Transcriptome Analysis of Hepatitis C Virus-Infected Hepatoma Cells Following Stringent Removal of Genomic DNA.
6 affiliations
- 1Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University, 35392 Giessen, Germany.
- 2RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany.
- 3Bioinformatics Core Facility Jena, Friedrich Schiller University, 07743 Jena, Germany.
- 4Bioinformatics and Systems Biology, Justus-Liebig-University, 35392 Giessen, Germany.
- 5National Emerging Infectious Diseases Laboratories (NEIDL), Department of Virology, Immunology, and Microbiology, Boston University Medical School, Boston, MA 02118, USA.
- 6Institute of Medical Virology, Justus-Liebig-University, National Reference Center for Hepatitis B and D Viruses, Giessen, and German Center for Infection Research (DZIF), Partner Site Giessen, 35392 Giessen, Germany.
Abstract
Hepatitis C Virus (HCV) is a positive strand RNA virus that infects hepatocytes and reprograms cellular gene expression, contributing to chronic liver disease and hepatocellular carcinoma. HCV replicates slowly and induces limited changes in the cellular transcriptome. Here, we improved analysis of low-abundance transcripts, including long non-coding RNAs (lncRNAs), in the context of HCV replication. We stringently removed genomic DNA from total RNA from Huh-7 hepatoma cell lines by a combination of TRIzol, acidic phenol, silica matrix columns and recombinant DNase I. RNA sequencing (RNA-Seq) and targeted validation were used to characterize Lnc-ITM2C-1 splice variants and expression of its neighboring gene, G protein-coupled receptor 55 (GPR55), to investigate their potential roles in HCV replication. Challenging our previous findings, under our improved experimental conditions, Lnc-ITM2C-1 and GPR55 were neither involved in a positive regulation circuit with HCV nor induced detectable transcriptome changes. Secondary analysis of RNA-Seq data according to HCV infection status revealed statistically robust HCV-induced expression of 21 host cell genes involved in pathways like stress response (in particular ATF3), lipid metabolism, cytoskeleton organization and growth regulation. In contrast, we found that expression changed for only a limited subset of previously reported HCV-associated lncRNAs (e.g., EGOT). This highlights the necessity of stringent gDNA removal for analysis of low-abundance transcripts like lncRNAs.
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BibTeX
@article{khajouei2026transcriptome,
title = {{Transcriptome Analysis of Hepatitis C Virus-Infected Hepatoma Cells Following Stringent Removal of Genomic DNA.}},
author = {Mozhdeh Khajouei and Elena Jost and Maximilian Collatz and Attiya Qadoos Malik and Gesche K Gerresheim and Nina Hofmann and Pan Hu and Nikolai Grahn and Ragna Weitz and Jan Dreute and Lena Soppa and Alexander Goesmann and Dieter Glebe and Manja Marz and Michael Niepmann},
journal = {Viruses},
year = {2026},
month = oct,
doi = {10.3390/v18101167},
url = {https://europepmc.org/article/MED/42944086},
note = {CC BY},
}
RIS
TY - JOUR
TI - Transcriptome Analysis of Hepatitis C Virus-Infected Hepatoma Cells Following Stringent Removal of Genomic DNA.
AU - Mozhdeh Khajouei
AU - Elena Jost
AU - Maximilian Collatz
AU - Attiya Qadoos Malik
AU - Gesche K Gerresheim
AU - Nina Hofmann
AU - Pan Hu
AU - Nikolai Grahn
AU - Ragna Weitz
AU - Jan Dreute
AU - Lena Soppa
AU - Alexander Goesmann
AU - Dieter Glebe
AU - Manja Marz
AU - Michael Niepmann
PY - 2026
DA - 2026/10/20
JO - Viruses
DO - 10.3390/v18101167
UR - https://europepmc.org/article/MED/42944086
AB - Hepatitis C Virus (HCV) is a positive strand RNA virus that infects hepatocytes and reprograms cellular gene expression, contributing to chronic liver disease and hepatocellular carcinoma. HCV replicates slowly and induces limited changes in the cellular transcriptome. Here, we improved analysis of low-abundance transcripts, including long non-coding RNAs (lncRNAs), in the context of HCV replication. We stringently removed genomic DNA from total RNA from Huh-7 hepatoma cell lines by a combination of TRIzol, acidic phenol, silica matrix columns and recombinant DNase I. RNA sequencing (RNA-Seq) and targeted validation were used to characterize Lnc-ITM2C-1 splice variants and expression of its neighboring gene, G protein-coupled receptor 55 (GPR55), to investigate their potential roles in HCV replication. Challenging our previous findings, under our improved experimental conditions, Lnc-ITM2C-1 and GPR55 were neither involved in a positive regulation circuit with HCV nor induced detectable transcriptome changes. Secondary analysis of RNA-Seq data according to HCV infection status revealed statistically robust HCV-induced expression of 21 host cell genes involved in pathways like stress response (in particular ATF3), lipid metabolism, cytoskeleton organization and growth regulation. In contrast, we found that expression changed for only a limited subset of previously reported HCV-associated lncRNAs (e.g., EGOT). This highlights the necessity of stringent gDNA removal for analysis of low-abundance transcripts like lncRNAs.
SN - 1999-4915
ER -