Maizbha Uddin Ahmed

Lung cancer risk in relation to nicotinic acetylcholine receptor, CYP2A6 and CYP1A1 genotypes in the Bangladeshi population

BACKGROUND CYP1A1, CYP2A6 and CHRNA5 are biologically plausible genes as risk factors for lung cancer but no studies have been reported in the Bangladeshi population. METHODS We conducted this study to determine the prevalence and role of CYP1A1, CYP2A6 and CHRNA5 polymorphisms together with tobacco smoking in the development of lung cancer in Bangladesh. A case-control study was carried out on 106 lung cancer patients and 116 controls to investigate three allelic variants of the CYP1A1 gene-rs4646903, rs1048943 and rs1799814; 2 variants of CYP2A6 (CYP2A6*1B1, CYP2A6*4) and 1 variant of CHRNA5 (rs16969968) using Polymerase Chain Reaction Restriction Fragment Length Polymorphism. RESULTS Lung cancer risk was estimated as odds ratio (OR) and 95% confidence interval (CI) using unconditional logistic regression models adjusting for age, sex and smoking. A significantly elevated lung cancer risk was associated with heterozygous, mutant and combined heterozygous plus mutant variants of CYP1A1 rs4646903. A significant association was also found for heterozygous and heterozygous plus mutant variants of rs1048943 which was in linkage disequilibrium with rs4646903. The risk of lung cancer was decreased significantly in individuals carrying at least one CYP2A6 deletion (CYP2A6*4) allele. No association with lung cancer risk was found for CHRNA5 rs16969968. When stratified by smoking, the effects of CYP1A1 and CYP2A6 polymorphisms on lung cancer susceptibility were found to be significant only in heavy smokers who had smoked 40 pack years or more (54% of all cases) but no associations were seen for lighter smokers. No association was also found with any polymorphism in the non-smokers in this study. CONCLUSIONS Our results indicate that the CYP1A1*2B allele (rs4646903 and rs1048943) is associated with an increased lung cancer risk and CYP2A6*4 is associated with a decreased lung cancer risk in the study population.

Loss of the proprioception and touch sensation channel PIEZO2 in siblings with a progressive form of contractures

Dominant mutations in PIEZO2, which codes for the principal mechanotransduction channel for proprioception and touch sensation, have been found to cause different forms of distal arthrogryposis. Some observations suggest that these dominant mutations induce a gain‐of‐function effect on the channel. Here, we report a consanguineous family with three siblings who showed short stature, scoliosis, gross motor impairment, and a progressive form of contractures involving the distal joints that is distinct from that found in patients with dominant mutations in PIEZO2. These siblings also displayed deficits in proprioception and touch sensation. Whole‐exome sequencing performed in the three affected siblings revealed the presence of a rare homozygous variant (c.2708C>G; p.S903*) in PIEZO2. This variant is predicted to disrupt PIEZO2 function by abolishing the pore domain. Sanger sequencing confirmed that all three siblings are homozygous whereas their parents and an unaffected sibling are heterozygous for this variant. Recessive mutations in PIEZO2 thus appear to cause a progressive phenotype that overlaps with, while being mostly distinct from that associated with dominant mutations in the same gene.

Breast cancer risk in relation to TP53 codon 72 and CDH1 gene polymorphisms in the Bangladeshi women.

