Biology subjects

Masson, E.

Publications and source records attributed to Masson, E..

10 recordsLinked to original sources

bioRxiv2026

Context-dependent variant interpretation from Mendelian disease to genetic predisposition: a proof-of-concept using LPL

As genomic sequencing evolves beyond rare disease diagnostics toward population screening and precision medicine, clinical variant interpretation is increasingly challenged by variants whose clinical consequences depend on biological context. Current frameworks, including the ACMG/AMP guidelines, generally assign a single classification to each variant regardless of inheritance state or genetic context, potentially failing to communicate context-dependent clinical consequences. Here, we address this issue using loss-of-function variants in LPL as a uniquely informative model system in which residual physiological LPL activity can be directly quantified in vivo. By systematically integrating published biallelic LPL genotypes, physiological measurements, functional studies, and clinical phenotypes, we identified a biologically meaningful transition at approximately 10% residual physiological LPL activity. Activity below this level was predominantly associated with classical childhood-onset familial chylomicronemia syndrome (FCS), whereas higher activity was associated with phenotypic attenuation and modifier-dependent clinical expression. Furthermore, heterozygous loss-of-function variants exhibited an estimated penetrance of 5-7% for severe hypertriglyceridemia. We therefore propose a context-dependent framework in which biallelic complete- or near-complete loss-of-function genotypes are interpreted as causative for FCS, whereas heterozygous variants are interpreted as predisposing to severe hypertriglyceridemia while retaining recognition of FCS carrier status. Together, our findings demonstrate that clinical variant interpretation should integrate available biological context--including, where relevant, allelic configuration, residual biological function, and penetrance--rather than rely on the intrinsic molecular consequence of the variant alone. More broadly, this framework provides a conceptual model for interpreting variants across the continuum from Mendelian disease to genetic predisposition in the era of precision medicine.

genetics↗

bioRxiv2025

When splicing is not all or none: Implications for variant classification

Variants with intermediate functional effects--those that neither eliminate nor fully maintain normal gene function--represent an underrecognized source of genetic complexity and constitute a grey zone that challenges variant classification. Here, we address this issue using GT>GC (+2T>C) 5' splice-site variants as a tractable model, as approximately 15% of such substitutions retain variable amounts of wild-type (WT) transcript. Using residual WT transcript as a quantitative readout, we first show that disease-associated GT>GC variants known to generate substantial WT transcript (for example, SPINK1 c.194+2T>C, HBB c.315+2T>C, and BRCA2 c.8331+2T>C) consistently complicate classification efforts. We then carried out a locus-wide assessment of all 26 GT>GC substitutions in CFTR, applying SpliceAI delta donor-loss scores as an initial screen and cross-checking classifications in expert-curated database. This evaluation indicated that three variants with low or intermediate SpliceAI scores are likely to retain WT transcript. Minigene analyses of four selected CFTR variants, together with additional examination of a BAP1 GT>GC variant with conflicting clinical interpretations, illustrate the methodological challenges in predicting and experimentally quantifying residual WT transcript. These results emphasize that (i) in silico predictors cannot reliably discriminate between complete and partial splice disruption and (ii) experimental systems differ in their ability to detect subtle splicing outcomes. Overall, our integrative analysis shows that GT>GC variants generating appreciable WT transcript exemplify a broader class of intermediate-effect alleles that complicate both computational prediction and experimental assessment, underscoring the need for classification frameworks that incorporate quantitative functional data and better capture the continuum of variant effects.

genetics↗

bioRxiv2022

Impact of membrane lipid polyunsaturation on dopamine D2 receptor ligand binding and signaling

The heterogenous and dynamic constitution of the membrane fine-tunes signal transduction. In particular, the polyunsaturated fatty acid (PUFA) tails of phospholipids influence the biophysical properties of the membrane, production of second messengers, or membrane partitioning. Few evidence mostly originating from studies of rhodopsin suggest that PUFAs directly modulate the conformational dynamic of transmembrane proteins. However, whether such properties translate to other G protein-coupled receptors remains unclear. We focused on the dopamine D2 receptor (D2R), a main target of antipsychotics. Membrane enrichment in n-3, but not n-6, PUFAs potentiates ligand binding. Molecular dynamics simulations show that the D2R preferentially interacts with n-3 over n-6 PUFAs. Furthermore, even though this mildly affects signalling in heterologous systems, in vivo n-3 PUFA deficiency blunts the effects of D2R ligands. These results suggest that n-3 PUFAs act as allosteric modulators of the D2R and provide a putative mechanism for their potentiating effect on antipsychotic efficacy.

