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Parkinson’s disease (PD) affects about 2-3% of the global population over 65 years of age and hence, it is the second most common neurodegenerative disorder in the world. This study explored the key genes and miRNA involved in PD. Microarray dataset (accession number GSE19587) comprising of two regions of medulla: dorsal motor nucleus of vagus (DMNV) and inferior olivary nucleus (ION) was downloaded from Gene Expression Omnibus (GEO) database. A total of 697 DEGs from ION (605 up-regulated genes and 92 down-regulated genes) and 663 DEGs from DMNV (638 up-regulated genes and 25 down-regulated genes) were screened. These DEGs were found to be enriched in 46 (DMNV) and 24 (ION) pathways common in DAVID and Comparative Toxicogenomics Database. In PPI network analysis, IGF1 and CD44 were identified as hub genes in DMNV whereas for ION, the hub genes identified were CSF2 and CD44. In TF-miRNA-target gene networks, an aggregate of 11 transcription factors and 46 miRNA were observed to influence the target genes. In drug-gene interaction studies, CYP3A5 and ESR1 had higher connective degrees and hence, they might be novel druggable targets for Parkinson’s disease.
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Parkinson’s disease (PD) affects about 2-3% of the global population over 65 years of age and hence, it is the second most common neurodegenerative disorder in the world. This study explored the key genes and miRNA involved in PD. Microarray dataset (accession number GSE19587) comprising of two regions of medulla: dorsal motor nucleus of vagus (DMNV) and inferior olivary nucleus (ION) was downloaded from Gene Expression Omnibus (GEO) database. A total of 697 DEGs from ION (605 up-regulated genes and 92 down-regulated genes) and 663 DEGs from DMNV (638 up-regulated genes and 25 down-regulated genes) were screened. These DEGs were found to be enriched in 46 (DMNV) and 24 (ION) pathways common in DAVID and Comparative Toxicogenomics Database. In PPI network analysis, IGF1 and CD44 were identified as hub genes in DMNV whereas for ION, the hub genes identified were CSF2 and CD44. In TF-miRNA-target gene networks, an aggregate of 11 transcription factors and 46 miRNA were observed to influence the target genes. In drug-gene interaction studies, CYP3A5 and ESR1 had higher connective degrees and hence, they might be novel druggable targets for Parkinson’s disease.
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OBJECTIVES@#To study the association of maternal methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) and methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) gene polymorphisms with congenital heart disease (CHD) in offspring.@*METHODS@#A hospital-based case-control study was conducted. The mothers of 683 children with CHD alone who attended Hunan Children's Hospital, from November 2017 to March 2020 were enrolled as the case group, and the mothers of 740 healthy children who attended the same hospital during the same period and did not have any deformity were enrolled as the control group. A questionnaire survey was performed to collect related exposure data, and then venous blood samples (5 mL) were collected from the mothers to detect MTHFD1 and MTHFD2 gene polymorphisms. A multivariate logistic regression analysis was used to evaluate the association of MTHFD1 and MTHFD2 gene polymorphisms with CHD. The four-gamete test in Haploview 4.2 software was used to construct haplotypes and evaluate the association between haplotypes and CHD. The generalized multifactor dimensionality reduction method and logistic regression analysis were used to examine gene-gene interaction and its association with CHD.@*RESULTS@#The multivariate logistic regression analysis showed that maternal MTHFD1 gene polymorphisms at rs11849530 (GA vs AA: OR=1.49; GG vs AA: OR=2.04) andat rs1256142 (GA vs GG: OR=2.34; AA vs GG: OR=3.25) significantly increased the risk of CHD in offspring (P<0.05), while maternal MTHFD1 gene polymorphisms at rs1950902 (AA vs GG: OR=0.57) and MTHFD2 gene polymorphisms at rs1095966 (CA vs CC: OR=0.68) significantly reduced the risk of CHD in offspring (P<0.05). The haplotypes of G-G-G (OR=1.86) and G-A-G (OR=1.35) in mothers significantly increased the risk of CHD in offspring (P<0.05). The gene-gene interaction analyses showed that the first-order interaction between MTHFD1 rs1950902 and MTHFD1 rs2236222 and the second-order interaction involving MTHFD1 rs1950902, MTHFD1 rs1256142, and MTHFD2 rs1095966 might be associated with risk of CHD (P<0.05).@*CONCLUSIONS@#Maternal MTHFD1 and MTHFD2 gene polymorphisms and their haplotypes, as well as the interaction between MTHFD1 rs1950902 and MTHFD1 rs2236222 and between MTHFD1 rs1950902, MTHFD1 rs1256142, and MTHFD2 rs1095966, are associated with the risk of CHD in offspring.
Subject(s)
Child , Female , Humans , Aminohydrolases/genetics , Case-Control Studies , Genetic Predisposition to Disease , Heart Defects, Congenital/genetics , Methylenetetrahydrofolate Dehydrogenase (NADP)/genetics , Minor Histocompatibility Antigens/genetics , Mothers , Multifunctional Enzymes/genetics , Polymorphism, Single Nucleotide , Risk FactorsABSTRACT
AIM: To investigate the association of dopamine D2 receptor (DRD2) and 5-hydroxytryptamine 2A receptor (5-HTR2A) gene polymorphisms and their interactions with efficacy of olanzapine in treatment of schizophrenic patients. METHODS: A total of 147 schizophrenic patients who treated with olanzapine alone were recruited. The positive and negative symptom scale (PANSS) was used to evaluate the efficacy of drugs. According to PANSS reduction rate ≥50% and <50%, patients were divided into the effective group and the ineffective group. The gene polymorphisms of DRD2 (rs1799978, rs1800497) and 5-HTR2A (rs6311, rs6313) were detected by improved multiple ligase detection reaction (iMLDR). Multivariate Logistic regression analysis was used to analyze the correlation between genotypes and olanzapine efficacy, and multifactor dimensionality reduction (MDR) was used to analyze gene-gene interactions. RESULTS: There were significant differences in genotype and allele frequencies of rs1799978 and rs6313 between the effective group and the ineffective group (P<0.05), while there was no difference in genotype and allele frequencies of rs1800497 and rs6311 (P<0.05). Patients with GA and GG of rs1799978 locus were more effective than those with wild type AA when treated with olanzapine, and the ORs (95%CI) were 5.101 (1.118-23.267) and 6.051 (2.454-14.925), respectively. Patients with CT and CC of rs6313 locus were more effective than those with wild type TT when treated with olanzapine, and the ORs (95%CI) were 2.623 (1.054-6.528) and 3.412 (1.180-9.869), respectively. There was a interaction between the gene polymorphisms of rs1799978, rs1800497 and rs6313. The interaction model was the optimal gene-gene interaction model (P<0.05) with the verify sample accuracy rate of 0.727 3 and a cross-validation consistency of 10/10. CONCLUSION: The gene polymorphisms of DRD2 (rs1799978) and 5-HTR2A (rs6313) may be associated with efficacy of olanzapine in treatment of schizophrenic patients, and there is a interaction between DRD2 (rs1799978, rs1800497) and 5-HTR2A (rs6313) on the efficacy of olanzapine.
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To date, multiple genetic susceptible genes/loci associated with rheumatoid arthritis (RA) have been identified and confirmed through large-scale genetic association studies and genome-wide association study (GWAS). However, the heritability of RA could be not fully explained by these genetic factors, and gene-gene interaction might account for part of the missing heritability. Indeed, genetic interaction study is a critical research direction in the field of genetic epidemiology of RA, and these studies have provided novel insights into the genetic basis and pathogenesis of RA. Additionally, these studies have also provided scientific reference for risk prediction and prevention of RA. This review is aimed to present a summary of recent progress in genetic interaction study of RA, thus implicate further research in this field.
