Shagufta Khaliq

P53 mutations, polymorphisms, and haplotypes in Pakistani ethnic groups and breast cancer patients

Inactivation of the p53 gene has been found to be associated with the pathogenesis of several neoplasias. Three biallelic polymorphisms in the p53 gene have been linked to predisposition to the development of various malignancies. These include a 16-bp duplication in intron 3 and BstU I and Msp I restriction fragment length polymorphisms (RFLPs) in exon 4 and intron 6, respectively. The prevalence of these polymorphisms was studied in breast cancer patients and nine major ethnic groups of Pakistan. Differences in allele frequencies for all three polymorphisms were observed among the various ethnic groups and breast cancer patients. The absence of the 16-bp duplication was common among the northern ethnic groups, being highest in the Hazara (0.90). The Msp I A1 allele frequency in the southern Makrani population was significantly higher in comparison with the other ethnic groups. In the cancer patients, the absence of the 16-bp duplication in combination with the BstU I Pro and absence of Msp I restriction site were the most frequent. In these patients, ten substitution mutations were found in the p53 gene, seven of which have been reported previously for breast cancer. The remaining three mutations have been found in other malignancies, but not in carcinoma of the breast.

The association of urinary interferon-gamma inducible protein-10 (IP10/CXCL10) levels with kidney allograft rejection

BackgroundInterferon-gamma inducible protein-10 (IP-10/CXCL10) is a chemokine involved in the alloimmune response against kidney allograft. We aimed to investigate the association of urinary CXCL10 protein levels with rejection in renal transplant patients.MethodsA total of 273 urine samples from (biopsy-proven) rejection and non-rejection patients and controls were included in this study. CXCL10 levels were analyzed for association with rejection.ResultsThe data showed statistically significant differences in the CXCL10 levels between rejection vs. non-rejection (pu2009<u20090.001). Among the rejection groups, statistically significant differences for CXCL10 levels were found between ACR vs. NAD (pu2009<u20090.001), ACR vs. BLR (pu2009=u20090.019) and AVR vs. NAD (pu2009=u20090.009). Receiver Operating Characteristic (ROC) curve analysis of CXCL10 showed an area under the curve (AUC) of 0.74 with 72% sensitivity and 71% specificity at 27.5xa0pg/ml between rejection and non-rejection group. Kaplan–Meier curve analysis among different levels of CXCL10 showed a better rejection-free graft survival in patients with <100xa0pg/ml when compared to >200xa0pg/ml (38u2009±u20096 vs. 12u2009±u20091.0 weeks; log-rank pu2009<u20090.001) and 100–200xa0pg/ml (38u2009±u20096 vs. 22u2009±u20099 weeks; log-rank pu2009=u20090.442) concentration.ConclusionThe results indicate significantly increased levels of CXCL10 protein in the urine at the time of allograft rejection. This association of urinary CXCL10 protein levels with rejection could provide an additional tool for the non-invasive monitoring of allograft rejection.

Unique molecular alteration patterns in von Hippel-Lindau (VHL) gene in a cohort of sporadic renal cell carcinoma patients from Pakistan.

BACKGROUNDnRenal cell carcinoma (RCC) is the most frequent form of kidney cancer in adults. Somatic mutations that inactivate the von Hippel-Lindau (VHL) gene are the most common cause of RCC. The frequencies of molecular changes in the VHL gene in RCCs vary among different populations. So far, a single chromosomal-based study has been reported from a South Asian population. This report presents, for the first time, the somatic changes and promoter hypermethylation in VHL in a cohort of 300 RCC patients from Pakistan.nnnMETHODSnTo identify mutations in the VHL gene, direct DNA sequencing was carried out. Epigenetic silencing was investigated by using methylation-specific polymerase chain reaction.nnnRESULTSnOur data showed molecular alterations in the VHL gene in 163 (54%) renal cell carcinoma patients. Somatic mutations were found in 87 (29%) patients and 35 novel mutations were identified. VHL promoter hyper-methylation analysis showed epigenetic changes in 106 (35%) out of 300 patients. Patients who had no evidence of molecular alterations in the VHL gene were significantly younger than patients who carried some molecular change. Molecular alterations in the VHL gene were not restricted to clear-cell RCCs (ccRCCs).nnnCONCLUSIONSnThis is the first report that identifies molecular aberrations in the VHL gene from a South Asian population. The frequency of somatic mutation is lower and that of promoter hypermethylation is higher when compared with data from other parts of the world. The data has important implications in the population-specific application of tailored preventive and therapeutic regimens in non-familial RCCs.

