Single-Nucleotide Polymorphisms of NKX2.5 Found in Congenital Heart Disease Patients of Mysore, South India

Conotruncal Heart Defects: A Narrative Review of Molecular Genetics, Genomics Research and Innovation

Congenital heart defects (CHDs) are most prevalent cardiac defects that occur at birth, leading to significant neonatal mortality and morbidity, especially in the developing nations. Among the CHDs, conotruncal heart defects (CTDs) are particularly noteworthy, comprising a significant portion of congenital cardiac anomalies. While advances in imaging and surgical techniques have improved the diagnosis, prognosis, and management of CTDs, their molecular genetics and genomic substrates remain incompletely understood. This expert review covers the recent advances from January 2016 onward and examines the complexities surrounding the genetic etiologies, prevalence, embryology, diagnosis, and clinical management of CTDs. We also emphasize the known copy number variants and single nucleotide variants associated with CTDs, along with the current planetary health research efforts aimed at CTDs in large cohort studies. In all, this comprehensive narrative review of molecular genetics and genomics research and innovation on CTDs draws from and highlights selected works from around the world and offers new ideas for advances in CTD diagnosis, precision medicine interventions, and accurate assessment of prognosis and recurrence risks.

The role of NKX2-5 gene polymorphisms in congenital heart disease (CHD): a systematic review and meta-analysis

BACKGROUND

The gene NKX2-5 is a key transcription factor that plays an essential role in normal cardiac development. Although some recent studies have studied the role of polymorphisms in the NKX2-5 gene in congenital heart diseases (CHDs), the results were not consistent and remained uncertain. Therefore, we conduct a review of literature and investigate the association of genetic polymorphisms with CHDs.

RESULTS

We selected seventeen studies regarding the association of NKX2-5 gene rs2277923 polymorphism with CHDs. Overall, in all the tested genetic models, the 63A > G polymorphism was not significantly associated with increased congenital heart defects risk. We used pooled odds ratios (OR) to calculate the association of CHDs with rs2277923 including allelic model: OR 1.00, 95% CI 0.82-1.21; homozygote model: OR 0.95, 95%CI 0.68-1.33, recessive model: OR 0.89 CI 0.70-1.13, heterozygote model: OR: 1.09, 95%CI 0.87-1.37, dominant model: OR 1.08 CI 0.82-1.42 and overdominant model: OR 1.17 CI 1.01-1.35. In addition, our analysis suggests that no publication bias exists in this meta-analysis.

CONCLUSIONS

Our findings suggested that 63A > G polymorphism in the NKX2-5 gene was not significantly associated with congenital heart defects. However, in the future, more studies with increased sample size are required that may provide us more definite conclusions.

Association between congenital heart disease and NKX2.5 gene polymorphisms: systematic review and meta-analysis

Aim: To analyze the association of NKX2.5 gene with congenital heart disease (CHD), and to determine if the variants rs703752, rs3729753 and rs2277923 increase the risk for developing CHD. Materials & methods: PubMed, EBSCO and Web of Science databases were screened to identify eligible studies. Through a comprehensive meta-analysis software, the association between NKX2.5 gene variants and susceptibility of CHD was calculated by pooled odd ratio (ORs) and 95% CI. Results: We observed that the allelic model of rs703752 and rs2277923 increased the risk in the overall population: OR = 1.24; 95% CI: 1.00-1.55; Z p-value = 0.049; OR = 1.18; 95% CI: 0.01-1.37; Z p-value = 0.036; respectively. Conclusion: Our results suggested that the rs703752 and rs2277923 polymorphisms of the NKX2.5 gene are associated with CHD.

Whole-exome sequencing and homozygosity mapping identify variants in NCOR1 and MAP2K3 associated with non-syndromic congenital heart defects

Background

Homozygosity mapping is an efficient gene mapping method applicable to recessive disorders. It can detect homozygous segments of identical haplotype structures shared at a higher frequency among ventricular septal defect (VSD) and tetralogy of Fallot (TOF) cases. This study aims to identify the recessive genes involved in congenital heart disease (CHD) cases by homozygosity mapping. A total of 36 CHD cases of Indian origin were recruited based on inclusion and exclusion criteria, disease severity, and hole size. Of these, ten prediagnosed VSD and TOF cases were selected for homozygosity mapping. For in silico validation of variations, overlapping gene variants were analyzed from 26 cases based on pathogenecity and haploinsufficiency scores.

