Loss of TDP-43 Splicing Repression Occurs in Myonuclei of Inclusion Body Myositis Patients
Chiseko Ikenaga MD, PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorAndrew B. Wilson PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorKatherine E. Irwin MS
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorAswathy Peethambaran Mallika PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorCollin Kilgore MS
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorIrika R. Sinha MS
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorElizabeth H. Michelle MD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorJonathan P. Ling PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorCorresponding Author
Philip C. Wong PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Address correspondence to Dr Thomas E. Lloyd, Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030. E-mail: [email protected]
Dr Philip C. Wong, Department of Pathology, Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Room 558D, Baltimore, MD 21205. E-mail: [email protected]
Search for more papers by this authorCorresponding Author
Thomas E. Lloyd MD, PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Department of Neurology, Baylor College of Medicine, Houston, TX
Address correspondence to Dr Thomas E. Lloyd, Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030. E-mail: [email protected]
Dr Philip C. Wong, Department of Pathology, Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Room 558D, Baltimore, MD 21205. E-mail: [email protected]
Search for more papers by this authorChiseko Ikenaga MD, PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorAndrew B. Wilson PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorKatherine E. Irwin MS
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorAswathy Peethambaran Mallika PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorCollin Kilgore MS
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorIrika R. Sinha MS
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorElizabeth H. Michelle MD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorJonathan P. Ling PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Search for more papers by this authorCorresponding Author
Philip C. Wong PhD
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Address correspondence to Dr Thomas E. Lloyd, Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030. E-mail: [email protected]
Dr Philip C. Wong, Department of Pathology, Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Room 558D, Baltimore, MD 21205. E-mail: [email protected]
Search for more papers by this authorCorresponding Author
Thomas E. Lloyd MD, PhD
Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD
Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD
Department of Neurology, Baylor College of Medicine, Houston, TX
Address correspondence to Dr Thomas E. Lloyd, Department of Neurology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030. E-mail: [email protected]
Dr Philip C. Wong, Department of Pathology, Johns Hopkins University School of Medicine, Ross Research Building, 720 Rutland Avenue, Room 558D, Baltimore, MD 21205. E-mail: [email protected]
Search for more papers by this authorAbstract
Objective
Inclusion body myositis (IBM) is an idiopathic inflammatory myopathy with muscle pathology characterized by endomysial inflammation, rimmed vacuoles, and cytoplasmic mislocalization of transactive response DNA-binding protein 43 (TDP-43). We aimed to determine whether loss of TDP-43 splicing repression led to the production of “cryptic peptides” that could be detected in muscle biopsies as a useful biomarker for IBM.
Methods
We used an antisera against a neoepitope encoded by a TDP-43-dependent cryptic exon within hepatoma-derived growth factor-like protein 2 (HDGFL2) for immunohistochemical analysis on muscle biopsy samples of 122 patients with IBM, 181 disease controls, and 16 healthy controls without abnormal muscle pathology. In situ hybridization was also utilized to detect the localization of cryptic HDGFL2 transcripts.
Results
We found cryptic HDGFL2 peptides localized within myonuclei from muscle biopsies in 79 of 122 patients with IBM (65%), and this staining correlated with TDP-43 depletion. In contrast, cryptic HDGFL2 immunoreactivity was absent in 197 muscle biopsies from a variety of disease controls, except for 2 patients with vacuolar myopathies. Notably, we show that cryptic HDGFL2 transcripts are accompanied by the detection of cryptic HDGFL2 in muscle fibers of IBM without rimmed vacuoles and TDP-43 aggregates.
Interpretation
Together, our findings establish that loss of TDP-43 splicing repression occurs in myonuclei of IBM skeletal muscle and suggest that detection of cryptic peptides in muscle biopsies may be a useful biomarker. We suggest that a therapeutic strategy designed to restore TDP-43 function should be considered to attenuate the degeneration of skeletal muscle in this devastating disease. ANN NEUROL 2025;97:629–641
Potential Conflicts of Interest
The authors declare the following competing interests. J.P.L. and P.C.W. are inventors on a provisional patent application submitted by Johns Hopkins University that covers the usage of TDP-43-associated cryptic exon-derived neoepitopes as biomarkers.
Open Research
Data Availability
The authors confirm that the data supporting the findings of this study are available within the article and its supplementary materials.
Supporting Information
| Filename | Description |
|---|---|
| ana27167-sup-0001-Supinfo.docWord document, 2.2 MB | Data S1. Supporting Information. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- 1Lindgren U, Pullerits R, Lindberg C, Oldfors A. Epidemiology, survival, and clinical characteristics of inclusion body myositis. Ann Neurol 2022; 92: 201–212.
- 2Michelle EH, Pinal-Fernandez I, Casal-Dominguez M, et al. Clinical subgroups and factors associated with progression in patients with inclusion body myositis. Neurology 2023; 100: e1406–e1417.
