Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist

Abstract

Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors.

CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins

“…With the above criteria, the CRISPR-Surfaceome website contains 216,530 sgRNAs spanning the 18,421 genes in the genome with an average of 12 sgRNAs per gene. The 1,344 surface proteins are defined using the information from a mass spectrometry database [31] as previously described [23] . Gene ontology analysis of the cellular components of the surface proteins shows that the majority is located on plasma membrane and/or extracellular matrix, rather than intracellular membranes ( Fig.…”

“…RVs were produced as previously described [23] . For RV infection, H1-Hela cells were seeded on to 96- or 12-well plates with a density of 2.0 × 10 4 cells per well.…”

“…Particularly, cell surface proteins are the most important targets for macromolecule drugs or cell-based therapeutics, which lack the access to intracellular components. We and others have constructed cell surface protein-focused CRISPR libraries and demonstrated the feasibility of targeting surface proteins for functional genomics studies [20] , [21] , [22] , [23] .…”

CRISPR-Cas9-Based Technology for Studying Enteric Virus Infection

“…Interestingly, SETD3 interacts with viral 2A protease regardless of its protease activity, and these interactions are required for viral replication, suggesting that the 2A protease has a previously undocumented pro-viral role unrelated to its protease activity ( Diep et al, 2019 ). Moreover, CRISPR-Cas9 screens identified OLFML3 which support rhinovirus replication via suppression of the interferon response and multiple host proteins (e.g., MGAT5 and COG1) required for EV-D68 infection ( Kim et al, 2017 ; Mei et al, 2021 ).…”

Correction: Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist

“…Following publication of the original article [ 1 ], the authors identified an error in the author affiliations presented in additional file 1 . The additional file has been updated and published in this correction.…”