The genetics of congenital heart disease: The role of advanced genomic approaches

As the leading non-infectious cause of paediatric morbidity and mortality worldwide, congenital heart disease (CHD) is a significant social and healthcare burden, especially in low- and lower-middle-income countries, including South Africa. The aetiology of CHD is poorly understood, though heritable genetic factors have been shown to contribute to the risk of CHD in individuals of European ancestry. In this review, we highlight the impact that advanced genomic approaches have had on the understanding of the role of genetics in CHD. We also summarise current knowledge of the genetics of CHD in Africa, and the challenges and opportunities for conducting genomic research in these populations. Chromosomal microarrays and next-generation sequencing platforms allow for high-throughput screening of patients for genetic mutations and show great potential for the identification of genetic causes of CHD. Advancing our understanding of the genetic architecture and risk factors associated with CHD in patients of African descent is the fi rst step towards improving CHD diagnosis and management. Therefore, exploring the genetics of CHD has the potential to improve the quality of life for children born with CHD in Africa, by enabling clinicians to identify familial inheritance patterns and predict recurrent risks and prognostic outcomes pre- and post-surgical intervention

Bariatric surgery and its impact on cardiovascular disease and mortality : A systematic review and meta-analysis

Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.Peer reviewedPostprin

STK39 polymorphisms and blood pressure: an association study in British Caucasians and assessment of cis-acting influences on gene expression

<p>Abstract</p> <p>Background</p> <p>Blood pressure (BP) has significant heritability, but the genes responsible remain largely unknown. Single nucleotide polymorphisms (SNPs) at the <it>STK39 </it>locus were recently associated with hypertension by genome-wide association in an Amish population; <it>in vitro </it>data from transient transfection experiments using reporter constructs suggested that altered <it>STK39 </it>expression might mediate the effect. However, other large studies have not implicated <it>STK39 </it>in hypertension. We determined whether reported SNPs influenced <it>STK39 </it>expression <it>in vivo</it>, or were associated with BP in a large British Caucasian cohort.</p> <p>Methods</p> <p>1372 members of 247 Caucasian families ascertained through a hypertensive proband were genotyped for reported risk variants in <it>STK39 </it>(rs6749447, rs3754777, rs35929607) using Sequenom technology. MERLIN software was used for family-based association testing. <it>Cis</it>-acting influences on expression were assessed <it>in vivo </it>using allelic expression ratios in cDNA from peripheral blood cells in 35 South African individuals heterozygous for a transcribed SNP in <it>STK39 </it>(rs1061471) and quantified by mass spectrometry (Sequenom).</p> <p>Results</p> <p>No significant association was seen between the SNPs tested and systolic or diastolic BP in clinic or ambulatory measurements (all p > 0.05). The tested SNPs were all associated with allelic expression differences in peripheral blood cells (p < 0.05), with the most significant association for the intronic SNP rs6749447 (P = 9.9 × 10^-4). In individuals who were heterozygous for this SNP, on average the G allele showed 13% overexpression compared to the T allele.</p> <p>Conclusions</p> <p><it>STK39 </it>expression is modified by polymorphisms acting in <it>cis </it>and the typed SNPs are associated with allelic expression of this gene, but there is no evidence for an association with BP in a British Caucasian cohort.</p

Increased Power for Detection of Parent-of-Origin Effects via the Use of Haplotype Estimation

Parent-of-origin (or imprinting) effects relate to the situation in which traits are influenced by the allele inherited from only one parent and the allele from the other parent has little or no effect. Given SNP genotype data from case-parent trios, the parent of origin of each allele in the offspring can often be deduced unambiguously; however, this is not true when all three individuals are heterozygous. Most existing methods for investigating parent-of-origin effects operate on a SNP-by-SNP basis and either perform some sort of averaging over the possible parental transmissions or else discard ambiguous trios. If the correct parent of origin at a SNP could be determined, this would provide extra information and increase the power for detecting the effects of imprinting. We propose making use of the surrounding SNP information, via haplotype estimation, to improve estimation of parent of origin at a test SNP for case-parent trios, case-mother duos, and case-father duos. This extra information is then used in a multinomial modeling approach for estimating parent-of-origin effects at the test SNP. We show through computer simulations that our approach has increased power over previous approaches, particularly when the data consist only of duos. We apply our method to two real datasets and find a decrease in significance of p values in genomic regions previously thought to possibly harbor imprinting effects, thus weakening the evidence that such effects actually exist in these regions, although some regions retain evidence of significant effects

Myocardial Ischemia and Reperfusion Leads to Transient CD8 Immune Deficiency and Accelerated Immunosenescence in CMV-Seropositive Patients

