Abstract
In TNF signaling, ubiquitination of RIP1 functions as an early cell-death checkpoint, which prevents the spatial transition of the signaling complex from complex-I to death-inducing complex-II. Here, we report that ankyrin repeat domain 13a (ANKRD13a) acts as a novel component of complex-II to set a higher signal threshold for the cytotoxic potential of TNF. ANKRD13a deficiency is sufficient to turn the response to TNF from survival to death by promoting the formation of complex-II without affecting NF-κB activation. ANKRD13a binds to ubiquitinated-RIP1 via its UIM, and subsequently limits the association of FADD and caspase-8 with RIP1. Moreover, high ANKRD13a expression is inversely correlated with apoptotic phenotypes in ovarian cancer tissues and is associated with poor prognosis. Our work identifies ANKRD13a as a novel gatekeeper of the early cell-death checkpoint, which may function as part of an escape mechanism from cell death in some cancers.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
Data availability
All data needed to evaluate the conclusion in this article are included in the paper and/or its supplementary information. The datasets used and/or analyzed in this study are available from the corresponding author on reasonable request.
References
Walczak H. TNF and ubiquitin at the crossroads of gene activation, cell death, inflammation, and cancer. Immunol Rev. 2011;244:9–28.
Micheau O, Tschopp J. Induction of TNF receptor I-mediated apoptosis via two sequential signaling complexes. Cell. 2013;114:181–90.
Ting AT, Bertrand MJM. More to Life than NF-kappaB in TNFR1 Signaling. Trends Immunol. 2016;37:535–45.
Kanayama A, Seth RB, Sun L, Ea CK, Hong M, Shaito A, et al. TAB2 and TAB3 activate the NF-kappaB pathway through binding to polyubiquitin chains. Mol Cell. 2004;15:535–48.
Ea CK, Deng L, Xia ZP, Pineda G, Chen ZJ. Activation of IKK by TNFalpha requires site-specific ubiquitination of RIP1 and polyubiquitin binding by NEMO. Mol Cell. 2006;22:245–57.
Wu CJ, Conze DB, Li T, Srinivasula SM, Ashwell JD. Sensing of Lys 63-linked polyubiquitination by NEMO is a key event in NF-kappaB activation. Nat Cell Biol. 2006;8:398–406.
Bertrand MJ, Milutinovic S, Dickson KM, Ho WC, Boudreault A, Durkin J, et al. cIAP1 and cIAP2 facilitate cancer cell survival by functioning as E3 ligases that promote RIP1 ubiquitination. Mol Cell. 2008;30:689–700.
Yin Q, Lamothe B, Darnay BG, Wu H. Structural basis for the lack of E2 interaction in the RING domain of TRAF2. Biochemistry. 2009;48:10558–67.
Gerlach B, Cordier SM, Schmukle AC, Emmerich CH, Rieser E, Haas TL, et al. Linear ubiquitination prevents inflammation and regulates immune signalling. Nature. 2011;471:591–6.
Silke J. The regulation of TNF signalling: what a tangled web we weave. Curr Opin Immunol. 2011;23:620–6.
Schneider-Brachert W, Tchikov V, Neumeyer J, Jakob M, Winoto-Morbach S, Held-Feindt J, et al. Compartmentalization of TNF receptor 1 signaling: internalized TNF receptosomes as death signaling vesicles. Immunity. 2004;21:415–28.
Brenner D, Blaser H, Mak TW. Regulation of tumour necrosis factor signalling: live or let die. Nat Rev Immunol. 2015;15:362–74.
Annibaldi A, Meier P. Checkpoints in TNF-induced cell death: implications in inflammation and cancer. Trends Mol Med. 2018;24:49–65.
Lee EG, Boone DL, Chai S, Libby SL, Chien M, Lodolce JP, et al. Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice. Science. 2000;289:2350–4.
Micheau O, Lens S, Gaide O, Alevizopoulos K, Tschopp J. NF-kappaB signals induce the expression of c-FLIP. Mol Cell Biol. 2001;21:5299–305.
Chen G, Goeddel DV. TNF-R1 signaling: a beautiful pathway. Science. 2002;296:1634–5.
Peltzer N, Darding M, Walczak H. Holding RIPK1 on the ubiquitin leash in TNFR1 signaling. Trends Cell Biol. 2016;26:445–61.
Dondelinger Y, Jouan-Lanhouet S, Divert T, Theatre E, Bertin J, Gough PJ, et al. NF-kappaB-independent role of IKKalpha/IKKbeta in preventing ripk1 kinase-dependent apoptotic and necroptotic cell death during TNF signaling. Mol Cell. 2015;60:63–76.
