Regulatory single nucleotide polymorphisms at the beginning of intron 2 of the human KRAS gene

Abstract

There are two regulatory single nucleotide polymorphisms (rSNPs) at the beginning of the second intron of the mouse K-ras gene that are strongly associated with lung cancer susceptibility. We performed functional analysis of three SNPs (rs12228277: T greater than A, rs12226937: G greater than A, and rs61761074: T greater than G) located in the same region of human KRAS. We found that rs12228277 and rs61761074 result in differential binding patterns of lung nuclear proteins to oligonucleotide probes corresponding two alternative alleles; in both cases, the transcription factor NF-Y is involved. G greater than A substitution (rs12226937) had no effect on the binding of lung nuclear proteins. However, all the nucleotide substitutions under study showed functional effects in a luciferase reporter assay. Among them, rs61761074 demonstrated a significant correlation with allele frequency in non-small-cell lung cancer (NSCLC). Taken together, the results of our study suggest that a T greater than G substitution at nucleotide position 615 in the second intron of the KRAS gene (rs61761074) may represent a promising genetic marker of NSCLC.

Influence of Genetic Variance on Biomarker Levels After Occupational Exposure to 1,6-Hexamethylene Diisocyanate Monomer and 1,6-Hexamethylene Diisocyanate Isocyanurate

“…Other studies have shown that intronic SNPs can impact enhancer activity and splicing, which can result in altered mRNA and protein expression and can change the characteristics of those genes (Wang et al, 2014;Wang and Sadee, 2016;Schwartz et al, 2017). Intergenic SNPs have also been observed to impact enhancer activity and the binding of transcription factors (Flora et al, 2013;Spasovski et al, 2013;Antontseva et al, 2015;Schierding et al, 2016). Thus, the intronic and intergenic SNPs we have identified could be impacting biomarker levels after isocyanate exposure by acting as modifiers of gene regulation and transcription.…”

Regulatory single nucleotide polymorphisms (rSNPs) at the promoters 1A and 1B of the human APC gene

“…Besides, we analysed two SNPs from promoter 1B (rs115658307: C > T and rs78429131: T > G) that did not change the protein binding pattern, because it is known that substitutions that do not affect the binding of nuclear-extract proteins can nevertheless influence the expression of a reporter [22]. …”

“…These differences represented either an increase or decrease in the affinity of some TFs, or even disappearance or appearance of binding sites for TFs. Such alterations in TF binding patterns can strongly influence gene expression [22, 34–36]. Indeed, the luciferase reporter assay suggested that all four analyzed SNPs (which demonstrated differential binding patterns in the EMSA) were functionally active.…”

“…As the second PCR template amplicons from the first PCR reactions were used adds primers. The presence of the mutations was confirmed by Sanger′s sequencing as described [22]. …”

Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer

“…According to the somatic mutation theory, the key point in cancer transformation is DNA damage, e.g., due to aberrantly regulated or nonfunctional DNA repair pathways [3]. Cancer cells accumulate mutations several times faster than the normal cells [4]. It contributes to deregulation of molecular pathways including those responsible for apoptosis, cell growth, metabolism, motility and immunosuppression [5,6].…”