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Bajdzienko J, Bremm A. Mammalian pexophagy at a glance. J Cell Sci 2024; 137:jcs259775. [PMID: 38752931 PMCID: PMC11166455 DOI: 10.1242/jcs.259775] [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] [Indexed: 05/21/2024] Open
Abstract
Peroxisomes are highly plastic organelles that are involved in several metabolic processes, including fatty acid oxidation, ether lipid synthesis and redox homeostasis. Their abundance and activity are dynamically regulated in response to nutrient availability and cellular stress. Damaged or superfluous peroxisomes are removed mainly by pexophagy, the selective autophagy of peroxisomes induced by ubiquitylation of peroxisomal membrane proteins or ubiquitin-independent processes. Dysregulated pexophagy impairs peroxisome homeostasis and has been linked to the development of various human diseases. Despite many recent insights into mammalian pexophagy, our understanding of this process is still limited compared to our understanding of pexophagy in yeast. In this Cell Science at a Glance article and the accompanying poster, we summarize current knowledge on the control of mammalian pexophagy and highlight which aspects require further attention. We also discuss the role of ubiquitylation in pexophagy and describe the ubiquitin machinery involved in regulating signals for the recruitment of phagophores to peroxisomes.
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Affiliation(s)
- Justyna Bajdzienko
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Anja Bremm
- Goethe University Frankfurt,Medical Faculty,Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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2
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Okarmus J, Agergaard JB, Stummann TC, Haukedal H, Ambjørn M, Freude KK, Fog K, Meyer M. USP30 inhibition induces mitophagy and reduces oxidative stress in parkin-deficient human neurons. Cell Death Dis 2024; 15:52. [PMID: 38225227 PMCID: PMC10789816 DOI: 10.1038/s41419-024-06439-6] [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: 12/08/2022] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024]
Abstract
Ubiquitination of mitochondrial proteins plays an important role in the cellular regulation of mitophagy. The E3 ubiquitin ligase parkin (encoded by PARK2) and the ubiquitin-specific protease 30 (USP30) have both been reported to regulate the ubiquitination of outer mitochondrial proteins and thereby mitophagy. Loss of E3 ligase activity is thought to be pathogenic in both sporadic and inherited Parkinson's disease (PD), with loss-of-function mutations in PARK2 being the most frequent cause of autosomal recessive PD. The aim of the present study was to evaluate whether mitophagy induced by USP30 inhibition provides a functional rescue in isogenic human induced pluripotent stem cell-derived dopaminergic neurons with and without PARK2 knockout (KO). Our data show that healthy neurons responded to CCCP-induced mitochondrial damage by clearing the impaired mitochondria and that this process was accelerated by USP30 inhibition. Parkin-deficient neurons showed an impaired mitophagic response to the CCCP challenge, although mitochondrial ubiquitination was enhanced. USP30 inhibition promoted mitophagy in PARK2 KO neurons, independently of whether left in basal conditions or treated with CCCP. In PARK2 KO, as in control neurons, USP30 inhibition balanced oxidative stress levels by reducing excessive production of reactive oxygen species. Interestingly, non-dopaminergic neurons were the main driver of the beneficial effects of USP30 inhibition. Our findings demonstrate that USP30 inhibition is a promising approach to boost mitophagy and improve cellular health, also in parkin-deficient cells, and support the potential relevance of USP30 inhibitors as a novel therapeutic approach in diseases with a need to combat neuronal stress mediated by impaired mitochondria.
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Affiliation(s)
- Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløws Vej 21, 5000, Odense C, Denmark
| | - Jette Bach Agergaard
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløws Vej 21, 5000, Odense C, Denmark
| | - Tina C Stummann
- Neuroscience, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - Henriette Haukedal
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegaardsvej 7, 1870, Frederiksberg C, Denmark
| | - Malene Ambjørn
- Neuroscience, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - Kristine K Freude
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegaardsvej 7, 1870, Frederiksberg C, Denmark
| | - Karina Fog
- Neuroscience, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, J.B. Winsløws Vej 21, 5000, Odense C, Denmark.
- Department of Neurology, Odense University Hospital, J.B. Winsløws Vej 4, 5000, Odense C, Denmark.
- BRIDGE-Brain Research Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000, Odense C, Denmark.
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3
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Fang TSZ, Sun Y, Pearce AC, Eleuteri S, Kemp M, Luckhurst CA, Williams R, Mills R, Almond S, Burzynski L, Márkus NM, Lelliott CJ, Karp NA, Adams DJ, Jackson SP, Zhao JF, Ganley IG, Thompson PW, Balmus G, Simon DK. Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model. Nat Commun 2023; 14:7295. [PMID: 37957154 PMCID: PMC10643470 DOI: 10.1038/s41467-023-42876-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Mutations in SNCA, the gene encoding α-synuclein (αSyn), cause familial Parkinson's disease (PD) and aberrant αSyn is a key pathological hallmark of idiopathic PD. This α-synucleinopathy leads to mitochondrial dysfunction, which may drive dopaminergic neurodegeneration. PARKIN and PINK1, mutated in autosomal recessive PD, regulate the preferential autophagic clearance of dysfunctional mitochondria ("mitophagy") by inducing ubiquitylation of mitochondrial proteins, a process counteracted by deubiquitylation via USP30. Here we show that loss of USP30 in Usp30 knockout mice protects against behavioral deficits and leads to increased mitophagy, decreased phospho-S129 αSyn, and attenuation of SN dopaminergic neuronal loss induced by αSyn. These observations were recapitulated with a potent, selective, brain-penetrant USP30 inhibitor, MTX115325, with good drug-like properties. These data strongly support further study of USP30 inhibition as a potential disease-modifying therapy for PD.
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Affiliation(s)
- Tracy-Shi Zhang Fang
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Yu Sun
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH, UK
| | - Andrew C Pearce
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Simona Eleuteri
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Mark Kemp
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Christopher A Luckhurst
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Rachel Williams
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Ross Mills
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Sarah Almond
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Laura Burzynski
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Nóra M Márkus
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | | | | | | | - Stephen P Jackson
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0RE, UK
| | - Jin-Feng Zhao
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Paul W Thompson
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK.
| | - Gabriel Balmus
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, 400191, Cluj-Napoca, Romania.
| | - David K Simon
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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4
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Waters CS, Angenent SB, Altschuler SJ, Wu LF. A PINK1 input threshold arises from positive feedback in the PINK1/Parkin mitophagy decision circuit. Cell Rep 2023; 42:113260. [PMID: 37851575 PMCID: PMC10668033 DOI: 10.1016/j.celrep.2023.113260] [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: 11/11/2022] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Mechanisms that prevent accidental activation of the PINK1/Parkin mitophagy circuit on healthy mitochondria are poorly understood. On the surface of damaged mitochondria, PINK1 accumulates and acts as the input signal to a positive feedback loop of Parkin recruitment, which in turn promotes mitochondrial degradation via mitophagy. However, PINK1 is also present on healthy mitochondria, where it could errantly recruit Parkin and thereby activate this positive feedback loop. Here, we explore emergent properties of the PINK1/Parkin circuit by quantifying the relationship between mitochondrial PINK1 concentrations and Parkin recruitment dynamics. We find that Parkin is recruited to mitochondria only if PINK1 levels exceed a threshold and then only after a delay that is inversely proportional to PINK1 levels. Furthermore, these two regulatory properties arise from the input-coupled positive feedback topology of the PINK1/Parkin circuit. These results outline an intrinsic mechanism by which the PINK1/Parkin circuit can avoid errant activation on healthy mitochondria.
