TDP43 negatively regulates TBK1-mediated IFN1 production through IRF7 pathway in neurodegenerative diseases

Abstract

Mutations in the genes encoding TAR DNA-binding protein 43 (TDP43) or TANK-binding kinase 1 (TBK1) have been strongly associated with neurological disorders, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. TDP43 is a key component of pathological protein aggregates found in more than 90% of ALS cases, while TBK1 plays a critical role in innate immune signaling and autophagy. Despite these associations, the precise molecular mechanisms linking TDP43 or TBK1 dysfunction to neurodegeneration remain poorly understood. The present study examined the impact of TDP43 on TBK1-mediated type I interferon (IFN1) production in HEK-293T cells. The findings demonstrated that co-expression of TDP43 and TBK1 resulted in a dose-dependent reduction in TBK1 and interferon regulatory factor (IRF) 7 protein levels. In addition, it led to decreased phosphorylation of IRF3 and TBK1. Interestingly, TDP43 knockout cells displayed elevated IRF7 protein levels. Moreover, co-expression of TDP43 and TBK1 significantly suppressed the IFN1 inductions and associated pro-inflammatory cytokines, a suppression reversed by IRF7 overexpression. Further, mechanistic analysis demonstrated that TDP43 facilitates TBK1 degradation through autophagy, resulting in diminished IFN1 induction. These findings uncover a new pathway through which TDP43 disrupts TBK1-mediated signaling through IRF7, potentially contributing to neurodegeneration. Overall, the disrupted TBK1-IRF7-IFN1 axis may therefore represent a critical pathway in TDP43-associated neurodegenerative diseases, offering potential targets for therapeutic intervention.

Graphical abstract

Keywords

Amyotrophic lateral sclerosis / TAR DNA-binding protein 43 / TANK-binding kinase 1 / Type I interferons / Interferon regulatory factor 7

Funding

This work was supported by the Natural Science Foundation of Shanxi Province (N202304031401121 to B.H., 202403021211044 to B.H., 202302130501011 to Y.Z, 202204051002032 to G.S), the Health Planning Commission foundation of Shanxi Province (N2019017 to B.H., 2024ZYY2A010 to B.H., Renal Disease Clinical and Research Innovation Base Project to Y.Z. and 2021XM to Y.Z.), the Development and Reform Commission Foundation of Shanxi Province (Shanxi Genetic Engineering Center for Experimental Animal Models to Y.Z. and B.H.), and the Shanxi Provincial Medical Administration and Medical Administration Bureau (Role and mechanism of electroacupuncture in the analgesic process of the APP/PS1-MRL/Lpr model to B.H., Y.Z., and J.H., Grant No. 2024ZYY2A010 to B.H., 2022TD2004 to Y.Z.). This work was also financially supported through a demonstration project targeting reform and high-quality development at public hospitals, funded by the Shanxi Provincial Department of Finance supports the (Jin Cai She [2023] No. 23 Project to Y.Z.). This work was also supported by the Shanxi University of Traditional Chinese Medicine (Innovative team cultivation project for the combination of acupuncture and medicine in the prevention and treatment of chronic kidney disease to Y.Z.).

Conflict of interest

The authors declared that they have no competing interests.

References

[1] Weskamp K, Tank EM, Miguez R, et al. Shortened TDP43 isoforms upregulated by neuronal hyperactivity drive TDP43 pathology in ALS. J Clin Invest. 2020; 130(3):1139-1155. doi: 10.1172/JCI130988

[2] Prasad A, Bharathi V, Sivalingam V, Girdhar A, Patel BK. Molecular mechanisms of TDP-43 misfolding and pathology in amyotrophic lateral sclerosis. Front Mol Neurosci. 2019;12:25. doi: 10.3389/fnmol.2019.00025

[3] Polymenidou M, Lagier-Tourenne C, Hutt KR, et al. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat Neurosci. 2011; 14(4):459-468. doi: 10.1038/nn.2779

[4] Liu G, Coyne AN, Pei F, et al. Endocytosis regulates TDP-43 toxicity and turnover. Nat Commun. 2017; 8(1):2092. doi: 10.1038/s41467-017-02017-x

[5] Xia Q, Wang H, Hao Z, et al. TDP-43 loss of function increases TFEB activity and blocks autophagosome-lysosome fusion. EMBO J. 2016; 35(2):121-142. doi: 10.15252/embj.201591998