- 3Rose MR, Group EIW. 188th ENMC international workshop: inclusion body myositis, 2-4 December 2011, Naarden, The Netherlands. Neuromuscul Disord 2013; 23: 1044–1055.
- 4Ikenaga C, Kubota A, Kadoya M, et al. Clinicopathologic features of myositis patients with CD8-MHC-1 complex pathology. Neurology 2017; 89: 1060–1068.
- 5Lloyd TE, Mammen AL, Amato AA, et al. Evaluation and construction of diagnostic criteria for inclusion body myositis. Neurology 2014; 83: 426–433.
- 6Pinkus JL, Amato AA, Taylor JP, Greenberg SA. Abnormal distribution of heterogeneous nuclear ribonucleoproteins in sporadic inclusion body myositis. Neuromuscul Disord 2014; 24: 611–616.
- 7Salajegheh M, Pinkus JL, Taylor JP, et al. Sarcoplasmic redistribution of nuclear TDP-43 in inclusion body myositis. Muscle Nerve 2009; 40: 19–31.
- 8Weihl CC, Temiz P, Miller SE, et al. TDP-43 accumulation in inclusion body myopathy muscle suggests a common pathogenic mechanism with frontotemporal dementia. J Neurol Neurosurg Psychiatry 2008; 79: 1186–1189.
- 9Donde A, Sun M, Ling JP, et al. Splicing repression is a major function of TDP-43 in motor neurons. Acta Neuropathol 2019; 138: 813–826.
- 10Ling JP, Pletnikova O, Troncoso JC, Wong PC. TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD. Science 2015; 349: 650–655.
- 11Sun M, Bell W, LaClair KD, et al. Cryptic exon incorporation occurs in Alzheimer's brain lacking TDP-43 inclusion but exhibiting nuclear clearance of TDP-43. Acta Neuropathol 2017; 133: 923–931.
- 12Britson KA, Ling JP, Braunstein KE, et al. Loss of TDP-43 function and rimmed vacuoles persist after T cell depletion in a xenograft model of sporadic inclusion body myositis. Sci Transl Med 2022; 14:eabi9196.
- 13Wischnewski S, Thäwel T, Ikenaga C, et al. Selective myofiber vulnerability in inclusion body myositis. Nat Aging 2024; 4: 969–983.
- 14Jeong YH, Ling JP, Lin SZ, et al. Tdp-43 cryptic exons are highly variable between cell types. Mol Neurodegener 2017; 12: 13.
- 15Irwin KE, Jasin P, Braunstein KE, et al. A fluid biomarker reveals loss of TDP-43 splicing repression in pre-symptomatic ALS. Nat Med 2024; 30: 382–393.
- 16Allenbach Y, Mammen AL, Benveniste O, et al. 224th ENMC international workshop:: Clinico-sero-pathological classification of immune-mediated necrotizing myopathies Zandvoort, The Netherlands, 14–16 October 2016. Neuromuscul Disord 2018; 28: 87–99.
- 17Hoogendijk JE, Amato AA, Lecky BR, et al. 119th ENMC international workshop: trial design in adult idiopathic inflammatory myopathies, with the exception of inclusion body myositis, 10-12 October 2003, Naarden, The Netherlands. Neuromuscul Disord 2004; 14: 337–345.
- 18Bucelli RC, Pestronk A. Immune myopathies with perimysial pathology: clinical and laboratory features. Neurol Neuroimmunol Neuroinflamm 2018; 5:e434.
- 19Connors GR, Christopher-Stine L, Oddis CV, Danoff SK. Interstitial lung disease associated with the idiopathic inflammatory myopathies: what progress has been made in the past 35 years? Chest 2010; 138: 1464–1474.
- 20Witt LJ, Curran JJ, Strek ME. The diagnosis and treatment of antisynthetase syndrome. Clin Pulm Med 2016; 23: 218–226.
- 21Blume G, Pestronk A, Frank B, Johns DR. Polymyositis with cytochrome oxidase negative muscle fibres. Early quadriceps weakness and poor response to immunosuppressive therapy. Brain 1997; 120: 39–45.
- 22Chariot P, Ruet E, Authier FJ, et al. Cytochrome c oxidase deficiencies in the muscle of patients with inflammatory myopathies. Acta Neuropathol 1996; 91: 530–536.
- 23Fayet G, Jansson M, Sternberg D, et al. Ageing muscle: clonal expansions of mitochondrial DNA point mutations and deletions cause focal impairment of mitochondrial function. Neuromuscul Disord 2002; 12: 484–493.
- 24Rygiel KA, Miller J, Grady JP, et al. Mitochondrial and inflammatory changes in sporadic inclusion body myositis. Neuropathol Appl Neurobiol 2015; 41: 288–303.
