Biology subjects

Tregouet, D.-A.

Publications and source records attributed to Tregouet, D.-A..

8 recordsLinked to original sources

bioRxiv2024

A genome wide search for non-additive allele effects identifies PSKH2 as involved in the variability of Factor V activity.

BackgroundFactor V (FV) is a key molecular player in the coagulation cascade. FV plasma levels have been associated with several human diseases, including thrombosis, bleeding and diabetic complications. So far, two genes have been robustly found through genome wide association analyses to contribute in the inter-individual variability of plasma FV levels: structural F5 gene and PLXDC2. MethodsWe used the underestimated Brown-Forsythe methodology implemented in the Quicktest software to search for non-additive genetic effects that could contribute to the inter-individual variability of FV plasma activity. QUICKTEST was applied to 4 independent GWAS studies (LURIC, MARTHA, MEGA and RETROVE) totaling 4,505 participants of European ancestry with measured FV plasma levels. Results obtained in the 4 cohorts were meta-analyzed using a fixed-effect model. Additional analyses involved exploring haplotype and genexgene interactions in downstream investigations. ResultsWe observed a genome-wide significant signal at PSKH2 locus, on chr8q21.3 with lead variant rs75463553 with no evidence for heterogeneity across cohorts (p = 0.518). Although rs75463553 did not show association with mean FV levels (p = 0.49), it demonstrated a robust significant (p = 8.4 10-9) association with the variance of FV plasma levels. Further analyses confirmed the reported association of PSKH2 with neutrophil biology and revealed that rs75463553 likely interact with two loci, GRIN2A and POM121L12, known for their involvement in smoking biology. ConclusionsThis comprehensive approach identifies the role of PSKH2 as a novel molecular player in the genetic regulation of FV, shedding light on the contribution of neutrophils to FV biology.

genetics↗

bioRxiv2023

Integrative Multiomics to Dissect the Lung Transcriptional Landscape of Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) remains an incurable and often fatal disease despite currently available therapies. Multiomics systems biology analysis can shed new light on PAH pathobiology and inform translational research efforts. Using RNA sequencing on the largest PAH lung biobank to date (96 disease and 52 control), we aim to identify gene co-expression network modules associated with PAH and potential therapeutic targets. Co-expression network analysis was performed to identify modules of co-expressed genes which were then assessed for and prioritized by importance in PAH, regulatory role, and therapeutic potential via integration with clinicopathologic data, human genome-wide association studies (GWAS) of PAH, lung Bayesian regulatory networks, single-cell RNA-sequencing data, and pharmacotranscriptomic profiles. We identified a co-expression module of 266 genes, called the pink module, which may be a response to the underlying disease process to counteract disease progression in PAH. This module was associated not only with PAH severity such as increased PVR and intimal thickness, but also with compensated PAH such as lower number of hospitalizations, WHO functional class and NT-proBNP. GWAS integration demonstrated the pink module is enriched for PAH-associated genetic variation in multiple cohorts. Regulatory network analysis revealed that BMPR2 regulates the main target of FDA-approved riociguat, GUCY1A2, in the pink module. Analysis of pathway enrichment and pink hub genes (i.e. ANTXR1 and SFRP4) suggests the pink module inhibits Wnt signaling and epithelial-mesenchymal transition. Cell type deconvolution showed the pink module correlates with higher vascular cell fractions (i.e. myofibroblasts). A pharmacotranscriptomic screen discovered ubiquitin-specific peptidases (USPs) as potential therapeutic targets to mimic the pink module signature. Our multiomics integrative study uncovered a novel gene subnetwork associated with clinicopathologic severity, genetic risk, specific vascular cell types, and new therapeutic targets in PAH. Future studies are warranted to investigate the role and therapeutic potential of the pink module and targeting USPs in PAH.

genomics↗

bioRxiv2022

Novel uAUG creating variants in the 5UTR of ENG causing Hereditary Hemorrhagic Telangiectasia

