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Cell Mol Immunol. 2021 Jun;18(6):1512-1527. doi: 10.1038/s41423-020-0362-6. Epub 2020 Feb 05.

The deubiquitinase OTUB1 augments NF-κB-dependent immune responses in dendritic cells in infection and inflammation by stabilizing UBC13.

Cellular & molecular immunology

Floriana Mulas, Xu Wang, Shanshan Song, Gopala Nishanth, Wenjing Yi, Anna Brunn, Pia-Katharina Larsen, Berend Isermann, Ulrich Kalinke, Antonio Barragan, Michael Naumann, Martina Deckert, Dirk Schlüter

Affiliations

  1. Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany.
  2. Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany.
  3. Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany. [email protected].
  4. Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany. [email protected].
  5. Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, 325035, Wenzhou, China. [email protected].
  6. Department of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
  7. Institute for Experimental Infection Research, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, 30625, Hannover, Germany.
  8. Institute for Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany.
  9. Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hannover Medical School, 30625, Hannover, Germany.
  10. Department of Molecular Biosciences, Stockholm University, 10691, Stockholm, Sweden.
  11. Institute for Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany.
  12. Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke University Magdeburg, 39120, Magdeburg, Germany. [email protected].
  13. Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625, Hannover, Germany. [email protected].
  14. Cluster of Excellence-Resolving Infection Susceptibility (RESIST), Hannover Medical School, 30625, Hannover, Germany. [email protected].

PMID: 32024978 PMCID: PMC8167118 DOI: 10.1038/s41423-020-0362-6

Abstract

Dendritic cells (DCs) are indispensable for defense against pathogens but may also contribute to immunopathology. Activation of DCs upon the sensing of pathogens by Toll-like receptors (TLRs) is largely mediated by pattern recognition receptor/nuclear factor-κB (NF-κB) signaling and depends on the appropriate ubiquitination of the respective signaling molecules. However, the ubiquitinating and deubiquitinating enzymes involved and their interactions are only incompletely understood. Here, we reveal that the deubiquitinase OTU domain, ubiquitin aldehyde binding 1 (OTUB1) is upregulated in DCs upon murine Toxoplasma gondii infection and lipopolysaccharide challenge. Stimulation of DCs with the TLR11/12 ligand T. gondii profilin and the TLR4 ligand lipopolysaccharide induced an increase in NF-κB activation in OTUB1-competent cells, resulting in elevated interleukin-6 (IL-6), IL-12, and tumor necrosis factor (TNF) production, which was also observed upon the specific stimulation of TLR2, TLR3, TLR7, and TLR9. Mechanistically, OTUB1 promoted NF-κB activity in DCs by K48-linked deubiquitination and stabilization of the E2-conjugating enzyme UBC13, resulting in increased K63-linked ubiquitination of IRAK1 (IL-1 receptor-associated kinase 1) and TRAF6 (TNF receptor-associated factor 6). Consequently, DC-specific deletion of OTUB1 impaired the production of cytokines, in particular IL-12, by DCs over the first 2 days of T. gondii infection, resulting in the diminished production of protective interferon-γ (IFN-γ) by natural killer cells, impaired control of parasite replication, and, finally, death from chronic T. encephalitis, all of which could be prevented by low-dose IL-12 treatment in the first 3 days of infection. In contrast, impaired OTUB1-deficient DC activation and cytokine production by OTUB1-deficient DCs protected mice from lipopolysaccharide-induced immunopathology. Collectively, these findings identify OTUB1 as a potent novel regulator of DCs during infectious and inflammatory diseases.

Keywords: OTUB1; dendritic cell; innate immunity; signal transduction; ubiquitination

