DNA Methylation Regulates a Set of Long Non-Coding RNAs Compromising Hepatic Identity during Hepatocarcinogenesis

Author:

Recalde MiriamORCID,Gárate-Rascón María,Herranz José MaríaORCID,Elizalde María,Azkona María,Unfried Juan P.ORCID,Boix Loreto,Reig MaríaORCID,Sangro BrunoORCID,Fernández-Barrena Maite G.ORCID,Fortes PuriORCID,Ávila Matías A.ORCID,Berasain CarmenORCID,Arechederra MaríaORCID

Abstract

Background: Long noncoding RNAs (lncRNAs) are emerging as key players in cancer, including hepatocellular carcinoma (HCC). Here we identify the mechanism implicated in the HCC inhibition of a set of lncRNAs, and their contribution to the process of hepatocarcinogenesis. Methods and Results: The top-ranked 35 lncRNAs downregulated in HCC (Top35 LNDH) were validated in several human HCC cohorts. We demonstrate that their inhibition is associated with promoter hypermethylation in HCC compared to control tissue, and in HCC human cell lines compared to primary hepatocytes. Moreover, demethylating treatment of HCC human cell lines induced the expression of these lncRNAs. The Top35 LNDH were preferentially expressed in the adult healthy liver compared to other tissues and fetal liver and were induced in well-differentiated HepaRG cells. Remarkably, their knockdown compromised the expression of other hepato-specific genes. Finally, the expression of the Top35 LNDH positively correlates with the grade of tumor differentiation and, more importantly, with a better patient prognosis. Conclusions: Our results demonstrate that the selected Top35 LNDH are not only part of the genes that compose the hepatic differentiated signature but participate in its establishment. Moreover, their downregulation through DNA methylation occurs during the process of hepatocarcinogenesis compromising hepatocellular differentiation and HCC patients’ prognosis.

Funder

Instituto de Salud Carlos III

Gobierno de Navarra

Ministerio de Ciencia, Innovación y Universidades

Fundación Científica Asociación Española Contra el Cáncer

Publisher

MDPI AG

Subject

Cancer Research,Oncology

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