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

Abstract

AbstractAlthough 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.