Evaluation of genetic and epigenetic changes of Tumor Necrosis Factor-Alpha gene in larynx cancer.

BACKGROUND:Tumor Necrosis Factor-Alpha (TNF-α) is a proinflammatory cytokine that plays a role in inflammation, which is one of the hallmarks of cancer, and its polymorphic variants have been associated with disease risk in many cancers in the literature. The aim of this study was to investigate four different polymorphic variants, differential methylation and expression status of the TNF-α gene and to determine the associations between these variants and disease risk, and to evaluate the relationship between the results and clinical parameters. We purposed to investigate the genetic and epigenetic alterations of the TNF-α gene in larynx cancer (LC). MATERIAL AND METHODS:After isolation of DNA/RNA from whole blood, tumor and normal tissue, polymorphic variant alleles differrential expression and methylation levels were analyzed by RFLP, semiquantitative RT-PCR, and restriction enzyme digestion, respectively. TNF-α expression and methylation levels were calculated using BIO1D software. The frequencies of the variants c.-238 G>A (rs361525), c.-857 C>T (rs1799724), c.-863 C>A (rs1800630), and c.-1031 T > C (rs1799964) in the promoter region of TNF-α in LC Turkish patients and healthy individuals were examined using the De-Finetti case-control program. Haplotype frequencies and linkage disequilibrium were analyzed using the SNPStats program. RESULTS:The frequency of genotype c.-1031 T > C was significantly lower in patients than in healthy individuals [TT vs TC: OR (%95CI) = 7.00 (1.75-27.93), p = 0.003, χ2 = 8.76]. The heterozygous variant of - 857 was associated with recurrence [T vs G: OR (%95CI) = 0.15 (0.02-0.95), p = 0.02, χ2 = 4.86]. For c.-238 G>A, c.-857 C>T, and c.-863 C>A, there was no statistically significant difference between the patient and healthy group in terms of disease risk. A significant association was found between c.-1031 T > C and disease risk of LC. Decreased expression was detected in 46% (23/50) and increased expression in 54% (27/50) of tumor tissue samples compared to the matched normal tissues of patients. Methylation-related loss of expression was detected in 53.3% (16/30) of patients. CONCLUSION:Our study is the first investigating four different polymorphic regions of the TNF-α promoter region and the expression/methylation status of TNF-α in the same LC patient and healthy cohort. According to our results, the c.-1031 T > C variant was reported to be significantly associated with a reduced risk of LC. In addition, the TNF-α variant c. -857 C>T suggests that it may be a potential biomarker for predicting the recurrence of LC. An association between c. -857 C>T variant and methylation-based expression status was observed.