Pharmacogenomic studies play a significant role in understanding the risk of breast cancer where genetic abnormalities are implicated as the etiology of cancer. Various polymorphisms of tumor suppressor gene TP53 and E-cadherin (CDH1) have been found to be associated with increased breast cancer risk worldwide. This study aimed to analyze the contribution of TP53 and CDH1 gene anomalies in breast cancer risk in the Bangladeshi breast cancer patients. For risk determination, 310 patients with breast cancer and 250 controls from Bangladeshi women were recruited who are matched up with age and use of contraceptives with patients. Genetic polymorphisms were detected by using polymerase chain reaction restriction fragment length polymorphism. A significant association was found between TP53Arg72Pro (rs1042522) and CDH1 -160 C/A (rs16260) polymorphisms and breast cancer risk. In case of P53rs1042522 polymorphism, Arg/Pro (P = 0.0053, odds ratio (OR) = 1.69) and Pro/Pro (P = 0.018, OR = 1.83) genotypes were associated with increased risk of breast cancer in comparison to the Arg/Arg genotype. Arg/Pro + Pro/Pro genotype and Pro allele also increased the risk of breast cancer (P = 0.002, OR = 1.73; P = 0.004, OR = 1.43, respectively). In case of CDH1rs16260 polymorphism, C/A heterozygote and combined C/A + A/A genotypes were found to be strongly associated (P = 0.005, OR = 1.67; P = 0.0037, OR = 1.68) with increased risk of breast cancer. The variant A allele also increased the breast cancer risk (P = 0.0058, OR = 1.52). The present study demonstrates that P53Arg72Pro and CDH1rs16260 polymorphisms are associated with elevated breast cancer risk in the Bangladeshi population.

Interaction of nalbuphine hydrochloride with deoxyribonucleic acid measured by fluorescence quenching.

The interaction of nalbuphine hydrochloride with calf thymus deoxyribonucleic acid was investigated by absorption and fluorescence titration techniques. Hypochromic effect was observed in the absorption spectra of nalbuphine. The fluorescence quenching of nalbuphine by DNA was found to be static according to Stern-Volmer constant at different temperature (2.257×103 L/mol and 1.678×103 L/mol at 298 K and 308 K respectively; binding constants (K) between calf thymus DNA and nalbuphine were 2.081×103 and 8.26×101 at 298 K and 308 K respectively). The binding numbers (n) were 0.9955 and 0.6762 with the standard deviation of 0.225 at 2 different temperatures which indicates mol ratio of Nalbuphine and DNA remains unchanged at different temperatures (298 K and 308 K). The binding affinity of nalbuphine to DNA was calculated at different temperatures and the stoichiometry of binding was characterized to be about 1 nalbuphine molecule per nucleotide. Calibration for nalbuphine, based on quenching titration data, was linear in the concentration range 6.3×10-6 to 6.4×10-4 mol/L. And these binding forces also indicate the binding site of Nalbuphine to be at the minor groove of DNA.

Genotypes and phenotypes of CYP3A in Bangladeshi population.

BACKGROUND To investigate whether interindividual variation in CYP3A levels can partly be explained by genetic polymorphisms, this study was designed to phenotype 200 healthy Bangladeshi subjects by measuring urinary ratio of 6β-hydroxy-cortisol/cortisol and to genotype all the subjects for the presence of CYP3A4*1B, *2, *4, *5, *6, *10 and *18 and CYP3A5*3 alleles. METHODS For phenotyping, cortisol and 6β-hydroxy-cortisol were extracted and quantified by HPLC from morning spot urine samples (n=200). Genotyping was done using the extracted genomic DNA from all the subjects followed by amplification of target alleles by PCR. Amplified DNA was digested by restriction enzymes (MboII, XcmI, BsmAI, ClaI, HinfI, HpyCH4III, HpaII and RsaI) followed by gel electrophoresis and sequencing to identify the targeted alleles. RESULTS The ratio of 6β-hydroxy-cortisol/cortisol ranged from 0.01 to 31.98 with an average of 3.91. No sample (n=200) was positive for CYP3A4*2, *4, *5, *6, *10 and *18 alleles. Two samples heterozygous for CYP3A4*1B (1.0%) and twenty six samples with the genotype CYP3A5*1/*1 (13.0%) were found to have relatively high 6β-hydroxy-cortisol/cortisol ratios. CONCLUSION CYP3A4 variant alleles are present at a low frequency in the Bangladeshi population whereas 50% of the Bangladeshi population carrying a CYP3A5*3/*3 genotype appear to show lower 6β-hydroxy-cortisol/cortisol ratios compared with those with a CYP3A5*1/*1 genotype.

