Article | Published:

Sumoylation coordinates the repression of inflammatory and anti-viral gene-expression programs during innate sensing

Nature Immunology volume 17, pages 140149 (2016) | Download Citation

Abstract

Innate sensing of pathogens initiates inflammatory cytokine responses that need to be tightly controlled. We found here that after engagement of Toll-like receptors (TLRs) in myeloid cells, deficient sumoylation caused increased secretion of transcription factor NF-κB–dependent inflammatory cytokines and a massive type I interferon signature. In mice, diminished sumoylation conferred susceptibility to endotoxin shock and resistance to viral infection. Overproduction of several NF-κB-dependent inflammatory cytokines required expression of the type I interferon receptor, which identified type I interferon as a central sumoylation-controlled hub for inflammation. Mechanistically, the small ubiquitin-like modifier SUMO operated from a distal enhancer of the gene encoding interferon-β (Ifnb1) to silence both basal and stimulus-induced activity of the Ifnb1 promoter. Therefore, sumoylation restrained inflammation by silencing Ifnb1 expression and by strictly suppressing an unanticipated priming by type I interferons of the TLR-induced production of inflammatory cytokines.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

    & Transcriptional control of the inflammatory response. Nat. Rev. Immunol. 9, 692–703 (2009).

  2. 2.

    & Pattern recognition receptors and inflammation. Cell 140, 805–820 (2010).

  3. 3.

    et al. Type I IFN modulates innate and specific antiviral immunity. J. Immunol. 164, 4220–4228 (2000).

  4. 4.

    , , , & Constitutive type I interferon modulates homeostatic balance through tonic signaling. Immunity 36, 166–174 (2012).

  5. 5.

    Type I interferonopathies: Mendelian type I interferon up-regulation. Curr. Opin. Immunol. 32, 7–12 (2015).

  6. 6.

    et al. Central role for type I interferons and Tyk2 in lipopolysaccharide-induced endotoxin shock. Nat. Immunol. 4, 471–477 (2003).

  7. 7.

    & Virus induction of human IFN β gene expression requires the assembly of an enhanceosome. Cell 83, 1091–1100 (1995).

  8. 8.

    et al. CD8+ T cell-mediated skin disease in mice lacking IRF-2, the transcriptional attenuator of interferon-α/β signaling. Immunity 13, 643–655 (2000).

  9. 9.

    & Concepts in sumoylation: a decade on. Nat. Rev. Mol. Cell Biol. 8, 947–956 (2007).

  10. 10.

    SUMO: a history of modification. Mol. Cell 18, 1–12 (2005).

  11. 11.

    & SUMO losing balance: SUMO proteases disrupt SUMO homeostasis to facilitate cancer development and progression. Genes Cancer 1, 748–752 (2010).

  12. 12.

    , & Interplay between viruses and host sumoylation pathways. Nat. Rev. Microbiol. 11, 400–411 (2013).

  13. 13.

    & Regulation of gene-activation pathways by PIAS proteins in the immune system. Nat. Rev. Immunol. 5, 593–605 (2005).

  14. 14.

    et al. SUMOylation of the inducible (c-Fos:c-Jun)/AP-1 transcription complex occurs on target promoters to limit transcriptional activation. Oncogene 33, 921–927 (2014).

  15. 15.

    , , , & Negative regulation of TLR inflammatory signaling by the SUMO-deconjugating enzyme SENP6. PLoS Pathog. 9, e1003480 (2013).

  16. 16.

    , , & NF-kappaB repression by PIAS3 mediated RelA SUMOylation. PLoS ONE 7, e37636 (2012).

  17. 17.

    et al. SENP2 negatively regulates cellular antiviral response by deSUMOylating IRF3 and conditioning it for ubiquitination and degradation. J. Mol. Cell Biol. 3, 283–292 (2011).

  18. 18.

    et al. Tripartite motif-containing protein 28 is a small ubiquitin-related modifier E3 ligase and negative regulator of IFN regulatory factor 7. J. Immunol. 187, 4754–4763 (2011).

  19. 19.

    , , , & MDA5 is SUMOylated by PIAS2β in the upregulation of type I interferon signaling. Mol. Immunol. 48, 415–422 (2011).

  20. 20.

    , , & SUMO conjugation of STAT1 protects cells from hyperresponsiveness to IFNγ. Blood 118, 1002–1007 (2011).

  21. 21.

    , , & SUMOylation of RIG-I positively regulates the type I interferon signaling. Protein Cell 1, 275–283 (2010).

  22. 22.

    & Nuclear receptor transrepression pathways that regulate inflammation in macrophages and T cells. Nat. Rev. Immunol. 10, 365–376 (2010).

  23. 23.

    et al. Differential SUMOylation of LXRα and LXRβ mediates transrepression of STAT1 inflammatory signaling in IFN-gamma-stimulated brain astrocytes. Mol. Cell 35, 806–817 (2009).

  24. 24.

    et al. Virus infection triggers SUMOylation of IRF3 and IRF7, leading to the negative regulation of type I interferon gene expression. J. Biol. Chem. 283, 25660–25670 (2008).