References

  1. Eisenbarth, S. C. Dendritic cell subsets in T cell programming: location dictates function. Nat. Rev. Immunol. 19, 89–103 (2019). - PubMed
  2. Rodrigues, P. F. et al. Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells. Nat. Immunol. 19, 711–722 (2018). - PubMed
  3. Andrade, W. A. et al. Combined action of nucleic acid-sensing Toll-like receptors and TLR11/TLR12 heterodimers imparts resistance to Toxoplasma gondii in mice. Cell Host Microbe 13, 42–53 (2013). - PubMed
  4. Yarovinsky, F. et al. TLR11 activation of dendritic cells by a protozoan Profilin-like protein. Science (80-.). 308, 1626–1629 (2005). - PubMed
  5. Raetz, M. et al. Cooperation of TLR12 and TLR11 in the IRF8-dependent IL-12 response to Toxoplasma gondii profilin. J. Immunol. 191, 4818–4827 (2013). - PubMed
  6. Roger, T. et al. Protection from lethal Gram-negative bacterial sepsis by targeting Toll-like receptor 4. Proc. Natl Acad. Sci. USA 106, 2348–2352 (2009). - PubMed
  7. Zheng, N. & Shabek, N. Ubiquitin ligases: structure, function, and regulation. Annu. Rev. Biochem. 86, 129–157 (2017). - PubMed
  8. Hodge, C. D. et al. Covalent inhibition of Ubc13 affects ubiquitin signaling and reveals active site elements important for targeting. ACS Chem. Biol. 10, 1718–1728 (2015). - PubMed
  9. Choi, K.-C. et al. Smad6 negatively regulates interleukin 1-receptor-Toll-like receptor signaling through direct interaction with the adaptor Pellino-1. Nat. Immunol. 7, 1057–1065 (2006). - PubMed
  10. Zhang, X., Zhang, J., Zhang, L., van Dam, H. & ten Dijke, P. UBE2O negatively regulates TRAF6-mediated NF-κB activation by inhibiting TRAF6 polyubiquitination. Cell Res. 23, 366–377 (2013). - PubMed
  11. Mevissen, T. E. T. & Komander, D. Mechanisms of deubiquitinase specificity and regulation. Annu. Rev. Biochem. 86, 159–192 (2017). - PubMed
  12. Xuan, N. T. et al. A20 expression in dendritic cells protects mice from LPS-induced mortality. Eur. J. Immunol. 45, 818–828 (2015). - PubMed
  13. Hammer, G. E. et al. Expression of A20 by dendritic cells preserves immune homeostasis and prevents colitis and spondyloarthritis. Nat. Immunol. 12, 1184–1193 (2011). - PubMed
  14. Kool, M. et al. The ubiquitin-editing protein A20 prevents dendritic cell activation, recognition of apoptotic cells, and systemic autoimmunity. Immunity 35, 82–96 (2011). - PubMed
  15. Li, Y. et al. Preventing abnormal NF-κB activation and autoimmunity by Otub1-mediated p100 stabilization. Cell Res. 29, 474–485 (2019). - PubMed
  16. Pasupala, N. et al. OTUB1 non-catalytically stabilizes the E2 ubiquitin-conjugating enzyme UBE2E1 by preventing its autoubiquitination. J. Biol. Chem. 293, 18285–18295 (2018). - PubMed
  17. Zhou, H. et al. OTUB1 promotes esophageal squamous cell carcinoma metastasis through modulating Snail stability. Oncogene 37, 3356–3368 (2018). - PubMed
  18. Zhao, L. et al. OTUB1 protein suppresses mTOR complex 1 (mTORC1) activity by deubiquitinating the mTORC1 inhibitor DEPTOR. J. Biol. Chem. 293, 4883–4892 (2018). - PubMed
  19. Dong, W. et al. Activated protein C ameliorates renal ischemia–reperfusion injury by restricting Y-Box binding protein-1 ubiquitination. J. Am. Soc. Nephrol. 26, 2789–2799 (2015). - PubMed
  20. Herhaus, L., Al-salihi, M., Macartney, T., Weidlich, S. & Sapkota, G. P. OTUB1 enhances TGFβ signalling by inhibiting the ubiquitylation and degradation of active SMAD2/3. Nat. Commun. 4, 1–13 (2013). - PubMed
  21. Goncharov, T. et al. OTUB1 modulates c-IAP1 stability to regulate signalling pathways. EMBO J. 32, 1103–1114 (2013). - PubMed
  22. Sun, X. & Dai, M. Deubiquitinating enzyme regulation of the p53 pathway: a lesson from Otub1. World J. Biol. Chem. 5, 75–85 (2014). - PubMed
  23. Zhou, X. et al. The deubiquitinase Otub1 controls the activation of CD8 - PubMed
