Several polymorphisms in the CYP1A1 locus have been identified and their genotypes appear to exhi... more Several polymorphisms in the CYP1A1 locus have been identified and their genotypes appear to exhibit population frequencies that depend on ethnicity. In this study, we assessed the role of CYP1A1 genotype in 388 head and neck cancer patients in Pakistani population via a case-control study. Polymerase chain reaction (PCR) and single stranded conformational polymorphism assays were used. Most of the patients (51%) enrolled for the study, were from the age group of 40 to 60 years (±16.59). Mean age of the cancer patients involved in the study was 48 ± 16.59 years. Statistical analysis has shown that, tobacco users have more chances of head and neck cancer (P 0.05). Jobless persons are more prone to head and neck cancer (P < 0.01) compared with employers and housewives. After the genetic analysis, it was found that no already reported variants of CYP1A1 gene were found in Pakistani population. A novel mutation in CYP1A1 gene at exon 2 in 21 patients (P < 0.001, Odd Ratio (OR) = 9...
The present study was designed to determine the association between the genetic polymorphisms/exp... more The present study was designed to determine the association between the genetic polymorphisms/expression variations of RB1 and CCND1 genes and brain tumor risk. For this purpose, 250 blood samples of brain tumor patients along with 250 controls (cohort I) and 96 brain tumor tissues (cohort II) with adjacent control section were collected. Mutation analysis of RB1 (rs137853294, rs121913300) and CCND1 (rs614367, rs498136) genes was performed using ARMS-PCR followed by sequencing, and expression analysis was performed using real-time PCR and immunohistochemistry. The results showed homozygous mutant genotype of RB1 gene polymorphism, rs121913300 (P=0.003) and CCND1 gene polymorphism rs614367 (P=0.01) were associated significantly with brain tumor risk. Moreover, significant down-regulation of RB1 (P=0.005) and up-regulation of CCND1 (P=0.0001) gene was observed in brain tumor sections vs controls. Spearman correlation showed significant negative correlation between RB1 vs proliferation...
PARP-1 gene plays an essential part in base excision repair pathway and its functional variations... more PARP-1 gene plays an essential part in base excision repair pathway and its functional variations result in several types of cancer. In this study we have explored the effect of genetic variations in PARP-1 gene in brain tumorigenesis. This case control study comprised of 500 brain tumor cases along with 500 healthy controls. Three polymorphisms of PARP-1 gene, rs1136410 (Val762Ala), rs1805404 (Asp81Asp) and rs1805414 (Ala284Ala) were analyzed using AS-PCR method followed by DNA sequencing. Joint effect model, haplotype analysis and linkage disequilibrium of these polymorphisms was assessed using Haploview 4.2. In rs1136410 (Val762Ala) heterozygous mutant genotype (CT) was observed notably lower (OR: 0.44., 95% CI: 0.33-0.57., p<0.0001) in brain tumor patients compared to controls and 2 fold increased frequency of homozygous mutant genotype (CC) was observed in brain tumor patients versus controls (OR: 1.51., 95%CI: 1.16-1.96, p = 0.001). In rs1805414 (Ala284Ala), frequency of heterozygous mutant genotype (CT) was observed lower (OR: 0.77., 95% CI: 0.60-0.99., p = 0.05) in patients versus controls. In rs1805404 (Asp81Asp), heterozygous mutant genotyping (CT) was observed lower in brain tumor patients compared with the healthy controls (OR: 0.63., 95% CI: 0.48-0.83., p = 0.001). However, homozygous mutant genotype (TT) was observed increased in patients compared to controls (OR: 1.41., 95% CI:1.07-1.85., p = 0.01). We assessed the fact that in combination the PARP-1 gene SNPs, rs1136410 (Val762Ala), rs1805414 (Ala284Ala) and rs1805404 (Asp81Asp) may increase the brain pathogenesis at least in Pakistani population.
We aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and ne... more We aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and neck cancer (HNC) in 400 patients and 400 controls. Five polymorphisms of XRCC2 gene G4234C (rs3218384), G4088T (rs3218373), G3063A (rs2040639), R188H (rs3218536) and rs7802034 were analyzed using Allele- specific polymerase chain reaction (ARMS-PCR) followed by sequence analysis. For rs3218373, the GG genotype indicated a statistically significant 3-fold increased risk of HNC (P < 0.001) after multivariate adjustment. For rs7802034, the GG genotype suggested statistically significant 2-fold increased risk of HNC (P < 0.001). For SNP of rs3218536, the AA genotype indicated a significant 3-fold increased risk of HNC (P < 0.001). Additionally, haplotype analysis revealed that TACAG, TGGAG, TACGG and TAGGA haplotypes of XRCC2 polymorphisms are associated with HNC risk. Two SNPs in XRCC2 (rs2040639 and rs3218384) were found increased in strong linkage disequilibrium. Furthermore, join...
Polymorphisms in DNA repair genes may alter the repair mechanism which makes the person susceptib... more Polymorphisms in DNA repair genes may alter the repair mechanism which makes the person susceptible to DNA damage. Polymorphic variants in these DNA repair pathway genes such as Poly (ADP-ribose) polymerase- 1 (PARP1) have been associated with susceptibility of several types of cancer including thyroid. Many studies have been published on PARP1 gene polymorphisms and carcinogenesis with inconsistent results. The present study was designed to explore the link between the PARP1 polymorphisms and thyroid cancer risk. This case-control study was comprised of 456 thyroid cancer patients and 400 healthy controls. Three SNPs of PARP1 gene; rs1136410, rs1805414 and rs1805404 were analyzed using ARMS-PCR. The combined genotype and haplotype analysis were performed using haploview software 4.2. Major allele homozygote (CC) of rs1136410 and combined genotype (TT+TC) of rs180414 showed a significant association with thyroid cancer risk (OR = 1.30; 95% CI 0.99-1.77; P = 0.05) and (OR = 0.43; 95%...