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Affiliation(s)
- Christopher S Waters
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sigurd B Angenent
- Mathematics Department, University of Wisconsin Madison, Madison, WI 53706, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
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5
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Clancy A, Rusilowicz-Jones EV, Wallace I, Swatek KN, Urbé S, Clague MJ. ISGylation-independent protection of cell growth by USP18 following interferon stimulation. Biochem J 2023; 480:1571-1581. [PMID: 37756534 PMCID: PMC10586769 DOI: 10.1042/bcj20230301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
Type 1 interferon stimulation highly up-regulates all elements of a ubiquitin-like conjugation system that leads to ISGylation of target proteins. An ISG15-specific member of the deubiquitylase family, USP18, is up-regulated in a co-ordinated manner. USP18 can also provide a negative feedback by inhibiting JAK-STAT signalling through protein interactions independently of DUB activity. Here, we provide an acute example of this phenomenon, whereby the early expression of USP18, post-interferon treatment of HCT116 colon cancer cells is sufficient to fully suppress the expression of the ISG15 E1 enzyme, UBA7. Stimulation of lung adenocarcinoma A549 cells with interferon reduces their growth rate but they remain viable. In contrast, A549 USP18 knock-out cells show similar growth characteristics under basal conditions, but upon interferon stimulation, a profound inhibition of cell growth is observed. We show that this contingency on USP18 is independent of ISGylation, suggesting non-catalytic functions are required for viability. We also demonstrate that global deISGylation kinetics are very slow compared with deubiquitylation. This is not influenced by USP18 expression, suggesting that enhanced ISGylation in USP18 KO cells reflects increased conjugating activity.
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Affiliation(s)
- Anne Clancy
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Emma V. Rusilowicz-Jones
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Iona Wallace
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Kirby N. Swatek
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Sylvie Urbé
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Michael J. Clague
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
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6
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Suresh K, Mattern M, Goldberg MS, Butt TR. The Ubiquitin Proteasome System as a Therapeutic Area in Parkinson's Disease. Neuromolecular Med 2023; 25:313-329. [PMID: 36739586 DOI: 10.1007/s12017-023-08738-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/28/2023] [Indexed: 02/06/2023]
Abstract
Parkinson's disease (PD) is the most common neurodegenerative movement disorder. There are no available therapeutics that slow or halt the progressive loss of dopamine-producing neurons, which underlies the primary clinical symptoms. Currently approved PD drugs can provide symptomatic relief by increasing brain dopamine content or activity; however, the alleviation is temporary, and the effectiveness diminishes with the inevitable progression of neurodegeneration. Discovery and development of disease-modifying neuroprotective therapies has been hampered by insufficient understanding of the root cause of PD-related neurodegeneration. The etiology of PD involves a combination of genetic and environmental factors. Although a single cause has yet to emerge, genetic, cell biological and neuropathological evidence implicates mitochondrial dysfunction and protein aggregation. Postmortem PD brains show pathognomonic Lewy body intraneuronal inclusions composed of aggregated α-synuclein, indicative of failure to degrade misfolded protein. Mutations in the genes that code for α-synuclein, as well as the E3 ubiquitin ligase Parkin, cause rare inherited forms of PD. While many ubiquitin ligases label proteins with ubiquitin chains to mark proteins for degradation by the proteasome, Parkin has been shown to mark dysfunctional mitochondria for degradation by mitophagy. The ubiquitin proteasome system participates in several aspects of the cell's response to mitochondrial damage, affording numerous therapeutic opportunities to augment mitophagy and potentially stop PD progression. This review examines the role and therapeutic potential of such UPS modulators, exemplified by both ubiquitinating and deubiquitinating enzymes.
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Affiliation(s)
- Kumar Suresh
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA.
