Analysis of human endogenous retrovirus in hepatocellular carcinomas using HERV-Fcount.

ABSTRACT:

Background

Human endogenous retroviruses (HERVs) are important in the development of human diseases, including cancers, and comprehensive study for hepatocellular carcinoma (HCC) is lacking.

Methods

We analyzed the impacts of HERVs on 254 HCC patients using total RNA sequencing (RNA-seq) and a new approach based on featureCounts (we call it HERV-Fcount), and then evaluated the alterations of HERVs in an HCC cell line after TP53 knockdown and alternative splicing (AS)-related small molecules treatment. We also compared the differences in HERVs detection between the Telescope and HERV-Fcount.

Results

In all, 206 HERVs with differential expression are correlated with patient survival and there are 299 genes located near the 206 survival-related differentially expressed (

SUBMITTER: Chang YS 

PROVIDER: S-EPMC12492642 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature