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

Hong Mei,Jia Liu,Wenping Li,Yusang Xie,Wei Wang,Xinxin Zhang,Yuege Huang,Zhao Zha,Jieming Qu,Dong Wei

doi:10.1186/s13059-021-02513-w

Abstract

BackgroundRhinoviruses (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.ResultsHerein, 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.ConclusionOur 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.

Highlights

Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases
Construction of genome-wide and surfaceome clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) libraries in H1-Hela cells To normalize for the quality of sgRNAs in the library, we performed side-by-side screening with RVs using genome-wide sub-library A and surfaceome library, which exhibited similar on-target and off-target scores (Additional file 1: Fig. S1b)
Surfaceome CRISPR screen involved 16,975 sgRNA targeting to 1344 genes

Summary

Introduction

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. RVs are known as the prevalent pathogen causing common cold [15] and have been found to be associated with other severe respiratory symptoms including asthma exacerbations [16] and chronic obstructive pulmonary disease [17]. Functional genomics has been employed to understand RV infections, including RNAi or haploid cell-based genetic screen [18, 19] and emerging CRISPR screens [3]. Conventional genome-wide genetic screen appeared to have limited efficiency and only a few novel host factors of RVs such as EXOC4 and SETD3 have been identified and validated to have clinical relevance [12, 18]

Methods

Results

Conclusion