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Diverse intracellular pathogens activate type III interferon expression from peroxisomes

Nature Immunology volume 15, pages 717–726 (2014)Cite this article

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Abstract

Type I interferon responses are considered the primary means by which viral infections are controlled in mammals. Despite this view, several pathogens activate antiviral responses in the absence of type I interferons. The mechanisms controlling type I interferon–independent responses are undefined. We found that RIG-I like receptors (RLRs) induce type III interferon expression in a variety of human cell types, and identified factors that differentially regulate expression of type I and type III interferons. We identified peroxisomes as a primary site of initiation of type III interferon expression, and revealed that the process of intestinal epithelial cell differentiation upregulates peroxisome biogenesis and promotes robust type III interferon responses in human cells. These findings highlight the importance of different intracellular organelles in specific innate immune responses.

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Figure 1: Peroxisomal MAVS induces Jak-STAT–dependent antiviral responses that have characteristics of type III interferon signaling.
Figure 2: Type III interferons are produced during viral infections and are important for the antiviral functions of human cells.
Figure 3: Similarities between type I and type III interferon regulation.
Figure 4: IFN-λ1 is regulated by a unique pathway that involves IRF1.
Figure 5: Peroxisomal MAVS selectively induces type III interferons.
Figure 6: The abundance and function of mitochondria and peroxisomes affects the quality of the interferon response.

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References

  1. Takeuchi, O. & Akira, S. Innate immunity to virus infection. Immunol. Rev. 227, 75–86 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Dixit, E. et al. Peroxisomes are signaling platforms for antiviral innate immunity. Cell 141, 668–681 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Noyce, R.S., Collins, S.E. & Mossman, K.L. Identification of a novel pathway essential for the immediate-early, interferon-independent antiviral response to enveloped virions. J. Virol. 80, 226–235 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Noyce, R.S. et al. Membrane perturbation elicits an IRF3-dependent, interferon-independent antiviral response. J. Virol. 85, 10926–10931 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Peltier, D.C., Lazear, H.M., Farmer, J.R., Diamond, M.S. & Miller, D.J. Neurotropic arboviruses induce interferon regulatory factor 3-mediated neuronal responses that are cytoprotective, interferon independent, and inhibited by Western equine encephalitis virus capsid. J. Virol. 87, 1821–1833 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Nakhaei, P., Genin, P., Civas, A. & Hiscott, J. RIG-I-like receptors: sensing and responding to RNA virus infection. Semin. Immunol. 21, 215–222 (2009).

    CAS  PubMed  Google Scholar 

  7. Kato, H. et al. Differential roles of MDA5 and RIG-I helicases in the recognition of RNA viruses. Nature 441, 101–105 (2006).

    CAS  PubMed  Google Scholar 

  8. Seth, R.B., Sun, L., Ea, C.K. & Chen, Z.J. Identification and characterization of MAVS, a mitochondrial antiviral signaling protein that activates NF-kappaB and IRF 3. Cell 122, 669–682 (2005).

    Article  CAS  PubMed  Google Scholar 

  9. Horner, S.M., Liu, H.M., Park, H.S., Briley, J. & Gale, M. Jr. Mitochondrial-associated endoplasmic reticulum membranes (MAM) form innate immune synapses and are targeted by hepatitis C virus. Proc. Natl. Acad. Sci. USA 108, 14590–14595 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Belgnaoui, S.M., Paz, S. & Hiscott, J. Orchestrating the interferon antiviral response through the mitochondrial antiviral signaling (MAVS) adapter. Curr. Opin. Immunol. 23, 564–572 (2011).

    CAS  PubMed  Google Scholar 

  11. Kotenko, S.V. IFN-lambdas. Curr. Opin. Immunol. 23, 583–590 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Sumpter, R. Jr. et al. Regulating intracellular antiviral defense and permissiveness to hepatitis C virus RNA replication through a cellular RNA helicase, RIG-I. J. Virol. 79, 2689–2699 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Frank, D.A., Mahajan, S. & Ritz, J. Fludarabine-induced immunosuppression is associated with inhibition of STAT1 signaling. Nat. Med. 5, 444–447 (1999).