Dondelinger Y, Delanghe T, Rojas-Rivera D, Priem D, Delvaeye T, Bruggeman I, et al. MK2 phosphorylation of RIPK1 regulates TNF-mediated cell death. Nat Cell Biol. 2017;19:1237–47.
Geng J, Ito Y, Shi L, Amin P, Chu J, Ouchida AT, et al. Regulation of RIPK1 activation by TAK1-mediated phosphorylation dictates apoptosis and necroptosis. Nat Commun. 2017;8:359.
Jaco I, Annibaldi A, Lalaoui N, Wilson R, Tenev T, Laurien L, et al. MK2 Phosphorylates RIPK1 to prevent TNF-induced cell death. Mol Cell. 2017;66:698–710.
Menon MB, Gropengießer J, Fischer J, Novikova L, Deuretzbacher A, Lafera J, et al. p38(MAPK)/MK2-dependent phosphorylation controls cytotoxic RIPK1 signalling in inflammation and infection. Nat Cell Biol. 2017;19:1248–59.
Lafont E, Draber P, Rieser E, Reichert M, Kupka S, de Miguel D, et al. TBK1 and IKKepsilon prevent TNF-induced cell death by RIPK1 phosphorylation. Nat Cell Biol. 2018;20:1389–99.
Hofmann K, Falquet LA. ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends Biochem Sci. 2001;26:347–50.
Riezman H. Cell biology: the ubiquitin connection. Nature. 2002;416:381–3.
Fisher RD, Wang B, Alam SL, Higginson DS, Robinson H, Sundquist WI, et al. Structure and ubiquitin binding of the ubiquitin-interacting motif. J Biol Chem. 2003;278:28976–84.
Polo S, Confalonieri S, Salcini AE, Di Fiore PP. EH and UIM: endocytosis and more. Sci STKE. 2003:re17.
Satpathy S, Wagner SA, Beli P, Gupta R, Kristiansen TA, Malinova D, et al. Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation. Mol Syst Biol. 2015;11:810.
Tanno H, Yamaguchi T, Goto E, Ishido S, Komada M. The Ankrd 13 family of UIM-bearing proteins regulates EGF receptor endocytosis from the plasma membrane. Mol Biol Cell. 2012;23:1343–53.
Burana D, Yoshihara H, Tanno H, Yamamoto A, Saeki Y, Tanaka K, et al. The Ankrd13 family of ubiquitin-interacting motif-bearing proteins regulates valosin-containing protein/p97 protein-mediated lysosomal trafficking of caveolin 1. J Biol Chem. 2016;291:6218–31.
Budczies J, Klauschen F, Sinn BV, Győrffy B, Schmitt WD, Darb-Esfahani S, et al. Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PLoS One. 2012;7:e51862.
Wertz IE, O’Rourke KM, Zhou H, Eby M, Aravind L, Seshagiri S, et al. De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature 2004;430:694–9.
Heyninck K, Beyaert R. A20 inhibits NF-kappaB activation by dual ubiquitin-editing functions. Trends Biochem Sci. 2005;30:1–4.
Lee S, Sohn KC, Choi DK, Won M, Park KA, Ju SK, et al. Ecdysone receptor-based singular gene switches for regulated transgene expression in cells and adult rodent tissues. Mol Ther-Nucl Acids. 2016;5:e36710.
Jin Z, Li Y, Pitti R, Lawrence D, Pham VC, Lill JR, et al. Cullin3-based polyubiquitination and p62-dependent aggregation of caspase-8 mediate extrinsic apoptosis signaling. Cell. 2009;137:721–35.
O’Donnell MA, Legarda-Addison D, Skountzos P, Yeh WC, Ting AT. Ubiquitination of RIP1 regulates an NF-kappaB-independent cell-death switch in TNF signaling. Curr Biol. 2007;17:418–24.
Jang TH, Zheng C, Li J, Richards C, Hsiao YS, Walz T, et al. Structural study of the RIPoptosome core reveals a helical assembly for kinase recruitment. Biochemistry 2014;53:5424–31.
Meng H, Liu Z, Li X, Wang H, Jin T, Wu G, et al. Death-domain dimerization-mediated activation of RIPK1 controls necroptosis and RIPK1-dependent apoptosis. Proc Natl Acad Sci USA. 2018;115:E2001–E9.
