The single-nucleotide polymorphism rs1990760 in the gene encoding the cytosolic viral sensor IFIH1 results in an amino-acid change (A946T; IFIH1T946) that is associated with multiple autoimmune diseases. The effect of this polymorphism on both viral sensing and autoimmune pathogenesis remains poorly understood. Here we found that human peripheral blood mononuclear cells (PBMCs) and cell lines expressing the risk variant IFIH1T946 exhibited heightened basal and ligand-triggered production of type I interferons. Consistent with those findings, mice with a knock-in mutation encoding IFIH1T946 displayed enhanced basal expression of type I interferons, survived a lethal viral challenge and exhibited increased penetrance in autoimmune models, including a combinatorial effect with other risk variants. Furthermore, IFIH1T946 mice manifested an embryonic survival defect consistent with enhanced responsiveness to RNA self ligands. Together our data support a model wherein the production of type I interferons driven by an autoimmune risk variant and triggered by ligand functions to protect against viral challenge, which probably accounts for its selection within human populations but provides this advantage at the cost of modestly promoting the risk of autoimmunity.
Subscribe to Journal
Get full journal access for 1 year
only $17.42 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Wandstrat, A. & Wakeland, E. The genetics of complex autoimmune diseases: non-MHC susceptibility genes. Nat. Immunol. 2, 802–809 (2001).
Theofilopoulos, A.N., Baccala, R., Beutler, B. & Kono, D.H. Type I interferons (α/β) in immunity and autoimmunity. Annu. Rev. Immunol. 23, 307–336 (2005).
Ferreira, R.C. et al. A type I interferon transcriptional signature precedes autoimmunity in children genetically at risk for type 1 diabetes. Diabetes 63, 2538–2550 (2014).
Münz, C., Lünemann, J.D., Getts, M.T. & Miller, S.D. Antiviral immune responses: triggers of or triggered by autoimmunity? Nat. Rev. Immunol. 9, 246–258 (2009).
Errett, J.S., Suthar, M.S., McMillan, A., Diamond, M.S. & Gale, M. Jr. The essential, nonredundant roles of RIG-I and MDA5 in detecting and controlling West Nile virus infection. J. Virol. 87, 11416–11425 (2013).
Loo, Y.-M. & Gale, M. Jr. Immune signaling by RIG-I-like receptors. Immunity 34, 680–692 (2011).
del Toro Duany, Y., Wu, B. & Hur, S. MDA5-filament, dynamics and disease. Curr. Opin. Virol. 12, 20–25 (2015).
Leung, D.W. & Amarasinghe, G.K. Structural insights into RNA recognition and activation of RIG-I-like receptors. Curr. Opin. Struct. Biol. 22, 297–303 (2012).
Kato, H. et al. Length-dependent recognition of double-stranded ribonucleic acids by retinoic acid-inducible gene-I and melanoma differentiation-associated gene 5. J. Exp. Med. 205, 1601–1610 (2008).
Pichlmair, A. et al. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J. Virol. 83, 10761–10769 (2009).
Rice, G.I. et al. Gain-of-function mutations in IFIH1 cause a spectrum of human disease phenotypes associated with upregulated type I interferon signaling. Nat. Genet. 46, 503–509 (2014).
Rutsch, F. et al. A specific IFIH1 gain-of-function mutation causes Singleton-Merten syndrome. Am. J. Hum. Genet. 96, 275–282 (2015).
Van Eyck, L. et al. Brief report: IFIH1 mutation causes systemic lupus erythematosus with selective IgA deficiency. Arthritis Rheumatol. 67, 1592–1597 (2015).
Funabiki, M. et al. Autoimmune disorders associated with gain of function of the intracellular sensor MDA5. Immunity 40, 199–212 (2014).
Smyth, D.J. et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat. Genet. 38, 617–619 (2006).
Nejentsev, S., Walker, N., Riches, D., Egholm, M. & Todd, J.A. Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324, 387–389 (2009).
Enevold, C. et al. Multiple sclerosis and polymorphisms of innate pattern recognition receptors TLR1-10, NOD1-2, DDX58, and IFIH1. J. Neuroimmunol. 212, 125–131 (2009).
Cunninghame Graham, D.S. et al. Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with systemic lupus erythematosus. PLoS Genet. 7, e1002341 (2011).
Li, Y. et al. Carriers of rare missense variants in IFIH1 are protected from psoriasis. J. Invest. Dermatol. 130, 2768–2772 (2010).
Martínez, A. et al. Association of the IFIH1-GCA-KCNH7 chromosomal region with rheumatoid arthritis. Ann. Rheum. Dis. 67, 137–138 (2008).
