Whole genome sequence analysis of platelet traits in the NHLBI trans-omics for precision medicine initiative

Platelets play a key role in thrombosis and hemostasis. Platelet count (PLT) and mean platelet volume (MPV) are highly heritable quantitative traits, with hundreds of genetic signals previously identified, mostly in European ancestry populations. We here utilize whole genome sequencing from NHLBI\u27s Trans-Omics for Precision Medicine Initiative (TOPMed) in a large multi-ethnic sample to further explore common and rare variation contributing to PLT (n = 61 200) and MPV (n = 23 485). We identified and replicated secondary signals at MPL (rs532784633) and PECAM1 (rs73345162), both more common in African ancestry populations. We also observed rare variation in Mendelian platelet related disorder genes influencing variation in platelet traits in TOPMed cohorts (not enriched for blood disorders). For example, association of GP9 with lower PLT and higher MPV was partly driven by a pathogenic Bernard-Soulier syndrome variant (rs5030764, p.Asn61Ser), and the signals at TUBB1 and CD36 were partly driven by loss of function variants not annotated as pathogenic in ClinVar (rs199948010 and rs571975065). However, residual signal remained for these gene-based signals after adjusting for lead variants, suggesting that additional variants in Mendelian genes with impacts in general population cohorts remain to be identified. Gene-based signals were also identified at several GWAS identified loci for genes not annotated for Mendelian platelet disorders (PTPRH, TET2, CHEK2), with somatic variation driving the result at TET2. These results highlight the value of whole genome sequencing in populations of diverse genetic ancestry to identify novel regulatory and coding signals, even for well-studied traits like platelet traits

Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus

AbstractMany individual genetic risk loci have been associated with multiple common human diseases. However, the molecular basis of this pleiotropy often remains unclear. We present an integrative approach to reveal the molecular mechanism underlying the PROCR locus, associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. We identify PROCR-p.Ser219Gly as the likely causal variant at the locus and protein C as a causal factor. Using genetic analyses, human recall-by-genotype and in vitro experimentation, we demonstrate that PROCR-219Gly increases plasma levels of (activated) protein C through endothelial protein C receptor (EPCR) ectodomain shedding in endothelial cells, attenuating leukocyte–endothelial cell adhesion and vascular inflammation. We also associate PROCR-219Gly with an increased pro-thrombotic state via coagulation factor VII, a ligand of EPCR. Our study, which links PROCR-219Gly to CAD through anti-inflammatory mechanisms and to VTE through pro-thrombotic mechanisms, provides a framework to reveal the mechanisms underlying similar cross-phenotype associations.</jats:p

Genetic and plasmatic variations of microRNAs : impact on haemostatic traits

Les microARNs (miARNs) sont les membres d’une classe de petits ARNs non codants d’environ 22 nucléotides, dont le mécanisme principal est de réguler l’expression des gènes dans le cytoplasme. Leurs importance est telle qu’il est estimé que la majorité des gènes humains sont régulés par ces petits ARNs, et ils sont ainsi potentiellement impliqués dans le développement de nombreuse pathologies. La séquence des miARNs peut-être soumise à des variations post- transcriptionnelles et des variations génétiques générant alors des séquences isoformes appelées isomiRs. Afin de détécter et quantifier précisemment l’expression des miARNs à partir de données de séquençage, cette hétérogénéité intra-miARN, due aux isomiRs, doit être prise en compte, tout comme l’homogénéité inter-miARN due aux miARNs paralogues. Le pipeline optimiR, développé dans le cadre de cette thèse, permet de surmonter ces challenges grâce notamment à l’intégration de l’information génétique des échantillons analysés, ainsi qu’à une stratégie d’alignement originale, qui permettent de détecter les isomiRs tout en distinguant les miARNs paralogues. Les données analysées lors de cette thèse proviennent de la cohorte MARTHA, composée de patients ayant développé une thrombose veineuse (VTE), parfois avec récidive. L’expression normalisée de 162 miARNs obtenue pour 344 patients a ensuite été utilisée afin d’analyser: 1) les déterminants génétiques de l’expression de ces miARNs; 2) l’association des miARNs avec le risque de récidive pour la VTE; 3) les corrélations avec certains paramètres biologiques de l’hémostase. Collectivement, ces analyses m’ont permis d’identifier des microARNs d’intérêt pour la recherche sur la thrombose veineuse et sur l’hémostase.MicroRNAs (miRNA) are small non coding RNAs with an average size of 22 nucleotides, mainly known to regulate gene expression in the cytoplasm. These small RNAs are estimated to regulate the majority of human genes, and are potentially involved in several diseases. MiRNA sequences might contain genetic variants and can undergo post-transcriptional variations, which generate miRNA isoforms called isomiRs. In order to accurately detect and quantify miRNA expression, isomiRs as well as paralogous miRNAs must be accounted for. The optimiR pipeline developed during this project overcome these challenges by integrating genetic information and by implementing an original strategy based on local alignement. Sequencing data were obtained from the MARTHA cohort, which is composed of french unrelated patients who experienced venous thrombosis (VTE). Normalized expression of 162 miRNAs from 334 patients were used to analyze: 1) the genetic determinants of miRNA expression; 2) the association of miRNA expression levels with VTE recurence; 3) the correlations between miRNA expression levels and hemostatic traits. As a whole, these analyses allowed me to identify miRNAs of interest for the study of VTE and hemostasis

