Molecular bases for HOIPINs-mediated inhibition of LUBAC and innate immune responses.


Journal

Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179

Informations de publication

Date de publication:
03 04 2020
Historique:
received: 10 08 2019
accepted: 27 02 2020
entrez: 5 4 2020
pubmed: 5 4 2020
medline: 16 6 2021
Statut: epublish

Résumé

The NF-κB and interferon antiviral signaling pathways play pivotal roles in inflammatory and innate immune responses. The LUBAC ubiquitin ligase complex, composed of the HOIP, HOIL-1L, and SHARPIN subunits, activates the canonical NF-κB pathway through Met1-linked linear ubiquitination. We identified small-molecule chemical inhibitors of LUBAC, HOIPIN-1 and HOIPIN-8. Here we show that HOIPINs down-regulate not only the proinflammatory cytokine-induced canonical NF-κB pathway, but also various pathogen-associated molecular pattern-induced antiviral pathways. Structural analyses indicated that HOIPINs inhibit the RING-HECT-hybrid reaction in HOIP by modifying the active Cys885, and residues in the C-terminal LDD domain, such as Arg935 and Asp936, facilitate the binding of HOIPINs to LUBAC. HOIPINs effectively induce cell death in activated B cell-like diffuse large B cell lymphoma cells, and alleviate imiquimod-induced psoriasis in model mice. These results reveal the molecular and cellular bases of LUBAC inhibition by HOIPINs, and demonstrate their potential therapeutic uses.

Identifiants

pubmed: 32246052
doi: 10.1038/s42003-020-0882-8
pii: 10.1038/s42003-020-0882-8
pmc: PMC7125101
doi:

Substances chimiques

Anti-Inflammatory Agents 0
Antineoplastic Agents 0
Enzyme Inhibitors 0
Inflammation Mediators 0
Intracellular Signaling Peptides and Proteins 0
SHARPIN protein, human 0
Sipl1 protein, mouse 0
Transcription Factors 0
Ubiquitins 0
RBCK1 protein, human EC 2.3.2.27
RNF31 protein, human EC 2.3.2.27
Rbck1 protein, mouse EC 2.3.2.27
Rnf31 protein, mouse EC 2.3.2.27
Ubiquitin-Protein Ligases EC 2.3.2.27
Imiquimod P1QW714R7M

