Gene Expression Profiling of Different Huh7 Variants Reveals Novel Hepatitis C Virus Host Factors

Abstract

Chronic Hepatitis C virus (HCV) infection still constitutes a major global health problem with almost half a million deaths per year. To date, the human hepatoma cell line Huh7 and its derivatives is the only cell line that robustly replicates HCV. However, even different subclones and passages of this single cell line exhibit tremendous differences in HCV replication efficiency. By comparative gene expression profiling using a multi-pronged correlation analysis across eight different Huh7 variants, we identified 34 candidate host factors possibly affecting HCV permissiveness. For seven of the candidates, we could show by knock-down studies their implication in HCV replication. Notably, for at least four of them, we furthermore found that overexpression boosted HCV replication in lowly permissive Huh7 cells, most prominently for the histone-binding transcriptional repressor THAP7 and the nuclear receptor NR0B2. For NR0B2, our results suggest a finely balanced expression optimum reached in highly permissive Huh7 cells, with even higher levels leading to a nearly complete breakdown of HCV replication, likely due to a dysregulation of bile acid and cholesterol metabolism. Our unbiased expression-profiling approach, hence, led to the identification of four host cellular genes that contribute to HCV permissiveness in Huh7 cells. These findings add to an improved understanding of the molecular underpinnings of the strict host cell tropism of HCV.

The Orphan Nuclear Receptor Gene NR0B2 Is a Favorite Prognosis Factor Modulated by Multiple Cellular Signal Pathways in Human Liver Cancers

“…Interestingly, higher NR0B2 expression is a favorite factor for overall survival in patients with viral hepatitis history (Figure 2F), especially for those without alcohol consumption and Asian male patients. These data were supported by a previous report that SHP protein suppressed HCV replication in human liver cancer HuH7 cells (27).…”

“…Chronic viral hepatitis is a substantial contributing factor for liver cancer development and progression (51). HCV infection was shown to increase NR0B2 gene expression in human liver cells (52), and NR0B2 gene silencing or an excessive overexpression all reduced HCV replication in Huh7 cells (27). This study found an interesting correlation of NR0B2 expression with over survival in liver cancer patients with viral hepatitis history (HR = 0.52, p = 0.0416), which was more significant in Asian male patients (HR = 0.33, p = 0.0157).…”

Identification of Genetic Risk Factors of Severe COVID-19 Using Extensive Phenotypic Data: A Proof-of-Concept Study in a Cohort of Russian Patients

“…THAP7 encodes a transcriptional repressor that acts via histone deacetylation [ 34 ]). Notably, THAP7 overexpression induces permissiveness of human hepatoma Huh7 cells to hepatitis C viral invasion [ 35 ]. These data suggest that both LZTR1 per se , as target genes affected by rs112544, may be involved in immune system function and anti-viral response.…”

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies

“…2×10 5 Lunet-CD81 high [49] cells per 6-well were seeded in 2 mL 16 hours prior to infection. To ensure simultaneous infection of all cells, cells were kept at 4°C for 30 min before medium aspiration and inoculation with pre-cooled PEG-precipitated HCV cc (Jc1) [50] at an MOI of 1 at 4°C for one hour (1 mL per 6-well). The inoculum was removed and cells were covered with 1 ml per well pre-warmed (37°C) medium and incubated for one hour at 37°C.…”

“…A strand-specific RT-qPCR protocol was used to quantify numbers of (+)- and (-)-strand RNA per cell [52]. TCID50 of supernatants was measured and calculated as described previously [50] and converted to PFU/mL.…”