Genetic polymorphisms in homologous recombination repair genes cause an abnormal development of c... more Genetic polymorphisms in homologous recombination repair genes cause an abnormal development of cancerous cells. In the present study we evaluated the possibility of breast cancer association with single nucleotide polymorphisms of RAD51, XRCC2 and XRCC3 genes. Polymorphisms selected in this study were RAD51 135G/C, XRCC2 Arg188His; and XRCC3 Thr241Met. Each polymorphism was genotyped using Polymerase chain reaction-restriction fragment length polymorphism in study cohort of 306 females (156 breast cancer patients and 150 controls). We observed that heterozygous variant genotype (GC) of RAD51 135 G/C polymorphism was associated with a significantly (OR=2.70; 95%CI (0.63-1.79); p<0.03) increased risk of breast cancer. In case of the XRCC3 gene we observed that frequency of heterozygous (OR=2.88; 95%CI (1.02-8.14); p<0.02) and homozygous (OR=1.46; 95%CI (0.89-2.40); p<0.04) genotype of Thr241Met polymorphism were significantly higher in breast cancer patients. For the Arg188His polymorphism of XRCC2, ~2fold increase in breast cancer risk (OR=1.6, 95%CI = 0.73-3.50) was associated with GA genotype with a p value for trend of 0.03. Our results suggest that the 135G/C polymorphism of the RAD51, Thr241Met polymorphism of XRCC3 and Arg188His polymorphism of XRCC2 can be independent markers of breast cancer risk in Pakistan.
Head and neck cancer is one of the leading causes of deaths worldwide. Two genes GSTM1 and GSTT1 ... more Head and neck cancer is one of the leading causes of deaths worldwide. Two genes GSTM1 and GSTT1 involved in phase II of carcinogen detoxification have been frequently studied in the literature. Their null genotypes are thought to be associated with increased head and neck cancer risk. However, the published reviews are not up to date and many important papers have been skipped. The current literature review was restricted to the null genotypes of the GSTM1 and GSTT1 genes with special emphasis on the genotypic status. We found that the size of study sample varied greatly and the oral cavity cancer was more influenced by GSTM1 and GSTT1 gene deletions. With respect to ethnicity Asians are more prone to head and neck cancers with these null genotypes as compared to Europeans and Americans. The current review showed significant associations (OR=9.0, 95%CI; 1.4-9.5; OR=3.7, 95%CI; 1.4-9.5) of GSTM1 and GSTT1 null genotypes with head and neck cancers. Review confirms the data of previous reviews that GSTM1 and GSTT1 gene polymorphisms may be risk factors for cancer initiation.
Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein which plays a central r... more Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein which plays a central role in the BER pathway. APEX1 gene being highly polymorphic in cancer patients and has been indicated to have a contributive role in Apurinic/apyrimidinic (AP) site accumulation in DNA and consequently an increased risk of cancer development. In this case-control study, all exons of the APEX1 gene and its exon/intron boundaries were amplified in 530 breast cancer patients and 395 matched healthy controls and then analyzed by single-stranded conformational polymorphism followed by sequencing. Sequence analysis revealed fourteen heterozygous mutations, seven 5'UTR, one 3´UTR, two intronic and four missense. Among identified mutations one 5'UTR (rs41561214), one 3'UTR (rs17112002) and one missense mutation (Ser129Arg, Mahjabeen et al., 2013) had already been reported while the remaining eleven mutations. Six novel mutations (g.20923366T>G,
Gaughan et al., 2000). MTHFR gene has two promoters and isoform (70 kDa and 77 kDa) (Tran et al.,... more Gaughan et al., 2000). MTHFR gene has two promoters and isoform (70 kDa and 77 kDa) (Tran et al., 2002). Human MTHFR gene is composed of eleven (11) exons that encode a protein of 656 amino acids. Analysis of promoter regions of MTHFR gene revealed that it does not have a TATA box that contain CpG islands, which have multiple binding sites for different transcription factors (Rozen,1997). MTHFR enzyme activity is inhibited with the binding of dihydrofolate (DHF) (Matthews & Daubner, 1982) and S-adenosylmethionine (SAM) (Jencks and Mathews, 1987).
The International journal of biological markers, Jan 23, 2016
PTEN is part of large family of tyrosine phosphatases and has been found inactivated in a wide va... more PTEN is part of large family of tyrosine phosphatases and has been found inactivated in a wide variety of human cancers. In the present study we have tried to determine the association of the expression patterns of this gene with carcinogenesis. First, a systematic review was carried out to ascertain the importance of the PTEN gene and its role in carcinogenesis. In the second phase, a case-control study was designed using different expression analysis techniques. Expression of PTEN mRNA was analyzed using reverse transcriptase polymerase chain reaction (RT-PCR). Significantly downregulated expression of PTEN was observed in patients with head and neck cancer (HNC) compared to adjacent normal-tissue controls. These results were confirmed with quantitative polymerase chain reaction (qPCR). Significant downregulation of the gene was observed in HNC patients compared to adjacent normal-tissue controls. PTEN expression was correlated with different histopathological parameters of the st...
