A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets

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.

Effects of immunophilin inhibitors and non-immunosuppressive analogs on coronavirus replication in human infection models

“…The potent antiviral effects of CsA have also been demonstrated for SARS-CoV-2 infection in several relevant preclinical models, such as phBECs ( Sauerhering et al., 2022 ), primary human nasal epithelial cells ( Kratzel et al., 2021 ), lung donor-derived precision cut lung slices, and the above-mentioned mouse model ( Sauerhering et al., 2022 ). Given the well-established antiviral properties of CsA, it is not surprising that several FDA-approved clinical trials are underway to investigate the effect of CsA on COVID-19 outcomes in more detail ( Devaux et al., 2021 ).…”

Kiaa1024L/Minar2 is essential for hearing by regulating cholesterol distribution in hair bundles

“…Since the region in Kiaa1024/Minar1/Ubtor that interacts with the Deptor protein is missing in the Kiaa1024L/Minar2 protein, the regulation of mTOR signaling is likely a function specific to the Kiaa1024/Minar1/Ubtor protein. Importantly, a recent study showed that Kiaa1024/Minar1/Ubtor is a host factor crucial for the replication of pathogenic human coronaviruses, including the SARS-CoV-2 that causes the COVID-19 (Kratzel et al, 2021). Previous studies showed that the replications of positive-strand RNA viruses including hepatitis C virus (HCV) and SARS-CoV-2 require rearranged intracellular membrane structures called replication organelle (Twu et al, 2021).…”

In silico analysis and preclinical findings uncover potential targets of anti-cervical carcinoma and COVID-19 in laminarin, a promising nutraceutical

“…A kinase phosphorylation study showed that SARS-CoV-2 regulated various signaling pathways, including autophagy ( Chatterjee and Thakur, 2022 ). A genome-wide CRISPR/Cas-9 knockout (KO) screening suggested that autophagy-related genes were required for SARS-CoV-2 replication ( Kratzel et al, 2021 ). More importantly, studies found that induction of autophagy is essential for the infection and replication of SARS-CoV-2 through the regulation of acute inflammatory responses ( Zhang X. et al, 2022 ).…”