Identification of microRNAs associated with invasive and aggressive phenotype in cutaneous melanoma by next-generation sequencing

Abstract

A comprehensive repertoire of human microRNAs (miRNAs) that could be involved in early melanoma invasion into the dermis remains unknown. To this end, we sequenced small RNAs (18-30 nucleotides) isolated from an annotated series of invasive melanomas (average invasive depth, 2.0 mm), common melanocytic nevi, and matched normal skin (n = 28). Our previously established bioinformatics pipeline identified 765 distinct mature known miRNAs and defined a set of top 40 list that clearly segregated melanomas into thin (0.75 mm) and thick (2.7 mm) groups. Among the top, miR-21-5p, let-7b-5p, let-7a-5p, miR-424-5p, miR-423-5p, miR-21-3p, miR-199b-5p, miR-182-5p, and miR-205-5p were differentially expressed between thin and thick melanomas. In a validation cohort (n = 167), measured expression of miR-21-5p and miR-424-5p, not previously reported in melanoma, were significantly increased in invasive compared with in situ melanomas (Po0.0001). Increased miR-21-5p levels were significantly associated with invasive depth (P = 0.038), tumor mitotic index (P = 0.038), lymphovascular invasion (P = 0.0036), and AJCC stage (P = 0.038). In contrast, let-7b levels were significantly decreased in invasive and in situ melanomas compared with common and dysplastic nevi (Po0.0001). Decreased let-7b levels were significantly associated with invasive depth (P = 0.011), Clark's level (P = 0.013), ulceration (P = 0.0043), and AJCC stage (P = 0.011). These results define a distinct set of miRNAs associated with invasive and aggressive melanoma phenotype. Notwithstanding the distinct sets of DNA and chromosomal alterations demonstrated in melanoma, the changes in the noncoding RNA transcriptome remain poorly understood. The microRNAs (miRNAs) are endogenous, noncoding small (18-24 nucleotides) RNAs, which can regulate gene expression in animals and plants by complementary base-pairing to the mRNAs of target genes to specify mRNA cleavage or translation repression. 1 Growing evidence has shown that particular miRNAs function predominately as tumor suppressors, eg, let-7 family 2,3 and miR-15a and miR-16; 4 and some as oncogenes, eg, miR-17~92 cluster. 5,6 A number of studies have demonstrated an evolving role of miRNAs in various aspects of melanoma biology and clinical behavior. For example, results showed a cell-specific upregulated Dicer expression in 81% of cutaneous, 80% of acrolentiginous, and 96% of metastatic melanomas compared with carcinomas or sarcomas of the skin. 7 Moreover, the expression of Dicer was significantly higher in melanomas compared with benign melanocytic nevi. Dicer, a member of the RNase III family of double-stranded RNases, is a central enzyme in a multi-component miRNA biogenesis pathway where the Drosha/DGCR8 complex and Dicer act sequentially to crop long primary and precursor miRNAs into functionally mature miRNAs. 8 In patients with cutaneous melanomas, Dicer upregulation was significantly associated with an increased tumor mitotic index, Breslow's depth of invasion, nodal metastasis, and a higher American Joi...

Circulating cell‐free microRNAs in cutaneous melanoma staging and recurrence or survival prognosis

“…miR-424-5p was significantly increased in invasive compared with in situ melanomas and dysplastic nevi (Babapoor et al, 2017).…”

“…(). A significant increase in miR‐21‐5p was observed also in melanoma tissues (Babapoor et al., ; Wandler et al., ). The correlation of this miRNA with melanoma aggressive phenotype has been linked to its targeting proteins that negatively modulate in proliferation, invasion, migration and apoptosis (Latchana et al., ; Mao et al., ), and its expression in melanoma tissues may thus have implications also as independent melanoma prognostic factor (Jiang et al., ).…”

“…miR‐424‐5p was significantly increased in invasive compared with in situ melanomas and dysplastic nevi (Babapoor et al., ). On the contrary, no data are reported about the involvement of miR‐103a‐3p in melanoma.…”

“…miR-423-5p was reported to be differentially expressed between thin and thick melanomas (Babapoor et al, 2017).…”

A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi

“…Numerous studies have analyzed miRNA expression at different stages of melanoma progression, collectively identifying over 500 miRNAs enriched in nevi or melanomas (Babapoor et al 2017;Kozubek et al 2013;Hanniford et al 2015;Jukic et al 2010;Satzger et al 2012;Sand et al 2013;Xu et al 2012;Komina et al 2016;Chen et al 2011;Latchana et al 2017). Our analyses have refined this expansive list to six miRNAs that reproducibly distinguish nevi from melanoma across independent datasets and profiling platforms.…”