Mitochondrial control region alterations and breast cancer risk: a study in South Indian population.

BACKGROUND: Mitochondrial displacement loop (D-loop) is the hot spot for mitochondrial DNA (mtDNA) alterations which influence the generation of cellular reactive oxygen species (ROS). Association of D-loop alterations with breast cancer has been reported in few ethnic groups; however none of the reports were documented from Indian subcontinent. METHODOLOGY: We screened the entire mitochondrial D-loop region (1124 bp) of breast cancer patients (n = 213) and controls (n = 207) of south Indian origin by PCR-sequencing analysis. Haplotype frequencies for significant loci, the standardized disequilibrium coefficient (D') for pair-wise linkage disequilibrium (LD) were assessed by Haploview Software. PRINCIPAL FINDINGS: We identified 7 novel mutations and 170 reported polymorphisms in the D-loop region of patients and/or controls. Polymorphisms were predominantly located in hypervariable region I (60%) than in II (30%) of D-loop region. The frequencies of 310'C' insertion (P = 0.018), T16189C (P = 0.0019) variants and 310'C'ins/16189C (P = 0.00019) haplotype were significantly higher in cases than in controls. Furthermore, strong LD was observed between nucleotide position 310 and 16189 in controls (D' = 0.49) as compared to patients (D' = 0.14). CONCLUSIONS: Mitochondrial D-loop alterations may constitute inherent risk factors for breast cancer development. The analysis of genetic alterations in the D-loop region might help to identify patients at high risk for bad progression, thereby helping to refine therapeutic decisions in breast cancer.

Association between fragile X premutation and premature ovarian failure: a case-control study and meta-analysis.

AIM: The aim of the present study was to investigate the association between FMR1 premutation and premature ovarian failure (POF) patients in Indian population, and a meta-analysis of published results was undertaken to clarify whether FMR1 premutation consistently contributed to the susceptibility. METHODS: A total of 289 POF samples and 360 control samples were included in the study. Repeat variation was checked using GeneScan technique. Results were analyzed with GeneMapper software. Meta-analysis was performed using the Open Meta-Analyst and STATA 12.0 software. The crude odds ratio with 95 % confidence interval (CI) was computed to assess the strength of the associations. RESULTS: The assayed case and control population showed 29 different CGG repeat sizes (alleles), ranging from 7 to 40. Within this population, we found that the CGG repeat length polymorphisms were within the normal range of 6-55 in both patients as well as control samples. Eleven case-control studies were included in the meta-analysis with a total of 1,313 POF cases and 3,132 control subjects. Our meta-analysis revealed that there was a significant difference in the incidence of FMR1 premutation between POF cases and control subjects with p value <0.001 (OR 5.41; 95 % CI 2.53, 11.61). CONCLUSIONS: We found no significant association between FMR1 CGG repeat premutation and POF in Indian population. However, the meta-analysis showed an increased risk of POF associated with a premutation, especially among populations from European descent. Further functional research should be performed to explain the inconsistent results in different ethnicities and POF susceptibility.

Screening of the galactose-1-phosphate uridyltransferase gene in Indian women with ovarian failure.

The present study was aimed at mutational screening of the gene coding for galactose-1-phosphate uridyltransferase in females with premature ovarian failure within an Indian population. A case-control-based study approach was used. It included females with premature ovarian failure (n = 108), primary amenorrhoea (n = 37) and secondary amenorrhoea (n = 9), and a control group of 136 women with a normal ovarian pattern. Gene sequencing analysis for the presence of mutations in the promoter and the coding regions of GALT has shown the absence of any mutation. A hexanucleotide deletion was found in the third intronic region of GALT in both cases and controls. These data support the hypothesis that there is no significant association between GALT mutations and ovarian failure, and hence the present authors conclude that there is no relationship between ovarian failure and GALT polymorphisms in Indian women.

Prevalence of chromosome defects in azoospermic and oligoastheno-teratozoospermic South Indian infertile men attending an infertility clinic.