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

163

Références

Lee, M. S. & Kim, Y. J. Signaling pathways downstream of pattern-recognition receptors and their cross talk. Annu. Rev. Biochem. 76, 447–480 (2007).
pubmed: 17328678 doi: 10.1146/annurev.biochem.76.060605.122847
Liu, J., Qian, C. & Cao, X. Post-translational modification control of innate immunity. Immunity 45, 15–30 (2016).
pubmed: 27438764 doi: 10.1016/j.immuni.2016.06.020
Hershko, A. & Ciechanover, A. The ubiquitin system for protein degradation. Annu. Rev. Biochem. 61, 761–807 (1992).
pubmed: 1323239 doi: 10.1146/annurev.bi.61.070192.003553
Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012).
pubmed: 22524316 doi: 10.1146/annurev-biochem-060310-170328
Marin, I. RBR ubiquitin ligases: diversification and streamlining in animal lineages. J. Mol. Evol. 69, 54–64 (2009).
pubmed: 19526189 doi: 10.1007/s00239-009-9252-3 pmcid: 19526189
Eisenhaber, B., Chumak, N., Eisenhaber, F. & Hauser, M. T. The ring between ring fingers (RBR) protein family. Genome Biol. 8, 209 (2007).
pubmed: 17367545 pmcid: 1868946 doi: 10.1186/gb-2007-8-3-209
Rittinger, K. & Ikeda, F. Linear ubiquitin chains: enzymes, mechanisms and biology. Open Biol. 7, 170026 (2017).
pubmed: 28446710 pmcid: 5413910 doi: 10.1098/rsob.170026
Iwai, K., Fujita, H. & Sasaki, Y. Linear ubiquitin chains: NF-κB signalling, cell death and beyond. Nat. Rev. Mol. Cell. Biol. 15, 503–508 (2014).
pubmed: 25027653 doi: 10.1038/nrm3836 pmcid: 25027653
Stieglitz, B., Morris-Davies, A. C., Koliopoulos, M. G., Christodoulou, E. & Rittinger, K. LUBAC synthesizes linear ubiquitin chains via a thioester intermediate. EMBO Rep. 13, 840–846 (2012).
pubmed: 22791023 pmcid: 3432797 doi: 10.1038/embor.2012.105
Stieglitz, B. et al. Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature 503, 422–426 (2013).
pubmed: 24141947 pmcid: 3838313 doi: 10.1038/nature12638
Smit, J. J. et al. The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension. EMBO J. 31, 3833–3844 (2012).
pubmed: 22863777 pmcid: 3463842 doi: 10.1038/emboj.2012.217
Lechtenberg, B. C. et al. Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation. Nature 529, 546–550 (2016).
pubmed: 26789245 pmcid: 4856479 doi: 10.1038/nature16511
de Almagro, M. C., Goncharov, T., Newton, K. & Vucic, D. Cellular IAP proteins and LUBAC differentially regulate necrosome-associated RIP1 ubiquitination. Cell Death Dis. 6, e1800 (2015).
pubmed: 26111062 pmcid: 4669837 doi: 10.1038/cddis.2015.158
Tokunaga, F. et al. Involvement of linear polyubiquitylation of NEMO in NF-κB activation. Nat. Cell Biol. 11, 123–132 (2009).
pubmed: 19136968 doi: 10.1038/ncb1821 pmcid: 19136968
Gerlach, B. et al. Linear ubiquitination prevents inflammation and regulates immune signalling. Nature 471, 591–596 (2011).
pubmed: 21455173 doi: 10.1038/nature09816 pmcid: 21455173
Goto, E. & Tokunaga, F. Decreased linear ubiquitination of NEMO and FADD on apoptosis with caspase-mediated cleavage of HOIP. Biochem. Biophys. Res. Commun. 485, 152–159 (2017).
pubmed: 28189684 doi: 10.1016/j.bbrc.2017.02.040 pmcid: 28189684
Fujita, H. et al. Mechanism underlying IκB kinase activation mediated by the linear ubiquitin chain assembly complex. Mol. Cell Biol. 34, 1322–1335 (2014).
pubmed: 24469399 pmcid: 3993567 doi: 10.1128/MCB.01538-13
Sasaki, Y. et al. Defective immune responses in mice lacking LUBAC-mediated linear ubiquitination in B cells. EMBO J. 32, 2463–2476 (2013).
pubmed: 23942237 pmcid: 3770953 doi: 10.1038/emboj.2013.184
Tokunaga, F. et al. SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex. Nature 471, 633–636 (2011).
pubmed: 21455180 doi: 10.1038/nature09815 pmcid: 21455180
Aksentijevich, I. & Zhou, Q. NF-κB pathway in autoinflammatory diseases: dysregulation of protein modifications by ubiquitin defines a new category of autoinflammatory diseases. Front. Immunol. 8, 399 (2017).
