Evidence map›Paper›PMID 41039219›Full record

ArticleBMC microbiology2025

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

Ya-Sian Chang, Ming-Hon Hsu, Chin-Chun Chung, I-Lu Lai, Ya-Ting Lee, Ju-Chen Yen, Chieh-Min Chang, Ta-Chih Liu, Jan-Gowth Chang

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Article in BMC microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

9 authors.

Ya-Sian ChangPrecision Gene and Cell Center, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan.
Ming-Hon HsuDepartment of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
Chin-Chun ChungDepartment of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
I-Lu LaiDepartment of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
Ya-Ting LeeDepartment of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
Ju-Chen YenDepartment of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
Chieh-Min ChangPrecision Gene and Cell Center, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan.
Ta-Chih LiuDepartment of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan.
Jan-Gowth ChangComputing Center for Precision Integration of Chinese and Western Genomic Medicines, Show Chwan Memorial Hospital, Changhua, Taiwan. jgchang99@gmail.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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

methodsWe 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.

resultsIn all, 206 HERVs with differential expression are correlated with patient survival and there are 299 genes located near the 206 survival-related differentially expressed (DE) HERVs. There are 14 HERVs whose expression is in the same direction as their nearby genes and also have survival significance. Among these, 11 are positive regulators, with 7 detected by both methods and 4 unique to HERV-Fcount, and 3 are negative regulators, with 2 detected by both methods and 1 unique to HERV-Fcount. Knockdown of TP53 results in dysregulation of survival-related DE HERVs and their nearby genes. The molecule modulating AS can influence the expressions of HERVs by regulating the host genes near HERVs.

conclusionsHERV-Fcount detects HERVs faster than the Telescope. In addition to total RNA-seq, which increases the detection of HERVs and their nearby genes, this phenomenon can also be observed with HERV-Fcount. HERVs activation results in dysregulation of nearby genes that could be associated with HCC development and prognosis.

Indexed as

Carcinoma, HepatocellularEndogenous RetrovirusesLiver NeoplasmsAlternative SplicingCell Line, TumorFemaleHumansMaleTumor Suppressor Protein p53TP53 protein, humanTumor Suppressor Protein p53Hepatocellular carcinomaHERV-FcountHuman endogenous retrovirusesTelescope

Identifiers

PMID41039219
PMCPMC12492642

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.