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Objective To investigate the dynamic changes of gene expressions in mouse jejunum after lethal dose abdomen irradiation (ABI).Methods RNA was extracted from mouse jejunum at 0 and 6 h,3.5 and 5 d after 14 Gy 137Cs γ-ray ABI and then subjected to RNA-sequence analysis.Gene with expressions changed more than 2-fold of control were identified as differentially expressed ones.The selected genes were subsequently analyzed using IPA,Funrich,GO and KEGG software.Results Gene analysis of mouse jejunum samples showed that radiation activated p53 pathway at 6 h and 3.5 d after ABI.Interaction network analysis of genes suggested that Lck,Cdkl and Fyn,genes could play an important role in jejunum damage at 3.5 d after ABI.The gene expression profiles demonstrated that ABI up-regulated DNA damage repair pathways and down-regulated cell adhesion molecules,focal adhesion and IgA production pathways.Conclusions The p53 signaling pathway and some key genes such as Lck,Cdkl,and Fyn may contribute to the radiation-induced intestinal injury.
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Objective To explore the interaction between tryptophan hydroxylase 2(TPH2) gene polymorphisms (rs4570625,rs11178997) and serotonin 1A receptor (5-HT1A) gene polymorpbisms (rs878567,rs1364043,rs6265) and the association with major depressive disorder (MDD) in a Chinese Han population.Methods The DNA isolated from peripheral blood samples of 288 MDD patients 288 healthy subjects was detected by single base primer extension assay (Snapshot).The generalized multifactor dimensionality reduction (GMDR) method was used to analyze the gene-gene interaction.Results Significant differences were found in the genotype (patients (TT:27,TA:152,AA:109),controls (TT:82,TA:105,AA:101),P＜0.01) and allele(patients (T:206,A:370),controls (T:269,A:307),P＜0.01) frequencies of rs1 1178997 within TPH2 between MDD patients and controls.Statistically,a greater risk of developing MDD was found in individuals with an rs1 1178997 A-allele(OR=1.574,95％CI=1.243-1.993).The interaction between TPH2 (rs4570625,rs1 1178997) and 5-HT1A (rs878567,rs1364043,rs6265) was considered as the best multi-locus model,and this showed a testing accuracy of 57.67％ and a CV consistency of 10/10.And this interaction had a significant effect on the risk of MDD (P=0.0107).Conclusion There may be an association between the interaction of TPH2 and 5-HT1A polymorphisms and MDD.
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Objective To investigate gene-gene interactions of suicidal behavior with single-nucleotide-polymorphism (SNP) in MAOA ,GAD1 and 5-HTR2C by multifactor dimensionality reduction .Methods For this case-control study ,six SNPs were captured in related genes and detected in blood samples obtained from 21 patients with suicidal behavior and 50 healthy individuals .The genotype frequency and allele frequency as well as the Hardy-Weinberg equilibrium (HWE) ,tests were performed and compared by plink software .The gene-gene interactions models were built by the MDR software .Results The HWE test for case group showed that rs3813928 rs518147 of 5-HTR2C gene was not in line with HWE ( P< 0 .05) .However ,the additive model analysis after adjustment by gender indicated that the polymorphism had a positive correlation with suicidal behavior in case group .The case and control groups differed significantly only in genotype frequencies of 5-HTR2C gene (χ2 =6 .18 , P=0 .04) .There was no significant difference in allele and genotype frequencies of the other genes ( P>0 .05) .The best combination model of MDR was rs5953210-rs769391 OR=20 .19 ,95% CI 4 .19-97 .38 , P<0 .01 ,with significant interaction . Conclusion The 5-HTR2C gene rs3813928 and rs518147 polymorphisms may play an important role in the susceptibility to suicidal behavior .The combination of MAOA with GAD1 has a significant interaction which may increase the risk of suicidal behavior .
