Causal SNP regulating FAM13B expression identified for the Chr. 5q31 atrial fibrillation susceptibility locus

AbstractRationaleOur prior RNA sequencing study found that FAM13B gene expression in human left atrial appendages was strongly associated with an atrial fibrillation (AF) susceptibility-associated variant on chr. 5q31.ObjectiveTo identify the common genetic variant responsible for regulating FAM13B expression and the effect of FAM13B expression on cardiomyocyte gene expression in order to gain insight into the functional mechanism of the chr. 5q31 AF susceptibility locus.Methods and ResultsBy taking advantage of a smaller linkage disequilibrium block in African descent subjects and available chromatin conformation data, we identified the common single nucleotide polymorphism (SNP) rs17171731 as a candidate genetic variant controlling FAM13B gene expression in the left atrium. Functional analysis demonstrated that the AF risk allele of rs17171731 had less enhancer activity than the protective allele. Gel mobility shift studies determined that the risk allele bound to an additional protein that may function as a transcriptional repressor. Knockdown of FAM13B expression in stem cell-derived human cardiomyocytes (iCM) altered the expression of >1000 genes and modified the sodium current, consistent with increased susceptibility to atrial fibrillation. Transfection of GFP tagged FAM13B into iCMs demonstrated expression on the plasma membrane and at the Z-disk.ConclusionsThe chr. 5q31 AF risk variant was identified as rs17171731, with the risk allele having less enhancer activity, leading to decreased expression of FAM13B, which resides on the plasma membrane and the Z-disk, and appears to play a role in the regulation of cardiomyocyte gene expression and the late sodium current.

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A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression

10.1101/362277 ◽

2018 ◽

Author(s):

Sarada Ketharnathan ◽

Megan Leask ◽

James Boocock ◽

Amanda J. Phipps-Green ◽

Jisha Antony ◽

...

Keyword(s):

Gene Expression ◽

Hepg2 Cells ◽

Molecular Mechanisms ◽

Genetic Variant ◽

Fluorescent Protein ◽

Serum Urate ◽

Specific Gene ◽

Specific Expression ◽

Enhancer Activity ◽

Tissue Specific

ABSTRACTSeveral dozen genetic variants associate with serum urate levels, but the precise molecular mechanisms by which they affect serum urate are unknown. Here we tested for functional linkage of the maximally-associated genetic variant rs1967017 at the PDZK1 locus to elevated PDZK1 expression.We performed expression quantitative trait locus (eQTL) and likelihood analyses followed by gene expression assays. Zebrafish were used to determine the ability of rs1967017 to direct tissue-specific gene expression. Luciferase assays in HEK293 and HepG2 cells measured the effect of rs1967017 on transcription amplitude.PAINTOR analysis revealed rs1967017 as most likely to be causal and rs1967017 was an eQTL for PDZK1 in the intestine. The region harboring rs1967017 was capable of directly driving green fluorescent protein expression in the kidney, liver and intestine of zebrafish embryos, consistent with a conserved ability to confer tissue-specific expression. The urate-increasing T-allele of rs1967017 strengthens a binding site for the transcription factor HNF4A. siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells. Luciferase assays showed that the T-allele of rs1967017 gains enhancer activity relative to the urate-decreasing C-allele, with T-allele enhancer activity abrogated by HNF4A depletion. HNF4A physically binds the rs1967017 region, suggesting direct transcriptional regulation of PDZK1 by HNF4A.With other reports our data predict that the urate-raising T-allele of rs1967017 enhances HNF4A binding to the PDZK1 promoter, thereby increasing PDZK1 expression. As PDZK1 is a scaffold protein for many ion channel transporters, increased expression can be predicted to increase activity of urate transporters and alter excretion of urate.

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Mendelian Randomization Integrating GWAS, eQTL, and mQTL Data Identified Genes Pleiotropically Associated With Atrial Fibrillation

Frontiers in Cardiovascular Medicine ◽

10.3389/fcvm.2021.745757 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yaozhong Liu ◽

Biao Li ◽

Yingxu Ma ◽

Yunying Huang ◽

Feifan Ouyang ◽

...

Keyword(s):

Gene Expression ◽

Atrial Fibrillation ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Variant ◽

