Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.

TitleIdentification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.
Publication TypeJournal Article
Year of Publication2021
AuthorsDaniloski, Z, Jordan, TX, Wessels, H-H, Hoagland, DA, Kasela, S, Legut, M, Maniatis, S, Mimitou, EP, Lu, L, Geller, E, Danziger, O, Rosenberg, BR, Phatnani, H, Smibert, P, Lappalainen, T, tenOever, BR, Sanjana, NE
Date Published2021 01 07
KeywordsA549 Cells, Alveolar Epithelial Cells, Angiotensin-Converting Enzyme 2, Biosynthetic Pathways, Cholesterol, Clustered Regularly Interspaced Short Palindromic Repeats, COVID-19, Endosomes, Gene Expression Profiling, Gene Knockdown Techniques, Gene Knockout Techniques, Genome-Wide Association Study, Host-Pathogen Interactions, Humans, rab GTP-Binding Proteins, rab7 GTP-Binding Proteins, RNA Interference, SARS-CoV-2, Single-Cell Analysis, Viral Load

To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.

Alternate JournalCell
PubMed ID33147445
PubMed Central IDPMC7584921
Grant ListR01 MH106842 / MH / NIMH NIH HHS / United States
R01 CA218668 / CA / NCI NIH HHS / United States
R01 AI110575 / AI / NIAID NIH HHS / United States
R01 AI123155 / AI / NIAID NIH HHS / United States
UM1 HG008901 / HG / NHGRI NIH HHS / United States
DP2 HG010099 / HG / NHGRI NIH HHS / United States
R01 HL142028 / HL / NHLBI NIH HHS / United States