    CAS  PubMed  Google Scholar 

  14. Stark, G.R. & Darnell, J.E. Jr. The JAK-STAT pathway at twenty. Immunity 36, 503–514 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Meydan, N. et al. Inhibition of acute lymphoblastic leukaemia by a Jak-2 inhibitor. Nature 379, 645–648 (1996).

    CAS  PubMed  Google Scholar 

  16. Sandberg, E.M. et al. Identification of 1,2,3,4,5,6-hexabromocyclohexane as a small molecule inhibitor of jak2 tyrosine kinase autophosphorylation. J. Med. Chem. 48, 2526–2533 (2005).

    CAS  PubMed  Google Scholar 

  17. Veomett, M.J. & Veomett, G.E. Species specificity of interferon action: maintenance and establishment of the antiviral state in the presence of a heterospecific nucleus. J. Virol. 31, 785–794 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Watling, D. et al. Complementation by the protein tyrosine kinase JAK2 of a mutant cell line defective in the interferon-gamma signal transduction pathway. Nature 366, 166–170 (1993).

    CAS  PubMed  Google Scholar 

  19. Berger Rentsch, M. & Zimmer, G. A vesicular stomatitis virus replicon-based bioassay for the rapid and sensitive determination of multi-species type I interferon. PLoS One 6, e25858 (2011).

    PubMed  PubMed Central  Google Scholar 

  20. Lee, S.J., Kim, W.J. & Moon, S.K. Role of the p38 MAPK signaling pathway in mediating interleukin-28A-induced migration of UMUC-3 cells. Int. J. Mol. Med. 30, 945–952 (2012).

    CAS  PubMed  Google Scholar 

  21. Iversen, M.B. & Paludan, S.R. Mechanisms of type III interferon expression. J. Interferon Cytokine Res. 30, 573–578 (2010).

    CAS  PubMed  Google Scholar 

  22. Onoguchi, K. et al. Viral infections activate types I and III interferon genes through a common mechanism. J. Biol. Chem. 282, 7576–7581 (2007).

    CAS  PubMed  Google Scholar 

  23. Osterlund, P.I., Pietila, T.E., Veckman, V., Kotenko, S.V. & Julkunen, I. IFN regulatory factor family members differentially regulate the expression of type III IFN (IFN-lambda) genes. J. Immunol. 179, 3434–3442 (2007).

    PubMed  Google Scholar 

  24. Lasfar, A. et al. Characterization of the mouse IFN-lambda ligand-receptor system: IFN-lambdas exhibit antitumor activity against B16 melanoma. Cancer Res. 66, 4468–4477 (2006).

    CAS  PubMed  Google Scholar 

  25. Hermant, P. et al. Human but not mouse hepatocytes respond to interferon-lambda in vivo . PLoS One 9, e87906 (2014).

    PubMed  PubMed Central  Google Scholar 

  26. Marukian, S. et al. Hepatitis C virus induces interferon-lambda and interferon-stimulated genes in primary liver cultures. Hepatology 54, 1913–1923 (2011).

    CAS  PubMed  Google Scholar 

  27. Sommereyns, C., Paul, S., Staeheli, P. & Michiels, T. IFN-lambda (IFN-lambda) is expressed in a tissue-dependent fashion and primarily acts on epithelial cells in vivo . PLoS Pathog. 4, e1000017 (2008).

    PubMed  PubMed Central  Google Scholar 

  28. Pott, J. et al. IFN-lambda determines the intestinal epithelial antiviral host defense. Proc. Natl. Acad. Sci. USA 108, 7944–7949 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. de Macedo, F.C. et al. Histologic, viral, and molecular correlates of dengue fever infection of the liver using highly sensitive immunohistochemistry. Diagn. Mol. Pathol. 15, 223–228 (2006).

    PubMed  Google Scholar 

  30. Bierne, H. et al. Activation of type III interferon genes by pathogenic bacteria in infected epithelial cells and mouse placenta. PLoS One 7, e39080 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Lebreton, A. et al. A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response. Science 331, 1319–1321 (2011).

