Altaf Ali

Mutational analysis of SCN5A gene in long QT syndrome

The SCN5A gene encodes for the INa channel implicated in long QT syndrome type-3 (LQTS-type-3). Clinical symptoms of this type are lethal as most patients had a sudden death during sleep. Screening of SCN5A in South Indian cohort by PCR-SSCP analyses revealed five polymorphisms — A29A (exon-2), H558R (exon-12), E1061E and S1074R (exon-17) and IVS25 + 65G > A (exon-25) respectively. In-silico and statistical analyses were performed on all the polymorphisms. Exon-2 of SCN5A gene revealed A282G polymorphism (rs6599230), resulting in alanine for alanine (A29A) silent substitution in the N-terminus of SCN5A protein. Exon-12 showed A1868G polymorphism (H558R — rs1805124) and its ‘AA’ genotype and ‘A’ allele frequency were found to be higher in LQTS patients pointing towards its role in LQTS etiology. Two polymorphisms A3378G (E1061E) and the novel C3417A (S1074R) were identified as compound heterozygotes/genetic compounds in exon-17 of SCN5A located in the DIIS6–DIIIS1 domain of the SCN5A transmembrane protein. IVS25 + 65G > A was identified in intron-25 of SCN5A. The ‘G’ allele was identified as the risk allele. Variations were identified in in-silico analyses which revealed that these genetic compounds may lead to downstream signaling variations causing aberrations in sodium channel functions leading to prolonged QTc. The compound heterozygotes of SCN5A gene polymorphisms revealed a significant association which may be deleterious/lethal leading to an aberrant sodium ion channel causing prolonged QTc.

Erratum to: Polymorphisms of extrinsic death receptor apoptotic genes (FAS −670 G>A, FASL −844 T>C) in coronary artery disease

Apoptosis plays an important role in atherogenesis and rupture of vulnerable plaques in coronary artery disease. FAS and FAS ligand (FASL) induce apoptosis when FAS binds to FAS-L. However sFas blocks apoptosis by binding to FAS and FASL or sFasL. The present study is sought to examine the role of extrinsic apoptotic genes (FAS, FASL) polymorphism and serum levels of FAS, FASL in the pathogenesis and susceptibility to CAD in south Indian population. The study included 300 CAD patients and 300 healthy controls. Lipid profiles, sFas, sFasL were estimated by commercially available kits. FAS −670 G>A, FASL −844 T>C genotypes were analyzed by PCR–RFLP. Secondary structures of pre mRNA were analyzed by the Vienna RNA webserver and gene–gene and gene–environment interactions were determined by MDR analysis. Total cholesterol, triglyceride and LDL levels were significantly high in CAD patients compared to the controls. Molecular analysis revealed that the frequency of the AA genotype of FAS (54 % vs 27 %) and CC genotypes of FASL (10.3 % vs 1.3 %) were high in CAD patients compared to controls. Secondary structure analysis of FAS and FASL confirmed our molecular analysis. sFas levels were low while serum sFasL were high in CAD patients. MDR analysis revealed synergistic effects of gene polymorphisms and additive effects of epidemiological factors on risk of CAD. Polymorphisms of FAS (−670 G/A), FASL (−844 T/C) and their circulating levels play an important role in the pathology of CAD.

MMP 1 circulating levels and promoter polymorphism in risk prediction of coronary artery disease in asymptomatic first degree relatives

Coronary artery disease (CAD) remains to be the prominent health problem in India, and its incidence is growing in developing countries as well. Matrix metalloproteinase 1 (MMP 1) is highly expressed in disruption-prone shoulder regions of the fibrous plaques. The present study aims to investigate association of MMP 1 gene polymorphisms (-1607 1G/2G) and serum circulating levels with CAD. The study includes 300 CAD patients, 100 FDRS, and 300 controls. ELISA and PCR-RFLP were performed to determine MMP 1 serum levels and genotypes respectively. MMP1 levels were high in CAD patients, followed by FDRS compared to controls (2.15±1.2ng/ml; 1.46±1.04ng/ml and 0.96±0.53ng/ml) respectively. ROC analysis showed the AUC at 95% CI of serum MMP-1 to be 0.83 and 0.73-0.94, respectively. The optimal cut-off point (sensitivity; specificity) of serum MMP 1 was >1.5ng/ml (0.74; 0.90). The 2G/2G genotype was associated with high MMP 1 circulating levels in CAD patients, and a similar trend was observed in FDRS and controls. The pre-mRNA secondary structure of the 2G allele is much more stable than 1G allele. Our results suggest MMP 1 serum levels and polymorphism as potential independent prognostic markers for future cardiovascular events. These may also help to stratify CAD patients and to identify susceptibility for CAD in asymptomatic healthy FDRS.

Atrial natriuretic peptide gene - a potential biomarker for long QT syndrome

This study highlights the possible implication of NPPA (natriuretic peptide precursor A) gene in the etiology of Long QT syndrome (LQTS) by population-based as well as familial study. Three SNPs of NPPA - C-664G, C1363A and T1766C were examined by molecular analyses in LQTS, controls and first degree relatives (FDRs). This study revealed a possible association of 1364 C>A SNP ‘C’ allele with LQTS (p = 0.0013). All three SNPs were in tight linkage disequilibrium. The familial study highlights the association of NPPA SNP with cLQTS and implicating it as a potential biomarker in South Indian population.

Biomarkers for Identifying Individuals at Risk of Alzheimer Disease

Background: Alzheimer Disease (AD), the most common form of dementia, is a progressive and irreversible neurodegenerative disorder. Promising preventative strategies includes identification of potential modifiable risk factors for AD that could help identify individual who are at risk of AD. This study focuses on identifying biochemical factors associated with non- familial AD. Methods: One hundred and ten individuals which included 55 AD patients and 55 healthy controls were recruited for the study. Patients clinically diagnosed by a neurologist as AD and controls with no clinical or family history of any neurological disease were subjected to Mini-Mental State Examination (MMSE) were evaluated for fourteen relevant biochemical markers using commercial kits. MDR analysis was carried out which is considered a basic machine learning tool for understanding the role of interaction and combination of the factors towards the outcome. PCA is performed to support the MDR interpretation. Through clustering analysis the probably causative factors towards the disease can be identified. Results: MDR analysis revealed that the overall best fit model included 10 factors which had a maximal testing accuracy of 61%, cross-validation consistency of 8/10. PCA analysis has further reduced the factors to Iron, TSAT, HDL, VitB12, FA, and Hcy which are important in disease initiation/progression. Apart from the cases, 9% of the controls who had lower MMSE also had low Iron, TSAT, HDL, VitB12, FA, and high Hcy. Conclusion: As per the results obtained, we would suggest a medical practice where, screening individuals above the age of 55 years with both MMSE and selected biochemical parameters (Iron, TSAT, HDL, VitB12, FA, and Hcy) should be carried out to identify those at risk of developing AD. Higher risk individuals can be suggested for modifications in diet/life style, enhancing certain nutritional components which may constitute promising strategies in postponing, slowing, and/or preventing cognitive decline in AD.

Genotype-phenotype correlation in long QT syndrome families.

Heterogeneity in clinical manifestations is a well-known feature in Long QT Syndrome (LQTS). The extent of this phenomenon became evident in families wherein both symptomatic and asymptomatic family members are reported. The study hence warrants genetic testing and/or screening of family members of LQTS probands for risk stratification and prediction. Of the 46 families screened, 18 probands revealed novel variations/compound heterozygosity in the gene/s screened. Families 1–4 revealed probands carrying novel variations in KCNQ1 gene along with compound heterozygosity of risk genotypes of the SCN5A, KCNE1 and NPPA gene/s polymorphisms screened. It was also observed that families- 5, 6 and 7 were typical cases of “anticipation” in which both mother and child were diagnosed with congenital LQTS (cLQTS). Families- 16 and 17 represented aLQTS probands with variations in IKs and INa encoding genes. First degree relatives (FDRs) carrying the same haplotype as the proband were also identified which may help in predictive testing and management of LQTS. Most of the probands exhibiting a family history were found to be genetic compounds which clearly points to the role of cardiac genes and their modifiers in a recessive fashion in LQTS manifestation.

AAT: A Comparative Study in HCM and DCM

Abstract Cardiomyopathies are the sub-acute, chronic disorders of the myocardium that result in cardiac muscle injury thus disrupting the normal contractile function of the heart. HCM and DCM are inflammatory disorders where the role of AAT as a disease marker and cardiac remodeler has been identified. AAT acts as a major serine protease inhibitor and immunomodulator with high degree of polymorphism. Its main role is inhibition of the matrix metalloproteinases, collagen and the enzyme elastase apart from ECM and microfibrillar components degradation. The present study aims to evaluate the role of AAT, in 83 HCM, 97 DCM patients and 100 Control individuals to identify its association with cardiomyopathy. Our results implicate the role of the Z and S alleles in the etiopathogenesis of HCM and DCM, and also their role in cardiomyocyte remodelling through ECM changes. Thus decreased production of AAT may lead to further damage of the myocardiocytes.