Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs

In order to identify novel SARS-CoV-2 Spike binding proteins, we carried out a whole genome CRISPR activation screen using the Calabrese Library Set A (Human CRISPR Activation Pooled Library, Addgene #92379). HEK293T cells stably expressing CRISPRa-SAM were transduced with Calabrese Set A library (Human CRISPR Activation Pooled Library, Addgene #92379). Cells were selected on puromycin and then incubated with SARS-CoV-2 Spike protein conjugated with Alexa Fluor 488. FACS was performed to identify Spike488-binding cells. Genomic DNA was isolated from sorted and unsorted cell populations and PCR performed to prepare samples for next generation sequencing. NGS fast files were processed using MAGeCK (v0.5.9) to produce read count tables. Three screens were carried out. Screen 1 used SARS-CoV-2 Hexapro Spike (Gift from Jason McLellan; Addgene, #154754) protein and 72 h puromycin selection. Screen 2 used SARS-CoV-2 (residues 1-1208, complete ectodomain) Spike (gift from Dr Florian Krammer) and 72h puromycin selection. Screen 3 used SARS-CoV-2 Hexapro Spike protein and 8 days puromycin selection.