Results

Genome-wide homozygosity mapping identified 34 homozygous regions with a maximum block length of 80 bp marked for the CHD samples under study. A total of 4863 genes were identified in these 34 homozygous regions, which were present across almost all chromosomes except chromosomes 4, 8, 12, and 13. The homozygosity region found in chromosome 17 revealed genes for CHD manifestation. This homozygous region contained VSD- and TOF-related genes—Nuclear Corepressor 1 (NCOR1) and Mitogen-Activated Protein Kinase Kinase 3 (MAP2K3). In silico validation identified damaging variants for NCOR1 and MAP2K3. Three variants, G207C, C241T, and G244A, were found on exon 2 in the transcript NM_001190438 for NCOR1. Three variants were also found for MAP2K3, namely G194T and C199T in exon 5 and C578T in exon 8 in the transcript NM_002756. All these variants were present in the protein kinase domain.

Conclusion

Presence of homozygous regions identifies recessive genes leading to disease severity. Defects in recessive genes NCOR1 and MAP2K3 are responsible for abnormal myogenesis, resulting in CHD manifestation.

Combined effects of AKT serine/threonine kinase 1 polymorphisms and environment on congenital heart disease risk: A case-control study

This study aimed to explore the combined association between AKT serine/threonine kinase 1 (AKT1) polymorphisms and congenital heart disease (CHD) risk, meanwhile, the role of AKT1 single polymorphism on CHD was also analyzed.In the first, AKT1 polymorphisms were genotyped in 130 CHD patients and 145 healthy people with the way of polymerase chain reaction-direct sequencing. The clinical data and genotypes, alleles between 2 groups were compared by χ test and the genotype distributions in the control group were checked by Hardy-Weinberg equilibrium. The relative risk strength of disease based on genetic variant was revealed using odds ratio (OR) with 95% confidence interval (95%CI).In 3 polymorphisms of AKT1 (rs1130214, rs2494732, rs3803300), the GT/TT genotype of rs1130214 in cases and controls had a significant frequency difference (P = .04) and was 1.71 times risk developing CHD, compared with AA (OR = 1.71, 95%CI = 1.02-2.86), and T allele had 1.63 times risk for carriers (OR = 1.63, 95%CI = 1.05-2.54). Similarly, both rs3803300 GG genotype and G allele had obvious differences between case and control groups (P < .05) and it was closely associated with CHD susceptibility. At the same time, the combined effects of rs1130214, rs3803300 and family history, smoking were found in our study.AKT1 rs1130214, rs3803300 polymorphisms are associated with the increased susceptibility to CHD. Environmental factors are found the interaction with AKT1 polymorphisms. Further study is needed to verify this conclusion.

A comprehensive in silico analysis, distribution and frequency of human Nkx2-5 mutations; A critical gene in congenital heart disease

Introduction: Congenital heart disease (CHD) affects 1% to 2 % of live births. The Nkx2-5 gene, is known as the significant heart marker during embryonic evolution and it is also necessary for the survival of cardiomyocytes and homeostasis in adulthood. In this study, Nkx2-5 mutations are investigated to identify the frequency, distribution, functional consequences of mutations by using computational tools.

Methods: A complete literature search was conducted to find Nkx2-5 mutations using the following key words: Nkx2-5 and/or CHD and mutations. The mutations were in silico analyzed using tools which predict the pathogenicity of the variants. A picture of Nkx2-5 protein and functional or structural effects of its variants were also figured using I-TASSER and STRING.

Results: A total number of 105 mutations from 18 countries were introduced. The most (24.1%) and the least (1.49%) frequency of Nkx2-5 mutations were observed in Europe and Africa, respectively. The c.73C>T and c.533C>T mutations are distributed worldwide. c.325G>T (62.5%) and c.896A>G (52.9%) had the most frequency. The most numbers of Nkx2-5 mutations were reported from Germany. The c.541C>T had the highest CADD score (Phred score = 38) and the least was for c.380C>A (Phred score=0.002). 41.9% of mutations were predicted as potentially pathogenic by all prediction tools.

Conclusion: This is the first report of the Nkx2-5 mutations evaluation in the worldwide. Given that the high frequency of mutation in Germany, and also some mutations were seen only in this country, therefore, presumably the main origin of Nkx2-5 mutations arise from Germany.

