microRNA network analysis identifies miR-29 cluster as key regulator of LAMA2 in ependymoma

Ependymomas (EPN) are enigmatic tumors which continue to present significant management challenges to clinicians as evidenced by the failure to cure up to 40% of cases [1]. Recent genomic and epigenomic studies have identified alterations in DNA copy number, gene expression [2,3], and methylation [4] and showed that EPN is a heterogeneous disease and consists of distinct molecular subtypes. However, the involvement of the microRNAs (miRNA) and their influence over mRNA translation into proteins, in EPN and their contribution to the complexity of the disease are still poorly understood. To identify miRNA-mRNA regulatory network, we systematically evaluated miRNA-mRNA associations using expression profiles of tumors from 64 EPN patients (mean age of 13.3 years, Additional file 1: Table S1 for more details). For each miRNA-mRNA pair, we measured the association between miRNA and mRNA using a Spearman rank correlation and filtered with sequence-based predicted miRNA-target interactions of miRanda and TargetScan databases Additional File 3: Materials and methods [5,6]. We selected miRNA-mRNA pairs with strong negative correlation (FDR < 0.005, 78,934 pairs) and evidence for target interaction as predicted by miRanda (score < −0.5), TargetS-can (context score < −0.2) and evolutionary conservation (miRanda conservation score > 0.5). We used these thresholds to obtain a high-confidence list of candidate miRNA-target interactions. The combination of the correlation and target prediction filters yielded 390 miRNA-mRNA pairs, significantly more than was expected by chance (P = 5.95 × 10 −08 , two-tailed binomial test, pairs). These 390 putative target interactions from EPN consisted of 107 evolutionarily conserved miRNAs and 305 target mRNAs (Additional file 1: Table S2). Remarkably, these miRNAs are significantly enriched for oncomiRs/ tumor suppressor miRNAs (2.01 fold enrichment; P = 9.41 × 10 −03 , Fisher's exact test. Additional file 2: Figure S1). They included let-7c, miR-125b, miR-29a/b, miR-15 family – miR-15a, miR-16, and miR-196 (tumor suppressors miRNA), miR-18a/b, miR-19a/b, and miR-17 family – miR-106a/b, miR-17, miR-20a/b, and miR-93 (onco miRNA). Growing evidences suggest that miR-17 miRNAs are involved in cell proliferation, development, and stem cell differentiation [7]. In addition, members of miR-17 directly target TGFBR2, attenuate TGF-β signaling that regulates multitude of cellular processes, and is particularly relevant not only during development, but also in cancer initiation and progression [7,8]. Targets genes regulated by miRNAs are enriched for biological processes or pathways such as multicellular organismal development (GO:0007275; FDR = 3.31 × 10 −04