Barrier-to-Autointegration Factor 1 Protects against a Basal cGAS-STING Response.

Hongming Ma,Sofia I Porter,Nima Mosammaparast,Michael S Diamond,Eugene M Oltz,Rong Zhang,Monika Bambouskova,Jonathan J Miner,Patrick L Collins,Wei Qian,Andrea K Byrum,Maxim Artyomov,Russell Vance

doi:10.1128/mbio.00136-20

Abstract

Although the pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immune-mediated damage. Using a genome-wide CRISPR-Cas9 screening approach to identify host factors that modulate interferon-stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. Ablation of Banf1 by gene editing resulted in chromatin activation near host defense genes with associated increased expression of ISGs, including Oas2, Rsad2 (viperin), Ifit1, and ISG15 The phenotype in Banf1-deficient cells occurred through a cGAS-, STING-, and IRF3-dependent signaling axis, was associated with reduced infection of RNA and DNA viruses, and was reversed in Banf1 complemented cells. Confocal microscopy and biochemical studies revealed that a loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline. Our study identifies an undescribed role for Banf1 in regulating the levels of cytoplasmic DNA and cGAS-dependent ISG homeostasis and suggests possible therapeutic directions for promoting or inhibiting cell-intrinsic innate immune responses.IMPORTANCE Although the interferon (IFN) signaling pathway is a key host mechanism to restrict infection of a diverse range of viral pathogens, its unrestrained activity either at baseline or in the context of an immune response can result in host cell damage and injury. Here, we used a genome-wide CRISPR-Cas9 screen and identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1) as a modulator of basal cell-intrinsic immunity. A loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline, which triggered IFN-stimulated gene expression via a cGAS-STING-IRF3 axis that did not require type I IFN or STAT1 signaling. Our experiments define a regulatory network in which Banf1 limits basal inflammation by preventing self DNA accumulation in the cytosol.

Highlights

The pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immunemediated damage
To rule out possible off-target effects, five additional small guide RNAs (sgRNA) against Barrier-to-autointegration factor 1 (Banf1) were tested in bulk cell lines (Fig. S2D); these cells showed that a deficiency of Banf1 expression resulted in enhanced interferon-stimulated gene (ISG) levels at baseline, even in the absence of exogenous IFN-␤ treatment
Of note, ⌬Banf1 cell line was not a complete null, since small amounts of Banf1 were detected in immunoblots (Fig. 1C); this expression pattern was anticipated as a complete loss of Banf1 is lethal during embryogenesis in invertebrates [20]

Summary

Introduction

The pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immunemediated damage. Using a genome-wide CRISPR-Cas screening approach to identify host factors that modulate interferon-stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. IMPORTANCE the interferon (IFN) signaling pathway is a key host mechanism to restrict infection of a diverse range of viral pathogens, its unrestrained activity either at baseline or in the context of an immune response can result in host cell damage and injury. A loss of Banf expression resulted in higher level of cytosolic double-stranded DNA at baseline, which triggered IFN-stimulated gene expression via a cGAS-STING-IRF3 axis that did not require type I IFN or STAT1 signaling. The suppressor of cytokine signaling (SOCS) family of proteins negatively regulates inflammation by targeting the tyrosine kinase activity of Janus kinases (JAK), which inhibits JAK/STAT signaling pathways and attenuates antiviral responses [8]

Methods

Results

Conclusion