pubmed: 28469620 pmcid: 5395695 doi: 10.3389/fimmu.2017.00399
Strickson, S. et al. The anti-inflammatory drug BAY 11-7082 suppresses the MyD88-dependent signalling network by targeting the ubiquitin system. Biochem. J. 451, 427–437 (2013).
pubmed: 23441730 pmcid: 3685219 doi: 10.1042/BJ20121651
Sakamoto, H. et al. Gliotoxin suppresses NF-κB activation by selectively inhibiting linear ubiquitin chain assembly complex (LUBAC). ACS Chem. Biol. 10, 675–681 (2015).
pubmed: 25494483 doi: 10.1021/cb500653y pmcid: 25494483
Yang, Y. et al. Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms. Cancer Discov. 4, 480–493 (2014).
pubmed: 24491438 pmcid: 3992927 doi: 10.1158/2159-8290.CD-13-0915
Aguilar-Alonso, F., Whiting, A. L., Kim, Y. J. & Bernal, F. Biophysical and biological evaluation of optimized stapled peptide inhibitors of the linear ubiquitin chain assembly complex (LUBAC). Bioorg. Med. Chem. 26, 1179–1188 (2018).
pubmed: 29246782 doi: 10.1016/j.bmc.2017.11.047 pmcid: 29246782
Fujita, H. et al. Cooperative domain formation by homologous motifs in HOIL-1L and SHARPIN plays a crucial role in LUBAC stabilization. Cell Rep. 23, 1192–1204 (2018).
pubmed: 29694895 pmcid: 6044281 doi: 10.1016/j.celrep.2018.03.112
De Cesare, V. et al. The MALDI-TOF E2/E3 ligase assay as universal tool for drug discovery in the ubiquitin pathway. Cell Chem. Biol., 25, 1117–1127 (2018).
pubmed: 30017913 pmcid: 6162346 doi: 10.1016/j.chembiol.2018.06.004
Johansson, H. et al. Fragment-based covalent ligand screening enables rapid discovery of inhibitors for the RBR E3 ubiquitin ligase HOIP. J. Am. Chem. Soc. 141, 2703–2712 (2019).
pubmed: 30657686 pmcid: 6383986 doi: 10.1021/jacs.8b13193
Katsuya, K. et al. High-throughput screening for Linear Ubiquitin Chain Assembly Complex (LUBAC) selective inhibitors using homogenous time-resolved fluorescence (HTRF)-based assay system. SLAS Discov. 23, 1018–1029 (2018).
pubmed: 30071751 pmcid: 30071751
Katsuya, K. et al. Small-molecule inhibitors of linear ubiquitin chain assembly complex (LUBAC), HOIPINs, suppress NF-κB signaling. Biochem Biophys. Res Commun. 509, 700–706 (2019).
pubmed: 30611571 doi: 10.1016/j.bbrc.2018.12.164 pmcid: 30611571
Haas, T. L. et al. Recruitment of the linear ubiquitin chain assembly complex stabilizes the TNF-R1 signaling complex and is required for TNF-mediated gene induction. Mol. Cell 36, 831–844 (2009).
pubmed: 20005846 doi: 10.1016/j.molcel.2009.10.013
Nakazawa, S. et al. Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis. Nat. Commun. 7, 12547 (2016).
pubmed: 27552911 pmcid: 4999505 doi: 10.1038/ncomms12547
Inn, K. S. et al. Linear ubiquitin assembly complex negatively regulates RIG-I- and TRIM25-mediated type I interferon induction. Mol. Cell 41, 354–365 (2011).
pubmed: 21292167 pmcid: 3070481 doi: 10.1016/j.molcel.2010.12.029
Belgnaoui, S. M. et al. Linear ubiquitination of NEMO negatively regulates the interferon antiviral response through disruption of the MAVS-TRAF3 complex. Cell Host Microbe 12, 211–222 (2012).
pubmed: 22901541 doi: 10.1016/j.chom.2012.06.009
Zinngrebe, J. et al. –LUBAC deficiency perturbs TLR3 signaling to cause immunodeficiency and autoinflammation. J. Exp. Med. 213, 2671–2689 (2016).
pubmed: 27810922 pmcid: 5110014 doi: 10.1084/jem.20160041
Khan, M., Syed, G. H., Kim, S. J. & Siddiqui, A. Hepatitis B virus-induced parkin-dependent recruitment of linear ubiquitin assembly complex (LUBAC) to mitochondria and attenuation of innate immunity. PLoS Pathog. 12, e1005693 (2016).
pubmed: 27348524 pmcid: 4922663 doi: 10.1371/journal.ppat.1005693
MacDuff, D. A. et al. HOIL1 is essential for the induction of type I and III interferons by MDA5 and regulates persistent murine norovirus infection. J. Virol. 92, e01368-18 (2018).
pubmed: 30209176 pmcid: 6232484 doi: 10.1128/JVI.01368-18