  25. 25.

    , , , & SUMO-1 conjugation selectively modulates STAT1-mediated gene responses. Blood 106, 224–226 (2005).

  26. 26.

    et al. Negative regulation of NF-κB signaling by PIAS1. Mol. Cell. Biol. 25, 1113–1123 (2005).

  27. 27.

    et al. PIAS1 selectively inhibits interferon-inducible genes and is important in innate immunity. Nat. Immunol. 5, 891–898 (2004).

  28. 28.

    , & SUMO-1 modification of IκBα inhibits NF-κB activation. Mol. Cell 2, 233–239 (1998).

  29. 29.

    et al. Sumoylation by Ubc9 regulates the stem cell compartment and structure and function of the intestinal epithelium in mice. Gastroenterology 140, 286–296 (2011).

  30. 30.

    et al. The SUMO pathway is essential for nuclear integrity and chromosome segregation in mice. Dev. Cell 9, 769–779 (2005).

  31. 31.

    et al. Host defense against viral infection involves interferon mediated down-regulation of sterol biosynthesis. PLoS Biol. 9, e1000598 (2011).

  32. 32.

    , , , & Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8, 265–277 (1999).

  33. 33.

    et al. A mouse model for Chikungunya: young age and inefficient type-I interferon signaling are risk factors for severe disease. PLoS Pathog. 4, e29 (2008).

  34. 34.

    et al. Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity 39, 454–469 (2013).

  35. 35.

    et al. Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation. Genome Res. 23, 1563–1579 (2013).

  36. 36.

    et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810–822 (2012).

  37. 37.

    et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).

  38. 38.

    et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell 51, 310–325 (2013).

  39. 39.

    , , & Enhancer RNAs and regulated transcriptional programs. Trends Biochem. Sci. 39, 170–182 (2014).

  40. 40.

    , & A distal locus element mediates IFN-γ priming of lipopolysaccharide-stimulated TNF gene expression. Cell Rep. 9, 1718–1728 (2014).

  41. 41.

    , & A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Res. 42, 12537–12554 (2014).

  42. 42.

    Experimental autoimmune encephalomyelitis (EAE). Curr. Protoc. Neurosci. Unit 9.7 Suppl. 14, 1–11 (2001).

  43. 43.

    et al. Type I IFN controls chikungunya virus via its action on nonhematopoietic cells. J. Exp. Med. 207, 429–442 (2010).

  44. 44.

    & Metabolic events mediating early killing of host cells infected by Shigella flexneri. Microb. Pathog. 3, 53–61 (1987).

  45. 45.

    et al. Preclinical studies of a modified vaccinia virus Ankara-based HIV candidate vaccine: antigen presentation and antiviral effect. J. Virol. 84, 5314–5328 (2010).

  46. 46.

    et al. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat. Protoc. 8, 539–554 (2013).

  47. 47.

    & Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  48. 48.

    , , , & deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–191 (2014).

  49. 49.

    et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 39, e35 (2011).

Download references

Acknowledgements

We thank M. Dasso (US National Institutes of Health) for antibody to SUMO-2; A. Garcia-Sastre(Icahn School of Medicine at Mount Sinai) for antibody to HA; A. Andrieux and J.-M. Carpier for technical help; Philippe Sansonetti (Pasteur Institute, Paris) for S. flexneri; and M. Yaniv for critical reading of the manuscript. Sequencing was performed by the Institut Génétique Biologie Moléculaire Cellulaire Microarray and Sequencing platform, a member of the 'France Génomique' consortium (ANR-10-INBS-0009). Supported by Institut National du Cancer (PLBIO13-057 to S.A.), Agence Nationale de la Recherche (ANR-14-CE16 to S.A.), Ligue Nationale Contre le Cancer (Equipes labellisées, A. Dejean and S.A.), Fondation pour la Recherche Médicale (FRM, AJE201212 to O.J.), Région-Midi-Pyrénées (NVEQ 2014 to O.J.), European Research Council ('SUMOSTRESS' to A. Dejean, 'DC-BIOX340046' to S.A., and 'HIVINNATE' (309848) to N.M.), Ecole Normale Supérieure (A. Decque) and Odyssey-RE (A. Decque).

Author information

Author notes

    • Adrien Decque
    • , Olivier Joffre
    • , Joao G Magalhaes
    •  & Jack-Christophe Cossec

    These authors contributed equally to this work.

    • Sebastian Amigorena
    •  & Anne Dejean

    These authors jointly directed this work.

Affiliations

  1. Nuclear Organization and Oncogenesis Unit, Institut Pasteur, Paris, France.

    • Adrien Decque
    • , Jack-Christophe Cossec
    • , Pierre Lapaquette
    • , Jacob-Sebastian Seeler
    •  & Anne Dejean
  2. INSERM, U993, Paris, France.

    • Adrien Decque
    • , Jack-Christophe Cossec
    • , Pierre Lapaquette
    • , Jacob-Sebastian Seeler
    •  & Anne Dejean
  3. Centre de Recherche, Institut Curie, Paris, France.