HLA class I and II polymorphisms in the Gujjar population from Pakistan

HLA polymorphisms at the HLA -A, -B, -C, -DRB and -DQB1 loci were investigated in the Gujjar population from the Punjab province of Pakistan. The Gujjars (nu2009=u200997) were genotyped using sequence specific primers for polymerase chain reaction. The allele and haplotype frequencies were calculated and a neighbor-joining (NJ) tree comparing the Gujjar with other populations was constructed. The class I allelic groups with a frequency greater than 10% include A*01, A*02, A*11, A*26 and A*31 at the HLA-A locus, B*08 and B*51 at the HLA-B locus and C*07 and C*14 at the HLA-C locus. Among the 12 allelic groups detected at the DRB1* locus, *03, *13, and *15 were present at frequencies higher than 10% whereas at the DQB1 locus, the allelic groups*06 and *02 accounted for over half of the Gujjar population. HLA-A*31-B*51-DRB1*13 was the most common (8.8%) haplotype in this population. A NJ tree revealed that the Pakistani Gujjar are closely related to the Golla tribe from Andhra Pradesh in India. The two populations are dedicated to the same profession, cattle breeding. HLA analyses of additional Punjab castes would provide valuable information for anthropological, organ transplantation and genetic disease studies.

Frequency of CCR5 Gene 32-bp deletion in Pakistani ethnic groups.

CCR5 is a G-protein-coupled chemokine receptor that is used as a co-factor by macrophage-tropic (M-tropic) isolates of human immunodeficiency virus-1 (HIV-1) to gain entry into host cells. A 32-bp deletion in the CCR5 gene (CCR5-Delta32) leads to the production of an altered gene product that prevents HIV-1 from entering the host cell. This study was carried out to determine prevalence of CCR5-Delta32 allele frequency in a large Pakistani population sample (n = 821) representing 10 ethnic groups. No individual was homozygous for the mutant allele and the frequency of the CCR5-Delta32 allele ranged from 0.62% to 3.57%. The CCR5-Delta32 allele frequency was generally lower in populations from southern Pakistan. The overall frequency of the CCR5-Delta32 allele in Pakistan was 2.31%, which is much lower than that found in European populations and similar to that in the Middle East. This is consistent with the historical records and genetic data that indicate a close genetic affinity among these populations. This study demonstrates that the Pakistani population is highly susceptible to M-tropic isolates of HIV-1 and public health measures need to be enforced with urgency if Pakistan is to avoid an HIV epidemic.

Analysis of the glutathione S-transferase genes polymorphisms in the risk and prognosis of renal cell carcinomas. Case-control and meta-analysis

BACKGROUNDnThe Glutathione S-transferases (GSTs) genes deletion polymorphisms have been associated with the progression of several cancers. The association studies between the 2 GSTs (GSTM1 and GSTT1) null polymorphisms with the susceptibility to renal cell carcinoma (RCC) have been inconclusive. Therefore, with the inclusion of our own data, we performed a comprehensive meta-analysis to assess the association between these 2 polymorphisms and the risk of RCC.nnnMETHODSnA systematic literature search was carried out for studies published in the PubMed, EMBASE, Cochrane library, and Google Scholar from 1997 to December 2014. Results were stated as pooled odds ratios (ORs) for nonparametric data after heterogeneity analysis with 95% CI using fixed effect or random effect model.nnnRESULTSnWe systematically selected 13 relevant studies after thorough searches from the databases. Data showed no association between the GSTM1 and the GSTT1 null genotypes and the risk of RCC (OR = 1.01; CI: 0.92-1.11; P = 0.89 for GSTM1 and OR = 1.14; CI: 0.91-1.42; P = 0.25 for GSTT1). No association was found when the data were stratified according to the geographical/ethnic basis, source of control, and the risk factor evaluation. Subgroup analysis of occupational exposure to pesticides showed an inverse association of the active genotypes of both GSTM1 and GSTT1 polymorphisms with the exposed group of RCC (P<0.00001 and P<0.00001, respectively). The combined null genotype of the GSTM1/GSTT1 significantly increased the susceptibility to RCC by 1.4-fold (P = 0.001). This association remained significant for the Asian populations in subgroup analysis (OR = 1.8; CI: 1.30-2.49; P = 0.0004).nnnCONCLUSIONnIn conclusion, this meta-analysis suggests that the 2 GSTs deletion polymorphisms independently have no association with the risk of RCC. However, combination of both deletions increases the risk of developing the RCC.