Hereditary Hemorrhagic Telangiectasia (HHT) is a rare vascular disorder causing abnormal vessel formation and characterized by autosomal dominant transmission. The associated considerable variability in symptoms and clinical severity complicate the management of the disease. In clinical routine, 3 main genes, ACVRL1 (also known as ALK1), ENG and SMAD4 are screened for pathogenic variants at the origin of HHT. About 80% of HHT cases are caused by pathogenic coding variants in ACVRL1 and ENG. However, at least 15% remain with no molecular explanations in the 3 main genes. We here report the identification of 2 never reported variants, c.-79C>T and c.-68G>A, in the 5UTR of ENG in 2 unrelated HHT patients. These 2 variants are predicted to create upstream AUGs (uAUGs) in the 5UTR, which are in frame with a stop codon located within the CoDing Sequence (CDS), thus generating Overlapping upstream Open reading frames (uoORFs). In other cases, uAUGs can lead to fully upstream ORFs (uORFs) when associated with stop codons located within the 5UTR or to elongated CDS (eCDS) when in frame with the CDS and associated with the main stop codon. In order to assess the pathogenicity of these ENG variants, we performed in vitro functional assays based on the expression of wild-type and mutant constructs in human cells. We found that these 5UTR ENG variants were associated with a decrease of protein levels in HeLa and HUVEC cells. They were also associated with a decreased ability to activate BMP9-stimulated ALK1 receptor in a BMP-response element (BRE) assay. This assay is a mandatory element before providing a definitive molecular diagnosis and has been so far applied only on coding ENG variants. We applied the same experimental workflow on 3 additional uoORF-creating variants (c.-142A>T, c.-127C>T and c.-10C>T) and one eCDS-creating variant (c.-9G>A) in the 5UTR of ENG previously reported in HHT patients. We found that all the analysed uoORF-creating variants alter endoglin levels and function. A comparison of our experimental results with patients clinical characteristics suggests that uoORF-creating variants leading to ENG protein levels [≤] 40% in vitro would be associated with HHT. Additional experiments relying on an artificial deletion in our mutated constructs show that created uAUGs predicted to create uoORFs are able to initiate the translation indicating that the associated effect is likely caused by an alteration of the translation mechanism. Overall, we here identified two never reported 5UTR ENG variations in HHT patients and shed new lights on the role of upstream ORFs on ENG regulation. Our findings contribute to the amelioration of molecular diagnosis in HHT.

molecular biology↗

bioRxiv2020

MORFEE: a new tool for detecting and annotating single nucleotide variants creating premature ATG codons from VCF files

SummaryVariants in 5UTR regions that create upstream translation initiation AUG codons are a class of neglected non coding variations. When they associate with a premature stop codon and create upstream open reading frames (uORFs) whose translation competes with that of natural proteins, they can have strong impact on human diseases. We here describe MORFEE, a new bioinformatics tool that detects, annotates and predicts, from a standard VCF file, the creation of uORF by any 5UTR variants on uORF creation. MORFEE was applied to two genomic resources and identified candidate functional variants that could explain statistical association signals observed in the context of Genome Wide Association Studies or could be responsible for rare forms of diseases. In conclusion MORFEE is an easy-to-use tool complementary to existing ones that can help resolving genetic investigations that remained so far unfruitful. Availability and implementationMORFEE is written in R with code and package available at https://github.com/daissi/MORFEE. Contactdavid-alexandre.tregouet@inserm.fr; david-alexandre.tregouet@u-bordeaux.fr

bioinformatics↗

bioRxiv2020

A novel rare c. -39C>T mutation in the PROS1 5'UTR causing PS deficiency by creating a new upstream translation initiation codon and inhibiting the production of the natural protein.

Inherited Protein S deficiency (PSD) (MIM176880) is a rare automosal dominant disorder caused by rare mutations, mainly located in the coding sequence of the structural PROS1 gene, and associated with an increased risk of venous thromboembolism. To identify the molecular defect underlying PSD observed in an extended French pedigree with 7 PSD affected members in who no candidate deleterious PROS1 mutation was detected by Sanger sequencing of PROS1 exons and their flanking intronic regions or via a MLPA approach, a whole genome sequencing strategy was adopted. This led to the identification of a never reported C to T substitution at c.-39 from the natural ATG codon of the PROS1 gene that completely segregates with PSD in the whole family. This substitution ACG->ATG creates a new start codon upstream of the main ATG. We experimentally demonstrated that the variant generates a novel overlapping ORF and inhibits the translation of the wild type protein from the main ORF in HeLa cells. This work describes the first example of 5UTR PROS1 mutation causing PSD through the creation of an upstream ORF, a mutation that is not predicted to be deleterious by standard annotation softwares.