Genomics and Epigenomics of Congenital Heart Defects: Expert Review and Lessons Learned in Africa

Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infrastructure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated. We present an expert review on CHD with lessons learned on Africa. We found variable CHD phenotype prevalence in Africa across countries and populations. There are important gaps and paucity in genomic studies of CHD in African populations. Among the available genomic studies, the key findings in Africa were variants in GATA4 (P193H), MTHFR 677TT, and MTHFR 1298CC that were associated with atrial septal defect, ventricular septal defect (VSD), Tetralogy of Fallot (TOF), and patent ductus arteriosus phenotypes and 22q.11 deletion, which is associated with TOF. There were no data on epigenomic association of CHD in Africa, however, other studies have shown an altered expression of miR-421 and miR-1233-3p to be associated with TOF and hypermethylation of CpG islands in the promoter of SCO2 gene also been associated with TOF and VSD in children with non-syndromic CHD. These findings signal the urgent need to develop and implement genetic and genomic research on CHD to identify the hereditary and genome-environment interactions contributing to CHD. These projected studies would also offer comparisons on CHD pathophysiology between African and other populations worldwide. Genomic research on CHD in Africa should be developed in parallel with next generation technology policy research and responsible innovation frameworks that examine the social and political factors that shape the emergence and societal embedding of new technologies.

Associations of NKX2-5 Genetic Polymorphisms with the Risk of Congenital Heart Disease: A Meta-analysis

The NKX2-5 gene is a vital regulator of cardiac formation and development. Recently, the roles of NKX2-5 63A>G polymorphism and 606G>C polymorphism in congenital heart disease (CHD) have been extensively studied, with conflicting results. The aim of the present study was to better elucidate the associations between NKX2-5 genetic polymorphisms and CHD risk through a meta-analysis. Eligible articles were searched in PubMed, MEDLINE, EMBASE, Google Scholar and CNKI up to December 2015. Odds ratios (ORs) and 95 % confidence intervals were used to detect any potential associations between NKX2-5 genetic polymorphisms and CHD risk. Heterogeneity between studies was assessed with Q test and I (2) statistic. Subgroup analysis and sensitivity analysis were performed to test the reliability and stability of the results, and funnel plots were applied to estimate publication bias. A total of 13 case-control studies including 2245 CHD patients and 1953 healthy controls were analyzed. The overall meta-analysis results showed that NKX2-5 63A>G polymorphism and 606G>C polymorphism were not significantly associated with CHD risk. Subgroup analysis was further performed for NKX2-5 63A>G polymorphism based on types of CHD and ethnicity of study population, and similar negative results were found in all subgroups. Our findings suggested that NKX2-5 63A>G polymorphism and 606G>C polymorphism may not be implicated in the pathogenesis of CHD.

A Comprehensive In Silico Analysis on the Structural and Functional Impact of SNPs in the Congenital Heart Defects Associated with NKX2-5 Gene-A Molecular Dynamic Simulation Approach

Congenital heart defects (CHD) presented as structural defects in the heart and blood vessels during birth contribute an important cause of childhood morbidity and mortality worldwide. Many Single nucletotide polymorphisms (SNPs) in different genes have been associated with various types of congenital heart defects. NKX 2–5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including Atrial septal defect (ASD), Atrial ventricular block (AVB), Tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional modification of its encoded protein. In this study, we retrieved SNPs from the database (dbSNP), followed by identification of potentially deleterious Non-synonymous single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein altering its biological function. The most important SNP that was found using our approach was rs137852685 R161P, which was predicted to cause the most damage to the structural features of the protein. Mapping nsSNPs in genes such as NKX 2–5 would provide valuable information about individuals carrying these polymorphisms, where such variations could be used as diagnostic markers.

Regulation of fetal gene expression in heart failure

During the processes leading to adverse cardiac remodeling and heart failure, cardiomyocytes react to neurohumoral stimuli and biomechanical stress by activating pathways that induce pathological hypertrophy. The gene expression patterns and molecular changes observed during cardiac hypertrophic remodeling bare resemblance to those observed during fetal cardiac development. The re-activation of fetal genes in the adult failing heart is a complex biological process that involves transcriptional, posttranscriptional and epigenetic regulation of the cardiac genome. In this review, the mechanistic actions of transcription factors, microRNAs and chromatin remodeling processes in regulating fetal gene expression in heart failure are discussed.

Transcription factor pathways and congenital heart disease

Congenital heart disease is a major cause of morbidity and mortality throughout life. Mutations in numerous transcription factors have been identified in patients and families with some of the most common forms of cardiac malformations and arrhythmias. This review discusses transcription factor pathways known to be important for normal heart development and how abnormalities in these pathways have been linked to morphological and functional forms of congenital heart defects. A comprehensive, current list of known transcription factor mutations associated with congenital heart disease is provided, but the review focuses primarily on three key transcription factors, Nkx2-5, GATA4, and Tbx5, and their known biochemical and genetic partners. By understanding the interaction partners, transcriptional targets, and upstream activators of these core cardiac transcription factors, additional information about normal heart formation and further insight into genes and pathways affected in congenital heart disease should result.