Showing papers by "Emmanuelle Masson published in 2021"

Scale and Scope of Gene-Alcohol Interactions in Chronic Pancreatitis: A Systematic Review.

Abstract: Background: Excessive alcohol consumption has long been known to be the primary cause of chronic pancreatitis (CP) but genetic risk factors have been increasingly identified over the past 25 years. The scale and scope of gene-alcohol interactions in CP nevertheless remain unclear. Methods: All studies that had obtained genetic variant data concurrently on alcoholic CP (ACP) patients, non-ACP (NACP) patients and normal controls were collated. Employing normal controls as a common baseline, paired ORACP and ORNACP (odds ratios associated with ACP and NACP, respectively) values were calculated and used to assess gene-alcohol interactions. Results: Thirteen variants involving PRSS1, SPINK1, CTRC, CLDN2, CPA1, CEL and CTRB1-CTRB2, and varying from very rare to common, were collated. Seven variants had an ORACP > ORNACP, which was regarded as an immediate indicator of gene-alcohol interactions in CP. Variants with an ORACP < ORNACP were also found to interact with alcohol consumption by virtue of their impact on age at first pancreatitis symptoms in ACP. Conclusions: This study revealed evidence for extensive gene-alcohol interactions in CP. Our findings lend support to the hypothesis that alcohol affects the expression of genetically determined CP and highlight a predominant role of weak-effect variants in the development of ACP.

NGS mismapping confounds the clinical interpretation of the PRSS1 p.Ala16Val (c.47C>T) variant in chronic pancreatitis.

Abstract: We read with interest the recent publication by Weiss and colleagues, which addressed the pitfalls of using next-generation sequencing (NGS) to diagnose PRSS1 variants in chronic pancreatitis (CP).1 Specifically, having failed to authenticate an NGS-identified ‘ PRSS1 c.47C>T (p.Ala16Val) variant’ by Sanger sequencing the PRSS1 gene in the supposed carrier, they postulated that this artefact could have arisen from sequence reads emanating from one of PRSS1 ’ highly homologous and closely linked (7q34) pseudogenes, PRSS3P2 . Herein, we address another NGS-related pitfall that contributes to confusion in relation to the clinical interpretation of PRSS1 p.Ala16Val. p.Ala16Val is the third most commonly detected rare PRSS1 variant in CP; its putative pathological involvement is supported by its ability to increase trypsinogen autoactivation.2 ClinVar, however, ascribes to it conflicting interpretations of pathogenicity (ie, likely benign (1); pathogenic (3) and uncertain significance (2)).3 The main reason for this appears to be its relatively high allele frequency (ie, 0.006607) in all gnomAD V.2.1.1 …

Chronic Pancreatitis: The True Pathogenic Culprit within the SPINK1 N34S-Containing Haplotype Is No Longer at Large.

Abstract: A diverse range of loss-of-function variants in the SPINK1 gene (encoding pancreatic secretory trypsin inhibitor) has been identified in patients with chronic pancreatitis (CP). The haplotype harboring the SPINK1 c.101A>G (p.Asn34Ser or N34S) variant (rs17107315:T>C) is one of the most important heritable risk factors for CP as a consequence of its relatively high prevalence worldwide (population allele frequency ≈ 1%) and its considerable effect size (odds ratio ≈ 11). The causal variant responsible for this haplotype has been intensively investigated over the past two decades. The different hypotheses tested addressed whether the N34S missense variant has a direct impact on enzyme structure and function, whether c.101A>G could affect pre-mRNA splicing or mRNA stability, and whether another variant in linkage disequilibrium with c.101A>G might be responsible for the observed association with CP. Having reviewed the currently available genetic and experimental data, we conclude that c.-4141G>T (rs142703147:C>A), which disrupts a PTF1L-binding site within an evolutionarily conserved HNF1A-PTF1L cis-regulatory module located ∼4 kb upstream of the SPINK1 promoter, can be designated as the causal variant beyond reasonable doubt. This case illustrates the difficulties inherent in determining the identity of the causal variant underlying an initially identified disease association.

Splicing Outcomes of 5' Splice Site GT>GC Variants That Generate Wild-Type Transcripts Differ Significantly Between Full-Length and Minigene Splicing Assays.

Abstract: Combining data derived from a meta-analysis of human disease-associated 5' splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15-18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated.

The reversion variant (p.Arg90Leu) at the evolutionarily adaptive p.Arg90 site in CELA3B predisposes to chronic pancreatitis.

Abstract: A gain-of-function missense variant in the CELA3B gene, pArg90Cys (c268C>T), has recently been reported to cause pancreatitis in an extended pedigree Herein, we sequenced the CELA3B gene in 644 genetically unexplained French chronic pancreatitis (CP) patients (all unrelated) and 566 controls No obvious loss-of-function variants were identified None of the six low-frequency or common missense variants detected showed significant association with CP Nor did the aggregate rare/very rare missense variants (n = 14) show any significant association with CP However, pArg90Leu (c269G>T), which was found in four patients but no controls, and affects the same amino acid as pArg90Cys, serves to revert pArg90 to the human elastase ancestral allele As pArg90Leu has previously been shown to exert a similar functional effect to that of pArg90Cys, our findings not only confirm the involvement of CELA3B in the etiology of CP but also pinpoint a new evolutionarily adaptive site in the human genome

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

Abstract: Since deregulation of intracellular Ca2+ can lead to intracellular trypsin activation, and stromal interaction molecule-1 (STIM1) 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 α-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) conformational change and enhanced SERCA pump activity leading to increased store-operated Ca2+ entry (SOCE). In 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.This article has an associated First Person interview with the first author of the paper.