Surfaceome CRISPR screening for SARS-CoV-2 virulent proteins

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19). Spike protein is the primary antigenic target for COVID vaccines and interfering with the interface between RBD (Receptor Binding Domain) of spike and ACE2 is the mechanism of action for the majority of existing therapeutic antibodies, indicating the importance of RBD and its binding to the cellular receptor for controlling SARS-CoV-2. It is unclear whether there are any intrinsic cellular proteins that inhibit viral entry of SARS-CoV-2. Our new preliminary data reveal that cellular entry of SARS-CoV-2 is inhibited by a novel inhibitory cellular protein, Leucin-rich repeat containing 15 (LRRC15). We generated a focused CRISPR activation (CRISPRa) library, named surfaceome, that covers all ~6000 known/predicted surface proteins on the cellular plasma membrane. The surfaceome CRISPRa screening was performed by staining cells with a recombinant spike protein to identify SARS-CoV-2 binding factors. Strikingly, LRRC15 inhibits spike-mediated viral entry not only in the same cells, but also in neighboring cells in trans. Expression of LRRC15 in ACE2+ cells blocked spike-mediated viral entry in ACE2+LRRC15- cells, providing a unique concept of viral entry inhibition by an inhibitory factor. This result suggests a protective role of LRRC15 in a physiological context. Our central hypothesis is that human LRRC15 acts as an inhibitory entry factor for SARS-CoV-2, acting in trans as a decoy receptor expressed in non-susceptible pathological fibroblasts in the lung. This proposal will explore the mechanism by which LRRC15 inhibits entry of SARS-CoV-2 in trans through three subaims of Aim 1. We will leverage the screening platform to identify cellular receptors for secreted virulence proteins of SARS-CoV-2, Orf3a, Orf7a, and Orf8. Importantly, the same screening platform is validated to be a efficient platform for secreted virulent proteins. In a separate screening for norovirus secreted virulence protein (NS1), the surfaceome screening successfully identified Syndecan-4 as a putative cellular receptor for norovirus NS1 (Li et al., In preparation). In the Aim 2, we will perform a surfaceome screening for Orf3a, Orf7a, and Orf8 and will discover putative cellular receptors for the secreted virulence proteins.