genetics↗

bioRxiv2020

ABO blood group, glycosyltransferase activity and risk of Venous Thrombosis

IntroductionABO blood group influence the risk of venous thrombosis (VT) by modifying A and B glycosyltransferases (AGT and BGT) activities that further modulates Factor VIII (FVIII) and von Willebrand Factor (VWF) plasma levels. The aim of this work was to evaluate the association of plasma GTs activities with VWF/FVIII plasma levels and VT risk in a case-control study. Materials and Methods420 cases were matched with 420 controls for age and ABO blood group. GT activities in plasma were measured using the quantitative transfer of tritiated N-acetylgalactosamine or galactose to the 2-fucosyl-lactose and expressed in disintegration per minute/30{micro}L of plasma and 2 hours of reaction (dpm/30{micro}L/2H). FVIII and VWF plasma levels were respectively measured using human FVIII-deficient plasma in a 1-stage factor assay and STA LIATEST VWF (Diagnostica Stago). ResultsA and B GT activities were significantly lower in cases than in controls (8119{+/-}4027 vs 9682{+/-}4177 dpm/30{micro}L/2H, p=2.03 x 10-5, and 4931{+/-}2305 vs 5524{+/-}2096 dpm/30{micro}L/2H, p=0.043 respectively). This association was observed whatever the ABO blood groups. The ABO A1 blood group was found to explain[~]80% of AGT activity. After adjusting for ABO blood groups, AGT activity was not correlated to VWF/FVIII plasma levels. Conversely, there was a moderate correlation ({rho}[~]0.30) between BGT activity and VWF/ FVIII plasma levels in B blood group carriers. ConclusionThis work showed, for the first time, that GT activities were decreased in VT patients in comparison to controls with the same ABO blood group. The biological mechanisms responsible for this association remained to be determined.

pathology↗

bioRxiv2018

OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.

Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs detection and quantification still remain a challenge as they can undergo different post transcriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).

bioinformatics↗

bioRxiv2018

Exome-wide association study on Albuminuria identifies a novel rare variant in CUBN and additional genes, in 33,985 Europeans with and without diabetes

Identifying rare coding variants associated with albuminuria may open new avenues for preventing chronic kidney disease (CKD) and end-stage renal disease which are highly prevalent in patients with diabetes. Efforts to identify genetic susceptibility variants for albuminuria have so far been limited with the majority of studies focusing on common variants.\n\nWe performed an exome-wide association study to identify coding variants in a two phase (discovery and replication) approach, totaling to 33,985 individuals of European ancestry (15,872 with and 18,113 without diabetes) and further testing in Greenlanders (n = 2,605). We identify a rare (MAF: 0.8%) missense (A1690V) variant in CUBN (rs141640975, {beta}=0.27, p=1.3 x 10-11) associated with albuminuria as a continuous measure in the combined European meta-analyses. Presence of each rare allele of the variant was associated with a 6.4% increase in albuminuria. The rare CUBN variant had 3 times stronger effect in individuals with diabetes compared to those without (pinteraction: 5.4 x 10-4, {beta}DM: 0.69, {beta}nonDM: 0.20) in the discovery meta-analyses. Geneaggregate tests based on rare and common variants identify three additional genes associated with albuminuria (HES1, CDC73, and GRM5) after multiple testing correction (P_bonferroni<2.7 x 10-6).\n\nThe current study identifies a rare coding variant in the CUBN locus and other potential genes associated with albuminuria in individuals with and without diabetes. These genes have been implicated in renal and cardiovascular dysfunction. These findings provide new insights into the genetic architecture of albuminuria and highlight novel target genes and pathways for prevention of diabetes-related kidney disease.\n\nSignificance statementIncreased albuminuria is a key manifestation of major health burdens, including chronic kidney disease and/or cardiovascular disease. Although being partially heritable, there is a lack of knowledge on rare genetic variants that contribute to albuminuria. The current study describes the discovery and validation, of a new rare gene mutation (~1%) in the CUBN gene which associates with increased albuminuria. Its effect multiplies 3 folds among diabetes cases compared to non diabetic individuals. The study further uncovers 3 additional genes modulating albuminuria levels in humans. Thus the current study findings provide new insights into the genetic architecture of albuminuria and highlight novel genes/pathways for prevention of diabetes related kidney disease.

genetics↗