Variation génétique et plasmatique des microARNs : impact sur les paramètres biologiques de l’hémostase

MicroRNAs (miRNA) are small non coding RNAs with an average size of 22 nucleotides, mainly known to regulate gene expression in the cytoplasm. These small RNAs are estimated to regulate the majority of human genes, and are potentially involved in several diseases. MiRNA sequences might contain genetic variants and can undergo post-transcriptional variations, which generate miRNA isoforms called isomiRs. In order to accurately detect and quantify miRNA expression, isomiRs as well as paralogous miRNAs must be accounted for. The optimiR pipeline developed during this project overcome these challenges by integrating genetic information and by implementing an original strategy based on local alignement. Sequencing data were obtained from the MARTHA cohort, which is composed of french unrelated patients who experienced venous thrombosis (VTE). Normalized expression of 162 miRNAs from 334 patients were used to analyze: 1) the genetic determinants of miRNA expression; 2) the association of miRNA expression levels with VTE recurence; 3) the correlations between miRNA expression levels and hemostatic traits. As a whole, these analyses allowed me to identify miRNAs of interest for the study of VTE and hemostasis.Les microARNs (miARNs) sont les membres d’une classe de petits ARNs non codants d’environ 22 nucléotides, dont le mécanisme principal est de réguler l’expression des gènes dans le cytoplasme. Leurs importance est telle qu’il est estimé que la majorité des gènes humains sont régulés par ces petits ARNs, et ils sont ainsi potentiellement impliqués dans le développement de nombreuse pathologies. La séquence des miARNs peut-être soumise à des variations post- transcriptionnelles et des variations génétiques générant alors des séquences isoformes appelées isomiRs. Afin de détécter et quantifier précisemment l’expression des miARNs à partir de données de séquençage, cette hétérogénéité intra-miARN, due aux isomiRs, doit être prise en compte, tout comme l’homogénéité inter-miARN due aux miARNs paralogues. Le pipeline optimiR, développé dans le cadre de cette thèse, permet de surmonter ces challenges grâce notamment à l’intégration de l’information génétique des échantillons analysés, ainsi qu’à une stratégie d’alignement originale, qui permettent de détecter les isomiRs tout en distinguant les miARNs paralogues. Les données analysées lors de cette thèse proviennent de la cohorte MARTHA, composée de patients ayant développé une thrombose veineuse (VTE), parfois avec récidive. L’expression normalisée de 162 miARNs obtenue pour 344 patients a ensuite été utilisée afin d’analyser: 1) les déterminants génétiques de l’expression de ces miARNs; 2) l’association des miARNs avec le risque de récidive pour la VTE; 3) les corrélations avec certains paramètres biologiques de l’hémostase. Collectivement, ces analyses m’ont permis d’identifier des microARNs d’intérêt pour la recherche sur la thrombose veineuse et sur l’hémostase

MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data

Availability and implementation: MACARON is written in python with codes available on the GENMED website (www.genmed.fr)International audiencePredicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings

Compositional certification: the CERCLES2 project

International audienceThe CERCLES2 project (in French: CERtification Compositionnelle des Logiciels Embarqués critiqueSet Sûrs 1 , that is to say: compositional certification of critical and safe embedded software) is a collabora-tion between two industrial partners (Sagem and Clearsy) and two academic partners (Pierre et MarieCurie and Paris Diderot universities) aiming at technically and economically improving the developmentprocess of safety-critical software, a typical target being avionics DO-178 level A software ([9])

