SNPs in microRNA binding sites as prognostic and predictive cancer biomarkers

Abstract

Single-nucleotide polymorphisms within microRNA (miRNA) binding sites comprise a novel genre of cancer biomarkers. Since miRNA regulation is dependent on sequence complementarity between the mRNA transcript and the miRNA, even single-nucleotide aberrations can have significant effects. Over the past few years, many examples of these functional miRNA binding site SNPs have been identified as cancer biomarkers. While most of the research to date focuses on associations with cancer risk, more and more studies are linking these SNPs to cancer prognosis and response to treatment as well. This review summarizes the state of the field and draws importance to this rapidly expanding area of cancer biomarkers.

FIGURE 1. Schematic of the luciferase reporter assay

(a) The 3'-UTR of the gene of interest is cloned downstream of the Renilla luciferase gene. Therefore, the effect of a SNP in the 3'-UTR will be observed via Renilla luciferase expression, as measured by a luminometer. The Firefly luciferase gene, which allows for normalization, can either be present in the same reporter construct (as pictured) or co-transfected with the reporter construct. The suspected miRNA or a negative control miRNA may also be co-transfected to test the specificity of the binding miRNA. (b) If the variant allele disrupts a miRNA binding site such that the miRNA can no longer suppress Renilla luciferase expression, the variant construct will have a higher luciferase value than the WT construct. (c) If the variant allele creates a novel miRNA binding site, Renilla luciferase expression will be suppressed by the binding miRNA.

FIGURE 2. The KRAS Variant and Tumorigenesis

The SNP rs61764370 is located within the 3'-UTR of KRAS in the binding site of the miRNA let-7. The variant allele (G) disrupts let-7 binding to the mRNA transcript and prevents let-7 mediated suppression, resulting in increased KRAS protein expression. By a still undefined mechanism, the variant allele is also associated with decreased let-7 levels. It is hypothesized that KRAS may induce Lin-28, a negative regulator of let-7. Both increased KRAS and decreased let-7 are associated with tumorigenesis. Let-7 is involved in a feedback loop such that low let-7 induces IL-6 expression, which activates the transcription factor STAT3, leading to tumorigenesis.