    CAS  PubMed  Google Scholar 

  32. Tamura, T., Yanai, H., Savitsky, D. & Taniguchi, T. The IRF family transcription factors in immunity and oncogenesis. Annu. Rev. Immunol. 26, 535–584 (2008).

    CAS  PubMed  Google Scholar 

  33. Miyamoto, M. et al. Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-beta gene regulatory elements. Cell 54, 903–913 (1988).

    CAS  PubMed  Google Scholar 

  34. Reis, L.F., Ruffner, H., Stark, G., Aguet, M. & Weissmann, C. Mice devoid of interferon regulatory factor 1 (IRF-1) show normal expression of type I interferon genes. EMBO J. 13, 4798–4806 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Stirnweiss, A. et al. IFN regulatory factor-1 bypasses IFN-mediated antiviral effects through viperin gene induction. J. Immunol. 184, 5179–5185 (2010).

    CAS  PubMed  Google Scholar 

  36. Siegel, R., Eskdale, J. & Gallagher, G. Regulation of IFN-lambda1 promoter activity (IFN-lambda1/IL-29) in human airway epithelial cells. J. Immunol. 187, 5636–5644 (2011).

    CAS  PubMed  Google Scholar 

  37. Ueki, I.F. et al. Respiratory virus-induced EGFR activation suppresses IRF1-dependent interferon lambda and antiviral defense in airway epithelium. J. Exp. Med. 210, 1929–1936 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Morrison, J., Aguirre, S. & Fernandez-Sesma, A. Innate immunity evasion by Dengue virus. Viruses 4, 397–413 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Stavru, F., Bouillaud, F., Sartori, A., Ricquier, D. & Cossart, P. Listeria monocytogenes transiently alters mitochondrial dynamics during infection. Proc. Natl. Acad. Sci. USA 108, 3612–3617 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Koshiba, T., Yasukawa, K., Yanagi, Y. & Kawabata, S. Mitochondrial membrane potential is required for MAVS-mediated antiviral signaling. Sci. Signal. 4, ra7 (2011).

    PubMed  Google Scholar 

  41. Stavru, F., Archambaud, C. & Cossart, P. Cell biology and immunology of Listeria monocytogenes infections: novel insights. Immunol. Rev. 240, 160–184 (2011).

    CAS  PubMed  Google Scholar 

  42. Schrader, M. et al. Expression of PEX11beta mediates peroxisome proliferation in the absence of extracellular stimuli. J. Biol. Chem. 273, 29607–29614 (1998).

    CAS  PubMed  Google Scholar 

  43. Narendra, D., Tanaka, A., Suen, D.F. & Youle, R.J. Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. J. Cell Biol. 183, 795–803 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Steinberg, S.J., Raymond, G.V., Braverman, N.E. & Moser, A.B. Peroxisome biogenesis disorders, Zellweger syndrome spectrum. in GeneReviews (eds., Pagon, R.A., Bird, T.D., Dolan, C.R., Stephens, K. and Adam, M.P.) (2003).

  45. Eichler, F. & Van Haren, K. Immune response in leukodystrophies. Pediatr. Neurol. 37, 235–244 (2007).

    PubMed  Google Scholar 

  46. Waterham, H.R. & Wanders, R.J. Metabolic functions and biogenesis of peroxisomes in health and disease. Biochim. Biophys. Acta 1822, 1325 (2012).

    CAS  PubMed  Google Scholar 

  47. Halbach, A. et al. Targeting of the tail-anchored peroxisomal membrane proteins PEX26 and PEX15 occurs through C-terminal PEX19-binding sites. J. Cell Sci. 119, 2508–2517 (2006).

    CAS  PubMed  Google Scholar 

  48. Sacksteder, K.A. et al. PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis. J. Cell Biol. 148, 931–944 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Hollinshead, M., Sanderson, J. & Vaux, D.J. Anti-biotin antibodies offer superior organelle-specific labeling of mitochondria over avidin or streptavidin. J. Histochem. Cytochem. 45, 1053–1057 (1997).

    CAS  PubMed  Google Scholar 

  50. Lencer, W.I., Delp, C., Neutra, M.R. & Madara, J.L. Mechanism of cholera toxin action on a polarized human intestinal epithelial cell line: role of vesicular traffic. J. Cell Biol. 117, 1197–1209 (1992).