    • Olivier Joffre
    • , Joao G Magalhaes
    • , Aymeric Silvin
    • , Nicolas Manel
    •  & Sebastian Amigorena
  4. INSERM, U932, Paris, France.

    • Olivier Joffre
    • , Joao G Magalhaes
    • , Aymeric Silvin
    • , Nicolas Manel
    •  & Sebastian Amigorena
  5. INSERM U1043, Centre de Physiopathologie de Toulouse-Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France.

    • Olivier Joffre
  6. Department of Immunology, Weizmann Institute, Rehovot, Israel.

    • Ronnie Blecher-Gonen
    •  & Ido Amit
  7. Laboratory of Dendritic Cell Immunobiology, Institut Pasteur, INSERM U818, Paris, France.

    • Pierre-Emmanuel Joubert
    •  & Matthew L Albert

Authors

  1. Search for Adrien Decque in:

  2. Search for Olivier Joffre in:

  3. Search for Joao G Magalhaes in:

  4. Search for Jack-Christophe Cossec in:

  5. Search for Ronnie Blecher-Gonen in:

  6. Search for Pierre Lapaquette in:

  7. Search for Aymeric Silvin in:

  8. Search for Nicolas Manel in:

  9. Search for Pierre-Emmanuel Joubert in:

  10. Search for Jacob-Sebastian Seeler in:

  11. Search for Matthew L Albert in:

  12. Search for Ido Amit in:

  13. Search for Sebastian Amigorena in:

  14. Search for Anne Dejean in:

Contributions

A. Decque, O.J., J.G.M. and J.-C.C. designed and performed all experiments, except those performed by R.B.-G., P.L., A.S., P.-E.J. and J.-S.S. (described below); R.B.-G. performed part of the ChIP-Seq experiments; P.L. performed infection with S. flexneri in vitro; A.S. performed viral infections in vitro, and N.M. assisted with experimental design; P.-E.J. performed infection with chikungunya virus in vivo; J.-S.S. generated the reporter-gene constructs; M.L.A. and I.A. assisted with experimental design and data analysis of ChIP-Seq and chikungunya virus infection and contributed to the writing of the manuscript; S.A. and A. Dejean conceived of and supervised the study; and A. Decque, O.J., J.G.M., J.-C.C., S.A. and A. Dejean wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Sebastian Amigorena or Anne Dejean.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7

  2. 2.

    Supplementary Table 7

    Full sequences of Luciferase reporter constructs

Excel files

  1. 1.

    Supplementary Table 1

    List of 224 genes differentially expressed in unstimulated Ubc9+/+ vs Ubc9-/- BMDCs as determined by microarray analysis in 3 biological replicates (fold change 2 or -2, p <0.05, Bonferroni).

  2. 2.

    Supplementary Table 2

    List of 880 genes differentially expressed in Ubc9+/+ vs Ubc9-/ BMDCs treated by LPS for 6h as determined by microarray analysis in 3 biological replicates performed in triplicates (fold change 2 or -2, p <0.05, Bonferroni).

  3. 3.

    Supplementary Table 3

    List of LPS-induced, -reduced and -unaffected SUMO-2 peaks in BMDCs.  In sheet 1, SUMO-2 peaks enriched at 2 h (as compared to the untreated sample) with a p < 10−5 are shown with their main features, including chromosomal location, p value, RefSeq and gene description. Peaks were ordered by p value. Peaks were color-coded as follows: green, intergenic; brown, non-coding; yellow, peaks surrounding TSS of RefSeq genes; dark blue, intronic; grey, exonic; orange, 3'UTR; light blue, 5'UTR; and red, TTS. In sheet 2, SUMO-2 peaks reduced at 2h (as compared to the untreated sample) with a p < 10−5 are shown as in sheet 1. In sheet 3, list of unaffected SUMO-2 peaks detected in untreated sample as in sheet 1.

  4. 4.

    Supplementary Table 4

    List of the LPS-stimulated genes associated with induced SUMO-2 peaks. The top 5 GO categories are shown.

  5. 5.

    Supplementary Table 5

    List of LPS-induced and non-induced SUMO-1 peaks in BMDCs. In sheet 1, SUMO-1 peaks enriched at 2 h (as compared to the untreated sample) with a p<10−5 are shown with their main features, including chromosomal location, p value, RefSeq and gene description. Peaks were ordered by p value. Peaks were color-coded as follows: green, intergenic; brown, non-coding; yellow, peaks surrounding TSS of RefSeq genes; dark blue, intronic; grey, exonic; orange, 3'UTR; light blue, 5'UTR; and red, TTS. In sheet 2, list of non-inducible SUMO-1 peaks detected in untreated sample as in sheet 1.

  6. 6.

    Supplementary Table 6

    List of primers and siRNAs used in this study. siRNAs and primers that were used for RT-qPCR, ChIP-qPCR and plasmid cloning are shown.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ni.3342

Further reading Further reading