Effect of socio-economic status and estimation of lipid peroxidation and antioxidant in preeclamptic pregnant women: a case-control study

Objective: Increased extent of lipid peroxidation and decreased antioxidant defense has been postulated as a major contributor to the development of preeclampsia. The present study was conducted to determine the serum level of malondialdehyde (MDA) and vitamin C in these patients. Methods: This research was conducted as a case–control study to assess the extent of lipid peroxidation and antioxidant status in 150 preeclampsia patients and 174 healthy pregnant women. Lipid peroxidation was assessed by measuring serum MDA level, and antioxidant defense was evaluated for serum vitamin C by UV spectrophotometric method. Independent sample t test and Pearson’s correlation test were used for the statistical analysis with statistical software package SPSS, version 16.0 (SPSS, Inc., Chicago, IL). Results: Our study found significantly higher level of MDA (p < 0.05) and significantly lower level of vitamin C (p < 0.05) in preeclampsia patients in comparison to the control subjects. Pearson’s correlation analysis revealed that there was negative correlation between the serum level of MDA and vitamin C for both patient (r = −0.057, p = 0.669) and control groups (r = −0.128, p = 0.487). Analysis of socio-economic data revealed that preeclampsia was more prevalent among the rural pregnant than the urban pregnant women (OR 1.44, 95% CI 0.665–3.14, p = 0.352). It was also observed that primigravida pregnant were at higher risk for the development of preeclampsia than the multigravida pregnant women (OR 1.87, 95% CI 0.868–4.04, p = 0.108). Conclusions: Elevated serum MDA and depleted serum vitamin C may be associated with the development of preeclampsia.

Prevalence of CYP2C19 alleles, pharmacokinetic and pharmacodynamic variation of clopidogrel and prasugrel in Bangladeshi population

The extent to which cytochrome P450 (CYP) 2C19 genotype influences the effectiveness of clopidogrel remains uncertain due to considerable heterogeneity between studies. We used the polymerase chain reaction restriction fragment length polymorphism (PCR‐RFLP) method for genotyping loss of function (LOF) allele, CYP2C19*2 and gain of function (GOF) allele, CYP2C19*17 in 163 patients undergoing PCI and 165 healthy volunteers from an ethnically distinctive Bangladeshi population. Thirty‐eight patients took prasugrel and 125 patients took clopidogrel among whom 30 patients had their clopidogrel active metabolites (CAM) determined by LC‐MS/MS 1–1.5 h after clopidogrel intake. All patients who underwent PCI had their P2Y12 per cent inhibition (PRI) measured by VerifyNow System. The impact of different genotypes on CAM and PRI were also determined. We did not find significant variation of CYP2C19*2 (P > 0.05) and CYP2C9*17 (P > 0.05) alleles among healthy volunteers and patients. CAM concentration as well as PRI by clopidogrel varied significantly (P < 0.05) based on genotypic variation of CYP2C19*2 and CYP2C19*17 individually. Such influence was not observed in case of prasugrel. Genotypic variation did not impact PRI but as a whole PRI by prasugrel was better than that of clopidogrel (P < 0.05). Due to presence of both of alleles the effect on PRI by clopidogrel could not be predicted, effectively indicating possible involvement of other factors. Genotype guided clopidogrel dose adjustment would be beneficial and therefore we propose mandatory genotyping before clopidogrel dosing. Prasugrel proved to be less affected by genotypic variability, but due to lack of sufficient long‐term toxicity data, caution would be adopted before substituting clopidogrel.

Genetic polymorphisms of GSTM1, GSTP1 and GSTT1 genes and lung cancer susceptibility in the Bangladeshi population

ABSTRACT Objective To verify possible associations between polymorphisms of glutathione S-transferase Mu (GSTM1), glutathione S-transferase θ (GSTT1) and glutathione S-transferase Pi (GSTP1) genes and susceptibility to lung cancer. Methods A total of 106 lung cancer patients and 116 controls were enrolled in a case-control study. The GSTM1 and GSTT1 were analyzed using PCR while GSTP1 was analyzed using PCR-restriction fragment length polymorphism. Risk of lung cancer was estimated as odds ratio at 95% confidence interval using unconditional logistic regression models adjusting for age, sex, and tobacco use. Results GSTM1 null and GSTT1 null genotypes did not show a significant risk for developing lung cancer. A significantly elevated lung cancer risk was associated with GSTP1 heterozygous, mutant and combined heterozygous+mutant variants of rs1695. When classified by tobacco consumption status, no association with risk of lung cancer was found in case of tobacco smokers and nonsmokers carrying null and present genotypes of GSTM1 and GSTT1. There is a three-fold (approximately) increase in the risk of lung cancer in case of both heterozygous (AG) and heterozygous+mutant homozygous (AG+GG) genotypes whereas there is an eight-fold increase in risk of lung cancer in cases of GG with respect to AA genotype in smokers. Conclusions Carrying the GSTM1 and GSTT1 null genotype is not a risk factor for lung cancer and GSTP1Ile105Val is associated with elevated risk of lung cancer.