Mendelian Randomization ◽

Regulation Of Transcription ◽

Eqtl Analysis ◽

Genome Wide Association Studies ◽

Trait Loci

Background: Atrial fibrillation (AF) is the most common arrhythmia. Genome-wide association studies (GWAS) have identified more than 100 loci associated with AF, but the underlying biological interpretation remains largely unknown. The goal of this study is to identify gene expression and DNA methylation (DNAm) that are pleiotropically or potentially causally associated with AF, and to integrate results from transcriptome and methylome.Methods: We used the summary data-based Mendelian randomization (SMR) to integrate GWAS with expression quantitative trait loci (eQTL) studies and methylation quantitative trait loci (mQTL) studies. The HEIDI (heterogeneity in dependent instruments) test was introduced to test against the null hypothesis that there is a single causal variant underlying the association.Results: We prioritized 22 genes by eQTL analysis and 50 genes by mQTL analysis that passed the SMR & HEIDI test. Among them, 6 genes were overlapped. By incorporating consistent SMR associations between DNAm and AF, between gene expression and AF, and between DNAm and gene expression, we identified several mediation models at which a genetic variant exerted an effect on AF by altering the DNAm level, which regulated the expression level of a functional gene. One example was the genetic variant-cg18693985-CPEB4-AF axis.Conclusion: In conclusion, our integrative analysis identified multiple genes and DNAm sites that had potentially causal effects on AF. We also pinpointed plausible mechanisms in which the effect of a genetic variant on AF was mediated by genetic regulation of transcription through DNAm. Further experimental validation is necessary to translate the identified genes and possible mechanisms into clinical practice.

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Abstract 18159: A Functional Variant for Atrial Fibrillation Affects PITX2c Expression by Interacting With TFAP2a

Circulation ◽

10.1161/circ.132.suppl_3.18159 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Jiangchuan Ye ◽

Nathan R Tucker ◽

Elena Dolmatova ◽

Patrick T Ellinor

Keyword(s):

Atrial Fibrillation ◽

Risk Allele ◽

Transcriptional Start Site ◽

Embryonic Stem ◽

Homozygous Deletion ◽

High Linkage Disequilibrium ◽

Mobility Shift ◽

Enhancer Activity ◽

Functional Variants ◽

Cap Analysis

Background: To date, 17 loci associated with atrial fibrillation (AF) have been identified, and there are 4 regions at 4q25 around PITX2 gene strongly associated with AF. However, the functional variants at all known AF loci remain elusive. Methods and Results: Among the 4 AF loci at 4q25, we focused on one associated region of ~84 kb extending from Chr4: 111,520,926 to 111,604,727 that includes the PITX2 gene itself (defined as all SNPs with r 2 > 0.6 from the sentinel SNP rs1448818). To identify potential functional variants , we analyzed DNase hypersensitivity, histone modification and mammalian conservation from ENCODE and Roadmap Epigenomics Project. Additionally, cap analysis of gene expression (CAGE) data was also investigated. We identified 13 candidate regions, 5 of which showed enhancer activity in zebrafish skeletal muscle and heart. Using luciferase assays in a mouse atrial cell line (HL-1), we then identified one SNP (rs2595104) in which the T risk allele was associated with 31% decreased activity compared to the G non-risk allele (p = 0.007). rs2595104 lies ~10 kb upstream of PITX2c transcriptional start site and is in high linkage disequilibrium (LD) (r 2 = 0.67) with rs1448818. In silico investigation of rs2595104 using UniPROBE and HaploReg database revealed differential binding of each allele to activating enhancer binding protein 2 alpha (TFAP2a). Electrophoretic mobility shift assays showed that TFAP2a bound robustly to the non-risk G allele at rs2595104 but not to the risk T allele. Chromatin immunopricipitation followed by allele-specific qPCR in human embryonic stem cell-derived cardiomyocytes (hESC-CM) further suggested that TFAP2a was preferentially recruited to the non-risk G allele at rs2595104 in an AF-relevant cell type. hESC-CMs with homozygous deletion of rs2595104-containing enhancer using CRSPR-Cas9 expressed less PITX2c (35 ± 6%, p = 0.036), compared to the wild-type hESC-CMs. Finally, mutating the G allele at rs2595104 to T allele by CRSPR-Cas9 led to 21% reduction in PITX2c level in hESC-CMs (p = 0.027). Conclusion: We have found that the AF-associated SNP rs2595104 alters PITX2c expression via interaction with TFAP2a. Such a pathway may ultimately contribute to AF susceptibility at the PITX2 locus.

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P2730 Thrombin-induced slowly inactivating sodium current by protease-activated receptor PAR1 activation in human cardiomyocytes

European Heart Journal ◽

10.1016/s0195-668x(03)95508-4 ◽

2003 ◽

Vol 24 (5) ◽

pp. 508

Author(s):

C PINET

Keyword(s):

Sodium Current ◽

Human Cardiomyocytes

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Faculty Opinions recommendation of A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727840927.793535628 ◽

2017 ◽

Author(s):

Andrew S McCallion ◽

Paul Hook

Keyword(s):

Gene Expression ◽

Genetic Variant ◽

Vascular Diseases ◽

Endothelin 1

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Variation in VKORC1 Is Associated with Vascular Dementia

Journal of Alzheimer s Disease ◽

10.3233/jad-201256 ◽

2021 ◽

Vol 80 (3) ◽

pp. 1329-1337

Author(s):

Jure Mur ◽

Daniel L. McCartney ◽

Daniel I. Chasman ◽

Peter M. Visscher ◽

Graciela Muniz-Terrera ◽

...

Keyword(s):

Atrial Fibrillation ◽

Vascular Dementia ◽

Genetic Variant ◽

Warfarin Dose ◽

Uk Biobank ◽

Parental History ◽

Genome Wide ◽

History Of ◽

First Time ◽

The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

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