Jin, Y., Andersen, G.H.L., Santorico, S.A. & Spritz, R.A. Multiple functional variants of IFIH1, a gene involved in triggering innate immune responses, protect against vitiligo. J. Invest. Dermatol. 137, 522–524 (2017).
Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).
Onengut-Gumuscu, S. et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat. Genet. 47, 381–386 (2015).
Concannon, P. et al. Genome-wide scan for linkage to type 1 diabetes in 2,496 multiplex families from the Type 1 Diabetes Genetics Consortium. Diabetes 58, 1018–1022 (2009).
Wang, C. et al. Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility. Genes Immun. 14, 217–222 (2013).
Liu, S. et al. IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells. Hum. Mol. Genet. 18, 358–365 (2009).
Chen, G. et al. Genetic variants in IFIH1 play opposite roles in the pathogenesis of psoriasis and chronic periodontitis. Int. J. Immunogenet. 39, 137–143 (2012).
Hoffmann, F.S. et al. Polymorphisms in melanoma differentiation-associated gene 5 link protein function to clearance of hepatitis C virus. Hepatology 61, 460–470 (2015).
Chistiakov, D.A., Voronova, N.V., Savost'Anov, K.V. & Turakulov, R.I. Loss-of-function mutations E6 27X and I923V of IFIH1 are associated with lower poly(I:C)-induced interferon-β production in peripheral blood mononuclear cells of type 1 diabetes patients. Hum. Immunol. 71, 1128–1134 (2010).
Kato, H. et al. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature 441, 101–105 (2006).
Dai, X. et al. A disease-associated PTPN22 variant promotes systemic autoimmunity in murine models. J. Clin. Invest. 123, 2024–2036 (2013).
Perry, D., Sang, A., Yin, Y., Zheng, Y.-Y. & Morel, L. Murine models of systemic lupus erythematosus. J. Biomed. Biotechnol. 2011, 271694 (2011).
Klarquist, J. & Janssen, E.M. The bm12 inducible model of systemic lupus erythematosus (SLE) in C57BL/6 mice. J. Vis. Exp. 105, e53319 (2015).
Ma, Z., Chen, F., Madaio, M.P., Cohen, P.L. & Eisenberg, R.A. Modulation of autoimmunity by TLR9 in the chronic graft-vs-host model of systemic lupus erythematosus. J. Immunol. 177, 7444–7450 (2006).
Robinson, T. et al. Autoimmune disease risk variant of IFIH1 is associated with increased sensitivity to IFN-α and serologic autoimmunity in lupus patients. J. Immunol. 187, 1298–1303 (2011).
Liddicoat, B.J. et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015).
Pestal, K. et al. Isoforms of RNA-editing enzyme ADAR1 independently control nucleic acid sensor MDA5-driven autoimmunity and multi-organ development. Immunity 43, 933–944 (2015).
Heraud-Farlow, J.E. & Walkley, C.R. The role of RNA editing by ADAR1 in prevention of innate immune sensing of self-RNA. J. Mol. Med. 94, 1095–1102 (2016).
Schlee, M. & Hartmann, G. Discriminating self from non-self in nucleic acid sensing. Nat. Rev. Immunol. 16, 566–580 (2016).
Rice, G.I. et al. Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature. Nat. Genet. 44, 1243–1248 (2012).
Niewold, T.B., Hua, J., Lehman, T.J.A., Harley, J.B. & Crow, M.K. High serum IFN-α activity is a heritable risk factor for systemic lupus erythematosus. Genes Immun. 8, 492–502 (2007).
Downes, K. et al. Reduced expression of IFIH1 is protective for type 1 diabetes. PLoS One 5, e12646 (2010).
Lincez, P.J., Shanina, I. & Horwitz, M.S. Reduced expression of the MDA5 gene IFIH1 prevents autoimmune diabetes. Diabetes 64, 2184–2193 (2015).
Buers, I., Nitschke, Y. & Rutsch, F. Novel interferonopathies associated with mutations in RIG-I like receptors. Cytokine Growth Factor Rev. 29, 101–107 (2016).
Rodero, M.P. & Crow, Y.J. Type I interferon-mediated monogenic autoinflammation: The type I interferonopathies, a conceptual overview. J. Exp. Med. 213, 2527–2538 (2016).
Fumagalli, M. et al. Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes. Mol. Biol. Evol. 27, 2555–2566 (2010).
Vasseur, E. et al. The selective footprints of viral pressures at the human RIG-I-like receptor family. Hum. Mol. Genet. 20, 4462–4474 (2011).
Vergara, C., Thio, C.L., Thomas, D. & Duggal, P. Polymorphisms in melanoma differentiation-associated gene 5 are not associated with clearance of hepatitis C virus in a European American population. Hepatology 63, 1061–1062 (2016).