    CAS  PubMed  Google Scholar 

  51. McLaughlin-Drubin, M.E. & Munger, K. Biochemical and functional interactions of human papillomavirus proteins with polycomb group proteins. Viruses 5, 1231–1249 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Warke, R.V. et al. Efficient dengue virus (DENV) infection of human muscle satellite cells upregulates type I interferon response genes and differentially modulates MHC I expression on bystander and DENV-infected cells. J. Gen. Virol. 89, 1605–1615 (2008).

    CAS  PubMed  Google Scholar 

  53. Furlong, D.B., Nibert, M.L. & Fields, B.N. Sigma 1 protein of mammalian reoviruses extends from the surfaces of viral particles. J. Virol. 62, 246–256 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Sabin, A.B. Research on dengue during World War II. Am. J. Trop. Med. Hyg. 1, 30–50 (1952).

    CAS  PubMed  Google Scholar 

  55. Lambeth, C.R., White, L.J., Johnston, R.E. & de Silva, A.M. Flow cytometry-based assay for titrating dengue virus. J. Clin. Microbiol. 43, 3267–3272 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Becavin, C. et al. Comparison of widely used Listeria monocytogenes strains EGD, 10403S, and EGD-e highlights genomic differences underlying variations in pathogenicity. MBio 5, e00969–14 (2014).

    Google Scholar 

  57. Amit, I. et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326, 257–263 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank members of the Kagan laboratory for helpful discussions, M. Fransen (Katholieke Universiteit, Leuven, Belgium) for providing cell lines and reagents, and B. Nelms for bioinformatic assistance. Microarray analyses were performed by members of the Molecular Genetics Core Facility at Boston Children's Hospital. J.C.K. is supported by US National Institutes of Health grants AI093589, AI072955 and P30 DK34854, and an unrestricted gift from Mead Johnson & Company. J.C.K. received an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund. C.O. is supported by a fellowship from the Crohn's and Colitis Foundation of America. F.S. is funded by the Agence National de la Recherche (ANR project Mitopatho). E.D. is supported by an Erwin Schrödinger Fellowship of the Austrian Science Fund (FWF). K.M.F. is supported through the Herchel Smith Graduate Fellowship Program. L.G. and J.C.K. are supported by a Massachusetts Institute of Technology–Boston Children's Hospital Collaborative grant. L.G. is supported by US National Institutes of Health grant CA159132. P.C. is supported by European Research Council Advanced Grant 233348 MODELIST and by Howard Hughes Medical Institute as a senior international research scholar.

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Author notes

  1. Helene Bierne

    Present address: Present address: INRA, Unité mixte de recherche (UMR) 1319 Micalis, Jouy-en-Josas, France, and AgroParis Tech, UMR Micalis, Jouy-en-Josas, France.,

  2. Evelyn Dixit and Fabrizia Stavru: These authors contributed equally to this work.

Authors and Affiliations

  1. Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, Massachusetts, USA

    Charlotte Odendall, Evelyn Dixit, Kate M Franz & Jonathan C Kagan

  2. Institut Pasteur, Unité des Interactions Bactéries Cellules, Institut National de la Santé et de la Recherche Médicale U604, Institut national de la recherche agronomique (INRA) USC2020, Paris, France

    Fabrizia Stavru, Helene Bierne & Pascale Cossart

  3. Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA

    Ann Fiegen Durbin & Lee Gehrke

  4. Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Ann Fiegen Durbin & Lee Gehrke

  5. Department of Infectious Diseases, Virology Schaller research group at CellNetworks and Deutsches Krebsforschungszentrum (DKFZ), University of Heidelberg, Heidelberg, Germany.,

    Steeve Boulant

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Contributions

C.O., E.D., A.F.D. and K.M.F. did and analyzed all experiments involving viral infections and peroxisome or mitochondria cell biology; F.S., H.B. and P.C. performed and analyzed all L. monocytogenes infection experiments. S.B. prepared and analyzed reovirus stocks. A.F.D. and L.G. prepared and analyzed DenV stocks. C.O. and J.C.K. wrote the manuscript. All authors edited the manuscript.

