CRISPRa screening with real world evidence identifies potassium channels as neuronal entry factors and druggable targets for SARS-CoV-2

Although vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been successful, there are no good treatments for those who are actively infected and potentially suffer from diverse neurological symptoms. While SARS-CoV-2 primarily infects the respiratory tract, clinical evid...

Full description

Saved in:
Bibliographic Details
Published in:bioRxiv 2021-07
Main Authors: Wang, Chengkun, Ravi, Dinesh, Qu, Yuanhao, Rustagi, Arjun, Cousins, Henry, Zengel, James, Guo, Yinglong, Hall, Taryn, Beck, Aimee, Tso, Luke, Erdemic, Elif, Tanudtanud, Kae, Ren, Sheng, Tzeng, Kathy Tzy-Hwa, Wilk, Aaron, Wang, Mengdi, Carette, Jan, Altman, Russ, Blish, Catherine, Le, Cong
Format: Article
Language:English
Subjects:
ACE2
Angiotensin-converting enzyme 2
Autopsy
Coronaviruses
COVID-19
CRISPR
Dosage
Histocompatibility antigen HLA
Infections
Major histocompatibility complex
Membrane proteins
Olfactory epithelium
Olig2 protein
Patent applications
Potassium
Potassium channels
Respiratory tract diseases
Sense organs
Severe acute respiratory syndrome coronavirus 2
Tropism
Viral infections
Citations: Items that cite this one
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Although vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been successful, there are no good treatments for those who are actively infected and potentially suffer from diverse neurological symptoms. While SARS-CoV-2 primarily infects the respiratory tract, clinical evidence indicates that cells from sensory organs, brain, and heart are also susceptible to infection. An understanding of factors critical for viral infection in these tissues may help identify novel therapeutics. To discover host factors involved in SARS-CoV-2 viral entry, we performed CRISPR activation (CRISPRa) screens targeting all 6000+ human membrane proteins in cells with and without overexpression of ACE2 using Spike-pseudotyped lentiviruses. We identified both novel as well as previously validated host factors. Notably, we used replication-competent SARS-CoV-2 to validate new viral-entry promoting genes, including potassium channel KCNA6, protease LGMN, and MHC-II component HLA-DPB1. We found that the overexpression of KCNA6 led to a marked increase in infection even in cells with undetectable levels of ACE2 expression. Our analysis of human olfactory neuroepithelium scRNA-seq data revealed that OLIG2+ cells--previously identified as sites of infection in COVID-19 autopsy studies--have high KCNA6 expression and minimal levels of ACE2, suggesting that the presence of KCNA6 may explain sensory/neuronal aspects of COVID-19 symptoms. Further, we demonstrate that FDA-approved compound dalfampridine, an inhibitor of KCNA-family potassium channels, suppresses viral entry in a dosage-dependent manner. Finally, we identified common prescription drugs likely to modulate the top screen hits. We then performed a retrospective analysis of insurance claims of ~8 million patients and found a clinical association between screen-identified drug classes, particularly those targeting potassium channels, and COVID-19 severity. We have thus identified the potassium channel KCNA6 as a SARS-CoV-2 host factor, expanded our understanding of potential viral tropism, and identified promising targets for drug repurposing and development. Competing Interest Statement Stanford University has filed patent applications based on this work. The authors will make all reagents openly available to the academic community.
DOI:10.1101/2021.07.01.450475