Association of TP53 codon 72 and CDH1 genetic polymorphisms with colorectal cancer risk in Bangladeshi population

Till now no pharmacogenetic study of TP53 codon 72 (Arg72Pro) and CDH1 rs16260 (-160C<A) genes has been reported on Bangladeshi population relating those with colorectal cancer. So the aim of the study is to determine whether there is an elevated risk of colorectal cancer development with TP53 codon 72 and CDH1 rs16260 genetic polymorphism in Bangladeshi population for the first time. To investigate the association of these two SNPs, we conducted a case-control study with 288 colorectal cancer patients and 295 healthy volunteers by using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. We found an increased risk of association between Arg/Pro heterozygosity (adjusted OR=2.58, 95% CI=1.77-3.77, p<0.05) and Pro/Pro mutant homozygosity (adjusted OR=2.92, 95% CI=1.78-4.78, p<0.05) along with the combined genotype (Arg/Pro+Pro/Pro) (adjusted OR=2.70, 95% CI=1.90-3.82, p<0.05) and colorectal cancer predisposition. In case of CDH1 rs16260 polymorphism, C/A heterozygous and A/A mutant homozygous are significantly (p<0.05) found to be associated with colorectal cancer risk with adjusted OR of 1.94 and 2.63, respectively. The combined genotype of C/A and A/A was also found to be strongly associated with colorectal cancer risk compared to C/C genotype (adjusted OR=2.02, 95% CI=1.42-2.87, p<0.05). In conclusion, heterozygosity and mutant homozygosity as well as the combination of both TP53 Arg72Pro and CDH1 rs16260 polymorphisms are responsible to increase the risk of colorectal cancer development in Bangladeshi population.

Genotype-phenotype variability in human CYP3A locus in Nepalese people residing in Bangladesh.

OBJECTIVES The study has been designed to phenotype 200 Nepalese people residing in Bangladesh by measuring urinary ratio of 6β-hydroxycortisol/cortisol (metabolic ratio) and to genotype all the subjects for the presence of CYP3A4*1B, *2, *4, *5, *6, *10, *18, CYP3A5*3, and *6 alleles. METHODS Cortisol and 6β-hydroxycortisol were extracted and quantified from morning spot urine samples (n = 200) by HPLC. Genotyping was carried out using the extracted genomic DNA by amplification of target alleles by PCR. Amplified DNA was digested by appropriate restriction enzymes followed by gel electrophoresis and sequencing to identify the targeted alleles. RESULTS A wide ratio of 6β-hydroxycortisol/cortisol was found (0.71 - 10.61) with an average of 4.41. No sample (n = 200) was found positive for CYP3A4*1B, *2, *4, *5, *6, *10, *18, and CYP3A5*6 alleles. CYP3A5*1/*1, *1/*3, and *3/*3 genotype frequency were found to be 20%, 20%, and 60%, respectively. A significantly higher mean metabolic ratio (MR) ± SD (MR = 6.28 ± 3.43) was found for CYP3A5*1/*1 compared to both CYP3A5*1/*3 (MR = 3.68 ± 1.37) and CYP3A5*3/*3 (MR = 3.58 ± 1.95). CONCLUSION This study demonstrates the absence of common CYP3A4 variant alleles in Nepalese people residing in Bangladesh whereas Nepalese people carrying the CYP3A5*1/*1 genotype appear to show a significantly higher 6β-hydroxycortisol/cortisol ratios compared to those with CYP3A5*3/*3 genotype.