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PURPOSE: Kawasaki disease (KD) is an acute systemic vasculitis. Both the etiology of KD and the erythema of Bacille Calmette-Guérin (BCG) injection sites observed in the disease are poorly understood. We investigated the association between KD and single nucleotide polymorphisms (SNPs) in two candidate genes: inositol 1,4,5-triphosphate 3-kinase (ITPKC), a well-studied KD-associated gene, and solute carrier 11a1 (SLC11A1), which is associated with the hypersensitive reaction to the BCG strain in Koreans. MATERIALS AND METHODS: Associations between KD and SNPs in two genes were evaluated. Potential associations between BCG injection site erythema and SNPs in two genes were also evaluated. Gene-gene interactions between ITPKC and SLC11A1 in KD and BCG injection site erythema were also analyzed. RESULTS: Three tagging SNPs in ITPKC and five tagging SNPs in SLC11A1 were genotyped in 299 KD patients and 210 control children. SNP rs28493229 in ITPKC was associated with KD and coronary artery complications. SNP rs77624405 in SLC11A1 was associated with KD. Comparisons of KD patients with and without BCG injection site erythema revealed that SNP rs17235409 in SLC11A1 was associated with erythema; no erythema-associated SNPs in ITPKC were identified. Interactions between ITPKC rs28493229_GG and SLC11A1 rs17235409_GA and between ITPKC rs10420685_GG and SLC11A1 rs17235409_AA were strongly associated with BCG injection site erythema. CONCLUSION: This study identified several important polymorphisms in the ITPKC and SLC11A1 genes in Koreans. The genetic variants identified in this study affected KD and erythema of BCG injection sites independently and through gene-gene interactions. Also, the effects of the polymorphisms were age-dependent.
Subject(s)
Child , Child, Preschool , Female , Humans , Infant , Male , Asian People/genetics , BCG Vaccine/administration & dosage , Case-Control Studies , Cation Transport Proteins/genetics , Epistasis, Genetic , Erythema/complications , Genetic Association Studies , Genetic Predisposition to Disease , Mucocutaneous Lymph Node Syndrome/genetics , Mutation Rate , Phosphotransferases (Alcohol Group Acceptor)/genetics , Polymorphism, Single Nucleotide/genetics , Republic of KoreaABSTRACT
Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotide polymorphism combinations to a binary variable with a value of high risk or low risk. This method has been widely expanded to own a specific objective. Among those expansions, fuzzy-MDR uses the fuzzy set theory for the membership of high risk or low risk and increases the detection rates of gene-gene interactions. Fuzzy-MDR is expanded by a maximum likelihood estimator as a new membership function in empirical fuzzy MDR (EFMDR). However, EFMDR is relatively slow, because it is implemented by R script language. Therefore, in this study, we implemented EFMDR using RCPP (c++ package) for faster executions. Our implementation for faster EFMDR, called EMMDR-Fast, is about 800 times faster than EFMDR written by R script only.
Subject(s)
Genotype , Methods , Multifactor Dimensionality ReductionABSTRACT
Objective To investigate the single nucleotide polymorphisms(SNPs) of 5-HT1BR(rs6298),5-HT2AR(rs6311,rs6313) and 5-HT2BR(rs765458) gene,and their gene-gene interactions on suicidal behavior in major depressive disorder.Methods The blood samples were taken from 281 depression patients with impulsive suicide attempt and 281 age-matched healthy controls from a hospital in Harbin city,Heilongjiang province.The DNA isolated from blood samples and was genotyped using TapMan SNP genotyping probe.χ2 test was used to compare differences in the distribution of gene alleles between cases and controls.Haplotype and linkage disequilibrium(LD) analysis was performed using Haploview 4.0 software.GMDR was used to analyze the gene-gene interaction.Results The rs6313 and rs6311 of the 5-HT2AR gene were in strong linkage disequilibrium (D=0.756,r2=0.375).There was a significant gene-gene interaction of 5-HT1BR (rs6298),5-HT2AR (rs6311,rs6313) and 5-HT2BR(rs765458) on suicidal behavior(P<0.05).In this model,the test accuracy was 0.6182 and CV value was 10/10.Conclusion A haplotype containing rs6311 and rs6313 of 5-HT2AR gene is associated with suicidal behavior.The interaction of 5-HT1BR gene (rs6298),5-HT2AR gene (rs6311,rs6313) and 5-HT2BR gene (rs765458) are associated with depression suicidal behavior.