The prevalence of chromosomal abnormalities in azoospermic and oligoastheno-teratozoospermic infertile men of South Indian origin undergoing assisted reproductive technologies was evaluated. In addition, the study aimed to investigate new abnormal karyotypes involving autosomes in azoospermia and sex chromosomes in oligoastheno-teratozoospermic individuals that are supposed to be rare. Metaphase chromosomes of 744 infertile men, including 272 men with azoospermia and 472 men with oligoastheno-teratozoospermia (OAT), were analysed using Giemsa-trypsin-Giemsa banding and fluorescence in-situ hybridization (FISH) wherever necessary. Chromosomal abnormalities were observed in 59 (7.9%) individuals of the total studied population. Among these, 30 out of 272 (11.0%) azoospermic men and 29 out of 472 (6.1%) infertile men with OAT showed chromosomal abnormalities. A strong and statistically significant association (OR = 1.89; P = 0.0235) of chromosomal abnormalities and sex chromosome abnormalities (OR = 4.29; P = 0.001) with azoospermia when compared with OAT was observed. In addition, six autosomal abnormalities associated with azoospermia and two abnormalities involving Y chromosome, which include a novel karyotype (mos 46,XY/51,XYYYYYY) in OAT individuals, were detected.

N-acetyl transferase 2 polymorphism and advanced stages of endometriosis in South Indian women.

Aylamine-N-acetyl transferase is a phase II detoxification enzyme encoded by the gene NAT2. Single nucleotide polymorphism (SNP) changes from the wild type NAT2 *4 allele result in allelic variants *5, *6 and *7. Homozygotes for the NAT2 *4 wild type are fast acetylators; heterozygotes with one wild-type allele and a variant NAT2 *5, *6 or *7 allele have reduced enzyme activity and individuals with two variant alleles are slow acetylators. Previous studies have implicated NAT2 as a susceptibility factor in endometriosis. This study investigated the NAT2 allele frequencies and genotype distributions in 252 unrelated women with endometriosis and 264 controls of South Indian origin. No differences were found between the frequencies of fast and slow acetylators in cases (34.9% and 65.1%) and controls (33.3% and 66.7%). Two NAT2 genotypes *7/*7 (1.2%) and *5/*6/*7 (1.6%) were detected in endometriosis cases only. Four new combinations, 6D (481 + 590 mutation), 7C (590 + 857), 7D (590 + 803 + 857) and 7E (481 + 590 + 803 + 857) were detected, which have not been reported earlier. Similar genotype and phenotype results were obtained in 33 affected sister-pairs. The case-control data from this study suggest there is no association between endometriosis and NAT2 in South Indian women; however, two new variant genotypes and seven SNP combinations were also identified in cases only, which suggests that the gene may still have some as yet undetermined role in the disease.

CYP1A1, GSTM1 and GSTT1 genetic polymorphism is associated with susceptibility to polycystic ovaries in South Indian women.

Polymorphic variants in the phase I enzyme, cytochrome P450 gene, may lead to increased toxification, whereas polymorphisms in the phase II enzyme, glutathione S-transferase genes, may result in impaired detoxification. Alterations in the activities of phase I drug metabolizing enzymes and phase II detoxification enzymes may cause abnormal functioning and formation of follicular cysts in the ovaries and thus causing an imbalance in the hormone profiles. This study aimed to investigate the relationship between genetic polymorphisms of CYP1A1 (T6235C), GSTM1 and GSTT1 in South Indian women with polycystic ovaries (PCO) using polymerase chain reaction-restriction fragment length polymorphism. The frequencies of variants of these genes were studied in 180 women with confirmed PCO and in 72 healthy fertile women with successful pregnancy record. No significant difference was found between the frequencies of GSTM1 and GSTT1 null genotypes in PCO cases and healthy controls. However, CYP1A1 Msp I homozygous mutants were strongly associated (P = 0.0139) with increased susceptibility to PCO. Three genotype combinations, CYP1A1 (mt/mt) with GSTM1 [-] and GSTT1 [-], CYP1A1 (wt/mt) with GSTM1 [-] and GSTT1 [-] and CYP1A1 (mt/mt) with GSTM1 [-], GSTT1 [+], were also observed in women with PCO. In conclusion, the presence of hyperinducible CYP1A1 (T6235C) mutant genotype and its mutants in combination with GSTM1 and GSTT1 null genotypes might cause an imbalance between phase I and phase II enzymes, and therefore may represent a risk factor for PCO.