Pedergnana, V. et al. Refined association of melanoma differentiation-associated gene 5 variants with spontaneous hepatitis C virus clearance in Egypt. Hepatology 63, 1059–1061 (2016).
Hartner, J.C. et al. Liver disintegration in the mouse embryo caused by deficiency in the RNA-editing enzyme ADAR1. J. Biol. Chem. 279, 4894–4902 (2004).
Laird, N.M., Horvath, S. & Xu, X. Implementing a unified approach to family-based tests of association. Genet. Epidemiol. 19 (Suppl. 1), S36–S42 (2000).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Sharma, S. et al. Widely divergent transcriptional patterns between SLE patients of different ancestral backgrounds in sorted immune cell populations. J. Autoimmun. 60, 51–58 (2015).
Börnsen, L. et al. Endogenous interferon-β-inducible gene expression and interferon-β-treatment are associated with reduced T cell responses to myelin basic protein in multiple sclerosis. PLoS One 10, e0118830 (2015).
Scheler, M. et al. Indoleamine 2,3-dioxygenase (IDO): the antagonist of type I interferon-driven skin inflammation? Am. J. Pathol. 171, 1936–1943 (2007).
Indraccolo, S. et al. Identification of genes selectively regulated by IFNs in endothelial cells. J. Immunol. 178, 1122–1135 (2007).
Vandesompele, J. et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034 (2002).
Jackson, S.W. et al. Opposing impact of B cell-intrinsic TLR7 and TLR9 signals on autoantibody repertoire and systemic inflammation. J. Immunol. 192, 4525–4532 (2014).
We thank K. Sommer for laboratory management and assistance with manuscript editing; the University of Washington Histology and Imaging Core and Benaroya Clinical Core; M. Kinsman for technical assistance with RNA preparation; and E. Whalen and V. Gersuk for assistance with Fluidigm assays. Supported by the US National Institutes of Health (DP3-DK097672 to J.H.B.; DP3-DK111802 to D.J.R.; R01-AI084914 to D.B.S.; R01-AI104002, R01-AI060389 and R01-AI127463 to M.G.; U19-AI083019 to M.G.; U19-AI100625 to M.G.; R01-DK106718 to P.C.; T32-AR007108 to J.A.G; and T32-GM007270 to K.P.), the Juvenile Diabetes Research Foundation (3-APF-2016-177-A-N to Y.G.), the Children's Guild Association Endowed Chair in Pediatric Immunology and the Benaroya Family Gift Fund (D.J.R.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 PBMCs from healthy human subjects with IFIH1R manifest increased ISG expression.
(a-b) PBMCs from healthy donors left unstimulated or stimulated with poly(I:C) and quantitative RT-PCR was performed to assess IFIH1 mRNA expression (as described in Fig 1). Each data point represents an individual subject. Bars represent mean. (a) Baseline IFIH1 mRNA levels. (b) IFIH1 mRNA levels following poly(I:C) stimulation for according to IFIH1 genotype or haplotype (as detailed in Fig 1). (c-d) Human PBMCs were thawed and rested for 24 hours and mRNA was analyzed using a custom high-throughput qPCR (Fluidigm) as in Fig 1 to assess ISG expression. Data points show log-transformed relative expression. Welch’s T test was used for statistical analysis. IFIH1R843 was held constant for all individuals. Each data point represents an individual subject. Bars represent median. (c) Additional ISGs with statistically significant increase in IFIH1R subjects. (d) ISGs reaching borderline statistical significance (defined as p=< 0.1). NR=non-risk (encoding IFIH1H843 and IFIH1A946); R=risk (encoding IFIH1R843 and IFIH1T946). *p<0.05.
Supplementary Figure 2 The mIFIH1 protective variant ablates innate signaling, while mIFIH1R promotes protection from West Nile virus.
(a-g) HEK293T cells were transfected with 1 μg of plasmid co-expressing either empty vector (EV) or the indicated mIFIH1 constructs described in Fig. 2. (a-b) Data from four biological replicates showing: (b) Geometric MFI and (c) Percent GFP+ for the histograms shown Fig. 2c. (c-d) IFN B1 mRNA expression in cells transfected with mIFIH1NR or mIFIH1P constructs at time points indicated showing: (c) Representative experiment from one of three biological replicates; (d) Mean ratio of 3 biological replicates. Error bars represent ± SEM. Statistical analysis using a two-tail student T test. (e-g) At 15 hours post-transfection with the indicated mIFIH1 constructs, cells were infected with West Nile Virus (WNV; MOI of 5) or left uninfected (mock) and harvested at the indicated time points. (e) Quantitative RT-PCR for IFNB1 mRNA expression with data normalized as in Fig. 2d. (f) WNV, IFIH1 and β-actin protein expression assessed by Western blotting. Whole cell lysates were resolved by SDS-PAGE and immuno-blotted with indicated antibodies. (+) represents plasmid or virus present, (-) represents plasmid or virus absent. (f) Densitometry analysis of WNV protein expression at the 30 hours normalized to β-actin levels and displayed as relative fold change. Representative data from one of three WNV infection experiments are displayed. **p<0.01, ****p<0.0001.
