Polymorphic genes expression analysis identified in patients with squamous cell carcinoma of base of tongue

Abstract

Inherited genetic alterations, such as single base genetic polymorphisms (SNPs) were associated with risk of squamous cell carcinoma (SCC) of head and neck (HN). The SCC of the base of tongue (BT) is important among the SCCHN due to high rates of morbidity and mortality, but the association of tumor with SNPs has not been established. Recently, we identified 6,609 new SNPs associated with altered risk of SCCBT. The study was conducted using large-scale genotyping of samples of peripheral blood of patients with SCCBT and healthy controls, using DNA microarrays (SNP 5.0 array, Affytmetrix®). Several SNPs were considered of interest located in the coding region of genes SPTA1 (rs863931), TREML2 (rs3747742), ZAN (rs17147735), IKBKAP (rs3204145), FAM24B (rs1891110), CASP5 (rs3181320), EXOC3L4 (rs2297067), LGALS14 (rs4830) and CPT1B (rs2269383). Since the quantity and functions of the proteins encoded by wild and variant alleles of these SNPs not yet been determined, we could not explain the association of them and SCCBT risk identified. Thus, the aim in this study is to assess whether the different genotypes (wild homozygous, heterozygous, variant homozygous) of these SNPs alter the expression of genes. To achieve this objective, we chose to analyze peripheral blood samples from healthy individuals. Genomic DNA samples will be analyzed to identify the genotypes of each polymorphism (wild homozygous, heterozygous, variant homozygous), by real time polymerase chain reaction (RT-PCR) using primers and TaqMan® probes (Applied Biosystems®). The total RNA of samples will be analyzed to identify the gene expression in individuals with different genotypes of each SNP, by quantitative polymerase chain reaction (qPCR) using specific primers and dye SYBR green (Applied Biosystems®). The statistical significance of differences in gene expression (””CT) between groups (wild homozygous, heterozygous, variant homozygous) will be assessed through tests and ANOVA, considering a P value <0.05. We believe that the results of this study will help define the role of wild and variant alleles of each SNP in the production of their proteins and thus define their roles in inherited predisposition to SCCBT. (AU)