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Microsomal epoxide hydrolase (mEH) is a crucial biotransformation enzyme that has capability to metabolize a large number of structurally divergent, highly reactive epoxides, and numerous environmentally exposed carcinogens. It catalyzes the conversion of xenobiotic epoxide compounds into more polar diol metabolites and may play important part of the enzymatic defense against adverse effects of foreign compounds. Most commonly, two functional polymorphisms affecting mEH enzyme activity have been identified: One in exon 3 and other in exon 4 of the mEH gene, which results in His113Tyr and Arg139His amino acid substitutions, respectively. Recent reports have shown that polymorphisms in mEH gene loci may an important risk factor for susceptibility of prostate cancers (PCs), worldwide, but inconsistent finding were also be illustrated. To the best of our knowledge, globally, there is no any systematic review has been published related to mEH gene polymorphisms and PC risk. Thus, in the current review, we have discussed the association between mEH gene polymorphisms, gene–environmental interaction, and PC risk.
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Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named “BOolean Operation-based Screening and Testing” (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.
Subject(s)
Cohort Studies , Diabetes Mellitus, Type 2 , Genetic Predisposition to Disease , Genome-Wide Association Study , Genotype , Korea , Linear Models , Logistic Models , Mass Screening , MethodsABSTRACT
Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups. The MDR method has been extended to various phenotypes and has been improved to provide a significance test for gene-gene interactions. In this paper, we propose a simple method, called accelerated failure time (AFT) UM-MDR, in which the idea of a unified model-based MDR is extended to the survival phenotype by incorporating AFT-MDR into the classification step. The proposed AFT UM-MDR method is compared with AFT-MDR through simulation studies, and a short discussion is given.
Subject(s)
Classification , Genome-Wide Association Study , Genotype , Methods , Multifactor Dimensionality Reduction , PhenotypeABSTRACT
Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.
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Blood Glucose , Classification , Diagnosis , Fasting , Glucose Tolerance Test , Glucose , Methods , Phenotype , Polymorphism, Single Nucleotide , World Health OrganizationABSTRACT
<p><b>OBJECTIVE</b>To investigate the mechanisms of Panax notoginseng saponins (PNS) in treating coronary heart disease (CHD) by integrating gene interaction network and functional enrichment analysis.</p><p><b>METHODS</b>Text mining was used to get CHD and PNS associated genes. Gene-gene interaction networks of CHD and PNS were built by the GeneMANIA Cytoscape plugin. Advanced Network Merge Cytoscape plugin was used to analyze the two networks. Their functions were analyzed by gene functional enrichment analysis via DAVID Bioinformatics. Joint subnetwork of CHD network and PNS network was identifified by network analysis.</p><p><b>RESULTS</b>The 11 genes of the joint subnetwork were the direct targets of PNS in CHD network and enriched in cytokine-cytokine receptor interaction pathway. PNS could affect other 85 genes by the gene-gene interaction of joint subnetwork and these genes were enriched in other 7 pathways. The direct mechanisms of PNS in treating CHD by targeting cytokines to relieve the inflflammation and the indirect mechanisms of PNS in treating CHD by affecting other 7 pathways through the interaction of joint subnetwork of PNS and CHD network. The genes in the 7 pathways could be potential targets for the immunologic adjuvant, anticoagulant, hypolipidemic, anti-platelet and anti-hypertrophic activities of PNS.</p><p><b>CONCLUSIONS</b>The key mechanisms of PNS in treating CHD could be anticoagulant and hypolipidemic which are indicated by analyzing biological functions of hubs in the merged network.</p>
Subject(s)
Humans , Coronary Disease , Drug Therapy , Genetics , Gene Expression Profiling , Gene Regulatory Networks , Panax notoginseng , Chemistry , Phytotherapy , Saponins , Pharmacology , Therapeutic UsesABSTRACT
Objective To investigate the joint action of CXCL16 G1850A and TNF-α T1031C genes polymorphisms in patients with atherosclerotic cerebral infarction (ACI). Methods CXCL16 gene, G1850A and TNF-α gene T1031C mononucleotide polymorphism were tested with polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) in 120 ACI patients and 75 healthy controls. Results The CXCL16 gene 1850 site AA genotype (35.8% vs 20.0%), A allele frequency (59.6% vs 44.0%), the TNF-αgene 1031 site CC genotype(2.5% vs 1.3%), C allele frequency(21.3% vs 11.3%)in ACI group were significantly higher than in the control group(P < 0.05). There was a positive correlation between the joint action of CXCL16 G1850A and TNF-α T1031C genes polymorphisms and ACI (χ2= 7.502,df = 2,P = 0.023). Conclusion The CXCL16 gene 1850, A allele and TNF-α gene 1031 C allele were risk factors for ACI. There is a positive correlation between the joint action of CXCL16 G1850A and TNF-α T1031C genes polymorphisms on ACI.