Kawai, T. & Akira, S. Toll-like receptors and their crosstalk with other innate receptors in infection and immunity. Immunity 34, 637–650 (2011).
pubmed: 21616434 doi: 10.1016/j.immuni.2011.05.006
Irie, T., Kiyotani, K., Igarashi, T., Yoshida, A. & Sakaguchi, T. Inhibition of interferon regulatory factor 3 activation by paramyxovirus V protein. J. Virol. 86, 7136–7145 (2012).
pubmed: 22532687 pmcid: 3416347 doi: 10.1128/JVI.06705-11
Wang, C. Y., Mayo, M. W. & Baldwin, A. S. Jr TNF- and cancer therapy-induced apoptosis: potentiation by inhibition of NF-κB. Science 274, 784–787 (1996).
pubmed: 8864119 doi: 10.1126/science.274.5288.784
Ikeda, F. et al. SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis. Nature 471, 637–641 (2011).
pubmed: 21455181 pmcid: 3085511 doi: 10.1038/nature09814
Walczak, H. TNF and ubiquitin at the crossroads of gene activation, cell death, inflammation, and cancer. Immunol. Rev. 244, 9–28 (2011).
pubmed: 22017428 doi: 10.1111/j.1600-065X.2011.01066.x pmcid: 22017428
Peltzer, N. et al. HOIP deficiency causes embryonic lethality by aberrant TNFR1-mediated endothelial cell death. Cell Rep. 9, 153–165 (2014).
pubmed: 25284787 doi: 10.1016/j.celrep.2014.08.066 pmcid: 25284787
Cabal-Hierro, L. & Lazo, P. S. Signal transduction by tumor necrosis factor receptors. Cell Signal. 24, 1297–1305 (2012).
pubmed: 22374304 doi: 10.1016/j.cellsig.2012.02.006 pmcid: 22374304
Dobashi, A. Molecular pathogenesis of diffuse large B-cell lymphoma. J. Clin. Exp. Hematop. 56, 71–78 (2016).
pubmed: 27980305 pmcid: 6144207 doi: 10.3960/jslrt.56.71
Knittel, G., Liedgens, P., Korovkina, D., Pallasch, C. P. & Reinhardt, H. C. Rewired NFκB signaling as a potentially actionable feature of activated B-cell-like diffuse large B-cell lymphoma. Eur. J. Haematol. 97, 499–510 (2016).
pubmed: 27526684 doi: 10.1111/ejh.12792 pmcid: 27526684
Dubois, S. M. et al. A catalytic-independent role for the LUBAC in NF-κB activation upon antigen receptor engagement and in lymphoma cells. Blood 123, 2199–2203 (2014).
pubmed: 24497531 doi: 10.1182/blood-2013-05-504019 pmcid: 24497531
Greb, J. E. et al. Psoriasis. Nat. Rev. Dis. Prim. 2, 16082 (2016).
pubmed: 27883001 doi: 10.1038/nrdp.2016.82 pmcid: 27883001
van der Fits, L. et al. Imiquimod-induced psoriasis-like skin inflammation in mice is mediated via the IL-23/IL-17 axis. J. Immunol. 182, 5836–5845 (2009).
pubmed: 19380832 doi: 10.4049/jimmunol.0802999 pmcid: 19380832
Feldman, S. R. & Yentzer, B. A. Topical clobetasol propionate in the treatment of psoriasis: a review of newer formulations. Am. J. Clin. Dermatol. 10, 397–406 (2009).
pubmed: 19824740 doi: 10.2165/11311020-000000000-00000 pmcid: 19824740
Eyerich, K. & Eyerich, S. Immune response patterns in non-communicable inflammatory skin diseases. J. Eur. Acad. Dermatol. Venereol. 32, 692–703 (2018).
pubmed: 29114938 pmcid: 5947562 doi: 10.1111/jdv.14673
Peltzer, N. & Walczak, H. Cell death and inflammation—a vital but dangerous liaison. Trends Immunol. 40, 387–402 (2019).
pubmed: 31003931 doi: 10.1016/j.it.2019.03.006 pmcid: 31003931
Heger, K. et al. OTULIN limits cell death and inflammation by deubiquitinating LUBAC. Nature 559, 120–124 (2018).
pubmed: 29950720 doi: 10.1038/s41586-018-0256-2 pmcid: 29950720
Lafont, E. et al. TBK1 and IKKepsilon prevent TNF-induced cell death by RIPK1 phosphorylation. Nat. Cell Biol. 20, 1389–1399 (2018).
pubmed: 30420664 pmcid: 6268100 doi: 10.1038/s41556-018-0229-6
Harden, J. L., Krueger, J. G. & Bowcock, A. M. The immunogenetics of psoriasis: a comprehensive review. J. Autoimmun. 64, 66–73 (2015).
pubmed: 26215033 pmcid: 4628849 doi: 10.1016/j.jaut.2015.07.008
Taraborrelli, L. et al. LUBAC prevents lethal dermatitis by inhibiting cell death induced by TNF, TRAIL and CD95L. Nat. Commun. 9, 3910 (2018).
pubmed: 30254289 pmcid: 6156229 doi: 10.1038/s41467-018-06155-8