  24. Wang, X. et al. OTUB1 inhibits CNS autoimmunity by preventing IFN-γ-induced hyperactivation of astrocytes. EMBO J. https://doi.org/10.15252/embj.2018100947 (2019). - PubMed
  25. Qian, C. & Cao, X. Dendritic cells in the regulation of immunity and inflammation. Semin. Immunol. 35, 3–11 (2018). - PubMed
  26. Mashayekhi, M. et al. CD8α - PubMed
  27. Peng, Y., Xu, R. & Zheng, X. HSCARG negatively regulates the cellular antiviral RIG-I like receptor signaling pathway by inhibiting TRAF3 ubiquitination via recruiting OTUB1. PLoS Pathog. 10, 1–10 (2014). - PubMed
  28. Li, S. et al. Regulation of virus-triggered signaling by OTUB1- and OTUB2-mediated deubiquitination of TRAF3 and TRAF6. J. Biol. Chem. 285, 4291–4297 (2010). - PubMed
  29. Baietti, M. F. et al. OTUB1 triggers lung cancer development by inhibiting RAS monoubiquitination. EMBO Mol. Med. 8, 288–303 (2016). - PubMed
  30. Yarovinsky, F. Innate immunity to Toxoplasma gondii infection. Nat. Rev. Immunol. 14, 109–121 (2014). - PubMed
  31. Plattner, F. et al. Toxoplasma profilin is essential for host cell invasion and TLR11-dependent induction of an interleukin-12 response. Cell Host Microbe 3, 77–87 (2008). - PubMed
  32. Caton, M. L., Smith-Raska, M. R. & Reizis, B. Notch-RBP-J signaling controls the homeostasis of CD8 - PubMed
  33. Kawai, T. & Akira, S. Signaling to NF-kappaB by Toll-like receptors. Trends Mol. Med. 13, 460–469 (2007). - PubMed
  34. Koblansky, A. A. et al. Recognition of profilin by Toll-like receptor 12 is critical for host resistance to Toxoplasma gondii. Immunity 38, 119–130 (2013). - PubMed
  35. Shi, J. H. & Sun, S. C. Tumor necrosis factor receptor-associated factor regulation of nuclear factor κB and mitogen-activated protein kinase pathways. Front. Immunol. 9, 1849 (2018). - PubMed
  36. Cusson-Hermance, N., Khurana, S., Lee, T. H., Fitzgerald, K. A. & Kelliher, M. A. Rip1 mediates the Trif-dependent Toll-like receptor 3- and 4-induced NF-κB activation but does not contribute to interferon regulatory factor 3 activation. J. Biol. Chem. 280, 36560–36566 (2005). - PubMed
  37. Shim, J. H. et al. TAK1, but not TAB1 or TAB2, plays an essential role in multiple signaling pathways in vivo. Genes Dev. 19, 2668–2681 (2005). - PubMed
  38. Hamidi, A. et al. Polyubiquitination of transforming growth factor β(TGFβ)-associated kinase 1 mediates nuclear factor-κB activation in response to different inflammatory stimuli. J. Biol. Chem. 287, 123–133 (2012). - PubMed
  39. Arthur, J. S. C. & Ley, S. C. Mitogen-activated protein kinases in innate immunity. Nat. Rev. Immunol. 13, 679–692 (2013). - PubMed
  40. Yamamoto, M. et al. Key function for the Ubc13 E2 ubiquitin-conjugating enzyme in immune receptor signaling. Nat. Immunol. 7, 962–970 (2006). - PubMed
  41. Fukushima, T. et al. Ubiquitin-conjugating enzyme Ubc13 is a critical component of TNF receptor-associated factor (TRAF)-mediated inflammatory responses. Proc. Natl Acad. Sci. USA 104, 6371–6376 (2007). - PubMed
  42. Nakada, S. et al. Non-canonical inhibition of DNA damage-dependent ubiquitination by OTUB1. Nature 466, 941–946 (2010). - PubMed
  43. Ordureau, A. et al. The IRAK-catalysed activation of the E3 ligase function of Pellino isoforms induces the Lys 63 -linked polyubiquitination of IRAK1. Biochem. J. 409, 43–52 (2008). - PubMed
  44. Shembade, N., Ma, A. & Harhaj, E. W. Inhibition of NF-kappaB signaling by A20 through disruption of ubiquitin enzyme complexes. Science 327, 1135–1139 (2010). - PubMed
  45. Edelmann, M. J. J. et al. Structural basis and specificity of human otubain 1-mediated deubiquitination. Biochem. J. 418, 379–390 (2008). - PubMed
  46. Zhang, Y. et al. Uev1A-Ubc13 catalyzes K63-linked ubiquitination of RHBDF2 to promote TACE maturation. Cell Signal. 42, 155–164 (2018). - PubMed