[6] Wang W, Wang L, Lu J, et al. The inhibition of TDP-43 mitochondrial localization blocks its neuronal toxicity. Nat Med. 2016; 22(8):869-878. doi: 10.1038/nm.4130

[7] Hiji M, Takahashi T, Fukuba H, Yamashita H, Kohriyama T, Matsumoto M. White matter lesions in the brain with frontotemporal lobar degeneration with motor neuron disease: TDP-43-immunopositive inclusions co-localize with p62, but not ubiquitin. Acta Neuropathol. 2008; 116(2):183-191. doi: 10.1007/s00401-008-0402-2

[8] Bose JK, Huang CC, James Shen CK. Regulation of autophagy by neuropathological protein TDP-43. J Biol Chem. 2011; 286(52):44441-44448. doi: 10.1074/jbc.M111.237115

[9] Foster AD, Downing P, Figredo E, et al. ALS-associated TBK1 variant p.G175S is defective in phosphorylation of p62 and impacts TBK1-mediated signalling and TDP-43 autophagic degradation. Mol Cell Neurosci. 2020;108:103539. doi: 10.1016/j.mcn.2020.103539

[10] Deng HX, Chen W, Hong ST, et al. Mutations in UBQLN2 cause dominant X-linked juvenile and adult-onset ALS and ALS/dementia. Nature. 2011; 477(7363):211-215. doi: 10.1038/nature10353

[11] Murray ME, DeJesus-Hernandez M, Rutherford NJ, et al. Clinical and neuropathologic heterogeneity of c9FTD/ ALS associated with hexanucleotide repeat expansion in C9ORF72. Acta Neuropathol. 2011; 122(6):673-690. doi: 10.1007/s00401-011-0907-y

[12] Smith BN, Vance C, Scotter EL, et al. Novel mutations support a role for profilin 1 in the pathogenesis of ALS. Neurobiol Aging. 2015; 36(3):1602.e17-e27. doi: 10.1016/j.neurobiolaging.2014.10.032

[13] Oakes JA, Davies MC, Collins MO. TBK1: A new player in ALS linking autophagy and neuroinflammation. Mol Brain. 2017; 10(1):5. doi: 10.1186/s13041-017-0287-x

[14] Marchlik E, Thakker P, Carlson T, et al. Mice lacking Tbk1 activity exhibit immune cell infiltrates in multiple tissues and increased susceptibility to LPS-induced lethality. J Leukoc Biol. 2010; 88(6):1171-1180. doi: 10.1189/jlb.0210071

[15] Chen T, Zhang W, Huang B, Chen X, Huang C. UBQLN2 promotes the production of type I interferon via the TBK1- IRF3 pathway. Cells. 2020; 9(5):1205. doi: 10.3390/cells9051205

[16] Liu YJ. IPC: Professional type 1 interferon-producing cells and plasmacytoid dendritic cell precursors. Annu Rev Immunol. 2005; 23:275-306. doi: 10.1146/annurev.immunol.23.021704.115633

[17] Honda K, Yanai H, Negishi H, et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature. 2005; 434(7034):772-777. doi: 10.1038/nature03464

[18] Wang J, Yang B, Hu Y, et al. Negative regulation of Nmi on virus-triggered type I IFN production by targeting IRF7. J Immunol. 2013; 191(6):3393-3399. doi: 10.4049/jimmunol.1300740

[19] Gorrie GH, Fecto F, Radzicki D, et al. Dendritic spinopathy in transgenic mice expressing ALS/dementia-linked mutant UBQLN2. Proc Natl Acad Sci U S A. 2014; 111(40):14524-14529. doi: 10.1073/pnas.1405741111

[20] Chen T, Huang B, Shi X, Gao L, Huang C. Mutant UBQLN2^P497Hin motor neurons leads to ALS-like phenotypes and defective autophagy in rats. Acta Neuropathol Commun. 2018; 6(1):122. doi: 10.1186/s40478-018-0627-9

[21] Wu Q, Liu M, Huang C, et al. Pathogenic Ubqln2 gains toxic properties to induce neuron death. Acta Neuropathol. 2015; 129(3):417-428. doi: 10.1007/s00401-014-1367-y

[22] Pilli M, Arko-Mensah J, Ponpuak M, et al. TBK-1 promotes autophagy-mediated antimicrobial defense by controlling autophagosome maturation. Immunity. 2012; 37(2):223-234. doi: 10.1016/j.immuni.2012.04.015