| | - Michael Mattern
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA
| | - Matthew S Goldberg
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Center for Neurodegeneration and Experimental Therapeutics, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tauseef R Butt
- Progenra Inc., 271A Great Valley Parkway, Malvern, PA, 19355, USA
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7
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Dong Y, Zhuang XX, Wang YT, Tan J, Feng D, Li M, Zhong Q, Song Z, Shen HM, Fang EF, Lu JH. Chemical mitophagy modulators: Drug development strategies and novel regulatory mechanisms. Pharmacol Res 2023; 194:106835. [PMID: 37348691 DOI: 10.1016/j.phrs.2023.106835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Maintaining mitochondrial homeostasis is a potential therapeutic strategy for various diseases, including neurodegenerative diseases, cardiovascular diseases, metabolic disorders, and cancer. Selective degradation of mitochondria by autophagy (mitophagy) is a fundamental mitochondrial quality control mechanism conserved from yeast to humans. Indeed, small-molecule modulators of mitophagy are valuable pharmaceutical tools that can be used to dissect complex biological processes and turn them into potential drugs. In the past few years, pharmacological regulation of mitophagy has shown promising therapeutic efficacy in various disease models. However, with the increasing number of chemical mitophagy modulator studies, frequent methodological flaws can be observed, leading some studies to draw unreliable or misleading conclusions. This review attempts (a) to summarize the molecular mechanisms of mitophagy; (b) to propose a Mitophagy Modulator Characterization System (MMCS); (c) to perform a comprehensive analysis of methods used to characterize mitophagy modulators, covering publications over the past 20 years; (d) to provide novel targets for pharmacological intervention of mitophagy. We believe this review will provide a panorama of current research on chemical mitophagy modulators and promote the development of safe and robust mitophagy modulators with therapeutic potential by introducing high methodological standards.
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Affiliation(s)
- Yu Dong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macau
| | - Xu-Xu Zhuang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macau
| | - Yi-Ting Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macau
| | - Jieqiong Tan
- Center for medical genetics, Central South University, Changsha 410031, Hunan, China
| | - Du Feng
- Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, College of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, Guangdong, China
| | - Min Li
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, 999077, Hong Kong Special Administrative Region
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, Hubei, China
| | - Han-Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, 999078, Macau
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway
| | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macau.
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O'Brien DP, Jones HBL, Guenther F, Murphy EJ, England KS, Vendrell I, Anderson M, Brennan PE, Davis JB, Pinto-Fernández A, Turnbull AP, Kessler BM. Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides. Mol Cell Proteomics 2023; 22:100609. [PMID: 37385347 PMCID: PMC10400906 DOI: 10.1016/j.mcpro.2023.100609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/07/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
Dampening functional levels of the mitochondrial deubiquitylating enzyme Ubiquitin-specific protease 30 (USP30) has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson's Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria, which is inherent to both familial and sporadic forms of the disease. Small-molecule inhibitors targeting USP30 are currently in development, but little is known about their precise nature of binding to the protein. We have integrated biochemical and structural approaches to gain novel mechanistic insights into USP30 inhibition by a small-molecule benzosulfonamide-containing compound, USP30inh. Activity-based protein profiling mass spectrometry confirmed target engagement, high selectivity, and potency of USP30inh for USP30 against 49 other deubiquitylating enzymes in a neuroblastoma cell line. In vitro characterization of USP30inh enzyme kinetics inferred slow and tight binding behavior, which is comparable with features of covalent modification of USP30. Finally, we blended hydrogen-deuterium exchange mass spectrometry and computational docking to elucidate the molecular architecture and geometry of USP30 complex formation with USP30inh, identifying structural rearrangements at the cleft of the USP30 thumb and palm subdomains. These studies suggest that USP30inh binds to this thumb-palm cleft, which guides the ubiquitin C terminus into the active site, thereby preventing ubiquitin binding and isopeptide bond cleavage, and confirming its importance in the inhibitory process. Our data will pave the way for the design and development of next-generation inhibitors targeting USP30 and associated deubiquitinylases.
