A diverse range of gene products are effectors of the type I interferon antiviral response

Abstract

The type I interferon response protects cells against invading viral pathogens. The cellular factors that mediate this defence are the products of interferon-stimulated genes (ISGs). Although hundreds of ISGs have been identified since their discovery more than 25 years ago, only a few have been characterized with respect to antiviral activity. For most ISG products, little is known about their antiviral potential, their target specificity and their mechanisms of action. Using an overexpression screening approach, here we show that different viruses are targeted by unique sets of ISGs. We find that each viral species is susceptible to multiple antiviral genes, which together encompass a range of inhibitory activities. To conduct the screen, more than 380 human ISGs were tested for their ability to inhibit the replication of several important human and animal viruses, including hepatitis C virus, yellow fever virus, West Nile virus, chikungunya virus, Venezuelan equine encephalitis virus and human immunodeficiency virus type-1. Broadly acting effectors included IRF1, C6orf150 (also known as MB21D1), HPSE, RIG-I (also known as DDX58), MDA5 (also known as IFIH1) and IFITM3, whereas more targeted antiviral specificity was observed with DDX60, IFI44L, IFI6, IFITM2, MAP3K14, MOV10, NAMPT (also known as PBEF1), OASL, RTP4, TREX1 and UNC84B (also known as SUN2). Combined expression of pairs of ISGs showed additive antiviral effects similar to those of moderate type I interferon doses. Mechanistic studies uncovered a common theme of translational inhibition for numerous effectors. Several ISGs, including ADAR, FAM46C, LY6E and MCOLN2, enhanced the replication of certain viruses, highlighting another layer of complexity in the highly pleiotropic type I interferon system.

Figure 1. FACS-based screen for identifying antiviral ISGs

a. Gateway-compatible bicistronic lentiviral vector. b. Schematic of overexpression screen showing hypothetical FACS plots of inhibitory versus non-inhibitory genes. Overlap of RFP (magenta) and GFP (green) is depicted as white. c. FACS plots showing IFI6-mediated inhibition of YFV in STAT1^−/−Fib. d. Distribution of HCV replication levels at 48 h normalized to Fluc control. The number of ISGs within standard deviation (S.D. or Z-score) ranges are shown in boxes. e. Dot plots of HCV replication levels at 48 h and 72 h normalized to Fluc control. Select ISGs are denoted in blue. Black line indicates population mean.

Figure 2. Identification of ISGs that inhibit or enhance virus replication

a. Dot plots of large-scale ISG screens against six viruses. Replication levels were normalized to Fluc control. Select ISGs are denoted in blue. Black line indicates population mean. b, d. Confirmation assays of selected ISGs. For HIV, Macaca mulatta (M.m.) TRIM5 was included as a control. Replication levels were normalized to Fluc control. Data are represented by box and whisker plots. n=8 for HCV, n=9 for other viruses. Statistical significance was determined by one-way ANOVA. (***,P<0.001, **,P<0.01, *,P<0.05, ns-not significant). c. Frequency of validated antiviral ISG prevalence across six screens.

Figure 3. Combinatorial action of inhibitory and enhancing ISGs

a. Anti-HCV ISGs were tested in 2-gene combinations (inset). Dashed red line denotes the strongest single-gene inhibitor, IRF1. b, d, e. Confirmation assays from two-gene screens for HCV (b), HIV(d), YFV(e). Data were normalized to Fluc control. n=8 for HCV, YFV, n=9 for HIV. Statistical significance was determined by one-way ANOVA. (***,P<0.001, **,P<0.01, *,P<0.05, ns-not significant). Inhibition of HIV IFNα is plotted for comparison. ISGs are color-coded: control (red), inhibitory (black), enhancing (green) c. Inhibition of HCV by IFNβ. Results are mean ± s.d., n=3.

Figure 4. Translational inhibition as a common mechanism of ISG-mediated antiviral action

a. ISG-expressing Huh-7 cells were transfected with HCV subgenomic replicon RNA and Gluc levels in cell supernatants were measured b. Inhibition of primary translation (left panel) or replication (right panel) was inferred from 4 h and 72 h data, respectively. Results are mean ± s.d., n=4. Statistical significance was determined by one-way ANOVA. (***,P<0.001, **,P<0.01, *,P<0.05, ns-not significant) d-g. C6orf150-mediated inhibition of SINV in STAT1^−/−Fib. C6orf150 inhibits SINV-GFP replication (d) and non-GFP SINV production(e). C6orf150 and IRF1 inhibit SINV(ts6) primary translation (f) and SINV-Fluc replication (g). Results are mean ± s.d., n=3.