An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae.

Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two "raw" transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture

Assigning protein function from domain-function associations using DomFun

Background: Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated using multiple indices based on tripartite network analysis. These domain-function associations are combined at the protein level, to generate protein-function predictions. Results: We analysed 16 tripartite networks connecting homologous superfamily and FunFam domains from CATH-Gene3D with functional annotations from the three Gene Ontology (GO) sub-ontologies, KEGG, and Reactome. We validated the results using the CAFA 3 benchmark platform for GO annotation, finding that out of the multiple association metrics and domain datasets tested, Simpson index for FunFam domain-function associations combined with Stouffer’s method leads to the best performance in almost all scenarios. We also found that using FunFams led to better performance than superfamilies, and better results were found for GO molecular function compared to GO biological process terms. DomFun performed as well as the highest-performing method in certain CAFA 3 evaluation procedures in terms of Fmax and Smin We also implemented our own benchmark procedure, Pathway Prediction Performance (PPP), which can be used to validate function prediction for additional annotations sources, such as KEGG and Reactome. Using PPP, we found similar results to those found with CAFA 3 for GO, moreover we found good performance for the other annotation sources. As with CAFA 3, Simpson index with Stouffer’s method led to the top performance in almost all scenarios. Conclusions: DomFun shows competitive performance with other methods evaluated in CAFA 3 when predicting proteins function with GO, although results vary depending on the evaluation procedure. Through our own benchmark procedure, PPP, we have shown it can also make accurate predictions for KEGG and Reactome. It performs best when using FunFams, combining Simpson index derived domain-function associations using Stouffer’s method. The tool has been implemented so that it can be easily adapted to incorporate other protein features, such as domain data from other sources, amino acid k-mers and motifs. The DomFun Ruby gem is available from https://rubygems.org/gems/DomFun. Code maintained at https://github.com/ElenaRojano/DomFun. Validation procedure scripts can be found at https://github.com/ElenaRojano/DomFun_project

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases

© 2020 Díaz-Santiago et al.Genetic and molecular analysis of rare disease is made difficult by the small numbers of affected patients. Phenotypic comorbidity analysis can help rectify this by combining information from individuals with similar phenotypes and looking for overlap in terms of shared genes and underlying functional systems. However, few studies have combined comorbidity analysis with genomic data. We present a computational approach that connects patient phenotypes based on phenotypic co-occurence and uses genomic information related to the patient mutations to assign genes to the phenotypes, which are used to detect enriched functional systems. These phenotypes are clustered using network analysis to obtain functionally coherent phenotype clusters. We applied the approach to the DECIPHER database, containing phenotypic and genomic information for thousands of patients with heterogeneous rare disorders and copy number variants. Validity was demonstrated through overlap with known diseases, co-mention within the biomedical literature, semantic similarity measures, and patient cluster membership. These connected pairs formed multiple phenotype clusters, showing functional coherence, and mapped to genes and systems involved in similar pathological processes. Examples include claudin genes from the 22q11 genomic region associated with a cluster of phenotypes related to DiGeorge syndrome and genes related to the GO term anterior/posterior pattern specification associated with abnormal development. The clusters generated can help with the diagnosis of rare diseases, by suggesting additional phenotypes for a given patient and potential underlying functional systems. Other tools to find causal genes based on phenotype were also investigated. The approach has been implemented as a workflow, named PhenCo, which can be adapted to any set of patients for which phenomic and genomic data is available. Full details of the analysis, including the clusters formed, their constituent functional systems and underlying genes are given. Code to implement the workflow is available from GitHub.The study was funded by grants from the The Spanish Ministry of Science and Innovation with European Regional Development Fund [PID2019-108096RB-C21 to J.A.G and PID2019- 108096RB-C22 to F.P.]; the Andalusian Government (Junta de Andalucia) with European Regional Development Fund [UMA18-FEDERJA102], and Biomedicine Research project [PI-0075- 2017] (Fundacion Progreso y Salud); and the Ramo´n Areces foundation, which funds project for the investigation of rare disease (National call for research on life and material sciences, XIX edition); Ramo´n y Cajal I3 projects through the Research Plan of the University of Malaga (Ayudas del I Plan Propio). The CIBERER is an initiative from the Carlos III Health Institute (Instituto de Salud Carlos III; ISCIII)

