Micro-RNA and mRNA integrative analysis revealed MMP1 as a predictor of lymph node metastasis in penile carcinomas

Abstract

Background: Penile carcinoma (PeCa), a relevant public health problem in poor and developing countries, has only recently been explored by genetic and epigenetic studies aiming to identify markers useful to the clinical practice. Herein, we aimed to integrate miRNA and mRNA profiles data to identify molecular drivers of PeCa development and progression. Methods: miRNA expression profile (TaqMan Human MicroRNA Array v2.0; Applied Biosystems) and mRNA expression data (4x44K, Agilent Technologies) were assayed in 23 PeCa tissues and 12 non-neoplastic penile tissues (NPT). Integrative analysis was based on predicted and experimentally validated miRNA/mRNA interaction. RT-qPCR confirmed the data in an independent set of cases (PeCa = 36; NPT = 27). Results: Eighty-one miRNA and 2,697 mRNAs differentially expressed were identified comparing tumor and non-neoplastic tissues. Integrated data analysis revealed that 255 mRNAs were specifically regulated by 68 miRNAs. Eight miRNAs and 10 mRNAs were evaluated by RT-qPCR in an array-dependent and -independent set of cases (PeCa = 36; NPT = 27), confirming the results. Molecular diagnostic classifiers including MMP1, MMP12 and PPARG transcripts were able to distinguish tumors from NPT with 92% of sensitivity and 83% of specificity. Similarly, three miRNAs (hsa-miR-31-5p, hsa-miR-224-5p, and hsa-miR-223-3p) revealed to have the potential to discriminate tumors from NPT (82% of sensitivity and 74% of specificity). Interestingly, higher MMP1 expression levels were capable to predict lymph node metastasis more efficiently than clinical-pathological data. Growth factors related pathways, human embryonic stem cell pluripotency and matrix metalloproteases were the main deregulated pathways in PeCa. Conclusions: The integrated data analysis revealed molecular markers and pathways involved in the PeCa development. Furthermore, MMP1 overexpression was identified as a new potential biomarker to predict lymph node metastasis.