Mitochondrial genes play important roles in cellular energy metabolism, free radical generation, ... more Mitochondrial genes play important roles in cellular energy metabolism, free radical generation, and apoptosis. Dysregulation of these genes have long been suspected to contribute to the generation of reactive oxygen species (ROS), increased proliferation and progression of cancer. A family of orthologues of yeast silent information regulator 3 (SIRT3), 4 (SIRT4) and mitochondrial tumor suppressor 1 (MTUS1) are important mitochondrial tumor suppressor genes which play an important role in the progression of multiple cancers. However, their role in the development of oxidative stress, enhanced proliferation and progression of head and neck squamous cell carcinoma (HNSCC) has not yet been studied. In this study we aimed to test the association between reduced mitochondrial tumor suppressor genes' activities and enhancement in tissue oxidative stress and cell proliferation in HNSCC cases. The expression of mitochondrial tumor suppressor genes (SIRT3, SIRT4 and MTUS1), mitochondrial DNA repair gene (OGG1-2a) and a proliferation marker (Ki-67) was studied in a study cohort of 120 HNSCC patients and controls with reverse transcriptase polymerase chain reaction (RT-PCR) and real-time PCR (qPCR) in order to determine the potential prognostic significance of these genes. A statistically significant downregulation of SIRT3 (p<0.001), SIRT4 (p<0.0001), MTUS1 (p<0.002) and OGG1 (p<0.0001) was observed in HNSCC compared to control samples. Ki-67 was also overexpressed (p<0.0001) in HNSCC versus control samples. Additionally, to explore gene-gene relationship, we observed a positive spearmen correlation between SIRT3 versus SIRT4 (r = 0.523***, p<0.0001), SIRT3 versus MTUS1 (r = 0.273***, p<0.001), SIRT3 versus OGG1-2a (r = 0.213*, p<0.03), SIRT4 versus OGG1 (r = 0.338***, p<0.0001) and MTUS1 versus OGG1-2a (r = 0.215*, p<0.03) in HNSCC cases. A negative spearman correlation was observed between OGG1 versus Ki-67 (r =-0.224**, p<0.01) and OGG1-2a versus Ki-67 (r =-0.224**, p<0.01) in HNSCC cases. Here we report that the deregulation of mitochondrial tumor suppressor genes (SIRT3, SIRT4 and MTUS1) in relation to decreased
The International Journal of Biological Markers, 2016
Introduction The excision repair cross-complementation group 2 (ERCC2) ATP-dependent helicase is ... more Introduction The excision repair cross-complementation group 2 (ERCC2) ATP-dependent helicase is an essential member of the DNA repair pathway. It has been observed to be differentially expressed in different cancers, which shows its involvement in carcinogenesis. Aim In the present study we have tried to determine the association of expression patterns of this gene with head and neck carcinogenesis. Method We first carried out a systematic review of the available studies on the role of ERCC2 in head and neck cancer (HNC). In order to test the hypothesis that the expression patterns of XPD/ERCC2 play a critical role in HNC pathogenesis, we then conducted a population based case-control study on 81 head and neck tumor samples and adjacent normal-tissue control samples. Reverse transcriptase polymerase chain reaction (RT-PCR) and quantitative polymerase chain reaction (qPCR) were used to assess ERCC2 deregulation at the mRNA level. Result Expression analysis showed that the ERCC2 expr...
In first part of this study association between OGG1 polymorphisms and breast cancer susceptibili... more In first part of this study association between OGG1 polymorphisms and breast cancer susceptibility was explored by meta-analysis. Second part of the study involved 925 subjects, used for mutational analysis of OGG1 gene using PCR-SSCP and sequencing. Fifteen mutations were observed, which included five intronic mutations, four splice site mutations, two 3′UTR mutations, three missense mutations, and a nonsense mutation. Significantly (p<0.001) increased (~29 fold) breast cancer risk was associated with a splice site variant g.9800972T>G and 3′UTR variant g.9798848G>A. Among intronic mutations, highest (~15 fold) increase in breast cancer risk was associated with g.9793680G>A (p<0.009). Similarly ~14-fold increased risk was associated with Val159Gly (p<0.01), ~17-fold with Gly221Arg (p<0.005), and ~18-fold with Ser326Cys (p<0.004) in breast cancer patients compared with controls, whereas analysis of nonsense mutation showed that ~13-fold (p<0.01) increased...
Polish journal of pathology : official journal of the Polish Society of Pathologists, 2012
Spleen tyrosine kinase (Syk) is an intracellular receptor protein kinase involved in cell prolife... more Spleen tyrosine kinase (Syk) is an intracellular receptor protein kinase involved in cell proliferation, differentiation and phagocytosis. Syk expression has been reported in cell lines of epithelial origin. The strong expression of Syk in mammary gland prompted research into its potential role in mammary carcinogenesis. Fresh Biopsy samples were collected from different hospitals of Pakistan. Single stranded conformational polymorphism and Semi quantitative reverse transcriptase polymerase chain reaction was used to investigate somatic mutations and expression alterations in twenty five breast cancer tumor tissues along with their adjacent normal control tissue. Statistical analysis was performed to explore Syk association with breast cancer risk. In the present study, DNA from tumor tissue was analyzed and mutations in the coding sequence and intronic sequence spanning the exonic region of the Syk gene were identified. Sequence analysis revealed two missense: g61096G>A, g65967G...
Asian Pacific journal of cancer prevention : APJCP, 2011
The PTEN gene, a candidate tumor suppressor, is one of the more commonly inactivated and extensiv... more The PTEN gene, a candidate tumor suppressor, is one of the more commonly inactivated and extensively studied genes in cancer. However, few data are available about the role of germ line mutations of this gene in sporadic breast cancer cases. The purpose of this study was to determine extent of involvement of this gene in breast cancer in Pakistan. To test the hypothesis that genetic variations of PTEN play a role in the etiology of breast cancer, a population based case-control study was conducted in 350 breast cancer patients along 400 healthy controls. After extracting DNA from blood, the whole coding sequence of PTEN along with intron/exon boundaries was genotyped by polymerase chain reaction-single stranded conformational polymorphism. Sequencing analysis revealed nineteen different types of mutations in different regions of PTEN (in exon 2, 4, 5, 6, 7 and splicing sites of intron 2 and 4 and also in the 3' UTR region), including 3 silent, 8 missense, 2 frame shift and 6 spl...