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Affiliation(s)
- Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
| | - Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Franziska Guenther
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Emma J Murphy
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Katherine S England
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Paul E Brennan
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - John B Davis
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
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9
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Rocha E, Chamoli M, Chinta SJ, Andersen JK, Wallis R, Bezard E, Goldberg M, Greenamyre T, Hirst W, Kuan WL, Kirik D, Niedernhofer L, Rappley I, Padmanabhan S, Trudeau LE, Spillantini M, Scott S, Studer L, Bellantuono I, Mortiboys H. Aging, Parkinson's Disease, and Models: What Are the Challenges? AGING BIOLOGY 2023; 1:e20230010. [PMID: 38978807 PMCID: PMC11230631 DOI: 10.59368/agingbio.20230010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Parkinson's disease (PD) is a chronic, neurodegenerative condition characterized by motor symptoms such as bradykinesia, rigidity, and tremor, alongside multiple nonmotor symptoms. The appearance of motor symptoms is linked to progressive dopaminergic neuron loss within the substantia nigra. PD incidence increases sharply with age, suggesting a strong association between mechanisms driving biological aging and the development and progression of PD. However, the role of aging in the pathogenesis of PD remains understudied. Numerous models of PD, including cell models, toxin-induced models, and genetic models in rodents and nonhuman primates (NHPs), reproduce different aspects of PD, but preclinical studies of PD rarely incorporate age as a factor. Studies using patient neurons derived from stem cells via reprogramming methods retain some aging features, but their characterization, particularly of aging markers and reproducibility of neuron type, is suboptimal. Investigation of age-related changes in PD using animal models indicates an association, but this is likely in conjunction with other disease drivers. The biggest barrier to drawing firm conclusions is that each model lacks full characterization and appropriate time-course assessments. There is a need to systematically investigate whether aging increases the susceptibility of mouse, rat, and NHP models to develop PD and understand the role of cell models. We propose that a significant investment in time and resources, together with the coordination and sharing of resources, knowledge, and data, is required to accelerate progress in understanding the role of biological aging in PD development and improve the reliability of models to test interventions.
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Affiliation(s)
- Emily Rocha
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Shankar J Chinta
- Buck Institute for Research on Aging, Novato, CA, USA
- Touro University California, College of Pharmacy, Vallejo, CA, USA
| | | | - Ruby Wallis
- The Healthy Lifespan Institute, Sheffield, United Kingdom
| | | | | | - Tim Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - We-Li Kuan
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Deniz Kirik
- Brain Repair and Imaging in Neural Systems (BRAINS), Lund, Sweden
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA
| | - Irit Rappley
- Recursion pharmaceuticals, Salt Lake City, UT, USA
| | | | - Louis-Eric Trudeau
- Department of pharmacology and physiology, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Maria Spillantini
- Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA
| | - Ilaria Bellantuono
- The Healthy Lifespan Institute, Sheffield, United Kingdom
- Department of Oncology and Metabolism, The Medical School, Sheffield, United Kingdom
| | - Heather Mortiboys
- The Healthy Lifespan Institute, Sheffield, United Kingdom
- Department of Neuroscience, Sheffield Institute of Translational Neuroscience (SITraN), University of Sheffield, Sheffield, United Kindgom
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10
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Clague MJ. Michael J Clague: mitophagy, pexophagy, & metabolism. Life Sci Alliance 2023; 6:e202302102. [PMID: 37100444 PMCID: PMC10133867 DOI: 10.26508/lsa.202302102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
Michael J Clague is a Professor of Molecular and Cellular Physiology at The University of Liverpool, Institute of Systems, Molecular and Integrative Biology. We asked him about his recent paper published in Life Science Alliance (LSA) and his experience in science thus far.
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Affiliation(s)
- Michael J Clague
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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11
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Barone FG, Urbé S, Clague MJ. Segregation of pathways leading to pexophagy. Life Sci Alliance 2023; 6:e202201825. [PMID: 36810161 PMCID: PMC9944197 DOI: 10.26508/lsa.202201825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Peroxisomes are organelles with key roles in metabolism including long-chain fatty acid production. Their metabolic functions overlap and interconnect with those of mitochondria, with which they share an overlapping but distinct proteome. Both organelles are degraded by selective autophagy processes termed pexophagy and mitophagy. Although mitophagy has received intense attention, the pathways linked to pexophagy and associated tools are less well developed. We have identified the neddylation inhibitor MLN4924 as a potent activator of pexophagy and show that this is mediated by the HIF1α-dependent up-regulation of BNIP3L/NIX, a known adaptor for mitophagy. We show that this pathway is distinct from pexophagy induced by the USP30 deubiquitylase inhibitor CMPD-39, for which we identify the adaptor NBR1 as a central player. Our work suggests a level of complexity to the regulation of peroxisome turnover that includes the capacity to coordinate with mitophagy, via NIX, which acts as a rheostat for both processes.