[23] Le NTT, Chang L, Kovlyagina I, et al. Motor neuron disease, TDP-43 pathology, and memory deficits in mice expressing ALS-FTD-linked UBQLN2 mutations. Proc Natl Acad Sci U S A. 2016; 113(47):7580-7589. doi: 10.1073/pnas.1608432113

[24] Xia Y, Yan LH, Huang B, Liu M, Liu X, Huang C. Pathogenic mutation of UBQLN2 impairs its interaction with UBXD8 and disrupts endoplasmic reticulum-associated protein degradation. J Neurochem. 2014; 129(1):99-106. doi: 10.1111/jnc.12606

[25] Dugger BN, Dickson DW. Pathology of neurodegenerative diseases. Cold Spring Harb Perspect Biol. 2017; 9(7):a028035. doi: 10.1101/cshperspect.a028035

[26] Smethurst P, Sidle KC, Hardy J. Review: Prion-like mechanisms of transactive response DNA binding protein of 43 kDa (TDP-43) in amyotrophic lateral sclerosis (ALS). Neuropathol Appl Neurobiol. 2015; 41(5):578-597. doi: 10.1111/nan.12206

[27] Ince PG, Highley JR, Kirby J, et al. Molecular pathology and genetic advances in amyotrophic lateral sclerosis: An emerging molecular pathway and the significance of glial pathology. Acta Neuropathol. 2011; 122(6):657-671. doi: 10.1007/s00401-011-0913-0

[28] Freischmidt A, Wieland T, Richter B, et al. Haploinsufficiency of TBK1 causes familial ALS and fronto-temporal dementia. Nat Neurosci. 2015; 18(5):631-636. doi: 10.1038/nn.4000

[29] Xu D, Jin T, Zhu H, et al. TBK1 suppresses RIPK1-driven apoptosis and inflammation during development and in aging. Cell. 2018; 174(6):1477-1491. doi: 10.1016/j.cell.2018.07.041

[30] Liu W, Wang Z, Liu L, et al. LncRNA Malat1 inhibition of TDP43 cleavage suppresses IRF3-initiated antiviral innate immunity. Proc Natl Acad Sci U S A. 2020; 117(38):23695-23706. doi: 10.1073/pnas.2003932117

[31] Yu CH, Davidson S, Harapas CR, et al. TDP-43 triggers mitochondrial DNA release via mPTP to activate cGAS/ STING in ALS. Cell. 2020; 183(3):636-649. doi: 10.1016/j.cell.2020.09.020

[32] Ma X, Helgason E, Phung QT, et al. Molecular basis of tank-binding kinase 1 activation by transautophosphorylation. Proc Natl Acad Sci U S A. 2012; 109(24):9378-9383. doi: 10.1073/pnas.1121552109

[33] Ahmad L, Zhang SY, Casanova JL, Sancho-Shimizu V. Human TBK1: A gatekeeper of neuroinflammation. Trends Mol Med. 2016; 22(6):511-527. doi: 10.1016/j.molmed.2016.04.006

[34] Trinchieri G. Type I interferon: Friend or foe? J Exp Med. 2010; 207(10):2053-2063. doi: 10.1084/jem.20101664

[35] Yu J, Zhou X, Chang M, et al. Regulation of T-cell activation and migration by the kinase TBK1 during neuroinflammation. Nat Commun. 2015;6:6074. doi: 10.1038/ncomms7074

[36] Zhao W. Negative regulation of TBK1-mediated antiviral immunity. FEBS Lett. 2013; 587(6):542-548. doi: 10.1016/j.febslet.2013.01.052

[37] McCoy CE, Carpenter S, Pålsson-McDermott EM, Gearing LJ, O’Neill LA. Glucocorticoids inhibit IRF3 phosphorylation in response to Toll-like receptor-3 and -4 by targeting TBK1 activation. J Biol Chem. 2008; 283(21):14277-14285. doi: 10.1074/jbc.M709731200

[38] Sin WX, Yeong JP, Lim TJF, Su IH, Connolly JE, Chin KC. IRF-7 mediates type I IFN responses in endotoxin-challenged mice. Front Immunol. 2020;11:640. doi: 10.3389/fimmu.2020.00640

[39] Ramesh N, Pandey UB. Autophagy dysregulation in ALS: When protein aggregates get out of hand. Front Mol Neurosci. 2017;10:263. doi: 10.3389/fnmol.2017.00263