cell biology↗

bioRxiv2020

RNA secondary structure mediated by Alu insertion as a novel disease-causing mechanism

We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3-UTR of the SPINK1 gene as the cause of a novel pediatric disease. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that Alu_Ins could independently disrupt mRNA 3 end formation and/or affect other post-transcriptional processes such as nuclear export and translation, due to its particular location. However, the presence of Alu_Ins in the 3-UTR resulted in only an ~50% reduction in luciferase reporter activity compared to the wild-type, suggesting the involvement of additional mechanisms. Using RepeatMasker, we identified two Alu elements within SPINK1s third intron, both of which resided in an orientation opposite to that of Alu_Ins. Through RNAfold predictions and full-length gene expression assays designed to examine orientation-dependent interactions between Alu repeats, we present evidence linking the detrimental effect of Alu_Ins to extensive double-stranded RNA structures formed between Alu_Ins and pre-existing intronic Alu sequences. Our results reveal a novel pathogenetic mechanism involving an Alu insertion, highlighting the importance of considering interactions between new and pre-existing Alu elements in inverted orientations within disease-associated genes.

genetics↗

bioRxiv2020

p.E152K-STIM1 mutation deregulates Ca2+ signaling contributing to chronic pancreatitis.

Since deregulation of intracellular Ca2+ can lead to intracellular trypsin activation and STIM1 (stromal interaction molecule-1) protein is the main regulator of Ca2+ homeostasis in pancreatic acinar cells, we explored the Ca2+ signaling in 37 STIM1 variants found in three pancreatitis patient cohorts. Extensive functional analysis of one particular variant, p.E152K, identified in three patients, provided a plausible link between dysregulated Ca2+ signaling within pancreatic acinar cells and chronic pancreatitis susceptibility. Specifically, p.E152K, located within the STIM1 EF-hand and sterile -motif domain, increased the release of Ca2+ from the endoplasmic reticulum in patient-derived fibroblasts and transfected HEK293T cells. This event was mediated by altered STIM1-sarco/endoplasmic reticulum calcium transport ATPase (SERCA) interactions and enhanced SERCA pump activity leading to increased Store Operated Calcium Entry (SOCE). In the pancreatic AR42J cells expressing the p.E152K variant, Ca2+-signaling perturbations correlated with defects in trypsin activation and secretion, and increased cytotoxicity after cholecystokinin stimulation. Summary statementp.E152K-STIM1 variant found in pancreatitis patients leads to intracellular changes in calcium homeostasis through SERCA interaction, enabling intracellular trypsin activation and pancreatic acinar cell death.

cell biology↗

bioRxiv2019

The experimentally obtained functional impact assessments of GT>GC 5' splice site variants differ markedly from those predicted

GT>GC 5 splice site (or +2T>C) variants have been frequently reported to cause human genetic disease. However, although we have demonstrated that GT>GC variants in human disease genes may not invariably be pathogenic, none of the currently available splicing prediction tools appear to be capable of reliably distinguishing those GT>GC variants that generate wild-type transcripts from those that do not. Recently, SpliceAI, a novel deep residual neural network tool, has been developed for splicing prediction. Methodologically distinct from previous approaches that either rely on human-engineered features and/or which focus on short nucleotide windows adjoining exon-intron boundaries, SpliceAI assesses splicing determinants by evaluating 10,000 nucleotides of flanking contextual sequence to predict the functional role in splicing of each position in the pre-mRNA transcript. Herein, we evaluated the performance of SpliceAI in the context of three datasets of GT>GC variants, all of which had been characterized functionally in terms of their impact on mRNA splicing. The first two datasets refer to our recently described "in vivo" dataset of 45 disease-causing GT>GC variants and the "in vitro" dataset of 103 GT>GC substitutions. The third dataset comprised 12 BRCA1 GT>GC variants that were recently analyzed by saturation genome editing. We processed all GT>GC variants using the default settings of SpliceAI. Comparison of the SpliceAI-predicted and experimentally obtained functional impact assessments of the analyzed GT>GC variants revealed that although SpliceAI performed rather better than other prediction tools, it was still far from perfect. A key issue is that the impact of GT>GC (as well as GT>GA or +2T>A) variants that generated wild-type transcripts represents a quantitative change that can vary from barely detectable to almost full expression of wild-type transcripts, with wild-type transcripts often co-existing with aberrantly spliced transcripts. Our findings highlight the challenges that we still face in attempting to accurately identify splice-altering variants.