Analysis of CYP2C9 polymorphisms (*2 and *3) in warfarin therapy patients in Pakistan. Association of CYP2C9 polymorphisms (*2 and*3) with warfarin dose, age, PT and INR

Warfarin is a widely used anticoagulant characterized by having a narrow therapeutic index and exhibiting a wide range of inter-individual and inter-ethnic variation. Single nucleotide polymorphisms in hepatic VKORC1 and CYP2C9 genes causes decreased and increased metabolism of warfarin respectively. The objective of this study was to evaluate the allele frequency of CYP2C9 polymorphic variants *2 and *3 and the association of these allelic variants with PT/INR and daily/weekly dose of warfarin. Seventy-four patients with heart valve replacement were selected. Patients taking low warfarin dose (4.90–17.50xa0mg weekly) for at least last 3xa0months and had a stable INR in the range of 2–3 were included in this study. CYP2C9 polymorphism was analyzed by polymerase chain reaction followed by restriction fragment length polymorphism (PCR–RFLP) technique. Among 74 patients, 9 (12.1xa0%) showed to have *2 allele, whereas 11 (14.1xa0%) had *3 allele. Genotype frequencies of wild and variant alleles were, 54.1, 17.6, 21.6 and 6.8xa0% for *1/*1, *1/*2, *1/*3 and *2/*3 respectively. None of the patient was homozygous for *2 and *3. Statistical analysis showed that low warfarin dose (weekly) is significantly associated with *1/*2 and *1/*3 genotypes (p valuexa0≥xa00.001), whereas PT/INR showed no significant association with the any genotypes of CYP2C9. Our study suggest that polymorphic variants of CYP2C9 (*2 and *3) might influence warfarin dose requirements and associated with the low dose of warfarin in patients.

Analysis of FANCC gene mutations (IVS4+4A>T, del322G, and R548X)in patients with Fanconi anemia in Pakistan

BACKGROUND/AIMnFanconi anemia (FA) is an autosomal recessive disease determined by mutations in at least 16 genes, with distinct distributions in different populations. To the best of our knowledge, there are no reports regarding the molecular basis of the disease in FA patients in Pakistan. The current study aimed to determine the frequency of FANCC gene mutations, i.e. IVS4+4A>T, del322G, and R548X, in FA patients.nnnMATERIALS AND METHODSnGenomic DNA was obtained from 36 FA patients. All samples were analyzed by polymerase chain reaction and restriction fragment length polymorphism techniques.nnnRESULTSnMutation IVS4+4A>T was identified in 26 (72.2%) patients. It was homozygous in 6 and heterozygous in 20 patients. Del322G and R548X were found with the following prevalences: del322G, 5.6%, and R548X, 5.6%. Patients with these two mutations were compound heterozygotes having concomitant IVS4+4A>T mutation.nnnCONCLUSIONnThese results suggest that mutation IVS4+4A>T is the most prevalent mutation in our group of patients. This analysis of Pakistani patients also suggests that there is no significant difference between IVS4+4A>T homozygotes and the rest of the patients with regard to severity of clinical phenotype.

The Origins of Pakistani Populations

In an attempt to investigate the origin of the present-day Pakistani populations, we have analysed a microsatellite locus (DYS19) and theAluinsertion polymorphism (YAP) in a sample of nine ethnic groups from the Northern (viz., Punjabi, Burusho, Pathan, Kalash, and Hazara) and the Southern (Brahui, Baloch, Makrani, and Sindhi) parts of the country. A north-south divide among the populations is evident. This separation is not only due to their geographic location but these two regional groups might have originated as a result of two distinct waves of migrations, one from North Africa and the other from Sub-Saharan region.

Screening of the LAMB2, WT1, NPHS1 and NPHS2 Genes in Paediatric Nephrotic Syndrome.

Mutations in the NPHS1, NPHS2, LAMB2, and the WT1 genes are responsible for causing nephrotic syndrome (NS) in two third of the early onset cases. This study was carried out to assess the frequencies of mutations in these genes in a cohort of pediatric NS patients. A total of 64 pediatric familial or sporadic SRNS cases were recruited. Among these, 74% had a disease onset of up to 3 years of age. We found one homozygous frameshift mutation in the NPHS1 gene in one CNS case and two homozygous mutations in the NPHS2 gene. Six mutations in four cases in the LAMB2 gene were also identified. No mutation was detected in the WT1 gene in isolated SRNS cases. LAMB2 gene missense mutations were segregating in NS cases with no extra-renal abnormalities. Analysis of the population genomic data (1000 genome and gnomAD databases) for the prevalence estimation revealed that NS is more prevalent than previously determined from clinical cohorts especially in Asian population compared with overall world populations (prevalence worldwide was 1in 189036 and in South-Asian was 1in 56689). Our results reiterated a low prevalence of mutations in the NPHS1, NPHS2, LAMB2, and WT1 genes in the studied population from Pakistan as compared to some European population that showed a high prevalence of mutations in these genes. This is a comprehensive screening of the genes causing early onset NS in sporadic and familial NS cases suggesting a more systematic and robust approach for mutation identification in all the 45 disease-causing genes in NS in our population is required.