Unraveling the Role of microRNA and isomiRNA Networks in Multiple Primary Melanoma Pathogenesis

Abstract

Background Malignant cutaneous melanoma (CM) is a potentially lethal form of skin cancer whose worldwide incidence has been constantly increasing over the past decades. During their lifetime about 8% of patients with CM will develop multiple primary melanomas (MPM). Patients affected by MPM could have a genetically determined susceptibility, though germline mutations in hereditary melanoma genes are rarely detected. Methods To better characterize the biology of this subset of melanomas, we explored the miRNome of 24 single and multiple primary melanomas, including multiple tumors from the same patient, using a smallRNA sequencing approach and bioinformatic detection of miRNA isoforms. The differential expression of specific miRNAs/isomiRs was obtained using quantitative PCR.Results From a supervised analysis, 22 miRNAs were differentially expressed in MPM compared to single CM, including key miRNAs involved in epithelial-mesenchymal transition (EMT). Moreover, the first and second melanoma from the same patient presented a different miRNA profile. Ten miRNAs, including miR-25-3p, 149-5p, 92b-3p, 211-5p, 125a-5p, 125b-5p, 205-5p, 200b-3p, 21-5p and 146a-5p, were further validated in a larger cohort of single and multiple melanoma samples (N=47). Overall, the Pathway Enrichment Analysis revealed a more differentiated and less invasive status of MPMs. Analyzing our smallRNA seq data, we detected a panel of melanoma-specific miRNA isoforms (isomiRs), which were validated in The Cancer Genome Atlas SKCM cohort. Specifically, we identified hsa-miR-125a-5p|0|-2 isoform as 10-fold over-represented in melanoma and differentially expressed in MPMs. IsomiR-specific target analysis revealed that the miRNA shortening confers a novel pattern of target gene regulations, including genes implicated in melanocyte differentiation and cell adhesion. Conclusions Overall we provided a comprehensive characterization of the miRNA/isomiRNA regulatory network of multiple primary melanomas, highlighting mechanisms of tumor development and correlating miRNA expression with MPM clinical characteristics.