Asian Pacific journal of cancer prevention : APJCP, 2011
In Pakistani culture tobacco use is very high and a well known risk factor for developing head an... more In Pakistani culture tobacco use is very high and a well known risk factor for developing head and neck cancer (HNC), tobacco smoke containing high quantities of chemical carcinogens such as aromatic amines and reactive oxygen species. OGG1 is the primary enzyme in the base excision repair (BER) pathway, responsible for the excision of 7, 8-dihydro-8-oxoguanine, a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species. Groups of 300 already diagnosed HNC patients along with normal controls were included in this study. PCR-single-strand conformation polymorphism and DNA sequencing were used to analyze the whole coding region of OGG1 gene. Sequence analysis revealed eight novel mutations (six missense and two frame shift mutations). Frequencies of missense mutations, Asp267Asn, Ser279Gly and Ile253Phe were 0.12, 0.13 and 0.06 respectively. Frequencies of other missense mutations, 1578A> T, 1582C> T and Ala399Glu (1542C> A) were 0.13, 0.13 and ...
Asian Pacific journal of cancer prevention : APJCP, 2011
Xenobiotics are metabolized by either phase I enzymes like CYP1A1 or phase II enzymes like GSTs. ... more Xenobiotics are metabolized by either phase I enzymes like CYP1A1 or phase II enzymes like GSTs. Polymorphisms in the encoding genes (CYP1A1, GSTM1, GSTT1 and GSTP1) potentially may therefore contribute towards risk association for oral cancer. These genes were investigated via a case control study consisting of 228 oral cancer patients and 150 cancer free normal individuals as controls. DNA was extracted from WBCs for genotyping. Polymerase chain reaction-single stranded conformational polymorphism (SSCP) was used for screening CYP1A1 and GSTP1 genes mutations. Deletion of GSTM1 and GSTT1 genes were analyzed by multiplex PCR. Two novel mutations were found in this study in relation to oral cancer. A substitution mutation of A2842 with C resulting in missense tyrosine to serine formation along with a frameshift mutation due to insertion of thymidine at nucleotide 2842 resulting in 495 nucleotide sequence to alter was found in oral cancer patients. GSTM1 and GSTT1 deletion polymorphi...
KAI1, also known as CD82, is a candidate metastasis suppressor gene and has been indicated in the... more KAI1, also known as CD82, is a candidate metastasis suppressor gene and has been indicated in the disease progression of certain solid tumours, including those of breast cancer. The present study aimed to investigate the importance of KAI1 as a potential metastasis suppressor in breast cancer cells. MDA-MB-231 and MCF-7 sublines with different patterns of KAI1 expression were created by way of anti-KAI1 transgene or transfection of KAI1 expression construct. Cell adhesion was markedly increased in cancer cells showing increased expression of KAI1 (MCF-7(KAI1EXP), p=0.021 vs. control cells), while it was significantly reduced in the KAI1 knockout subline, MDA-MB-231(KAI1KO) (p=0.002 and 0.0004, respectively). Significant increase of cell migration of MCF-7(KAI1EXP) cells (p=0.024 vs. control) and restricted motility of MDA-MB-231(KAI1KO) cells (p=0.003) were observed. Furthermore, MCF-7(KAI1EXP) cells also showed reduced cell invasion (p=0.022), while MDA-MB-231(KAI1KO) cell line sho...
Background Cyclin-dependent kinase 4 (CDK4) together with its regulatory subunit cyclin D1, gover... more Background Cyclin-dependent kinase 4 (CDK4) together with its regulatory subunit cyclin D1, governs cell cycle progression through G1 phase. Cyclin-dependent kinase inhibitors, including p16INK4A in turn regulate CDK4. In particular, deregulation of the p16/CDK4/cyclin D1 complex has been established in a variety of human tumors including gliomas, sarcomas, melanoma, breast and colorectal cancer. However, changes in CDK4 have rarely been observed. Method In this study we used a combination of PCR-SSCP and direct sequencing for mutational screening of CDK4. DNA was isolated from peripheral blood leukocyte of patients with squamous cell carcinoma of head and neck, for screening germline mutations in coding regions of CDK4. Results Variations observed in exon 2 and 5 were three missense mutations, g5051G > C (Ser52Thr), g5095G > C (Glu67Gln), g5906C > A, g5907C > G (Pro194Ser) and novel frame shift mutations g7321_23delTGA, g7121_7122insG, g7143delG in exon 7 and 3′UTR resp...
Differentiation-related gene-1, DRG1, is a metastasis suppressor gene whose expression has been s... more Differentiation-related gene-1, DRG1, is a metastasis suppressor gene whose expression has been shown to be dysregulated in a number of malignancies. The current study examines the expression of DRG1 in a clinical breast cohort and its association with a number of clinical pathological factors using quantitative polymerase chain reaction. Additionally, DRG1 expression is targeted in vitro using ribozyme transgene technology to explore the function of DRG1 in two human breast cancer cell lines. Low levels of DRG1 were found in patients who developed metastasis (p = 0.036) and who died of breast cancer (p = 0.0048) compared to disease free patients. Knockdown of DRG1 also resulted in significantly increased invasion and motility, but decreased matrix-adhesion in MCF7 cells. Knockdown of DRG1 seemed to have minimal impact on the cellular functions of the MDA-MB-231 breast cancer cell line causing no significant differences in cell growth, invasion, motility or matrix-adhesion. Thus, DRG1 appears to be linked to development of metastasis and death in patients who died as a result of breast cancer and may be useful as a prognostic factor as its knockdown appears to be linked with increased invasion and motility and decreased adhesion in MCF7 breast cancer cells.
