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Ko VI, Ong K, Cleveland DW, Yu H, Ravits JM. CK1δ/ε kinases regulate TDP-43 phosphorylation and are therapeutic targets for ALS-related TDP-43 hyperphosphorylation. Neurobiol Dis 2024; 196:106516. [PMID: 38677657 DOI: 10.1016/j.nbd.2024.106516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024] Open
Abstract
Hyperphosphorylated TAR DNA-binding protein 43 (TDP-43) aggregates in the cytoplasm of neurons is the neuropathological hallmark of amyotrophic lateral sclerosis (ALS) and a group of neurodegenerative diseases collectively referred to as TDP-43 proteinopathies that includes frontotemporal dementia, Alzheimer's disease, and limbic onset age-related TDP-43 encephalopathy. The mechanism of TDP-43 phosphorylation is poorly understood. Previously we reported casein kinase 1 epsilon gene (CSNK1E gene encoding CK1ε protein) as being tightly correlated with phosphorylated TDP-43 (pTDP-43) pathology. Here we pursued studies to investigate in cellular models and in vitro how CK1ε and CK1δ (a closely related family sub-member) mediate TDP-43 phosphorylation in disease. We first validated the binding interaction between TDP-43 and either CK1δ and CK1ε using kinase activity assays and predictive bioinformatic database. We utilized novel inducible cellular models that generated translocated phosphorylated TDP-43 (pTDP-43) and cytoplasmic aggregation. Reducing CK1 kinase activity with siRNA or small molecule chemical inhibitors resulted in significant reduction of pTDP-43, in both soluble and insoluble protein fractions. We also established CK1δ and CK1ε are the primary kinases that phosphorylate TDP-43 compared to CK2α, CDC7, ERK1/2, p38α/MAPK14, and TTBK1, other identified kinases that have been implicated in TDP-43 phosphorylation. Throughout our studies, we were careful to examine both the soluble and insoluble TDP-43 protein fractions, the critical protein fractions related to protein aggregation diseases. These results identify CK1s as critical kinases involved in TDP-43 hyperphosphorylation and aggregation in cellular models and in vitro, and in turn are potential therapeutic targets by way of CK1δ/ε inhibitors.
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Affiliation(s)
- Vivian I Ko
- Neuroscience Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Kailee Ong
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - Haiyang Yu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA
| | - John M Ravits
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0624, USA.
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Haider R, Shipley B, Surewicz K, Hinczewski M, Surewicz WK. Pathological C-terminal phosphomimetic substitutions alter the mechanism of liquid-liquid phase separation of TDP-43 low complexity domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586202. [PMID: 38585945 PMCID: PMC10996529 DOI: 10.1101/2024.03.21.586202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
C-terminally phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) marks the proteinaceous inclusions that characterize a number of age-related neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal lobar degeneration and Alzheimer's disease. TDP-43 phosphorylation at S403/S404, and especially at S409/S410, is in fact accepted as a biomarker of proteinopathy. These residues are located within the low complexity domain (LCD), which also drives the protein's liquid-liquid phase separation (LLPS). The impact of phosphorylation at these LCD sites on phase separation of the protein is a topic of great interest, as these post-translational modifications and LLPS are both implicated in proteinopathies. Here, we employed a combination of experimental and simulation-based approaches to explore this question on a phosphomimetic model of the TDP-43 LCD. Our turbidity and fluorescence microscopy data show that Ser-to-Asp substitutions at residues S403, S404, S409 and S410 alter the LLPS behavior of TDP-43 LCD. In particular, in contrast to the unmodified protein, the phosphomimetic variants display a biphasic dependence on salt concentration. Through coarse-grained modeling, we find that this biphasic salt dependence is derived from an altered mechanism of phase separation, in which LLPS-driving short-range intermolecular hydrophobic interactions are modulated by long-range attractive electrostatic interactions. Overall, this in vitro and in silico study provides a physiochemical foundation for understanding the impact of pathologically-relevant C-terminal phosphorylation on the LLPS of the TDP-43 in a more complex cellular environment.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Brandon Shipley
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, United States
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States