Anderton, H., Rickard, J. A., Varigos, G. A., Lalaoui, N. & Silke, J. Inhibitor of apoptosis proteins (IAPs) limit RIPK1-mediated skin inflammation. J. Invest. Dermatol. 137, 2371–2379 (2017).
pubmed: 28647349 doi: 10.1016/j.jid.2017.05.031 pmcid: 28647349
Weischenfeldt, J. & Porse, B. Bone marrow-derived macrophages (BMM): isolation and applications. CSH Protoc. 2008, pdb prot5080 (2008).
Tokunaga, F. et al. Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation. EMBO J. 31, 3856–3870 (2012).
pubmed: 23032187 pmcid: 3463848 doi: 10.1038/emboj.2012.241
Sarkar, S. N., Smith, H. L., Rowe, T. M. & Sen, G. C. Double-stranded RNA signaling by Toll-like receptor 3 requires specific tyrosine residues in its cytoplasmic domain. J. Biol. Chem. 278, 4393–4396 (2003).
pubmed: 12509442 doi: 10.1074/jbc.C200655200 pmcid: 12509442
Kato, K. et al. Structural and functional analyses of DNA-sensing and immune activation by human cGAS. PLoS ONE 8, e76983 (2013).
pubmed: 24116191 pmcid: 3792152 doi: 10.1371/journal.pone.0076983
Ohtake, F., Saeki, Y., Ishido, S., Kanno, J. & Tanaka, K. The K48-K63 branched ubiquitin chain regulates NF-κB signaling. Mol. Cell 64, 251–266 (2016).
doi: 10.1016/j.molcel.2016.09.014
Kabsch, W. Xds. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).
pubmed: 2815665 pmcid: 2815665 doi: 10.1107/S0907444909047337
Collaborative Computational Project, N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D. Biol. Crystallogr. 50, 760–763 (1994).
doi: 10.1107/S0907444994003112
Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997).
doi: 10.1107/S0021889897006766
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol. Crystallogr 60, 2126–2132 (2004).
pubmed: 15572765 doi: 10.1107/S0907444904019158 pmcid: 15572765
Zwart, P. H. et al. Automated structure solution with the PHENIX suite. Methods Mol. Biol. 426, 419–435 (2008).
pubmed: 18542881 doi: 10.1007/978-1-60327-058-8_28 pmcid: 18542881
Mizukami, Y., Sugawara, K., Kira, Y. & Tsuruta, D. Sorafenib stimulates human skin type mast cell degranulation and maturation. J. Dermatol. Sci. 88, 308–319 (2017).
pubmed: 28843624 doi: 10.1016/j.jdermsci.2017.08.005 pmcid: 28843624

Auteurs

Daisuke Oikawa (D)

Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Yusuke Sato (Y)

Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.
Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan.

Fumiaki Ohtake (F)

Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.

Keidai Komakura (K)

Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan.
Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Kazuki Hanada (K)

Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, JT Inc., Kanagawa, Japan.

Koji Sugawara (K)

Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Seigo Terawaki (S)

Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Yukari Mizukami (Y)

Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Hoang T Phuong (HT)

Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Kiyosei Iio (K)

Chemical Research Laboratories, Central Pharmaceutical Research Institute, JT Inc., Osaka, Japan.

Shingo Obika (S)

Chemical Research Laboratories, Central Pharmaceutical Research Institute, JT Inc., Osaka, Japan.

Masaya Fukushi (M)

Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.

Takashi Irie (T)

Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.

Daisuke Tsuruta (D)

Department of Dermatology, Graduate School of Medicine, Osaka City University, Osaka, Japan.

Shinji Sakamoto (S)

Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, JT Inc., Kanagawa, Japan.

Keiji Tanaka (K)

Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

Yasushi Saeki (Y)

Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.

Shuya Fukai (S)

Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.

Fuminori Tokunaga (F)

Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan. ftokunaga@med.osaka-cu.ac.jp.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH