Long Intergenic Non Coding RNA and MicroRNA Profiles of Pheochromocytoma and Paraganglioma as Prognostic Biomarkers

Abstract

Abstract microRNAs (miRNAs) and long intergenic noncoding RNAs (lincRNAs) have been reported as important markers for many cancers. In search of new markers for the metastatic or aggressive phenotypes in the neuroendocrine tumor pheochromocytomas and paragangliomas (PCPG), we analyzed the non-coding transcriptome from patient gene expression data in The Cancer Genome Atlas. We used differential expression analysis and an elastic-net machine-learning model to identify miRNA and lincRNA transcriptomic signature specific to PCPG molecular subtypes. Similarly, miRNAs and lincRNAs specific to aggressive PCPGs were identified, and univariate and multivariate analysis were performed for identifying factors associated with metastasis-free survival. Upregulation of 13 lincRNAs and 4 miRNAs was found to be associated with aggressive/metastatic PCPGs. RT-PCR validation in tumor samples from PCPG patients confirmed the overexpression of 4 miRNAs and 4 lincRNAs in metastatic compared to non-metastatic PCPGs. Kaplan-Meier analysis identified 3 miRNAs and 5 lincRNAs as prognostic markers for metastasis-free survival of patients in PCPGs. In a multivariate Cox regression analysis combining these miRNA and lincRNA expression signatures with the previously identified clinically relevant parameters like SDHB germline mutation, ATRX somatic mutation, tumor location and hormone secretion phenotypes, we identified the miRNA miR-182 and lincRNA HIF1A-AS2 as independent predictors of poor metastasis-free survival. We formulated a risk-score model using multivariate analysis of lincRNA and miRNA expression profiles, presence of SDHB and ATRX mutations, tumor location, and hormone secretion phenotypes. Stratification of PCPG patients with this risk-score showed significant differences in metastasis-free survival.