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The incidence trends of colorectal cancer have varied over time, and there is wide geographical variation across the world. Regarding colorectal cancer, diverse modifiable environmental or intrinsic risk factors have been investigated. This review summarizes the effects of both dietary intake of vitamin D and calcium in particular and diet-associated genetic factors on colorectal cancer risk. We searched the electronic database PubMed for articles published between January 2000 and March 2015. We reviewed case-control studies that included dietary factors, genetic polymorphisms, and gene-diet interactions in association with colorectal cancer risk. Overall, 21 studies were selected as eligible studies. These studies demonstrated that dietary consumption of vitamin D and calcium may decrease the risk of colorectal cancer or adenoma. Colorectal carcinogenesis was discussed in conjunction with dietary factors and mediating genetic factors. The epidemiological findings suggested that the gene-diet interactions may possibly alter the associations between dietary intake, genetic polymorphisms, and the risk of colorectal cancer. However, the reported effects of the same potential factors on colorectal cancer risk were inconsistent, depending on the study population and geographical location. This finding may imply the necessity of considering the environmental differences and genetic variations existing between individuals or specified populations. Therefore, further studies are required to investigate modifiable risk factors in diverse locations to derive useful implications for colorectal neoplasia.
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Adenoma , Calcium , Carcinogenesis , Case-Control Studies , Colorectal Neoplasms , Gene-Environment Interaction , Genetic Variation , Incidence , Negotiating , Polymorphism, Genetic , Risk Factors , Vitamin D , VitaminsABSTRACT
BACKGROUND AND AIM: p73, a novel P53 homolog and plays an important role in modulating cell cycle control, apoptosis and cell growth while P21, functions to negatively control the cell cycle. P53 up regulates p21 expression in response to deoxyribonucleic acid damage leading to cell cycle arrest at G1 checkpoint. In the present study, we are targeting p21 codon 31 and p73 gene variants of G4C14‑to‑A4T14 (Exon 2) polymorphism for bladder cancer (BC) risk in North Indians. MATERIALS AND METHODS: The above gene variants of P21 and P73 were assessed in the case‑control study comprising of 200 BC cases and 200 healthy controls of the same age, gender and similar ethnicity. Genotyping was performed by polymerase chain reaction (PCR) restriction fragment length polymorphism method and PCR‑based confronting two‑pair primers (PCR with CTPP). RESULTS: The variant genotype of p73Exon 2 polymorphism showed significant risk for BC (p = 0.014). While combining with heterozygous genotype, variant genotype of p73Exon2 showed a significant association with BC risk (p = 0.010). While in case of p21 codon31 showed no significant association for BC risk at genotypic level. Significant association between p73Exon2 polymorphism and smoking was observed for BC risk. Furthermore, gene combination analysis revealed that AT/AT‑Ser/Ser is associated with risk for BC. Variant genotype of P73Exon2 was associated with reduced risk of recurrence (p = 0.039) in superficial BC patients receiving Bacillus Calmette‑Guerin treatment thus showing least survival (log rank = 0.029). CONCLUSION: Our study provided evidence that the p73 G4C14 > A4T14 (Exon2) polymorphisms were associated with higher risk of BC in North Indian population.
Subject(s)
Adult , Aged , BCG Vaccine/therapeutic use , Female , Genotype , Humans , Immunotherapy/therapeutic use , India/epidemiology , Male , Middle Aged , Polymorphism, Genetic , Survival Analysis , Urinary Bladder Neoplasms/epidemiology , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/therapyABSTRACT
Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene (GxG) interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.