- 25Temiz P, Weihl CC, Pestronk A. Inflammatory myopathies with mitochondrial pathology and protein aggregates. J Neurol Sci 2009; 278: 25–29.
- 26Chang K, Ling JP, Redding-Ochoa J, et al. Loss of TDP-43 splicing repression occurs early in the aging population and is associated with Alzheimer's disease neuropathologic changes and cognitive decline. Acta Neuropathol 2023; 147: 4.
- 27Ikenaga C, Date H, Kanagawa M, et al. Muscle transcriptomics shows overexpression of cadherin 1 in inclusion body myositis. Ann Neurol 2022; 91: 317–328.
- 28Gao K, Xu C, Jin X, et al. HDGF-related protein-2 (HRP-2) acts as an oncogene to promote cell growth in hepatocellular carcinoma. Biochem Biophys Res Commun 2015; 458: 849–855.
- 29Greenberg SA, Pinkus JL, Amato AA. Nuclear membrane proteins are present within rimmed vacuoles in inclusion-body myositis. Muscle Nerve 2006; 34: 406–416.
- 30Seddighi S, Qi YA, Brown AL, et al. Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD. Sci Transl Med 2024; 16:eadg7162.
- 31Calliari A, Daughrity LM, Albagli EA, et al. HDGFL2 cryptic proteins report presence of TDP-43 pathology in neurodegenerative diseases. Mol Neurodegener 2024; 19: 29.
- 32Forcina L, Cosentino M, Musarò A. Mechanisms regulating muscle regeneration: insights into the interrelated and time-dependent phases of tissue healing. Cells 2020; 9:1297.
- 33Vogler TO, Wheeler JR, Nguyen ED, et al. TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle. Nature 2018; 563: 508–513.
- 34Brady S, Squier W, Sewry C, et al. A retrospective cohort study identifying the principal pathological features useful in the diagnosis of inclusion body myositis. BMJ Open 2014; 4:e004552.
- 35D'Agostino C, Nogalska A, Engel WK, Askanas V. In sporadic inclusion body myositis muscle fibres TDP-43-positive inclusions are less frequent and robust than p62 inclusions, and are not associated with paired helical filaments. Neuropathol Appl Neurobiol 2011; 37: 315–320.
- 36Dubourg O, Wanschitz J, Maisonobe T, et al. Diagnostic value of markers of muscle degeneration in sporadic inclusion body myositis. Acta Myol 2011; 30: 103–108.
- 37Hiniker A, Daniels BH, Lee HS, Margeta M. Comparative utility of LC3, p62 and TDP-43 immunohistochemistry in differentiation of inclusion body myositis from polymyositis and related inflammatory myopathies. Acta Neuropathol Commun 2013; 1:29.
- 38Küsters B, van Hoeve BJ, Schelhaas HJ, et al. TDP-43 accumulation is common in myopathies with rimmed vacuoles. Acta Neuropathol 2009; 117: 209–211.
- 39Milisenda JC, Pinal-Fernandez I, Lloyd TE, et al. Accumulation of autophagosome cargo protein p62 is common in idiopathic inflammatory myopathies. Clin Exp Rheumatol 2021; 39: 351–356.
- 40Fischer N, Preuße C, Radke J, et al. Sequestosome-1 (p62) expression reveals chaperone-assisted selective autophagy in immune-mediated necrotizing myopathies. Brain Pathol 2020; 30: 261–271.
- 41Dimitri D, Benveniste O, Dubourg O, et al. Shared blood and muscle CD8+ T-cell expansions in inclusion body myositis. Brain 2006; 129: 986–995.
- 42Goyal NA, Coulis G, Duarte J, et al. Immunophenotyping of inclusion body myositis blood T and NK cells. Neurology 2022; 98: e1374–e1383.
- 43Greenberg SA, Pinkus JL, Kong SW, et al. Highly differentiated cytotoxic T cells in inclusion body myositis. Brain 2019; 142: 2590–2604.
- 44Amemiya K, Granger RP, Dalakas MC. Clonal restriction of T-cell receptor expression by infiltrating lymphocytes in inclusion body myositis persists over time. Studies in repeated muscle biopsies. Brain 2000; 123: 2030–2039.
- 45Fyhr IM, Moslemi AR, Mosavi AA, et al. Oligoclonal expansion of muscle infiltrating T cells in inclusion body myositis. J Neuroimmunol 1997; 79: 185–189.
- 46Salajegheh M, Rakocevic G, Raju R, et al. T cell receptor profiling in muscle and blood lymphocytes in sporadic inclusion body myositis. Neurology 2007; 69: 1672–1679.
- 47Baude A, Aaes TL, Zhai B, et al. Hepatoma-derived growth factor-related protein 2 promotes DNA repair by homologous recombination. Nucleic Acids Res 2016; 44: 2214–2226.
- 48Zhang X, Chen Y, Pan J, et al. iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig. BMC Genomics 2016; 17: 137.
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