Gerresheim et al. 2019 (PRJNA525090)

General Details

Title Cellular gene expression during Hepatitis C Virus replication revealed by Ribosome profiling
Organism
Number of Samples 6
Release Date 2019/03/01 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP187206
ENA SRP187206
GEO GSE127713
BioProject PRJNA525090

Publication

Title
Authors Gerresheim GK,Bathke J,Michel AM,Andreev DE,Shalamova LA,Rossbach O,Hu P,Glebe D,Fricke M,Marz M,Goesmann A,Kiniry SJ,Baranov PV,Shatsky IN,Niepmann M
Journal International journal of molecular sciences
Publication Date 2019 Mar 15
Abstract Hepatitis C virus (HCV) infects human liver hepatocytes, often leading to liver cirrhosis and hepatocellular carcinoma (HCC). It is believed that chronic infection alters host gene expression and favors HCC development. In particular, HCV replication in Endoplasmic Reticulum (ER) derived membranes induces chronic ER stress. How HCV replication affects host mRNA translation and transcription at a genome wide level is not yet known. We used Riboseq (Ribosome Profiling) to analyze transcriptome and translatome changes in the Huh-7.5 hepatocarcinoma cell line replicating HCV for 6 days. Established viral replication does not cause global changes in host gene expression-only around 30 genes are significantly differentially expressed. Upregulated genes are related to ER stress and HCV replication, and several regulated genes are known to be involved in HCC development. Some mRNAs ( PPP1R15A / GADD34 , DDIT3 / CHOP , and TRIB3 ) may be subject to upstream open reading frame (uORF) mediated translation control. Transcriptional downregulation mainly affects mitochondrial respiratory chain complex core subunit genes. After establishing HCV replication, the lack of global changes in cellular gene expression indicates an adaptation to chronic infection, while the downregulation of mitochondrial respiratory chain genes indicates how a virus may further contribute to cancer cell-like metabolic reprogramming ('Warburg effect') even in the hepatocellular carcinoma cells used here.
PMC PMC6470931
PMID 30875926
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR8649954 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
SRR8649955 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
SRR8649956 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
SRR8649960 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
SRR8649961 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
SRR8649962 PRJNA525090 Homo sapiens Huh-7.5 Ribo-Seq Cycloheximide
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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