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite

12 páginas, 7 figuras, 2 tablas. Te online version contains supplementary material available at https://doi.org/ 10.1038/s41598-021-94343-w . Code is available at the bioconductor landing page https://bioconductor.org/packages/ExpHunterSuite. Te latest version of the code can be found at https://github.com/seoanezonjic/ExpHunterSuite. Tere is a specifc github site for the simulated data and case-studies at: https://github.com/fmjabato/ExpHunterSuiteExamples. Te dataset supporting the results of this article are available in the Sequence Read Archive SRA [https://www.ncbi.nlm.nih.gov/sra/PRJNA746239 (Lafora Disease) and ttps://www.ncbi.nlm.nih.gov/sra/PRJNA747153 (PMM2-CDG)] ; all FASTQ fles as well as important processed data necessary to repeat analysis have been made available.High-throughput gene expression analysis is widely used. However, analysis is not straightforward. Multiple approaches should be applied and methods to combine their results implemented and investigated. We present methodology for the comprehensive analysis of expression data, including co-expression module detection and result integration via data-fusion, threshold based methods, and a Naïve Bayes classifier trained on simulated data. Application to rare-disease model datasets confirms existing knowledge related to immune cell infiltration and suggest novel hypotheses including the role of calcium channels. Application to simulated and spike-in experiments shows that combining multiple methods using consensus and classifiers leads to optimal results. ExpHunter Suite is implemented as an R/Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite . It can be applied to model and non-model organisms and can be run modularly in R; it can also be run from the command line, allowing scalability with large datasets. Code and reports for the studies are available from https://github.com/fmjabato/ExpHunterSuiteExamplesTis work was supported by Te Spanish Ministry of Economy and Competitiveness with European Regional Development Fund [PID2019-108096RB-C21]; the Andalusian Government with European Regional Development Fund [projects: UMA18-FEDERJA-102 and PAIDI-2020-PY20-00372]; biomedicine research project [PI-0075-2017] (Fundación Progreso y Salud); the Carlos III Health Institue [PI19/01155]; the Ramón Areces foundation for rare disease investigation (National call for research on life and material sciences, XIX edition); the National Institute of Health (NIH-NINDS) [P01NS097197], which established the Lafora Epilepsy Cure Initiative (LECI); the Madrid Government [B2017/BMD-3721], and the Fundación Isabel Gemio/Fundacion La Caixa [LCF/PR/PR16/11110018]. Te CIBERER is an initiative from the Carlos III Health Institute (Instituto de Salud Carlos III).Peer reviewe

Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer

Exhaustive and comprehensive analysis of pathological traits is essential to understanding genetic diseases, performing precise diagnosis and prescribing personalized treatments. It is particularly important for disease cohorts, as thoroughly detailed phenotypic profiles allow patients to be compared and contrasted. However, many disease cohorts contain patients that have been ascribed low numbers of very general and relatively uninformative phenotypes. We present Cohort Analyzer, a tool that measures the phenotyping quality of patient cohorts. It calculates multiple statistics to give a general overview of the cohort status in terms of the depth and breadth of phenotyping, allowing us to detect less well-phenotyped patients for re-examining or excluding from further analyses. In addition, it performs clustering analysis to find subgroups of patients that share similar phenotypic profiles. We used it to analyse three cohorts of genetic diseases patients with very different properties. We found that cohorts with the most specific and complete phenotypic characterization give more potential insights into the disease than those that were less deeply characterised by forming more informative clusters. For two of the cohorts, we also analysed genomic data related to the patients, and linked the genomic data to the patient-subgroups by mapping shared variants to genes and functions. The work highlights the need for improved phenotyping in this era of personalized medicine. The tool itself is freely available alongside a workflow to allow the analyses shown in this work to be applied to other datasets.This work was supported by The Spanish Ministry of Economy and Competitiveness with European Regional Development Fund [PID2019-108096RB-C21]; the Andalusian Government with European Regional Development Fund [UMA18-FEDERJA-102 and PAIDI 2020:PY20-00372]; biomedicine research project [PI-0075-2017] (Fundación Progreso y Salud); the Carlos III Health Institute [PI19/01155]; the Madrid Government [B2017/BMD-3721]; the Ramón Areces foundation for rare disease investigation (National call for research on life and material sciences, XIX edition). We thank the patients and patients’ families for their collaboration and consent. PMM2-CDG research is supported by national grants from the National Plan on I+D+I, cofinanced by ISCIII (Subdirección General de Evaluación y Fomento de la Investigación Sanitaria) and FEDER (Fondo Europeo de Desarrollo Regional) [PI14/00021; PI17/00101 ]. Dr. Serrano’s research work is supported by a grant from the Generalitat de Catalunya [PERIS SLT008/18/00194]. The CIBERER is an initiative from the Carlos III Health Institute (Instituto de Salud Carlos III).Ye

Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model.

To investigate food allergy-tolerance mechanisms induced through allergen-specific immunotherapy we used RNA-Sequencing to measure gene expression in lymph-node-derived dendritic cells from Pru p 3-anaphylactic mice after immunotherapy with glycodendropeptides at 2 nM and 5 nM, leading to permanent tolerance and short-term desensitization, respectively. Gene expression was also measured in mice receiving no immunotherapy (anaphylaxis); and in which anaphylaxis could never occur (antigen-only). Compared to anaphylaxis, the antigen-only group showed the greatest number of expression-changes (411), followed by tolerant (186) and desensitized (119). Only 29 genes changed in all groups, including Il12b, Cebpb and Ifngr1. The desensitized group showed enrichment for genes related to chronic inflammatory response, secretory granule, and regulation of interleukin-12 production; the tolerant group showed genes related to cytokine receptor activity and glucocorticoid receptor binding, suggesting distinct pathways for similar outcomes. We identified genes and processes potentially involved in the restoration of long-term tolerance via allergen-specific immunotherapy, representing potential prognostic biomarkers