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Haider R, Penumutchu S, Boyko S, Surewicz WK. Phosphomimetic substitutions in TDP-43's transiently α-helical region suppress phase separation. Biophys J 2024; 123:361-373. [PMID: 38178578 PMCID: PMC10870169 DOI: 10.1016/j.bpj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/10/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024] Open
Abstract
Phosphorylated TAR DNA-binding protein of 43 kDa (TDP-43) is present within the aggregates of several age-related neurodegenerative disorders, such as amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer's disease, to the point that the presence of phosphorylated TDP-43 is considered a hallmark of some of these diseases. The majority of known TDP-43 phosphorylation sites detected in amyotrophic lateral sclerosis and frontotemporal lobar degeneration patients is located in the low-complexity domain (LCD), the same domain that has been shown to be critical for TDP-43 liquid-liquid phase separation (LLPS). However, the effect of these LCD phosphorylation sites on TDP-43 LLPS has been largely unexplored, and any work that has been done has mainly focused on sites near the C-terminal end of the LCD. Here, we used a phosphomimetic approach to explore the impact of phosphorylation at residues S332 and S333, sites located within the transiently α-helical region of TDP-43 that have been observed to be phosphorylated in disease, on protein LLPS. Our turbidimetry and fluorescence microscopy data demonstrate that these phosphomimetic substitutions greatly suppress LLPS, and solution NMR data strongly suggest that this effect is at least in part due to the loss of α-helical propensity of the phosphomimetic protein variant. We also show that the S332D and S333D substitutions slow TDP-43 LCD droplet aging and fibrillation of the protein. Overall, these findings provide a biophysical basis for understanding the effect of phosphorylation within the transiently α-helical region of TDP-43 LCD on protein LLPS and fibrillation, suggesting that phosphorylation at residues 332 and 333 is not necessarily directly related to the pathogenic process.
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Affiliation(s)
- Raza Haider
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Srinivasa Penumutchu
- Northeast Ohio High Field NMR Facility, Case Western Reserve University, Cleveland, Ohio
| | - Solomiia Boyko
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio.
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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TDP-43 pathology: from noxious assembly to therapeutic removal. Prog Neurobiol 2022; 211:102229. [DOI: 10.1016/j.pneurobio.2022.102229] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
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Eck RJ, Kraemer BC, Liachko NF. Regulation of TDP-43 phosphorylation in aging and disease. GeroScience 2021; 43:1605-1614. [PMID: 34032984 PMCID: PMC8492835 DOI: 10.1007/s11357-021-00383-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/06/2021] [Indexed: 12/20/2022] Open
Abstract
Insoluble inclusions of phosphorylated TDP-43 occur in disease-affected neurons of most patients with amyotrophic lateral sclerosis (ALS) and about half of patients with frontotemporal lobar degeneration (FTLD-TDP). Phosphorylated TDP-43 potentiates a number of neurotoxic effects including reduced liquid-liquid phase separation dynamicity, changes in splicing, cytoplasmic mislocalization, and aggregation. Accumulating evidence suggests a balance of kinase and phosphatase activities control TDP-43 phosphorylation. Dysregulation of these processes may lead to an increase in phosphorylated TDP-43, ultimately contributing to neurotoxicity and neurodegeneration in disease. Here we summarize the evolving understanding of major regulators of TDP-43 phosphorylation as well as downstream consequences of their activities. Interventions restoring kinase and phosphatase balance may be a generalizable therapeutic strategy for all TDP-43 proteinopathies including ALS and FTLD-TDP.
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Affiliation(s)
- Randall J Eck
- Neuroscience Graduate Program, University of Washington, Seattle, WA, 98195, USA.,Geriatric Research Education and Clinical Center, Seattle Veterans Affairs Puget Sound Health Care System, 1660 South Columbian Way, Seattle, WA, 98108, USA
| | - Brian C Kraemer
- Neuroscience Graduate Program, University of Washington, Seattle, WA, 98195, USA.,Geriatric Research Education and Clinical Center, Seattle Veterans Affairs Puget Sound Health Care System, 1660 South Columbian Way, Seattle, WA, 98108, USA.,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA.,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98104, USA
| | - Nicole F Liachko
- Geriatric Research Education and Clinical Center, Seattle Veterans Affairs Puget Sound Health Care System, 1660 South Columbian Way, Seattle, WA, 98108, USA. .,Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.
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