Identification of TMEM106B as proviral host factor for SARS-CoV-2

Abstract

SUMMARYThe ongoing COVID-19 pandemic is responsible for worldwide economic damage and nearly one million deaths. Potent drugs for the treatment of severe SARS-CoV-2 infections are not yet available. To identify host factors that support coronavirus infection, we performed genome-wide functional genetic screens with SARS-CoV-2 and the common cold virus HCoV-229E in non-transgenic human cells. These screens identified PI3K type 3 as a potential drug target against multiple coronaviruses. We discovered that the lysosomal protein TMEM106B is an important host factor for SARS-CoV-2 infection. Furthermore, we show that TMEM106B is required for replication in multiple human cell lines derived from liver and lung and is expressed in relevant cell types in the human airways. Our results identify new coronavirus host factors that may potentially serve as drug targets against SARS-CoV-2 or to quickly combat future zoonotic coronavirus outbreaks.

Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors

“…Of the predicted interactome, we were able to assign a putative functional role for 87 out of 332 (26%) unique genes. This finding is in contrast to a number of recent studies that performed genome-scale CRISPR-Cas9 screens in VeroE6, Huh-7, Huh-7.5.1, Huh-7.5, and ACE2-overexpressing A549 cells, which failed to identify significant enrichment of the same PPI network ( Baggen et al., 2020 ; Daniloski et al., 2020 ; Heaton et al., 2020 ; Schneider et al, 2020 ; Wang et al., 2020 ; Wei et al., 2020 ; Zhu et al., 2020 ). We speculate that this difference might be due in part to well-established advantages of focused screens, including (1) improved signal-to-noise ratios in the absence of sgRNAs targeting genes that are likely to dominate the screen (e.g., the SARS-CoV-2 cellular receptor, ACE2), (2) increased coverage by including more sgRNAs per gene (ten versus four), (3) feasibility of exploring multiple screening conditions (e.g., different viruses and temperatures), and (4) higher screen representation (i.e., >1,500-fold versus < 750-fold), as well as the lower propensity of Huh-7.5 cells to undergo syncytia formation in relation to ACE2-overexpressing A549 cells, which potentially confounds pooled screening results ( DeWeirdt et al., 2020 ; Doench, 2018 ; Parnas et al., 2015 ; Schneider et al, 2020 ).…”

“…The urgency of the ongoing SARS-CoV-2 pandemic has advanced coronavirus research at unprecedented speed. Several groups performed genome-wide CRISPR-Cas9 screens to identify host factors required by SARS-CoV-2 ( Baggen et al., 2020 ; Daniloski et al., 2020 ; Heaton et al., 2020 ; Schneider et al, 2020 ; Wang et al., 2020 ; Wei et al., 2020 ; Zhu et al., 2020 ) with the hope that these screens would not only uncover the biology underlying this virus, but also identify druggable host factors that could be targeted to prevent virus spread or lessen disease. Other groups conducted drug repurposing screens using compound libraries enriched with FDA-approved or clinical-phase drug candidates to identify off-the-shelf interventions ( Dittmar et al., 2020 ; Zhou et al., 2020 ).…”

Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

“…Another group performed SARS-CoV-2 and HCoV-229E screens using Huh-7 cells and highlighted TMEM106B , similar to Wang et al. (2020) and our study, as well as TMEM41B , the focus of this study and our accompanying manuscript describing TMEM41B as a pan-flavivirus host factor ( Baggen et al., 2020 ; Hoffmann et al., 2020a ). Most recently, Daniloski et al.…”

“…Second, Huh-7.5 cells were chosen based on their infectivity by multiple CoVs, but they are not airway cells. Nevertheless, the present study and recent work have demonstrated that hits in Huh-7 cells translate to human cells of lung origin ( Baggen et al., 2020 ). Furthermore, as shown in Figure S5 , the majority of genes identified here are expressed in human cells and tissues known to be infected by SARS-CoV-2.…”

“…CoV host factor discovery and validation is an active area of research, with multiple studies appearing in press and on preprint servers in recent months ( Baggen et al., 2020 ; Daniloski et al., 2020 ; Heaton et al., 2020 ; Hoffmann et al., 2020b ; Wang et al., 2020 ; Wei et al., 2020 ; Zhu et al., 2020b ). One group performed genome-wide CRISPR screens in the African green monkey kidney cell line VeroE6 and reported strong dependency on ACE2 and CTSL , consistent with our study ( Wei et al., 2020 ).…”