Several polymorphisms in the CYP1A1 locus have been identified and their genotypes appear to exhi... more Several polymorphisms in the CYP1A1 locus have been identified and their genotypes appear to exhibit population frequencies that depend on ethnicity. In this study, we assessed the role of CYP1A1 genotype in 388 head and neck cancer patients in Pakistani population via a case-control study. Polymerase chain reaction (PCR) and single stranded conformational polymorphism assays were used. Most of the patients (51%) enrolled for the study, were from the age group of 40 to 60 years (±16.59). Mean age of the cancer patients involved in the study was 48 ± 16.59 years. Statistical analysis has shown that, tobacco users have more chances of head and neck cancer (P 0.05). Jobless persons are more prone to head and neck cancer (P < 0.01) compared with employers and housewives. After the genetic analysis, it was found that no already reported variants of CYP1A1 gene were found in Pakistani population. A novel mutation in CYP1A1 gene at exon 2 in 21 patients (P < 0.001, Odd Ratio (OR) = 9...
The present study was designed to determine the association between the genetic polymorphisms/exp... more The present study was designed to determine the association between the genetic polymorphisms/expression variations of RB1 and CCND1 genes and brain tumor risk. For this purpose, 250 blood samples of brain tumor patients along with 250 controls (cohort I) and 96 brain tumor tissues (cohort II) with adjacent control section were collected. Mutation analysis of RB1 (rs137853294, rs121913300) and CCND1 (rs614367, rs498136) genes was performed using ARMS-PCR followed by sequencing, and expression analysis was performed using real-time PCR and immunohistochemistry. The results showed homozygous mutant genotype of RB1 gene polymorphism, rs121913300 (P=0.003) and CCND1 gene polymorphism rs614367 (P=0.01) were associated significantly with brain tumor risk. Moreover, significant down-regulation of RB1 (P=0.005) and up-regulation of CCND1 (P=0.0001) gene was observed in brain tumor sections vs controls. Spearman correlation showed significant negative correlation between RB1 vs proliferation...
PARP-1 gene plays an essential part in base excision repair pathway and its functional variations... more PARP-1 gene plays an essential part in base excision repair pathway and its functional variations result in several types of cancer. In this study we have explored the effect of genetic variations in PARP-1 gene in brain tumorigenesis. This case control study comprised of 500 brain tumor cases along with 500 healthy controls. Three polymorphisms of PARP-1 gene, rs1136410 (Val762Ala), rs1805404 (Asp81Asp) and rs1805414 (Ala284Ala) were analyzed using AS-PCR method followed by DNA sequencing. Joint effect model, haplotype analysis and linkage disequilibrium of these polymorphisms was assessed using Haploview 4.2. In rs1136410 (Val762Ala) heterozygous mutant genotype (CT) was observed notably lower (OR: 0.44., 95% CI: 0.33-0.57., p<0.0001) in brain tumor patients compared to controls and 2 fold increased frequency of homozygous mutant genotype (CC) was observed in brain tumor patients versus controls (OR: 1.51., 95%CI: 1.16-1.96, p = 0.001). In rs1805414 (Ala284Ala), frequency of heterozygous mutant genotype (CT) was observed lower (OR: 0.77., 95% CI: 0.60-0.99., p = 0.05) in patients versus controls. In rs1805404 (Asp81Asp), heterozygous mutant genotyping (CT) was observed lower in brain tumor patients compared with the healthy controls (OR: 0.63., 95% CI: 0.48-0.83., p = 0.001). However, homozygous mutant genotype (TT) was observed increased in patients compared to controls (OR: 1.41., 95% CI:1.07-1.85., p = 0.01). We assessed the fact that in combination the PARP-1 gene SNPs, rs1136410 (Val762Ala), rs1805414 (Ala284Ala) and rs1805404 (Asp81Asp) may increase the brain pathogenesis at least in Pakistani population.
We aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and ne... more We aimed to investigate the effect of hotspot variations of XRCC2 gene on the risk of head and neck cancer (HNC) in 400 patients and 400 controls. Five polymorphisms of XRCC2 gene G4234C (rs3218384), G4088T (rs3218373), G3063A (rs2040639), R188H (rs3218536) and rs7802034 were analyzed using Allele- specific polymerase chain reaction (ARMS-PCR) followed by sequence analysis. For rs3218373, the GG genotype indicated a statistically significant 3-fold increased risk of HNC (P < 0.001) after multivariate adjustment. For rs7802034, the GG genotype suggested statistically significant 2-fold increased risk of HNC (P < 0.001). For SNP of rs3218536, the AA genotype indicated a significant 3-fold increased risk of HNC (P < 0.001). Additionally, haplotype analysis revealed that TACAG, TGGAG, TACGG and TAGGA haplotypes of XRCC2 polymorphisms are associated with HNC risk. Two SNPs in XRCC2 (rs2040639 and rs3218384) were found increased in strong linkage disequilibrium. Furthermore, join...
Polymorphisms in DNA repair genes may alter the repair mechanism which makes the person susceptib... more Polymorphisms in DNA repair genes may alter the repair mechanism which makes the person susceptible to DNA damage. Polymorphic variants in these DNA repair pathway genes such as Poly (ADP-ribose) polymerase- 1 (PARP1) have been associated with susceptibility of several types of cancer including thyroid. Many studies have been published on PARP1 gene polymorphisms and carcinogenesis with inconsistent results. The present study was designed to explore the link between the PARP1 polymorphisms and thyroid cancer risk. This case-control study was comprised of 456 thyroid cancer patients and 400 healthy controls. Three SNPs of PARP1 gene; rs1136410, rs1805414 and rs1805404 were analyzed using ARMS-PCR. The combined genotype and haplotype analysis were performed using haploview software 4.2. Major allele homozygote (CC) of rs1136410 and combined genotype (TT+TC) of rs180414 showed a significant association with thyroid cancer risk (OR = 1.30; 95% CI 0.99-1.77; P = 0.05) and (OR = 0.43; 95%...
