Identification of Long Noncoding RNAs Deregulated in Papillary Thyroid Cancer and Correlated with BRAFV600E Mutation by Bioinformatics Integrative Analysis

Lucas Goedert,Cesar Seigi Fuziwara,Jessica Rodrigues Plaça,Jair Figueredo Dos Santos,Enilza Maria Espreafico,Amanda Cristina Corveloni,Palloma Porto Almeida,Illy Enne Gomes Pereira,Maiaro Cabral Rosa Machado,Desirée Rodrigues Plaça,Marcela Motta De Castro,Wilson Araújo Silva,Talita Perez Sanches,Edna Teruko Kimura

doi:10.1038/s41598-017-01957-0

Abstract

Papillary Thyroid Cancer (PTC) is an endocrine malignancy in which BRAFV600E oncogenic mutation induces the most aggressive phenotype. In this way, considering that lncRNAs are arising as key players in oncogenesis, it is of high interest the identification of BRAFV600E-associated long noncoding RNAs, which can provide possible candidates for secondary mechanisms of BRAF-induced malignancy in PTC. In this study, we identified differentially expressed lncRNAs correlated with BRAFV600E in PTC and, also, extended the cohort of paired normal and PTC samples to more accurately identify differentially expressed lncRNAs between these conditions. Indirectly validated targets of the differentially expressed lncRNAs in PTC compared to matched normal samples demonstrated an involvement in surface receptors responsible for signal transduction and cell adhesion, as well as, regulation of cell death, proliferation and apoptosis. Targets of BRAFV600E-correlated lncRNAs are mainly involved in calcium signaling pathway, ECM-receptor interaction and MAPK pathway. In summary, our study provides candidate lncRNAs that can be either used for future studies related to diagnosis/prognosis or as targets for PTC management.

Highlights

Thyroid oncogenesis is still under investigation, a high frequency (70%) of activating mutations in components of the mitogen-activated protein kinase (MAPK) pathway was reported, such as BRAFV600E 5, 6 and HRAS/NRAS/KRAS point mutations[7, 8]
Hierarchical clustering was used to organize patients or long noncoding RNAs (lncRNAs) into groups according to the expression levels of differentially expressed (DE) lncRNAs. Results demonstrated that this set of lncRNAs is capable of clustering, majorly, normal and cancer patients in two distinct groups (Supplemental Fig. S2A)
As almost the totality of the identified DE lncRNAs in both conditions (Normal × Tumor and wild type (WT) × BRAFV600E) is uncharacterized, we used prediction methods to identify a possible interaction between lncRNAs and mRNAs/microRNAs

Summary

Introduction

Thyroid oncogenesis is still under investigation, a high frequency (70%) of activating mutations in components of the mitogen-activated protein kinase (MAPK) pathway was reported, such as BRAFV600E 5, 6 and HRAS/NRAS/KRAS point mutations[7, 8]. BRAFV600E-associated mRNA signature was determined in a mouse model and human samples[24], which identified new genes not previously reported as related to BRAF mutation in thyroid cancer (e.g. MMD, ITPR3, AACS, LAD1, PVRL3, ALDH3B1, and RASA1) that will provide further support for future research on BRAF-induced PTC24. This analysis did not evaluate the expression of long noncoding RNAs (lncRNAs), which are progressively shown to be of fundamental importance in other types of cancer[25, 26]. LncRNAs are RNAs longer than 200 nucleotides that have no coding potential[27] and are involved in several processes, such as gene expression regulation through chromatin modulation[28, 29], epigenetic control[30], association with translational apparatus[31], improving other mRNA stability[32], serving as a scaffold for protein[33], acting as decoys for miRNAs34, altering protein turnover[35], among others

Methods

Results

Conclusion