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Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE243139 | GEO | 2025/08/05

REPOSITORIES: GEO

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Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD

Project description:Decoding the Variant-to-Function Relationship for LIPA, a Risk Locus for CAD

| PRJNA1016418 | ENA

Insights into function and regulation of microRNAs by decoding degradation dynamics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-20 | E-GEOD-72656 | biostudies-arrayexpress

Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-03-29 | GSE241691 | GEO

Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.

Project description:BackgroundSeveral genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray datasets in order to determine if the genotype had effect on expression of any gene transcript in aorta, mammary artery, carotid plaque and lymphoblastoid cells.Methodology/principal findingsAfter multiple testing correction, no genes were found to have relation to the rs2891168 risk genotype, either on a genome-wide scale or on a regional (8 MB) scale. The neighbouring ANRIL gene was found to have eight novel transcript variants not previously known from literature and these varied by tissue type. We therefore performed a detailed probe-level analysis and found small stretches of significant relation to genotype but no consistent associations. In all investigated tissues we found an inverse correlation between ANRIL and the MTAP gene and a positive correlation between ANRIL and CDKN2A and CDKN2B.Conclusions/significanceInvestigation of relation of the risk genotype to gene expression is complicated by the transcript complexity of the locus. With our investigation of a range of relevant tissue we wish to underscore the need for careful attention to the complexity of the alternative splicing issues in the region and its implications to the design of future gene expression studies.

| S-EPMC2765615 | biostudies-literature

Identification of a novel transcriptional variant in the mouse Sry locus

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-10-01 | GSE151474 | GEO

A regulator of RNA Polymerase III at tRNA genes revealed by locus-specific proteome decoding

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-21 | GSE227470 | GEO

Insights into function and regulation of microRNAs by decoding degradation dynamics

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-01-20 | GSE72656 | GEO

High Shear Stress Enhances Endothelial Permeability in the presence of a CAD Risk Locus

Project description:Single nucleotide polymorphisms are exceedingly common in non-coding loci, yet their impact on cellular dysfunction–especially under stressed conditions associated with coronary artery disease (CAD)–is still unclear. Here we show that when exposed to external stressors, the presence of polymorphisms in the non-coding 9p21.3 locus increases endothelial monolayer and microvessel dysfunction; endothelial cells (ECs) derived from induced pluripotent stem cells of patients homozygous for this risk haplotype (R/R WT) differentiated similarly to their non-risk (N/N) and isogenic knockout (R/R KO) counterparts; monolayers exhibited greater permeability and ROS signaling when the risk locus was present. Addition of the inflammatory cytokine TNFa further enhanced EC monolayer permeability but independent of risk haplotype. When wall shear stress was applied to ECs in a microfluidic vessel, R/R WT vessels were more permeable at lower shear stresses than R/R KO vessels. Transcriptomes of sheared cells clustered more by risk haplotype than by patient or clone, resulting in significant differential regulation of EC function and junction genes versus static conditions. A subset of previously identified CAD risk genes invert expression patterns in the presence of high shear concomitant with aberrant cell-cell adhesion, vessel permeability, and the risk haplotype, suggesting that shear stress could be a unique regulator of non-coding loci and its impact on CAD.

2021-06-08 | GSE167861 | GEO

HoxD locus

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-23 | E-GEOD-45242 | biostudies-arrayexpress

Interaction between a haptoglobin genetic variant and coronary artery disease (CAD) risk factors on CAD severity in Singaporean Chinese population.

Project description:BackgroundHaptoglobin (Hp) is a plasma protein with strong anti-inflammation and antioxidant activities. Its plasma level is known to be inversely associated with many inflammatory diseases, including cardiovascular diseases. However, the association of HP genetic variants with coronary artery disease (CAD) severity/mortality, and how they interact with common CAD risk factors are largely unknown.MethodsWe conducted the analysis in a Singaporean Chinese CAD population with Gensini severity scores (N = 582) and subsequently evaluated the significant findings in an independent cohort with cardiovascular mortality (excluding stroke) as outcome (917 cases and 19,093 controls). CAD risk factors were ascertained from questionnaires, and stenosis information from medical records. Mortality was identified through linkage with the nationwide registry of births and deaths in Singapore. Linear regression analysis between HP genetic variant (rs217181) and disease outcome were performed. Interaction analyses were performed by introducing an interaction term in the same regression models.ResultsAlthough rs217181 was not significantly associated with CAD severity and cardiovascular mortality (excluding stroke) in all subjects, when stratified by hypertension status, hypertensive individuals with the minor T allele have more severe CAD (β = 0.073, SE = 0.030, p = 0.015) and non-hypertensive individuals with the T allele have lower risk for mortality (odds ratio = 0.771 (0.607-0.980), p = 0.033).ConclusionHP genetic variant is not associated with CAD severity and mortality in the general population. However, hypertensive individuals with the rs217181 T allele associated with higher Hp levels had more severe CAD while non-hypertensive individuals with the same allele had lower risk for mortality in the Chinese population.

| S-EPMC7549588 | biostudies-literature

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