Genetic polymorphisms in homologous recombination repair genes cause an abnormal development of c... more Genetic polymorphisms in homologous recombination repair genes cause an abnormal development of cancerous cells. In the present study we evaluated the possibility of breast cancer association with single nucleotide polymorphisms of RAD51, XRCC2 and XRCC3 genes. Polymorphisms selected in this study were RAD51 135G/C, XRCC2 Arg188His; and XRCC3 Thr241Met. Each polymorphism was genotyped using Polymerase chain reaction-restriction fragment length polymorphism in study cohort of 306 females (156 breast cancer patients and 150 controls). We observed that heterozygous variant genotype (GC) of RAD51 135 G/C polymorphism was associated with a significantly (OR=2.70; 95%CI (0.63-1.79); p<0.03) increased risk of breast cancer. In case of the XRCC3 gene we observed that frequency of heterozygous (OR=2.88; 95%CI (1.02-8.14); p<0.02) and homozygous (OR=1.46; 95%CI (0.89-2.40); p<0.04) genotype of Thr241Met polymorphism were significantly higher in breast cancer patients. For the Arg188His polymorphism of XRCC2, ~2fold increase in breast cancer risk (OR=1.6, 95%CI = 0.73-3.50) was associated with GA genotype with a p value for trend of 0.03. Our results suggest that the 135G/C polymorphism of the RAD51, Thr241Met polymorphism of XRCC3 and Arg188His polymorphism of XRCC2 can be independent markers of breast cancer risk in Pakistan.
Head and neck cancer is one of the leading causes of deaths worldwide. Two genes GSTM1 and GSTT1 ... more Head and neck cancer is one of the leading causes of deaths worldwide. Two genes GSTM1 and GSTT1 involved in phase II of carcinogen detoxification have been frequently studied in the literature. Their null genotypes are thought to be associated with increased head and neck cancer risk. However, the published reviews are not up to date and many important papers have been skipped. The current literature review was restricted to the null genotypes of the GSTM1 and GSTT1 genes with special emphasis on the genotypic status. We found that the size of study sample varied greatly and the oral cavity cancer was more influenced by GSTM1 and GSTT1 gene deletions. With respect to ethnicity Asians are more prone to head and neck cancers with these null genotypes as compared to Europeans and Americans. The current review showed significant associations (OR=9.0, 95%CI; 1.4-9.5; OR=3.7, 95%CI; 1.4-9.5) of GSTM1 and GSTT1 null genotypes with head and neck cancers. Review confirms the data of previous reviews that GSTM1 and GSTT1 gene polymorphisms may be risk factors for cancer initiation.
Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein which plays a central r... more Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein which plays a central role in the BER pathway. APEX1 gene being highly polymorphic in cancer patients and has been indicated to have a contributive role in Apurinic/apyrimidinic (AP) site accumulation in DNA and consequently an increased risk of cancer development. In this case-control study, all exons of the APEX1 gene and its exon/intron boundaries were amplified in 530 breast cancer patients and 395 matched healthy controls and then analyzed by single-stranded conformational polymorphism followed by sequencing. Sequence analysis revealed fourteen heterozygous mutations, seven 5'UTR, one 3´UTR, two intronic and four missense. Among identified mutations one 5'UTR (rs41561214), one 3'UTR (rs17112002) and one missense mutation (Ser129Arg, Mahjabeen et al., 2013) had already been reported while the remaining eleven mutations. Six novel mutations (g.20923366T>G,
Gaughan et al., 2000). MTHFR gene has two promoters and isoform (70 kDa and 77 kDa) (Tran et al.,... more Gaughan et al., 2000). MTHFR gene has two promoters and isoform (70 kDa and 77 kDa) (Tran et al., 2002). Human MTHFR gene is composed of eleven (11) exons that encode a protein of 656 amino acids. Analysis of promoter regions of MTHFR gene revealed that it does not have a TATA box that contain CpG islands, which have multiple binding sites for different transcription factors (Rozen,1997). MTHFR enzyme activity is inhibited with the binding of dihydrofolate (DHF) (Matthews & Daubner, 1982) and S-adenosylmethionine (SAM) (Jencks and Mathews, 1987).
The International journal of biological markers, Jan 23, 2016
PTEN is part of large family of tyrosine phosphatases and has been found inactivated in a wide va... more PTEN is part of large family of tyrosine phosphatases and has been found inactivated in a wide variety of human cancers. In the present study we have tried to determine the association of the expression patterns of this gene with carcinogenesis. First, a systematic review was carried out to ascertain the importance of the PTEN gene and its role in carcinogenesis. In the second phase, a case-control study was designed using different expression analysis techniques. Expression of PTEN mRNA was analyzed using reverse transcriptase polymerase chain reaction (RT-PCR). Significantly downregulated expression of PTEN was observed in patients with head and neck cancer (HNC) compared to adjacent normal-tissue controls. These results were confirmed with quantitative polymerase chain reaction (qPCR). Significant downregulation of the gene was observed in HNC patients compared to adjacent normal-tissue controls. PTEN expression was correlated with different histopathological parameters of the st...
