The Ca2+ sensor STIM1 regulates the type I interferon response by retaining the signaling adaptor STING at the endoplasmic reticulum

Abstract

Stimulator of interferon genes (STING) is an endoplasmic reticulum (ER) signaling adaptor that is essential for the type I interferon response to DNA pathogens. Aberrant activation of STING is linked to the pathology of autoimmune and autoinflammatory diseases. The rate-limiting step for the activation of STING is its translocation from the ER to the ER-Golgi intermediate compartment. Here, we found that deficiency in the Ca2+ sensor stromal interaction molecule 1 (STIM1) caused spontaneous activation of STING and enhanced expression of type I interferons under resting conditions in mice and a patient with combined immunodeficiency. Mechanistically, STIM1 associated with STING to retain it in the ER membrane, and coexpression of full-length STIM1 or a STING-interacting fragment of STIM1 suppressed the function of dominant STING mutants that cause autoinflammatory diseases. Furthermore, deficiency in STIM1 strongly enhanced the expression of type I interferons after viral infection and prevented the lethality of infection with a DNA virus in vivo. This work delineates a STIM1-STING circuit that maintains the resting state of the STING pathway.

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Fig. 1: STIM1 deficiency spontaneously induces type I IFN response in murine and human cells.
Fig. 2: STING-TBK1-IRF3 pathway links loss of STIM1 expression to Ifnb1 transcription.
Fig. 3: STIM1 deficiency causes enhanced type I IFN response in patient cells.
Fig. 4: STIM1 interacts with STING for its retention in the ER.
Fig. 5: STIM1 inhibits STING trafficking to the ERGIC.
Fig. 6: Ablation of STIM1 enhances host defense towards DNA viruses and HIV by priming type I IFN responses.
Fig. 7: STIM1 deficiency enhances host defense against HSV-1 infection in vivo.

Data availability

The data that support the findings of this study are available from the corresponding authors upon request. The manuscript describing the clinical phenotype of the STIM1 patient is available from OSR Preprints (https://doi.org/10.31219/osf.io/4duxt).

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Acknowledgements

We thank S. Bensinger (UCLA) for sharing THP1 cells, and X. Liu and S. Smale (UCLA) for BMDM differentiation protocols and reagents. We thank N.-H. Park, K.-H. Shin, M.K. Kang, R. Kim, Y. Wang, and T.M. Vondriska for sharing their confocal imaging facilities. We thank J.-L. Casanova (Rockefeller University) for providing STIM1 patient B cell line. This work was supported by the National Institutes of Health grants AI083432 and DE028432 (Y.G.) and AI130653 (S. Srikanth). This work was also supported in part by CA180779, CA200422, AI073099, AI116585, AI129496, AI140705, DE023926, DE027888, the Fletcher Jones Foundation, and the Whittier Foundation (J.U.J.).

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Contributions

Y.G. and S.S. designed the research. S.S. performed all of the in vitro experiments using MEFs, THP1, and BMDMs with technical help from J.L. J.S.W. performed biochemical experiments of interaction between STIM1 and STING, SAVI mutant analyses, and in vivo HSV infection experiments with help from B.W. Y.M.E.-S., L.R., and S. Savic collected and analyzed patient samples together with S.S. and J.S.W. K.C. and D.S.A. performed the HIV infection experiments. G.J.S. and J.U.J. provided reagents and protocols for in vitro HSV infections. G.C. helped with statistical analysis. C.R. and E.C. provided reagents and protocols for in vivo HSV infections. T.T.W. and R.S. provided reagents and protocols for MHV-68 infections. S.S. and Y.G. wrote the manuscript with input from all authors and supervised the project.

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Correspondence to Sonal Srikanth or Yousang Gwack.

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Integrated supplementary information

Supplementary Figure 1 Sequencing data for STIM1−/− THP1 clones generated using CRISPR–Cas9 system.

Top: alignment of sequences within exons 2 and 3 of human STIM1 gene with the ones from individual clones (sg#2 and sg#3). The sgRNA sequences are highlighted in red. Below: sequencing results of individual clones. Boxed areas mark the indel sites. Clone sg#2 shows insertion of three nucleotides and deletion of two nucleotides, whereas sg#3 shows deletion of five nucleotides

Supplementary Figure 2 Lack of spontaneous induction of the type I IFN response in STIM2−/− THP1 cells.

Left, immunoblot showing expression of STIM2 in control or STIM2−/− THP1 cells generated using two independent sgRNAs (sg#1 and sg#2). Loss of STIM2 does not alter expression of STIM1 or STING in these cells. Right: qPCR analysis of IFNB1 transcripts in unstimulated control and STIM2−/− THP1 cells. Data show representative triplicates from two independent experiments

Supplementary Figure 3 STIM1 deficiency induces dimerization of STING.

a, Immunoblots from two representative experiments (Exp. no. 1 and no. 2) showing endogenous STING in control, Stim1−/−, and Orai1−/− MEFs under non-reducing SDS–PAGE conditions. *The position of monomeric and dimeric STING. b, Lysates from untreated or DSP-treated (0.125, 0.25, 0.5, 1.0, and 2.0 mM, 1 h on ice) control or STIM1−/− HEK293T cells expressing STING-FLAG were immunoblotted for detection of STING under non-reducing conditions (left). Bar graph shows averaged ratio of STING (dimer/monomer) from three independent experiments (right). *P <0.05 (unpaired/two-tailed t-test)