Eur Heart J Suppl

MicroRNAs (miRNAs) are small regulatory RNAs participating to several biological processes and known to be involved in various pathologies. Measurable in body fluids, miRNAs have been proposed to serve as efficient biomarkers for diseases and/or associated traits. Here, we performed a next-generation-sequencing based profiling of plasma miRNAs in 344 patients with venous thrombosis (VT) and assessed the association of plasma miRNA levels with several haemostatic traits and the risk of VT recurrence. Among the most significant findings, we detected an association between hsa-miR-199b-3p and haematocrit levels (P = 0.0016), these two markers having both been independently reported to associate with VT risk. We also observed suggestive evidence for association of hsa-miR-370-3p (P = 0.019), hsa-miR-27b-3p (P = 0.016) and hsa-miR-222-3p (P = 0.049) with VT recurrence, the observations at the latter two miRNAs confirming the recent findings of Wang et al. Besides, by conducting Genome-Wide Association Studies on miRNA levels and meta-analyzing our results with some publicly available, we identified 21 new associations of single nucleotide polymorphisms with plasma miRNA levels at the statistical significance threshold of P < 5 × 10−8, some of these associations pertaining to thrombosis associated mechanisms. In conclusion, this study provides novel data about the impact of miRNAs’ variability in haemostasis and new arguments supporting the association of few miRNAs with the risk of recurrence in patients with venous thrombosis.Los micro-ARN (miARN) son pequeñas moléculas de ARN reguladoras que participan en varios procesos biológicos y están implicados en diversas patologías. Mensurables en los líquidos corporales, se ha planteado que los miARN pueden ser biomarcadores eficaces para el diagnóstico de enfermedades y/o características asociadas. Aquí hemos llevado a cabo un análisis de miARN plasmático con tecnología de secuenciación de última generación en 344 pacientes con trombosis venosa (TV) y hemos evaluado la asociación de los niveles de miARN con distintas características hemostáticas y el riesgo de recidiva de TV. Entre los hallazgos más significativos, hemos detectado una asociación entre hsa-miR-199b-3p y los niveles de hematocritos (p = 0,0016); dos marcadores que se habían asociado de forma independiente con el riesgo de sufrir TV. Asimismo, hemos observado una evidencia indicativa de asociación entre hsa-miR-370-3p (p = 0,019), hsa-miR-27b-3p (p = 0,016) y hsa-miR-222-3p (p = 0,049) y la recidiva de TV; los resultados los dos últimos miARN confirman los hallazgos recientes de Wang et al. (Clin Epigenetics, 2019). Además, al efectuar estudios de asociación del genoma completo sobre los niveles de miARN y al metaanalizar nuestros resultados con otros disponibles públicamente, hemos identificado 21 asociaciones nuevas de polimorfismos de un solo nucleótido (PSN) con niveles de miARN plasmático con un umbral de significación estadística de p < 5 × 10−8; algunas de estas asociaciones pertenecen a los mecanismos patogénicos de la trombosis.Como conclusión, en este estudio se proporcionan nuevos datos sobre el impacto de la variabilidad de miARN en la hemostasia y nuevos argumentos que apoyan la asociación de algunas secuencias de miARN con el riesgo de recidiva en pacientes con trombosis venosa

Bayesian Network Analysis of plasma microRNA sequencing data in patients with venous thrombosis

International audienceMicroRNAs (miRNAs) are small regulatory RNAs participating to several biological processes and known to be involved in various pathologies. Measurable in body fluids, miRNAs have been proposed to serve as efficient biomarkers for diseases and/or associated traits. We here performed a next-generation-sequencing based profiling of plasma miRNAs in 344 patients with venous thrombosis (VT) and assessed the association of plasma miRNA levels with several haemostatic traits and the risk of VT recurrence. Among the most significant findings, we detected an association between hsa-miR-199b-3p and hematocrit 2 levels (p = 0.0016), these two markers having both been independently reported to associate with VT risk. We also observed suggestive evidence for association of hsa-miR-370-3p (p = 0.019), hsa-miR-27b-3p (p = 0.016) and hsa-miR-222-3p (p = 0.049) with VT recurrence, the observations at the latter two miRNAs confirming the recent findings of Wang et al. (Clin Epigenetics 2019). Besides, by conducting Genome Wide Association Studies on miRNA levels and meta-analyzing our results with some publicly available, we identified 21 new associations of SNP with plasma miRNA levels at the statistical significance threshold of p < 5 × 10-8 , some of these associations pertaining to thrombosis associated mechanisms. In conclusion, this study provides novel data about the impact of miRNAs' variability in haemostasis and new arguments supporting the association of few miRNAs with the risk of recurrence in patients with venous thrombosis