Mitochondrial genes play important roles in cellular energy metabolism, free radical generation, ... more Mitochondrial genes play important roles in cellular energy metabolism, free radical generation, and apoptosis. Dysregulation of these genes have long been suspected to contribute to the generation of reactive oxygen species (ROS), increased proliferation and progression of cancer. A family of orthologues of yeast silent information regulator 3 (SIRT3), 4 (SIRT4) and mitochondrial tumor suppressor 1 (MTUS1) are important mitochondrial tumor suppressor genes which play an important role in the progression of multiple cancers. However, their role in the development of oxidative stress, enhanced proliferation and progression of head and neck squamous cell carcinoma (HNSCC) has not yet been studied. In this study we aimed to test the association between reduced mitochondrial tumor suppressor genes' activities and enhancement in tissue oxidative stress and cell proliferation in HNSCC cases. The expression of mitochondrial tumor suppressor genes (SIRT3, SIRT4 and MTUS1), mitochondrial DNA repair gene (OGG1-2a) and a proliferation marker (Ki-67) was studied in a study cohort of 120 HNSCC patients and controls with reverse transcriptase polymerase chain reaction (RT-PCR) and real-time PCR (qPCR) in order to determine the potential prognostic significance of these genes. A statistically significant downregulation of SIRT3 (p<0.001), SIRT4 (p<0.0001), MTUS1 (p<0.002) and OGG1 (p<0.0001) was observed in HNSCC compared to control samples. Ki-67 was also overexpressed (p<0.0001) in HNSCC versus control samples. Additionally, to explore gene-gene relationship, we observed a positive spearmen correlation between SIRT3 versus SIRT4 (r = 0.523***, p<0.0001), SIRT3 versus MTUS1 (r = 0.273***, p<0.001), SIRT3 versus OGG1-2a (r = 0.213*, p<0.03), SIRT4 versus OGG1 (r = 0.338***, p<0.0001) and MTUS1 versus OGG1-2a (r = 0.215*, p<0.03) in HNSCC cases. A negative spearman correlation was observed between OGG1 versus Ki-67 (r =-0.224**, p<0.01) and OGG1-2a versus Ki-67 (r =-0.224**, p<0.01) in HNSCC cases. Here we report that the deregulation of mitochondrial tumor suppressor genes (SIRT3, SIRT4 and MTUS1) in relation to decreased
The International Journal of Biological Markers, 2016
Introduction The excision repair cross-complementation group 2 (ERCC2) ATP-dependent helicase is ... more Introduction The excision repair cross-complementation group 2 (ERCC2) ATP-dependent helicase is an essential member of the DNA repair pathway. It has been observed to be differentially expressed in different cancers, which shows its involvement in carcinogenesis. Aim In the present study we have tried to determine the association of expression patterns of this gene with head and neck carcinogenesis. Method We first carried out a systematic review of the available studies on the role of ERCC2 in head and neck cancer (HNC). In order to test the hypothesis that the expression patterns of XPD/ERCC2 play a critical role in HNC pathogenesis, we then conducted a population based case-control study on 81 head and neck tumor samples and adjacent normal-tissue control samples. Reverse transcriptase polymerase chain reaction (RT-PCR) and quantitative polymerase chain reaction (qPCR) were used to assess ERCC2 deregulation at the mRNA level. Result Expression analysis showed that the ERCC2 expr...
In first part of this study association between OGG1 polymorphisms and breast cancer susceptibili... more In first part of this study association between OGG1 polymorphisms and breast cancer susceptibility was explored by meta-analysis. Second part of the study involved 925 subjects, used for mutational analysis of OGG1 gene using PCR-SSCP and sequencing. Fifteen mutations were observed, which included five intronic mutations, four splice site mutations, two 3′UTR mutations, three missense mutations, and a nonsense mutation. Significantly (p<0.001) increased (~29 fold) breast cancer risk was associated with a splice site variant g.9800972T>G and 3′UTR variant g.9798848G>A. Among intronic mutations, highest (~15 fold) increase in breast cancer risk was associated with g.9793680G>A (p<0.009). Similarly ~14-fold increased risk was associated with Val159Gly (p<0.01), ~17-fold with Gly221Arg (p<0.005), and ~18-fold with Ser326Cys (p<0.004) in breast cancer patients compared with controls, whereas analysis of nonsense mutation showed that ~13-fold (p<0.01) increased...
Polish journal of pathology : official journal of the Polish Society of Pathologists, 2012
Spleen tyrosine kinase (Syk) is an intracellular receptor protein kinase involved in cell prolife... more Spleen tyrosine kinase (Syk) is an intracellular receptor protein kinase involved in cell proliferation, differentiation and phagocytosis. Syk expression has been reported in cell lines of epithelial origin. The strong expression of Syk in mammary gland prompted research into its potential role in mammary carcinogenesis. Fresh Biopsy samples were collected from different hospitals of Pakistan. Single stranded conformational polymorphism and Semi quantitative reverse transcriptase polymerase chain reaction was used to investigate somatic mutations and expression alterations in twenty five breast cancer tumor tissues along with their adjacent normal control tissue. Statistical analysis was performed to explore Syk association with breast cancer risk. In the present study, DNA from tumor tissue was analyzed and mutations in the coding sequence and intronic sequence spanning the exonic region of the Syk gene were identified. Sequence analysis revealed two missense: g61096G>A, g65967G...
Asian Pacific journal of cancer prevention : APJCP, 2011
The PTEN gene, a candidate tumor suppressor, is one of the more commonly inactivated and extensiv... more The PTEN gene, a candidate tumor suppressor, is one of the more commonly inactivated and extensively studied genes in cancer. However, few data are available about the role of germ line mutations of this gene in sporadic breast cancer cases. The purpose of this study was to determine extent of involvement of this gene in breast cancer in Pakistan. To test the hypothesis that genetic variations of PTEN play a role in the etiology of breast cancer, a population based case-control study was conducted in 350 breast cancer patients along 400 healthy controls. After extracting DNA from blood, the whole coding sequence of PTEN along with intron/exon boundaries was genotyped by polymerase chain reaction-single stranded conformational polymorphism. Sequencing analysis revealed nineteen different types of mutations in different regions of PTEN (in exon 2, 4, 5, 6, 7 and splicing sites of intron 2 and 4 and also in the 3' UTR region), including 3 silent, 8 missense, 2 frame shift and 6 spl...