  47. Deng, L. et al. Activation of the Iκb kinase complex by TRAF6 requires a dimeric ubiquitin-conjugating enzyme complex and a unique polyubiquitin chain. Cell 103, 351–361 (2000). - PubMed
  48. Sato, Y. et al. Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13. J. Biol. Chem. 287, 25860–25868 (2012). - PubMed
  49. Hodge, C. D. et al. Ubc13: the Lys63 ubiquitin chain building machine. Oncotarget 7, 64471–64504 (2016). - PubMed
  50. Carlile, C. M., Pickart, C. M., Matunis, M. J. & Cohen, R. E. Synthesis of free and proliferating cell nuclear antigen-bound polyubiquitin chains by the RING E3 ubiquitin ligase Rad5. J. Biol. Chem. 284, 29326–29334 (2009). - PubMed
  51. Saldana, M. et al. Otubain 1: a non-canonical deubiquitinase with an emerging role in cancer. Endocr. Relat. Cancer 26, R1–R14 (2019). - PubMed
  52. Cui, W. et al. TrCP-mediated IRAK1 degradation releases TAK1-TRAF6 from the membrane to the cytosol for TAK1-dependent NF-κB activation. Mol. Cell. Biol. 32, 3990–4000 (2012). - PubMed
  53. Xia, Z. P. et al. Direct activation of protein kinases by unanchored polyubiquitin chains. Nature 461, 114–119 (2009). - PubMed
  54. Kimura, Y. et al. An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. Cell 137, 549–559 (2009). - PubMed
  55. Pertel, T. et al. TRIM5 is an innate immune sensor for the retrovirus capsid lattice. Nature 472, 361–365 (2011). - PubMed
  56. Hu, L. et al. Oligomerization-primed coiled-coil domain interaction with Ubc13 confers processivity to TRAF6 ubiquitin ligase activity. Nat. Commun. 8, 814 (2017). - PubMed
  57. Gilda, J. E. et al. Western blotting inaccuracies with unverified antibodies: need for a Western blotting minimal reporting standard (WBMRS). PLoS ONE 10, e0135392 (2015). - PubMed
  58. Koblansky, A. A. et al. The innate immune receptor NLRX1 functions as a tumor suppressor by reducing colon tumorigenesis and key tumor-promoting signals. Cell Rep. 14, 2562–2575 (2016). - PubMed
  59. Yoshimura, S., Bondeson, J., Foxwell, B. M. J., Brennan, F. M. & Feldmann, M. Effective antigen presentation by dendritic cells is NF-κB dependent: coordinate regulation of MHC, co-stimulatory molecules and cytokines. Int. Immunol. 13, 675–683 (2001). - PubMed
  60. Liu, C.-H. et al. Cutting edge: dendritic cells are essential for in vivo IL-12 production and development of resistance against Toxoplasma gondii infection in mice. J. Immunol. 177, 31–35 (2006). - PubMed
  61. Hou, B., Benson, A., Kuzmich, L., DeFranco, A. L. & Yarovinsky, F. Critical coordination of innate immune defense against Toxoplasma gondii by dendritic cells responding via their Toll-like receptors. Proc. Natl Acad. Sci. USA 108, 278–283 (2011). - PubMed
  62. Ge, Y. et al. Natural killer cell intrinsic toll-like receptor MyD88 signaling contributes to IL-12-dependent IFN-γ production by mice during infection with Toxoplasma gondii. Int. J. Parasitol. 44, 475–484 (2014). - PubMed
  63. Trinchieri, G. Interleukin-12 and the regulation of innate resistance and adaptive immunity. Nat. Rev. Immunol. 3, 133–146 (2003). - PubMed
  64. Lambert, H., Hitziger, N., Dellacasa, I., Svensson, M. & Barragan, A. Induction of dendritic cell migration upon Toxoplasma gondii infection potentiates parasite dissemination. Cell Microbiol. 8, 1611–1623 (2006). - PubMed
  65. Lachenmaier, S. M., Deli, M. A., Meissner, M. & Liesenfeld, O. Intracellular transport of Toxoplasma gondii through the blood–brain barrier. J. Neuroimmunol. 232, 119–130 (2011). - PubMed
  66. Kanatani, S. et al. Voltage-dependent calcium channel signaling mediates GABAA receptor-induced migratory activation of dendritic cells infected by Toxoplasma gondii. PLoS Pathog. 13, e1006739 (2017). - PubMed
  67. Dalod, M. et al. Dendritic cell responses to early murine cytomegalovirus infection: subset functional specialization and differential regulation by interferon α/β. J. Exp. Med. 197, 885–898 (2003). - PubMed