(a) Strategy for generating the Ifih1R knock-in mice with introduction of point mutation within exon 15 of Ifih1 designed to introduce the risk variant allele. Also shown are location of neomycin cassette with flanking FRT sites and the location of LoxP sites introduced in order to permit future generation of lineage-specific Ifih1deletion via intercrossing with Cre-expressing strains. (b) DNA sequencing reaction showing the Ifih1 coding change from GCA (Ala) to ACA (Thr) in homologous knock-in (Ifih1R/R) mice. (c) Quantitative RT-PCR to assess Ifih1 mRNA expression. Ct values were normalized to Hprt. (d) Splenocytes were isolated from 2-12 month old animals of the indicated genotypes. Fold increase relative to the average WT values for each experiment is displayed. Each dot represents an individual animal. Error bars represent ± SEM and significance was assessed using one-way ANOVA (c) or Kruskal-Wallis test (d).
(a-b) Mice were injected with STZ for 4 days (55 mg/kg) and monitored for development of diabetes as described in Figure 5c. Tissues were harvested at week 15 post-STZ treatment for genotypes that developed disease [Ifih1NR/NRPtpn22NR/R (n=2) or Ifih1NR/RPtpn22NR/R (n=2)] and analyzed in a blinded fashion for histological changes. Scale bars equal 100 μm. (a) STZ treated heterozygous Ifih1NR/NRPtpn22NR/R mice. Both diabetic (A1, 20X) and nondiabetic (A2, 20X) animals had mild cellular changes evident in islets in H&E stained sections. Immuno-histochemical stains revealed reduced numbers of dark brown insulin positive cells in diabetics (B1, 20X) compared to nondiabetics (B2, 20X). Inflammation was rare and scant. (b) Compound heterozygous Ifih1NR/RPtpn22NR/R diabetic mice exhibited inflammatory changes in the pancreas with lesion severity ranging from scattered mild lymphocytic insulitis (arrow, C1, 40X) to atrophy and sclerosis with replacement by fibrous tissue containing pancreatic ductal remnants (arrows, C2, 10X). Immuno-histochemical staining for insulin and CD3 demonstrated atrophic and fibrosing pancreatitis containing whole or fragments of islets (arrows showing brown foci, D1, 20X) or CD3+ inflammatory cells (scattered brown foci, D2, 20X) dispersed among an isolated islet (arrow) and remnants of pancreatic ducts (stars). (b-c) BM12 CD4+ T cell were adoptively transferred into mice of indicated genotypes as described in Figure 5. Each dot represents results from an individual animal. (b) ELISAs for IgG anti-smRNP (upper panel) and IgG2c anti-smRNP (lower panel) autoantibodies at time points indicated. (c) Splenic cell numbers at week 15 post injection. Error bars represent ± SEM.
(a) Full western blot from Fig. 2b immuno-blotted with anti-IFIH1 (left) and anti-β-actin (right) antibodies. (b) Full western blots from Sup. Fig. 2f immuno-blotted with anti-IFIH1 (top), anti-β-actin (middle), and anti-WNV (bottom) antibodies. The rightmost three lanes are from an unrelated experiment. Positions of loading controls used to assess relative protein molecular weight are indicated.
About this article
Cite this article
Gorman, J., Hundhausen, C., Errett, J. et al. The A946T variant of the RNA sensor IFIH1 mediates an interferon program that limits viral infection but increases the risk for autoimmunity. Nat Immunol 18, 744–752 (2017). https://doi.org/10.1038/ni.3766
Intracellular virus sensor MDA5 exacerbates vitiligo by inducing the secretion of chemokines in keratinocytes under virus invasion
Cell Death & Disease (2020)
Transcriptome profiling analysis of lung tissue of Chinese soft-shell turtle infected by Trionyx sinensis Hemorrhagic Syndrome Virus
Fish & Shellfish Immunology (2020)
Frontiers in Endocrinology (2020)
The African-American population with a low allele frequency of SNP rs1990760 (T allele) in IFIH1 predicts less IFN-beta expression and potential vulnerability to COVID-19 infection