Rationale: There is mounting evidence of a higher incidence of coronary heart disease (CHD) in cytomegalovirus (CMV) seropositive individuals. Objective: The aim of this study was to investigate whether acute MI triggers an inflammatory T-cell response that might lead to accelerated immunosenescence in CMV-seropositive patients. Methods and Results: Thirty-four patients with acute MI undergoing primary PCI (PPCI) were longitudinally studied within 3 months following reperfusion (Cohort A). In addition, 54 patients with acute and chronic MI were analyzed in a cross-sectional study (Cohort B). CMV-seropositive patients demonstrated a greater fall in the concentration of terminally differentiated CD8 effector memory T cells (TEMRA) in peripheral blood during the first 30 min of reperfusion compared with CMV-seronegative patients (-192 vs. -63 cells/µl; p=0.008), correlating with the expression of programmed cell death-1 (PD-1) before PPCI (r=0.8; p=0.0002). A significant proportion of TEMRA cells remained depleted for at least 3 months in CMV-seropositive patients. Using high-throughput 13-parameter flow cytometry and HLA class I CMV-specific dextramers, we confirmed an acute and persistent depletion of terminally differentiated TEMRA and CMV-specific CD8+ cells in CMV-seropositive patients. Long-term reconstitution of the TEMRA pool in chronic CMV-seropositive post-MI patients was associated with signs of terminal differentiation including an increase in KLRG1 and shorter telomere length in CD8+ T cells (2225 bp vs. 3397 bp; p<0.001). Conclusions: Myocardial ischemia and reperfusion in CMV-seropositive patients undergoing PPCI leads to acute loss of antigen-specific, terminally differentiated CD8 T-cells, possibly through PD-1-dependent programmed cell death. Our results suggest that acute MI and reperfusion accelerate immunosenescence in CMV-seropositive patients

Stroke following percutaneous coronary intervention : type-specific incidence, outcomes and determinants seen by the British Cardiovascular Intervention Society 2007-12

Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: [email protected] reviewedPostprin

A novel RNA-mediated mechanism causing down-regulation of insulating promoter interactions in human embryonic stem cells

From Springer Nature via Jisc Publications RouterHistory: received 2021-02-10, accepted 2021-11-15, registration 2021-11-16, collection 2021-12, pub-electronic 2021-12-01, online 2021-12-01Publication status: PublishedFunder: British Heart Foundation; doi: http://dx.doi.org/10.13039/501100000274; Grant(s): RG/15/12/31616Funder: University of Manchester; doi: http://dx.doi.org/10.13039/501100000770Abstract: The genome-wide promoter interactome is primarily maintained and regulated by architectural proteins such as CTCF and cohesin. However, some studies suggest a role for non-coding RNAs (ncRNAs) in this process. We aimed to characterise the regulatory role of RNA-mediated promoter interactions in the control of gene expression. We integrated genome-wide datasets of RNA-chromatin and promoter-genome interactions in human embryonic stem cells (hESCs) to identify putative RNA-mediated promoter interactions. We discovered that CTCF sites were enriched in RNA-PIRs (promoter interacting regions co-localising with RNA-chromatin interaction sites) and genes interacting with RNA-PIRs containing CTCF sites showed higher expression levels. One of the long noncoding RNAs (lncRNAs) expressed in hESCs, Syntaxin 18-Antisense 1 (STX18-AS1), appeared to be involved in an insulating promoter interaction with the neighbouring gene, MSX1. By knocking down STX18-AS1, the MSX1 promoter-PIR interaction was intensified and the target gene (MSX1) expression was down-regulated. Conversely, reduced MSX1 promoter-PIR interactions, resulting from CRISPR-Cas9 deletion of the PIR, increased the expression of MSX1. We conclude that STX18-AS1 RNA antagonised local CTCF-mediated insulating promoter interactions to augment gene expression. Such down-regulation of the insulating promoter interactions by this novel mechanism may explain the higher expression of genes interacting with RNA-PIRs linked to CTCF sites

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

Alternative splicing—the production of multiple messenger RNA isoforms from a single gene—is regulated in part by RNA binding proteins. While the RBPs transformer2 alpha (Tra2α) and Tra2β have both been implicated in the regulation of alternative splicing, their relative contributions to this process are not well understood. Here we find simultaneous—but not individual—depletion of Tra2α and Tra2β induces substantial shifts in splicing of endogenous Tra2β target exons, and that both constitutive and alternative target exons are under dual Tra2α–Tra2β control. Target exons are enriched in genes associated with chromosome biology including CHEK1, which encodes a key DNA damage response protein. Dual Tra2 protein depletion reduces expression of full-length CHK1 protein, results in the accumulation of the DNA damage marker γH2AX and decreased cell viability. We conclude Tra2 proteins jointly control constitutive and alternative splicing patterns via paralog compensation to control pathways essential to the maintenance of cell viability

Data on cardiac lncRNA STX18-AS1 expression in developing human hearts and function during in vitro hESC-cardiomyocyte differentiation

This article presents data concerning STX18-AS1, a long noncoding RNA gene identified from a Genome-wide association study of Atrial Septal Defect (ASD). The data describes its expression patterns in human tissues and functions in regulating cardiomyocyte differentiation in vitro. STX18-AS1 is a lncRNA with a higher abundance in developing tissues, including hearts. Its transcription distribution within the embryonic hearts during key heart septation stages supports STX18-AS1’s association with risk SNPs for ASD. The CRISPR stem cell pool in which STX18-AS1 was knocked down, showed reduced CM differentiation efficiency and lower expression of key cardiac transcriptional factors. This indicated its regulative role in supporting the lineage specification from cardiac mesoderm into cardiac progenitors and cardiomyocytes. These data can benefit the understanding of human embryonic heart developmental biology, and the time-course changes of cardiac transcriptional factors during in vitro cardiomyocyte differentiation from human embryonic stem cells