Asian Pacific journal of cancer prevention : APJCP, 2011
In Pakistani culture tobacco use is very high and a well known risk factor for developing head an... more In Pakistani culture tobacco use is very high and a well known risk factor for developing head and neck cancer (HNC), tobacco smoke containing high quantities of chemical carcinogens such as aromatic amines and reactive oxygen species. OGG1 is the primary enzyme in the base excision repair (BER) pathway, responsible for the excision of 7, 8-dihydro-8-oxoguanine, a mutagenic base byproduct that occurs as a result of exposure to reactive oxygen species. Groups of 300 already diagnosed HNC patients along with normal controls were included in this study. PCR-single-strand conformation polymorphism and DNA sequencing were used to analyze the whole coding region of OGG1 gene. Sequence analysis revealed eight novel mutations (six missense and two frame shift mutations). Frequencies of missense mutations, Asp267Asn, Ser279Gly and Ile253Phe were 0.12, 0.13 and 0.06 respectively. Frequencies of other missense mutations, 1578A> T, 1582C> T and Ala399Glu (1542C> A) were 0.13, 0.13 and ...
Asian Pacific journal of cancer prevention : APJCP, 2011
Xenobiotics are metabolized by either phase I enzymes like CYP1A1 or phase II enzymes like GSTs. ... more Xenobiotics are metabolized by either phase I enzymes like CYP1A1 or phase II enzymes like GSTs. Polymorphisms in the encoding genes (CYP1A1, GSTM1, GSTT1 and GSTP1) potentially may therefore contribute towards risk association for oral cancer. These genes were investigated via a case control study consisting of 228 oral cancer patients and 150 cancer free normal individuals as controls. DNA was extracted from WBCs for genotyping. Polymerase chain reaction-single stranded conformational polymorphism (SSCP) was used for screening CYP1A1 and GSTP1 genes mutations. Deletion of GSTM1 and GSTT1 genes were analyzed by multiplex PCR. Two novel mutations were found in this study in relation to oral cancer. A substitution mutation of A2842 with C resulting in missense tyrosine to serine formation along with a frameshift mutation due to insertion of thymidine at nucleotide 2842 resulting in 495 nucleotide sequence to alter was found in oral cancer patients. GSTM1 and GSTT1 deletion polymorphi...
KAI1, also known as CD82, is a candidate metastasis suppressor gene and has been indicated in the... more KAI1, also known as CD82, is a candidate metastasis suppressor gene and has been indicated in the disease progression of certain solid tumours, including those of breast cancer. The present study aimed to investigate the importance of KAI1 as a potential metastasis suppressor in breast cancer cells. MDA-MB-231 and MCF-7 sublines with different patterns of KAI1 expression were created by way of anti-KAI1 transgene or transfection of KAI1 expression construct. Cell adhesion was markedly increased in cancer cells showing increased expression of KAI1 (MCF-7(KAI1EXP), p=0.021 vs. control cells), while it was significantly reduced in the KAI1 knockout subline, MDA-MB-231(KAI1KO) (p=0.002 and 0.0004, respectively). Significant increase of cell migration of MCF-7(KAI1EXP) cells (p=0.024 vs. control) and restricted motility of MDA-MB-231(KAI1KO) cells (p=0.003) were observed. Furthermore, MCF-7(KAI1EXP) cells also showed reduced cell invasion (p=0.022), while MDA-MB-231(KAI1KO) cell line sho...
Background Cyclin-dependent kinase 4 (CDK4) together with its regulatory subunit cyclin D1, gover... more Background Cyclin-dependent kinase 4 (CDK4) together with its regulatory subunit cyclin D1, governs cell cycle progression through G1 phase. Cyclin-dependent kinase inhibitors, including p16INK4A in turn regulate CDK4. In particular, deregulation of the p16/CDK4/cyclin D1 complex has been established in a variety of human tumors including gliomas, sarcomas, melanoma, breast and colorectal cancer. However, changes in CDK4 have rarely been observed. Method In this study we used a combination of PCR-SSCP and direct sequencing for mutational screening of CDK4. DNA was isolated from peripheral blood leukocyte of patients with squamous cell carcinoma of head and neck, for screening germline mutations in coding regions of CDK4. Results Variations observed in exon 2 and 5 were three missense mutations, g5051G > C (Ser52Thr), g5095G > C (Glu67Gln), g5906C > A, g5907C > G (Pro194Ser) and novel frame shift mutations g7321_23delTGA, g7121_7122insG, g7143delG in exon 7 and 3′UTR resp...
Differentiation-related gene-1, DRG1, is a metastasis suppressor gene whose expression has been s... more Differentiation-related gene-1, DRG1, is a metastasis suppressor gene whose expression has been shown to be dysregulated in a number of malignancies. The current study examines the expression of DRG1 in a clinical breast cohort and its association with a number of clinical pathological factors using quantitative polymerase chain reaction. Additionally, DRG1 expression is targeted in vitro using ribozyme transgene technology to explore the function of DRG1 in two human breast cancer cell lines. Low levels of DRG1 were found in patients who developed metastasis (p = 0.036) and who died of breast cancer (p = 0.0048) compared to disease free patients. Knockdown of DRG1 also resulted in significantly increased invasion and motility, but decreased matrix-adhesion in MCF7 cells. Knockdown of DRG1 seemed to have minimal impact on the cellular functions of the MDA-MB-231 breast cancer cell line causing no significant differences in cell growth, invasion, motility or matrix-adhesion. Thus, DRG1 appears to be linked to development of metastasis and death in patients who died as a result of breast cancer and may be useful as a prognostic factor as its knockdown appears to be linked with increased invasion and motility and decreased adhesion in MCF7 breast cancer cells.
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Papers by MAHMOOD KAYANI