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Correspondence to Jonathan C Kagan.

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Integrated supplementary information

Supplementary Figure 1 JAK/STAT signaling and the type III interferon pathway.

(A) STAT1 and (B) JAK2 were knocked down in Huh7 cells. (C) Human Huh7.5 cells were incubated with mouse IFNλ2 or IFNβ, and STAT1 phosphorylation was assessed by western immunoblotting. (D) 293T cells expressing luciferase under the control of an ISRE promoter were incubated with mouse IFNλ2, human IFNλ1 or mouse or human IFNβ. Cells were then assessed for their ability to respond to IFNs by producing luciferase. Error bars represent mean ± SEM of triplicate readings for one experiment representative of 3. **, P < 0.01; ***, P < 0.001; ****, P < 0.0001 (One-way ANOVA).

Supplementary Figure 2 Knockdowns of components of the type III interferon pathway.

(A) Polarized T84 cells were treated with inhibitors of the JAK/STAT pathway: Fludarabine (STAT1), Pyridone 6 (JAKs) and AG490 (JAK2). Cells were subsequently infected with Reovirus, and expression of the ISG viperin was assessed by western immunoblotting. Huh7 cells (B) or JEG3 trophoblasts (C) were transfected with scrambled (Scr) or MAVS siRNA oligo. Efficient MAVS knockdown was monitored by western immunoblotting. (D) IRF3 depletion in Huh7 cells. ERK (E) or p38 (F) were knocked down in Huh7 cells. (G) IRF1 was knocked down in Huh7 cells. Cells were infected with SeV, inducing IRF1 in control cells transfected with a scrambled (Scr) siRNA oligo but not in cells transfected with an IRF1 siRNA oligo. (H) Huh7 cells were stably transduced with MAVS chimera localized on peroxisomes (Pex), mitochondria (Mito), both (WT) or neither (Cyto). MAVS transgenes include GFP whose expression is controlled by an IRES. Equivalent transgene expression was assessed by western immunoblotting against GFP. (I) Similar to H except JEG3 trophoblasts were transiently transfected with the indicated MAVS transgenes. Equivalent transgene expression was assessed by western blotting against GFP. (J) ERK1/2 was knocked down in MAVS-KO MEFs expressing MAVS-Pex.**, P < 0.01;****, P < 0.0001 (Student's t-test (D), One-way ANOVA (G)). Error bars represent mean ± SEM of triplicate readings for one experiment representative of 3.

Supplementary Figure 3 Peroxisome and mitochondria abundance in T84 cells.

T84 epithelial cells were polarized on transwells. Peroxisomes were labeled with Pex14, Mitochondria were visualized with Alexa-conjugated streptavidin that recognizes the high concentration of biotin in mitochondria.

Supplementary Figure 4 Localization of peroxisomal markers in Zellweger cells.

Human skin fibroblasts of indicated genotype were stained for peroxisomes using PMP70 and catalase antibodies.

Supplementary Figure 5 MAVS localization in Zellweger cells.

Human skin fibroblasts of indicated genotype were transfected with Pex13-GFP to label peroxisomes. Mitochondria were visualized with anti-mtHSP70 and endogenous MAVS with anti-MAVS.

Supplementary Figure 6 Transcriptome analysis in Zellweger cells.

Gene expression profiles of Pex19-deficient and reconstituted cells were determined by microarray analysis 9 and 16 hrs after reovirus infection. (A) Table of the most significantly enriched “GO-terms” in regulated genes of Pex19-deficient and reconstituted cells. Pairwise comparisons of both genotypes (B) and time points (C) are depicted in log-log scale scatter plots. The slope of the weighted linear fit indicates stronger gene induction in Pex19-deficient cells (B) and the later time point of infection (C) as the fitted slope is significantly greater than 1. (D) Overview of the 20 most highly upregulated genes in Pex19 reconstituted cells in comparison to Pex19-deficient cells.

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Odendall, C., Dixit, E., Stavru, F. et al. Diverse intracellular pathogens activate type III interferon expression from peroxisomes. Nat Immunol 15, 717–726 (2014). https://doi.org/10.1038/ni.2915

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