Biology subjects

Goyette, P.

Publications and source records attributed to Goyette, P..

6 recordsLinked to original sources

bioRxiv2025

Inflammatory bowel disease risk gene C1ORF106 regulates actin dynamics in intestinal epithelial cells

Background and aimsC1ORF106 has previously been associated with inflammatory bowel diseases (IBD) via large-scale genetic studies. Increased intestinal permeability is a hallmark of IBD and is observed in at-risk individuals prior to the appearance of clinical symptoms. C1ORF106 was previously shown to regulate intestinal barrier permeability through the regulation of adherens junction stability and through the formation of tight junctions, which impacted actin assembly. However, the downstream impact and molecular mechanisms involved in actin regulation by C1ORF106 havent been explored. Our study aimed at identifying which pathways involved in intestinal epithelial barrier regulation and F-actin regulation are impacted by C1ORF106 and its IBD-associated variant. MethodsWe knocked down (KD) the expression of C1ORF106 in human colonic epithelial cells and characterized the function of the 333F variant in intestinal epithelial spheroid cultures obtained from patient-derived human induced pluripotent stem cell (hiPSC). We measured barrier permeability and characterized spheroid formation, actin regulation and cell migration though immunofluorescence, western blots and permeability assays. ResultsC1ORF106 KD leads to impaired cortical actin belt dynamics and regulation of stress fiber formation, resulting in increased cell constriction, impaired barrier permeability, cell polarity and cell migration. Moreover, we demonstrated that an inhibition of ROCK rescues the actin belt and cell polarity phenotypes in C1ORF106 KD cells, demonstrating that C1ORF106 regulates these phenotypes through a ROCK-dependent mechanism. We also observed an altered nmMYO2-P localization in C1ORF106 KD cells associated with the formation of Vacuolar Apical Compartments (VACs), which are important for 3D epithelial spheroid formation. We observed a similar impact on cell polarity in intestinal epithelial spheroids obtained from hiPSC carrying the 333F variant, providing additional support that this pathway is involved in disease development. ConclusionWe provide insights into the molecular mechanisms by which C1ORF106 controls actin dynamics to regulate intestinal epithelial integrity. summaryC1ORF106 and its inflammatory bowel disease-associated genetic variant regulate intestinal barrier permeability through the regulation of tight junction formation and cell polarity in epithelial cells. This regulation is associated with altered F-actin dynamics that are ROCK-dependent.

genetics↗

bioRxiv2022

Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases

BackgroundGenome wide association studies (GWAS) have identified and validated more than 200 genomic loci associated with the inflammatory bowel disease (IBD), although for most the causal gene remains unknown. Given the importance of myeloid cells in IBD pathogenesis, the current study aimed to uncover the role of genes within IBD genetic loci that are endogenously expressed in this cell lineage. MethodsThe open reading frames (ORF) of 43 genes from IBD-associated loci were expressed via lentiviral transfer in the THP-1 model of human monocytes and the impact of each of these on the cells transcriptome was analyzed using a novel RNA sequencing-based approach. We used a combination of genetic and pharmacologic approaches to validate our findings in the THP-1 line with further validation in human induced pluripotent stem cell (hiPSC)-derived-monocytes. ResultsThis functional genomics screen provided evidence that genes in four IBD GWAS loci (PTGIR, ZBTB40, SLC39A11 and NFKB1) are involved in controlling S100A8 and S100A9 genes expression, which encode the two subunits of calprotectin (CP). We demonstrated that increasing PTGIR expression and/or stimulating PTGIR signaling resulted in increased CP expression in THP-1. This was further validated in hiPSC-derived monocytes. Conversely, knocking-down PTGIR endogenous expression and/or inhibiting PTGIR signaling led to decreased CP expression. These analyses were extended to the known IBD gene PTGER4, whereby its specific agonist also led to increased CP expression. Furthermore, we demonstrated that the PTGIR and PTGER4 mediated control of CP expression was dependent on signaling via adenylate cyclase and STAT3. Finally, we demonstrated that LPS-mediated increases in CP expression could be potentiated by agonists of PTGIR and PTGER4, or diminished by their antagonists, with an opposite effect on TNF-alpha expression. ConclusionOur results support a causal role for the PTGIR, ZBTB40, SLC39A11 and NFKB1 genes in IBD, with all four genes regulating the expression of CP in myeloid cells, as well as an important role for the prostacyclin/prostaglandin biogenesis and signaling pathways in IBD susceptibility and pathogenesis. Author SummaryCrohns Disease and Ulcerative colitis are the two main types of inflammatory bowel diseases (IBD). These are debilitating chronic inflammatory diseases of the digestive tract. IBD pathogenesis is complex and involves multiple different cell types within the intestinal mucosa. While over 200 regions of the genome have been associated with susceptibility to IBD, for most the causal gene remains to be identified. In the current study we have focused on genes from IBD loci that are endogenously expressed in monocytes or macrophages, given the importance of these cells in IBD pathogenesis. Specifically, we modulated the expression of 43 genes from within validated IBD loci, in a human monocyte/macrophage cell line, and determined the impact of this increased expression on the rest of the transcriptome. We found evidence that four of these genes (PTGIR, ZBTB40, SLC39A11 and NFKB1) control the expression of calprotectin, which is a proinflammatory molecule that is used as a marker of intestinal mucosal inflammation. We then elucidated how prostaglandin signaling via prostaglandin receptors PTGIR and PTGER4, another IBD gene, regulates calprotectin expression. This work provides evidence that all five genes are causal and provide the first link between calprotectin and disease susceptibility.