genetics↗

bioRxiv2019

5’ splice site GC>GT variants differ from GT>GC variants in terms of their functionality and pathogenicity

In the human genome, most 5 splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the non-canonical GC dinucleotide. The functionality and pathogenicity of 5 splice site GT>GC (i.e., +2T>C) variants have been extensively studied but we still know very little about 5 splice site GC>GT (+2C>T) variants. Herein, we sought to address this deficiency by performing a meta-analysis of identified +2C>T pathogenic variants together with a functional analysis of +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish a proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and pathogenicity and suggest that, in sharp contrast with +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants but might also improve our understanding of the evolutionary basis of switching between GT and GC 5 splice sites in mammalian genomes.

genetics↗

bioRxiv2019

Genetic analysis of the STIM1 gene in chronic pancreatitis

Chronic pancreatitis is a complex disease that involves many factors, both genetic and environmental. Over the past two decades, molecular genetic analysis of five genes that are highly expressed in human pancreatic acinar cells, namely PRSS1, PRSS2, SPINK1, CTRC and CTRB1/CTRB2, has established that a trypsin-dependent pathway plays a key role in the etiology of chronic pancreatitis. Since Ca2+ deregulation can lead to intracellular trypsin activation in experimental acute pancreatitis, we analyzed STIM1 (encoding stromal interaction molecule-1, the main regulator of Ca2+ homeostasis in pancreatic acinar cells) as a candidate modifier gene in French, German and Chinese patients with chronic pancreatitis. The French and German subjects were analyzed by Sanger sequencing whereas the Chinese subjects were analyzed by targeted next-generation sequencing confirmed by Sanger sequencing. A total of 37 rare coding variants (35 missense and 2 nonsense) were identified, which were enriched in patients as compared with controls [2.28% (47/2,057) vs. 0.99% (33/3,322); odds ratio = 2.33, P = 0.0001]. This is the first large case-control study to demonstrate a putative association of rare STIM1 coding variants with chronic pancreatitis. Functional analysis will be required to clarify whether or not the rare STIM1 variants detected predispose to pancreatitis.

genetics↗

bioRxiv2019

Artisanal and farmers bread making practices differently shape fungal species diversity in French sourdoughs

AO_SCPLOWBSTRACTC_SCPLOWPreserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to the Kazachstania genus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence of Kazachstania humilis in sourdoughs made with artisanal-like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and nonsourdough strains were found for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities.

ecology↗

bioRxiv2018

First estimation of the scale of canonical 5’ splice site GT>GC mutations generating wild-type transcripts and their medical genetic implications

It has long been known that canonical 5 splice site (5SS) GT>GC mutations may be compatible with normal splicing. However, to date, the true scale of canonical 5SS GT>GC mutations generating wild-type transcripts, both in the context of the frequency of such mutations and the level of wild-type transcripts generated from the mutation alleles, remain unknown. Herein, combining data derived from a meta-analysis of 45 informative disease-causing 5SS GT>GC mutations (from 42 genes) and a cell culture-based full-length gene splicing assay of 103 5SS GT>GC mutations (from 30 genes), we estimate that [~]15-18% of the canonical GT 5SSs are capable of generating between 1 and 84% normal transcripts as a consequence of the substitution of GT by GC. We further demonstrate that the canonical 5SSs whose substitutions of GT by GC generated normal transcripts show stronger complementarity to the 5 end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were able to accurately predict the functional impact of 5SS GT>GC mutations. Our findings imply that 5SS GT>GC mutations may not invariably cause human disease but should also help to improve our understanding of the evolutionary processes that accompanied GT>GC subtype switching of U2-type introns in mammals.

genetics↗