver A1 - Jahn, Niels A1 - Klages, Sven A1 - Kren, Vladimir A1 - Kube, Michael A1 - Kuhl, Heiner A1 - Kuramoto, Takashi A1 - Kuroki, Yoko A1 - Lechner, Doris A1 - Lee, Young-Ae A1 - Lopez-Bigas, Nuria A1 - Lathrop, G Mark A1 - Mashimo, Tomoji A1 - Medina, Ignacio A1 - Mott, Richard A1 - Patone, Giannino A1 - Perrier-Cornet, Jeanne-Antide A1 - Platzer, Matthias A1 - Pravenec, Michal A1 - Reinhardt, Richard A1 - Sakaki, Yoshiyuki A1 - Schilhabel, Markus A1 - Schulz, Herbert A1 - Serikawa, Tadao A1 - Shikhagaie, Medya A1 - Tatsumoto, Shouji A1 - Taudien, Stefan A1 - Toyoda, Atsushi A1 - Voigt, Birger A1 - Zelenika, Diana A1 - Zimdahl, Heike A1 - Hubner, Norbert KW - Animals KW - Chromosome Mapping KW - Databases, Genetic KW - Genome KW - Haplotypes KW - Linkage Disequilibrium KW - Phylogeny KW - Polymorphism, Single Nucleotide KW - Quantitative Trait Loci KW - Rats KW - Rats, Inbred Strains KW - Recombination, Genetic AB -

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

VL - 40 IS - 5 U1 - https://www.ncbi.nlm.nih.gov/pubmed/18443594?dopt=Abstract ER - TY - JOUR T1 - FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. JF - Nucleic Acids Res Y1 - 2007 A1 - Al-Shahrour, Fátima A1 - Minguez, Pablo A1 - Tárraga, Joaquín A1 - Medina, Ignacio A1 - Alloza, Eva A1 - Montaner, David A1 - Dopazo, Joaquin KW - Amino Acid Motifs KW - Animals KW - Binding Sites KW - Computational Biology KW - Gene Expression Profiling KW - Genes KW - Genomics KW - Humans KW - Internet KW - Oligonucleotide Array Sequence Analysis KW - Programming Languages KW - Software KW - Systems Integration KW - Transcription Factors AB -

The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org.

VL - 35 IS - Web Server issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/17478504?dopt=Abstract ER - TY - JOUR T1 - ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. JF - Nucleic Acids Res Y1 - 2007 A1 - Conde, Lucia A1 - Montaner, David A1 - Burguet-Castell, Jordi A1 - Tárraga, Joaquín A1 - Medina, Ignacio A1 - Al-Shahrour, Fátima A1 - Dopazo, Joaquin KW - Animals KW - Cluster Analysis KW - Computational Biology KW - Computer Graphics KW - Gene Expression Profiling KW - Humans KW - Internet KW - Models, Genetic KW - Nucleic Acid Hybridization KW - Oligonucleotide Array Sequence Analysis KW - Programming Languages KW - Software KW - Systems Integration KW - User-Computer Interface AB -

We present the ISACGH, a web-based system that allows for the combination of genomic data with gene expression values and provides different options for functional profiling of the regions found. Several visualization options offer a convenient representation of the results. Different efficient methods for accurate estimation of genomic copy number from array-CGH hybridization data have been included in the program. Moreover, the connection to the gene expression analysis package GEPAS allows the use of different facilities for data pre-processing and analysis. A DAS server allows exporting the results to the Ensembl viewer where contextual genomic information can be obtained. The program is freely available at: http://isacgh.bioinfo.cipf.es or within http://www.gepas.org.

VL - 35 IS - Web Server issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/17468499?dopt=Abstract ER -