genetics↗

bioRxiv2021

Human enteric viruses shape disease phenotype through divergent innate immunomodulation

Altered enteric microorganisms in concert with host genetics shape inflammatory bowel disease (IBD) phenotypes. However, insight is limited to bacteria and fungi. We found virus like particles (VLPs) enriched from normal human colon resections, containing eukaryotic viruses and bacteriophages (collectively, the virome), actively elicited atypical anti-inflammatory innate immune programs. Conversely, IBD patient VLPs provoked inflammation, which was successfully dampened by healthy VLPs. The IBD colon tissue virome was perturbed, including enriched Picornovirus Enterovirus B, not previously observed in fecal virome studies. Mice with humanized healthy colon tissue viromes had attenuated intestinal inflammation while those with IBD-derived viromes exhibited exacerbated inflammation in a nucleic acid sensing-dependent fashion. Furthermore, there were detrimental consequences for IBD-associated MDA5 loss-of-function on patient intestinal epithelial cells exposed to healthy or IBD viromes. Our results demonstrate that innate recognition of either healthy or IBD human viromes autonomously influences disease phenotypes in IBD. Harnessing the virome may offer therapeutic and biomarker potential. One Sentence SummaryHuman viromes divergently shape host immunity and disease

immunology↗

bioRxiv2021

Functional screen of Inflammatory Bowel Disease genes reveals key epithelial functions

BackgroundGenetic studies have been tremendously successful in identifying genomic regions associated with a wide variety of phenotypes, although the success of these studies in identifying causal genes, their variants, and their functional impacts have been more limited. MethodsWe identified 145 genes from IBD-associated genomic loci having endogenous expression within the intestinal epithelial cell compartment. We evaluated the impact of lentiviral transfer of the open reading frame (ORF) of these IBD genes into the HT-29 intestinal epithelial cell line via transcriptomic analyses. Comparing the genes whose expression was modulated by each ORF, as well as the functions enriched within these gene lists, identified ORFs with shared impacts and their putative disease-relevant biological functions. ResultsAnalysis of the transcriptomic data for cell lines expressing the ORFs for known causal genes such as HNF4a, IFIH1 and SMAD3 identified functions consistent for what is known for these genes. These analyses also identified two major cluster of genes: Cluster 1 contained the known IBD causal genes IFIH1, SBNO2, NFKB1 and NOD2, as well as genes from other IBD loci (ZFP36L1, IRF1, GIGYF1, OTUD3, AIRE and PITX1), whereas Cluster 2 contained the known causal gene KSR1 and implicated DUSP16 from another IBD locus. Our analyses highlight how multiple IBD gene candidates impact on epithelial structure and function, including the protection of the mucosa from intestinal microbiota, and demonstrate that DUSP16, acts a regulator of MAPK activity and contributes to mucosal defense, in part via its regulation of the polymeric immunoglobulin receptor, involved in the protection of the intestinal mucosa from enteric microbiota. ConclusionsThis functional screen, based on expressing IBD genes within an appropriate cellular context, in this instance intestinal epithelial cells, resulted in changes to the cells transcriptome that are relevant to their endogenous biological function(s). This not only helped in identifying likely causal genes within genetic loci but also provided insight into their biological functions. Furthermore, this work has highlighted the central role of intestinal epithelial cells in IBD pathophysiology, providing a scientific rationale for a drug development strategy that targets epithelial functions in addition to the current therapies targeting immune functions.