Mollah S, Wertz IE, Phung Q, Arnott D, Dixit VM, Lill JR. Targeted mass spectrometric strategy for global mapping of ubiquitination on proteins. Rapid Commun Mass Spectrom. 2007;21:3357–64.
de Almagro MC, Goncharov T, Izrael-Tomasevic A, Duttler S, Kist M, Varfolomeev E, et al. Coordinated ubiquitination and phosphorylation of RIP1 regulates necroptotic cell death. Cell Death Differ. 2017;24:26–37.
Zhang X, Zhang H, Xu C, Li X, Li M, Wu X, et al. Ubiquitination of RIPK1 suppresses programmed cell death by regulating RIPK1 kinase activation during embryogenesis. Nat Commun. 2019;10:4158.
Hicke L, Schubert HL, Hill CP. Ubiquitin-binding domains. Nat Rev Mol Cell Biol. 2005;6:610–21.
Hurley JH, Lee S, Prag G. Ubiquitin-binding domains. Biochem J. 2006;399:361–72.
Dikic I, Wakatsuki S, Walters KJ. Ubiquitin-binding domains-from structures to functions. Nat Rev Mol Cell Biol. 2009;10:659–71.
Hadian K, Griesbach RA, Dornauer S, Wanger TM, Nagel D, Metlitzky M, et al. NF-kappaB essential modulator (NEMO) interaction with linear and lys-63 ubiquitin chains contributes to NF-kappaB activation. J Biol Chem. 2011;286:26107–17.
Polo S, Sigismund S, Faretta M, Guidi M, Capua MR, Bossi G, et al. A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins. Nature. 2002;416:451–5.
Wang X, Lin Y. Tumor necrosis factor and cancer, buddies or foes? Acta Pharm Sin. 2008;29:1275–88.
Laha D, Grant R, Mishra P, Nilubol N. The role of tumor necrosis factor in manipulating the immunological response of tumor microenvironment. Front Immunol. 2021;12:656908.
Psyrri A, Yu Z, Bamias A, Weinberger PM, Markakis S, Kowalski D, et al. Evaluation of the prognostic value of cellular inhibitor of apoptosis protein in epithelial ovarian cancer using automated quantitative protein analysis. Cancer Epidemiol Biomark Prev. 2006;15:1179–83.
Gadducci A, Cosio S, Tana R, Genazzani AR. Serum and tissue biomarkers as predictive and prognostic variables in epithelial ovarian cancer. Crit Rev Oncol Hematol. 2009;69:12–27.
Funding
This work as supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2020R1A2C2005317; No. 2017R1A5A2015385; No. 2018R1C1B6005332).
Author information
Authors and Affiliations
Contributions
MW and KAP participated in the design of the study, carried out bench experiments and analyzes data. EJ helped carrying out bench experiments related to this study. SK, MY and JMK carried out immunohistochemical experiments and statistical analysis. YK and HY provided clinical ovarian cancer tissues. SYK and SWN carried out the pan-cancer cohort analysis. JL and JO carried out yeast two-hybrid screening to identify novel A20-interacting proteins. EGL helped the experiments for in vitro ubiquitination assay. HR carried out the experiments for the construction of teb-inducible expression plasmid. H-MS helped drafting the manuscript by providing critical intellectual input. GMH. designed this study and wrote the manuscript with comments from the coauthors, and all authors collaborated on the work. This work as supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2020R1A2C2005317; No. 2017R1A5A2015385; No. 2018R1C1B6005332).
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Ethical approval
All studies in human subjects were approved by the Institutional Review Board of Chungnam National University Hospital (approval No. 2016-12-027-001).
Informed consent
The written informed consents were obtained from each patient by research team before surgical operation for malignant ovarian cancers, according to the Declaration of Helsinki.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Edited by M. Piacentini
Supplementary information
Rights and permissions
About this article
Cite this article
Won, M., Park, K.A., Kim, S. et al. ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-κB. Cell Death Differ 29, 1152–1163 (2022). https://doi.org/10.1038/s41418-021-00906-9
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41418-021-00906-9
This article is cited by
-
Comprehensive analysis Neddylation-related genes identified UBB as a prognostic biomarker for clear cell renal cell carcinoma
Discover Oncology (2025)
-
Identification and validation of a thirteen-gene signature based on ubiquitin related genes in cervical cancer
Discover Oncology (2025)
-
Integrative analysis indicates the potential values of ANKRD53 in stomach adenocarcinoma
Discover Oncology (2024)
-
The double-edged functions of necroptosis
Cell Death & Disease (2023)
-
The resurrection of RIP kinase 1 as an early cell death checkpoint regulator—a potential target for therapy in the necroptosis era
Experimental & Molecular Medicine (2022)
