Congenital septal defects in Karachi, Pakistan: an update of mutational screening by high-resolution melting (HRM) analysis of MTHFR C677T.

BACKGROUND: Congenital heart defects (CHDs) are the heart structural malformations present at birth. Septal defects account for 40% of CHD, including atrial, ventricular and atrioventricular septal defects. In Pakistan, the prevalence of CHD is 3.4 in 1000, and a study estimated that 60,000 babies are born with CHD annually. Methylenetetrahydrofolate reductase (MTHFR), a chief enzyme, involved in the folate metabolism. The missense mutation, C677T (rs1801133), exists in MTHFR gene, results in a MTHFR thermolabile variant having low enzymatic activity. The study is aim to identify the MTHFR C677T variant association with septal defects. METHODS: Samples of 194 CHD patients (age [Formula: see text]= 5.8 ± 5.1) and 50 normal echo controls (age [Formula: see text]= 6.0 ± 4.9), confirmed by pediatric consultant, were collected. Extracted DNA, quantified by agarose gel electrophoresis and nanodrop, was screened for SNP by high-resolution melting (HRM). Further, HRM results were confirmed using restriction analysis and sequencing. HRM was simply and precisely genotyped the samples within 3 h at low cost. RESULTS: Genotypic data suggested that heterozygous mutant (CT) was frequent in congenital septal defect patients (0.26) which was higher than controls (0.143), p > 0.05. Mutant (TT) genotype was not found in this study. CONCLUSIONS: rs1801133 has lack of significant association with congenital septal defects. The absence of TT genotype in this study suggesting the role of natural selection in targeted population. HRM is an easy, fast and next generation of PCR, which may be used for applied genomics.

Tetra-primers ARMS-PCR Based Association Analyses of Synonymous and Intronic Variants in the ADAM12 Gene with Susceptibility to Knee Osteoarthritis: A Case-Control Study.

Genetic variations in a disintegrin and metalloprotease 12 (ADAM12) gene may contribute to develop Osteoarthritis (OA) that is characterized by cartilage matrix degradation and osteophytes formation. Therefore, the aim of present study was to analyze the association between the ADAM12 gene variants and knee OA predisposition. Tetra-primers ARMS-PCR was employed, to genotype the ADAM12 gene polymorphisms (rs1044122 and rs1871054) in 400 knee OA patients and equal number of age-matched controls. The association between ADAM12 gene variants and OA susceptibility was estimated using the Chi-square, logistic regression, haplotypes and linkage analyses. A significant association of rs1044122 (genotype: χ2 = 18.94; P < 0.001, allele: χ2 = 19.10; P < 0.001) and rs1871054 (genotype: χ2 = 10.04; P = 0.007, allele: χ2 = 10.57; P = 0.001) was observed with increased OA susceptibility. The variant genotype of rs1044122 increased OA risk more than twice [odds ratio (OR) 2.20; P = 0.001] and the risk was higher in females (OR 2.43; P = 0.001). The variant genotype of rs1871054 was perceived to almost double the risk in females (OR 1.97; P = 0.003). Moreover, a significant association of rs1044122 and rs1871054 under the additive genetic model (P < 0.001 and P = 0.002, respectively) was observed. The targeted ADAM12 gene polymorphisms, showed significant association with knee OA susceptibility. Females harboring the polymorphisms might be at risk. Besides, the haplotype CC of rs1044122 and rs1871054 in the ADAM12 gene may double knee OA risk. These findings may help in determining the etiology of OA and recognizing the people at risk of developing knee OA.

Association between obesity and risk of knee osteoarthritis.

The study was designed to investigate the association between obesity and the risk of knee osteoarthritis, recruiting 400 knee osteoarthritis patients and an equal number of controls. After the informed consent, diagnosed patients from Jinnah Post Graduate Medical Centre, Karachi were included as "cases". Age-matched individuals without the disease were included as "controls". Sociodemographic data were taken from each participant. Characteristics were compared by odds ratio and chi-square using SPSS 20 software. Obesity (OR 3.29; 95% CI 2.40-4.51), female gender (OR 2.87; 95% CI 1.94-4.25) and family history (OR 3.61; 95% CI 2.69-4.85) were found to be significantly associated with osteoarthritis (p<0.001). Highest OR was found in case of stair climbing >10 flights/d (OR 6.08; 95% CI 4.16-8.89; p<0.001), whereas heavy lifting (>25 kg/d for > 4 hr) was observed as another major factor with OR of 5.24 (95% CI 3.54-7.75; p<0.001) that elevates the risk. The study concluded that obesity is significantly associated with osteoarthritis and obese individuals (BMI>25 kg/m2) are at high risk of disease development. Furthermore, family history, prolonged standing (>2 h/d for >1 yr), heavy lifting (>25 kg/d for > 4 hr), stair climbing (>10 flights/d) and sitting on the floor (>5 h/d) might also be associated with knee osteoarthritis.

Phylogenetic analysis of HDV isolates from HBsAg positive patients in Karachi, Pakistan.

BACKGROUND: In spite of a high occurrence of Hepatitis Delta in the province of Sindh in Pakistan, no genetic study of Hepatitis Delta virus (HDV) isolates from this region was carried out. The aim of this study is to analyze the genetic proximity within local HDV strains, and relationship with other clades of HDV, using phylogenetic analysis. RESULTS: Phylogenetic analysis of nucleotide sequences of the Hepatitis Delta Antigen (HDAg) R0 region obtained in this study, showed considerable diversity among the local strains with a potential subgroup formation within clade I. The multiple sequence alignment of predicted amino acids within clade I showed many uncommon amino acid substitutions within some conserved regions that are crucial for replication and assembly of HDV. CONCLUSIONS: The studied strains showed a range of genetic diversity within HDV clade I. There is clustering of sequences into more than one group, along with formation of potential subgroup within clade I. Clustering shows the genetic closeness of strains and indicates a common origin of spread of HDV infection. Further phylogeny-based studies may provide more information about subgroup formation within clade I and may be used as an effective tool in checking and/or preventing the spread of hepatitis D virus infection in this region.

Nuclear hormone receptor co-regulators.

The critical role of nuclear hormone receptor co-activators in gene expression has been extensively studied for the past few years. Co-regulators (co-activators and co-repressors) are known to utilize various enzymatic activities, in addition to molecular interactions, to modulate gene expression in response to hormonal signals. Recent studies that demonstrate the role of co-regulators in cancer and developmental disorders have revealed their possible role as targets of therapy. A greater understanding of the cellular physiology of co-regulators is necessary to explore the pathological ramifications of hormone-dependent diseases, and to discover new treatments.