Biology subjects

Tregouët, D.-A.

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

3 recordsLinked to original sources

bioRxiv2026

Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican

BackgroundSingle nucleotide variants in the non-coding genome can significantly alter disease risk, but identifying the function of SNVs is a challenge. Increasing numbers of variants of unknown significance have been associated with the risk of Stroke, Cerebral Small Vessel Disease and burden of White Matter Hyperintensities, but without biological validation, the significance of these findings is uncertain. MethodsWe use a Multiplexed Parallel Reporter Assay (MPRA) to assay the function of 44 SNVs associated with Cerebral Small Vessel Disease and stroke in EFEMP1, FOXF2, HAAO, KCNK3, NMT1, OPA1, RASL12, STAT3 and VCAN. A functional SNV in versican was further probed using transcriptional reporter and Chromatin Immunoprecipitation assays. ResultsWe identify 26 allele-specific enhancers in where the SNV either increases or decreases transcriptional activity. We validate rs13176921 as an SNV that significantly modulates an intronic enhancer in the matrisome protein Versican and show it affects mRNA levels of the gene. We identify that the transcription factor NKX3.1 binds to the region of this SNV. ConclusionsThus, using MRPA we were able to gain mechanistic insight into which GWAS-identified SNVs modulate transcriptional activity, and validate a functionally important SNV in Versican and provide a mechanism by which it controls its transcription.

genetics↗

bioRxiv2025

From paleness to albinism: Contribution of OCA2 exon 10 skipping to hypopigmentation

Pathogenic variants in the OCA2 gene result in oculocutaneous albinism. In humans and several other mammalian species, OCA2 is transcribed into two coding mRNAs, a major transcript that encodes the full-length protein and a minor transcript that skips in-frame exon 10 and has no identified function. By contrast, rodents and non-mammalian vertebrates only express the major transcript. Several rare variants of human OCA2 have been reported to be pathogenic due to increased exon 10 skipping. To understand the vulnerability of human OCA2 to exon 10 skipping and its impact on pigmentation, we first functionally tested a series of rare missense variants spread across exon 10. We found that each variant significantly influences the skipping ratio either positively or negatively. By combining human and murine sequences in functional assays, we found that the skipping ratio depends on particular exonic and intronic combinations. Next, we focused on the most frequent exonic single nucleotide variant of human OCA2, rs1800404-T (c.1065G>A/p.Ala355=), located in exon 10. We show that this variant significantly promotes exon 10 skipping on its own and exhibits an additive effect in cis to previously identified splicing variants likely contributing to their pathogenicity. Association studies reveal that rs1800404-T is tightly associated with lighter skin and hair pigmentation in a representative European population, as has been observed in other populations around the world. Our structural models of the skipped transcript-derived protein support causality by predicting that it could exert a dominant-negative effect, which is consistent with a dose-dependent hypopigmentation response in both pathological and physiological contexts. Overall, the modulation of OCA2 exon 10 skipping by both benign and pathogenic variants provides a basis for improving the genetic diagnosis of albinism, and paves the way for research into the molecular and evolutionary mechanisms behind human pigmentation diversity.

genetics↗

bioRxiv2021

Testing for association with rare variants in the coding and non-coding genome: RAVA-FIRST, a new approach based on CADD deleteriousness score

Rare variant association tests (RVAT) have been developed to study the contribution of rare variants widely accessible through high-throughput sequencing technologies. RVAT require to aggregate rare variants in testing units and to filter variants to retain only the most likely causal ones. In the exome, genes are natural testing units and variants are usually filtered based on their functional consequences. However, when dealing with whole-genome sequence (WGS) data, both steps are challenging. No natural biological unit is available for aggregating rare variants. Sliding windows procedures have been proposed to circumvent this difficulty, however they are blind to biological information and result in a large number of tests. We propose a new strategy to perform RVAT on WGS data: "RAVA-FIRST" (RAre Variant Association using Functionally-InfoRmed STeps) comprising three steps. (1) New testing units are defined genome-wide based on functionally-adjusted Combined Annotation Dependent Depletion (CADD) scores of variants observed in the GnomAD populations, which are referred to as "CADD regions". (2) A region-dependent filtering of rare variants is applied in each CADD region. (3) A functionally-informed burden test is performed with sub-scores computed for each genomic category within each CADD region. Both on simulations and real data, RAVA-FIRST was found to outperform other WGS-based RVAT. Applied to a WGS dataset of venous thromboembolism patients, we identified an intergenic region on chromosome 18 that is enriched for rare variants in early-onset patients and that was that was missed by standard sliding windows procedures. RAVA-FIRST enables new investigations of rare non-coding variants in complex diseases, facilitated by its implementation in the R package Ravages. Author SummaryTechnological progresses have made possible whole genome sequencing at an unprecedented scale, opening up the possibility to explore the role of genetic variants of low frequency in common diseases. The challenge is now methodological and requires the development of novel methods and strategies to analyse sequencing data that are not limited to assessing the role of coding variants. With RAVA-FIRST, we propose a novel strategy to investigate the role of rare variants in the whole-genome that takes benefit from biological information. Especially, RAVA-FIRST relies on testing units that go beyond genes to gather rare variants in the association tests. In this work, we show that this new strategy presents several advantages compared to existing methods. RAVA-FIRST offers an easy and straightforward analysis of genome-wide rare variants, especially the intergenic ones which are frequently left behind, making it a promising tool to get a better understanding of the biology of complex diseases.

genetics↗