genetics↗

bioRxiv2019

The effect of sex and underlying disease on the genetic association of QT interval and sudden cardiac death

BackgroundSudden cardiac death (SCD) accounts for ~300,000 deaths annually in the US. Men have a higher risk of SCD and are more likely to have underlying coronary artery disease (CAD) than women. In contrast, women are more likely to have arrhythmic events in the setting of inherited or acquired QT prolongation. Moreover, there is evidence of sex differences in the underlying genetics of QT interval duration. Using sex- and CAD-stratified analyses, we assess differences in genetic association between prolonged QT interval and SCD risk.\n\nMethodsWe examined 2,282 SCD subjects with autopsy-confirmed underlying disease from the Fingesture cohort and 3,561 Finnish controls. The SCD subjects were stratified by underlying disease (ischemic vs. non-ischemic) and by sex. We used logistic regression to test for association between the top QT interval associated SNP, rs12143842 (in the NOS1AP locus), and SCD risk. We also performed Mendelian randomization to test for causal association of QT interval in the various subgroups.\n\nResultsFemale SCD victims with underlying non-ischemic disease had the strongest association between rs12143842 and SCD risk (OR=1.37; 95% CI, 1.07-1.75) and the strongest causal association, established using Mendelian randomization, between prolonged QT interval and SCD (OR in SCD risk per SD increase in QT, 3.60; 95% CI, 1.22-10.49). Ischemic SCD victims, irrespective of sex, did not show an association between rs12143842 and SCD risk or a causal association for QT interval.\n\nConclusionsThis study provides evidence that the causal effect of QT prolongation on SCD risk differs by sex and underlying disease.

genetics↗

bioRxiv2017

A Comprehensive Evaluation of the Genetic Architecture of Sudden Cardiac Arrest

BackgroundSudden cardiac arrest (SCA) accounts for 10% of adult mortality in Western populations. While several risk factors are observationally associated with SCA, the genetic architecture of SCA in the general population remains unknown. Furthermore, understanding which risk factors are causal may help target prevention strategies.\n\nMethodsWe carried out a large genome-wide association study (GWAS) for SCA (n=3,939 cases, 25,989 non-cases) to examine common variation genome-wide and in candidate arrhythmia genes. We also exploited Mendelian randomization methods using cross-trait multi-variant genetic risk score associations (GRSA) to assess causal relationships of 18 risk factors with SCA.\n\nResultsNo variants were associated with SCA at genome-wide significance, nor were common variants in candidate arrhythmia genes associated with SCA at nominal significance. Using cross-trait GRSA, we established genetic correlation between SCA and (1) coronary artery disease (CAD) and traditional CAD risk factors (blood pressure, lipids, and diabetes), (2) height and BMI, and (3) electrical instability traits (QT and atrial fibrillation), suggesting etiologic roles for these traits in SCA risk.\n\nConclusionsOur findings show that a comprehensive approach to the genetic architecture of SCA can shed light on the determinants of a complex life-threatening condition with multiple influencing factors in the general population. The results of this genetic analysis, both positive and negative findings, have implications for evaluating the genetic architecture of patients with a family history of SCA, and for efforts to prevent SCA in highrisk populations and the general community.

genetics↗