Supplementary Figure 4 Overexpression or deletion of STING affects SOCE and STIM1 translocation kinetics.

a, Representative traces of averaged SOCE from HEK293T cells expressing empty vector (24 cells) or that encoding STING (27 cells) after passive depletion of intracellular Ca2+ stores with 1 μM TG in the presence of external solution containing 2 mM Ca2+, as indicated. b, Representative traces of averaged SOCE from Jurkat T cells expressing empty vector (54 cells) or that encoding STING (49 cells). c, Representative traces of averaged SOCE from Jurkat T cells expressing empty vector (49 cells) or that encoding STING (53 cells) after stimulation with 10 µg ml−1 α-CD3 antibody or 0.5 µM ionomycin in the presence of external solution containing 2 mM Ca2+, as indicated. d, Representative epifluorescence (left) and TIRF (right) images of WT or Sting−/− MEFs stably expressing STIM1-YFP under resting conditions or 10 min after depletion of intracellular Ca2+ stores using 1 μM TG. Scale bar, 10 µm. Line graph on the right shows mean normalized fluorescence intensity ± s.e.m. of STIM1-YFP in WT (6 cells) and Tmem173−/− MEFs (9 cells) from 2 independent experiments. e, Left, immunoblot showing expression of indicated proteins in control and TMEM173−/− Jurkat T cells. Right panels show representative traces of averaged SOCE from control (54 cells) and TMEM173−/− (58 cells) Jurkat T cells. f, Representative traces of averaged SOCE from control (66 cells) and TMEM173−/− (60 cells) Jurkat T cells after stimulation with anti-CD3 antibody (2 μg ml−1) in the presence of external solution containing 2 mM Ca2+, as indicated. Bar graphs in panels ac, e, and f show averaged baseline subtracted peak SOCE (±s.e.m.) from three independent experiments. *P <0.05, **P <0.005, ***P <0.0005 (unpaired/two-tailed t-test)

Supplementary Figure 5 Functional interaction of constitutively active STING mutants with STIM1.

a, FLAG immunoprecipitates from lysates of HEK293T cells stably expressing FLAG-tagged WT or indicated mutants of STING were immunoblotted for detection of endogenous STIM1 proteins (left). Bar graph (right) shows densitometry analysis of normalized (relative to WT STING) fold change in STIM1 band intensity from seven independent experiments. b, Reporter assay for Ifnb1 promoter activity in HEK293T cells transfected with WT or mutant STING proteins and full-length STIM1 or its N-terminal fragment (a.a. 1–249) for 24 h (right). Data show representative triplicates from two independent experiments. c, Representative confocal microscopy images of MEFs stably expressing WT STING-GFP or indicated SAVI mutants without or with STIM1. Cells were either stained for endogenous p58 (ERGIC marker, left three panels) or STIM1 (+STIM1, right three panels). Scale bar, 10 µm. Images are representative of 25–30 cells for each condition. *P <0.05, **P <0.005, and ***P <0.0005 (unpaired/two-tailed t-test, a; one-way ANOVA, b)

Supplementary Figure 6 STIM1 plays a Ca2+-independent role in the antiviral immune response.

a, qPCR analysis of GFP (left) and Ifnb1 (right) transcripts in WT, Orai1−/−, or Stim1−/− MEFs uninfected or HSV-1-GFP-infected with indicated MOI. b, qPCR analysis of GFP (left) transcripts in HSV-GFP-infected (MOI 0.5, 24 h) WT or Stim1−/− MEFs in the presence or absence of indicated amounts of tofacitinib. Cells were preincubated with the inhibitor for 30 min before infection. Data show representative triplicates from two independent experiments. Data are shown as mean ± s.e.m. *P <0.05, **P <0.005, and ***P <0.0005 (two-way ANOVA, a; unpaired/two-tailed t-test, b)

Supplementary Figure 7 Generation of mice with conditionally targeted Orai1 deficiency.

a, Schematic showing the architecture of mouse Orai1 gene. Exon 2 of the Orai1 gene was targeted. By homologous recombination, Orai1+/fl mice with loxP sites (red arrowheads) flanking exon 2 were generated. Germ-line transmission of flox alleles was validated by genotyping PCR (lower panel). The location of the primer pair is indicated as green (5′ and 3′) arrows. A 378-base pair (bp) band is derived from the flox allele while a 200-bp band denotes the WT allele. b, qPCR analysis of Orai1 transcripts in control (Orai1fl/fl) or Orai1−/− BMDMs 7 d after differentiation. Data show representative triplicates (mean ± s.e.m., unpaired/two-tailed t-test) from two independent experiments c, Representative traces of averaged SOCE from Orai1fl/fl (36 cells) and Orai1−/− (41 cells) BMDMs 7 d after differentiation and after passive depletion of intracellular Ca2+ stores with 1 μM TG in the presence of external solution containing 2 mM Ca2+, as indicated. Data are representative of three independent experiments

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Srikanth, S., Woo, J.S., Wu, B. et al. The Ca2+ sensor STIM1 regulates the type I interferon response by retaining the signaling adaptor STING at the endoplasmic reticulum. Nat Immunol 20, 152–162 (2019). https://doi.org/10.1038/s41590-018-0287-8

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