Study of the Genetic polymorphism and Methylation profile in the Wnt signaling pathway with risk for occurrence of Lung cancer in North Indian population

Abstract

Background: Wnt pathway has been implicated in the process of lung carcinogenesis. The genetic differences and methylation profile in the Wnt antagonist genes (DKK, Axin2 and sFRP) may lead to chronic activation of this cascade. Objectives: To evaluate the role of Single nucleotide polymorphic variants of DKK3 (rs2291599, rs3206824 and rs7391689), DKK2 (rs447372, rs419558 and rs17037102) and DKK4 (rs2073664) genes, Axin2 (148 C/T, 1365 G/A, 432 T/C, 956+16 A/G, 1712+19 G/T, 1386 C/T and 2062 C/T), sFRP3 ( rs7775 and rs228326) and sFRP4 ( rs1802073 and rs1802074). Also, to detect the methylation status of sFRP1, DKK2, DKK3 and Axin2 gene. Methodology: Genotyping of genomic DNA was carried out using PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) for each polymorphic site under study. Total number of subjects genotyped in case of DKK, Axin2 and sFRP genetic variants were 600 (300 cases and 300 controls), 608 (303 cases and 305 controls) and 610 (300 cases and 310 controls) respectively. Further association analysis was carried out using logistic regression approach to obtain adjusted odds ratio and statistical significance. MDR and CART analysis were applied to evaluate high order interactions between the SNP s of same gene. Also, MDR and CART was also used to analyze the high order interaction between the genetic variants of different genes. Overall Survival was estimated using Kaplan meier survival analysis and adjusted hazards ratio was obtained using cox regression method. DNA isolated from plasma samples of 100 lung cancer patients were screened for the methylation status of promoter region of sFRP1, DKK2, DKK3 and Axin2 gene using methylation specific PCR. Further, the methylation status was correlated with the clincopathological parameters such as stage, primary tumor extension, lymph node involvement and distant metastasis using logistic regression approach. Results: DKK4 (rs2073664) did not confer any effect on lung cancer susceptibility.