Allele-Specific MicroRNA-Mediated Regulation of a Glycolysis Gatekeeper PDK1 in Cancer Metabolism

SIMPLE SUMMARY: MicroRNAs are small non-coding RNAs that regulate gene expression. Single Nucleotide Polymorphisms (SNPs), which have been previously associated with cancer risk may interfere with the function of microRNAs by changing the binding of microRNA to its target gene. We sought to identify the role of prostate cancer risk associated SNPs in regulating a vital enzyme of cancer metabolism, pyruvate dehydrogenase kinase 1 (PDK1) via microRNAs. The microRNA and gene interaction was studied using computational predictions and by various laboratory assays. Our study highlighted the role of PDK1 and its regulation by microRNAs in cancer metabolism and disease progression. The findings from this study suggest that analysis of microRNAs and their interactions with SNPs could provide valuable insights into the complicated mechanisms of prostate cancer risk associated SNPs and identify suitable moleculer pathways for targeted therapy. ABSTRACT: Background: Emerging evidence has revealed that genetic variations in microRNA (miRNA) binding sites called miRSNPs can alter miRNA binding in an allele-specific manner and impart prostate cancer (PCa) risk. Two miRSNPs, rs1530865 (G > C) and rs2357637 (C > A), in the 3′ untranslated region of pyruvate dehydrogenase kinase 1 (PDK1) have been previously reported to be associated with PCa risk. However, these results have not been functionally validated. Methods: In silico analysis was used to predict miRNA–PDK1 interactions and was tested using PDK1 knockdown, miRNA overexpression and reporter gene assay. Results: PDK1 expression was found to be upregulated in PCa metastasis. Further, our results show that PDK1 suppression reduced the migration, invasion, and glycolysis of PCa cells. Computational predictions showed that miR-3916, miR-3125 and miR-3928 had a higher binding affinity for the C allele than the G allele for the rs1530865 miRSNP which was validated by reporter gene assays. Similarly, miR-2116 and miR-889 had a higher affinity for the A than C allele of the rs2357637 miRSNP. Overexpression of miR-3916 and miR-3125 decreased PDK1 protein levels in cells expressing the rs1530865 SNP C allele, and miR-2116 reduced in cells with the rs2357637 SNP A allele. Conclusions: The present study is the first to report the regulation of the PDK1 gene by miRNAs in an allele-dependent manner and highlights the role of PDK1 in metabolic adaption associated with PCa progression.