  68. Tabeta, K. et al. Toll-like receptors 9 and 3 as essential complonents of innate immune defense against mouse cytomegalovirus infection. Proc. Natl Acad. Sci. USA 101, 3516–3521 (2004). - PubMed
  69. Zucchini, N. et al. Cutting edge: overlapping functions of TLR7 and TLR9 for innate defense against a herpesvirus infection. J. Immunol. 180, 5799–5803 (2008). - PubMed
  70. Puttur, F. et al. Conventional dendritic cells confer protection against mouse cytomegalovirus infection via TLR9 and MyD88 signaling. Cell Rep. 17, 1113–1127 (2016). - PubMed
  71. Krug, A. et al. TLR9-dependent recognition of MCMV by IPC and DC generates coordinated cytokine responses that activate antiviral NK cell function. Immunity 21, 107–119 (2004). - PubMed
  72. Tegtmeyer, P. K. et al. STING induces early IFN-β in the liver and constrains myeloid cell-mediated dissemination of murine cytomegalovirus. Nat. Commun. 10, 2830 (2019). - PubMed
  73. Rosadini, C. V. & Kagan, J. C. Early innate immune responses to bacterial LPS. Curr. Opin. Immunol. 44, 14–19 (2017). - PubMed
  74. Motshwene, P. G. et al. An oligomeric signaling platform formed by the Toll-like receptor signal transducers MyD88 and IRAK-4. J. Biol. Chem. 284, 25404–25411 (2009). - PubMed
  75. Schauvliege, R., Janssens, S. & Beyaert, R. Pellino proteins are more than scaffold proteins in TLR/IL-1R signalling: a role as novel RING E3-ubiquitin-ligases. FEBS Lett. 580, 4697–4702 (2006). - PubMed
  76. Lork, M., Verhelst, K. & Beyaert, R. CYLD, A20 and OTULIN deubiquitinases in NF-κB signaling and cell death: so similar, yet so different. Cell Death Differ. 24, 1172–1183 (2017). - PubMed
  77. Ishikawa, H., Ma, Z. & Barber, G. N. STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity. Nature 461, 788–792 (2009). - PubMed
  78. Stempel, M., Chan, B. & Brinkmann, M. M. Coevolution pays off: herpesviruses have the license to escape the DNA sensing pathway. Med. Microbiol. Immunol. 208, 495–512 (2019). - PubMed
  79. Chan, B. et al. The murine cytomegalovirus M35 protein antagonizes type I IFN induction downstream of pattern recognition receptors by targeting NF-κB mediated transcription. PLoS Pathog. 13, e1006382 (2017). - PubMed
  80. Stempel, M. et al. The herpesviral antagonist m152 reveals differential activation of STING‐dependent IRF and NF‐κB signaling and STING’s dual role during MCMV infection. EMBO J. 38, e100983 (2019). - PubMed
  81. Jin, J. et al. Epigenetic regulation of the expression of Il12 and Il23 and autoimmune inflammation by the deubiquitinase Trabid. Nat. Immunol. 17, 259–268 (2016). - PubMed
  82. Schlüter, D., Löhler, J., Deckert, M., Hof, H. & Schwendemann, G. Toxoplasma encephalitis of immunocompetent and nude mice: immunohistochemical characterisation of Toxoplasma antigen, infiltrates and major histocompatibility complex gene products. J. Neuroimmunol. 31, 185–198 (1991). - PubMed
  83. Schmid, U. et al. The deubiquitinating enzyme cylindromatosis dampens CD8+ T cell responses and is a critical factor for experimental cerebral malaria and blood–brain barrier damage. Front. Immunol. 8, 27 (2017). - PubMed
  84. Wang, X. et al. Astrocytic A20 ameliorates experimental autoimmune encephalomyelitis by inhibiting NF-κB- and STAT1-dependent chemokine production in astrocytes. Acta Neuropathol. 126, 711–724 (2013). - PubMed
  85. Hjerpe, R. et al. Efficient protection and isolation of ubiquitylated proteins using tandem ubiquitin-binding entities. EMBO Rep. 10, 1250–1258 (2009). - PubMed
  86. Stahl, F. R. et al. Mck2-dependent infection of alveolar macrophages promotes replication of MCMV in nodular inflammatory foci of the neonatal lung. Mucosal Immunol. 8, 57–67 (2015). - PubMed

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