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Updated: Oct 8, 2025
Genome-wide RNAi Screening to Identify Host Factors That Modulate Oncolytic Virus Therapy
Published on: April 3, 2018
A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets
Annika Kratzel1,2,3, Jenna N Kelly1,2,4, Philip V'kovski1,2
1Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland.
Abstract:
Over the past 20 years, 3 highly pathogenic human coronaviruses (HCoVs) have emerged-Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and, most recently, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-demonstrating that coronaviruses (CoVs) pose a serious threat to human health and highlighting the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycles. Herein, we conducted 2 independent genome-wide CRISPR/Cas-9 knockout (KO) screens to identify MERS-CoV and HCoV-229E host dependency factors (HDFs) required for HCoV replication in the human Huh7 cell line. Top scoring genes were further validated and assessed in the context of MERS-CoV and HCoV-229E infection as well as SARS-CoV and SARS-CoV-2 infection. Strikingly, we found that several autophagy-related genes, including TMEM41B, MINAR1, and the immunophilin FKBP8, were common host factors required for pan-CoV replication. Importantly, inhibition of the immunophilin protein family with the compounds cyclosporine A, and the nonimmunosuppressive derivative alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures, which recapitulate the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrated that these factors constitute potential targets for therapeutic intervention by clinically approved drugs.
Insights
Common host factors, including autophagy genes and immunophilins, are essential for human coronavirus replication. Targeting these factors with drugs like cyclosporine A inhibits viral spread, offering new therapeutic avenues.
Area of Science:
- Virology and Molecular Biology
- Infectious Diseases
- Drug Discovery
Background:
- Emergence of three highly pathogenic human coronaviruses (HCoVs) - SARS-CoV, MERS-CoV, and SARS-CoV-2 - underscores the urgent need for effective antiviral therapies.
- Coronaviruses rely on host cell machinery for replication, suggesting conserved host dependency factors (HDFs) across different viral strains.
Purpose of the Study:
- To identify host factors essential for the replication of MERS-CoV and HCoV-229E using genome-wide CRISPR screens.
- To validate identified HDFs across multiple human coronaviruses, including SARS-CoV and SARS-CoV-2.
- To evaluate the therapeutic potential of targeting identified host factors with existing drugs.
Main Methods:
- Conducted two independent genome-wide CRISPR/Cas-9 knockout screens in Huh7 cells to identify MERS-CoV and HCoV-229E HDFs.
- Validated top-scoring genes in the context of MERS-CoV, HCoV-229E, SARS-CoV, and SARS-CoV-2 infections.
- Assessed the antiviral efficacy of immunophilin inhibitors (cyclosporine A, alisporivir) in primary human nasal epithelial cell cultures.
Main Results:
- Identified several autophagy-related genes (TMEM41B, MINAR1) and the immunophilin FKBP8 as common HDFs crucial for pan-coronavirus replication.
- Demonstrated that inhibition of the immunophilin protein family with cyclosporine A and alisporivir dose-dependently reduced CoV replication.
- Validated findings in primary human nasal epithelial cells, mimicking natural infection sites.
Conclusions:
- Autophagy-related genes and immunophilins are critical host factors for diverse human coronavirus replication.
- Targeting these conserved host factors with clinically approved drugs represents a promising therapeutic strategy against coronaviruses.
- This study provides a foundation for developing broad-spectrum antiviral therapies against emerging and existing HCoVs.
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