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Affiliation(s)
- Francesco G Barone
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michael J Clague
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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12
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Tufi R, Clark EH, Hoshikawa T, Tsagkaraki C, Stanley J, Takeda K, Staddon JM, Briston T. High-content phenotypic screen to identify small molecule enhancers of Parkin-dependent ubiquitination and mitophagy. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:73-87. [PMID: 36608804 DOI: 10.1016/j.slasd.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/13/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023]
Abstract
Mitochondrial dysfunction and aberrant mitochondrial homeostasis are key aspects of Parkinson's disease (PD) pathophysiology. Mutations in PINK1 and Parkin proteins lead to autosomal recessive PD, suggesting that defective mitochondrial clearance via mitophagy is key in PD etiology. Accelerating the identification and/or removal of dysfunctional mitochondria could therefore provide a disease-modifying approach to treatment. To that end, we performed a high-content phenotypic screen (HCS) of ∼125,000 small molecules to identify compounds that positively modulate mitochondrial accumulation of the PINK1-Parkin-dependent mitophagy initiation marker p-Ser65-Ub in Parkin haploinsufficiency (Parkin +/R275W) human fibroblasts. Following confirmatory counter-screening and orthogonal assays, we selected compounds of interest that enhance mitophagy-related biochemical and functional endpoints in patient-derived fibroblasts. Identification of inhibitors of the ubiquitin-specific peptidase and negative regulator of mitophagy USP30 within our hits further validated our approach. The compounds identified in this work provide a novel starting point for further investigation and optimization.
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Affiliation(s)
- Roberta Tufi
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Emily H Clark
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Tamaki Hoshikawa
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Christiana Tsagkaraki
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Jack Stanley
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Kunitoshi Takeda
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - James M Staddon
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Thomas Briston
- Neurology Innovation Centre, Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom.
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13
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Wilhelm LP, Zapata-Muñoz J, Villarejo-Zori B, Pellegrin S, Freire CM, Toye AM, Boya P, Ganley IG. BNIP3L/NIX regulates both mitophagy and pexophagy. EMBO J 2022; 41:e111115. [PMID: 36215693 PMCID: PMC9753467 DOI: 10.15252/embj.2022111115] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/15/2023] Open
Abstract
Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.
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Affiliation(s)
- Léa P Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Juan Zapata-Muñoz
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Beatriz Villarejo-Zori
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Stephanie Pellegrin
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | | | - Ashley M Toye
- School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Research Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Madrid, Spain
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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14
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Tsefou E, Ketteler R. Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin. Int J Mol Sci 2022; 23:12105. [PMID: 36292958 PMCID: PMC9603086 DOI: 10.3390/ijms232012105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
The quality control of mitochondria is critical for the survival of cells, and defects in the pathways required for this quality control can lead to severe disease. A key quality control mechanism in cells is mitophagy, which functions to remove damaged mitochondria under conditions of various stresses. Defective mitophagy can lead to a number of diseases including neurodegeneration. It has been proposed that an enhancement of mitophagy can improve cell survival, enhance neuronal function in neurodegeneration and extend health and lifespans. In this review, we highlight the role of deubiquitinating enzymes (DUBs) in the regulation of mitophagy. We summarise the current knowledge on DUBs that regulate mitophagy as drug targets and provide a list of small molecule inhibitors that are valuable tools for the further development of therapeutic strategies targeting the mitophagy pathway in neurodegeneration.
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Affiliation(s)
- Eliona Tsefou
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- UCL:Eisai Therapeutic Innovation Group, Translational Research Office, University College London, London W1T 7NF, UK
| | - Robin Ketteler
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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15
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Wang F, Gao Y, Zhou L, Chen J, Xie Z, Ye Z, Wang Y. USP30: Structure, Emerging Physiological Role, and Target Inhibition. Front Pharmacol 2022; 13:851654. [PMID: 35308234 PMCID: PMC8927814 DOI: 10.3389/fphar.2022.851654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/04/2022] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-specific protease 30 (USP30) is a deubiquitinating enzyme (DUB) belonging to the USP subfamily, which was found localized in the mitochondrial outer membrane and peroxisomes owing to its unique transmembrane domain. Structural study revealed that USP30 employed a unique catalytic triad and molecular architecture to preferentially cleave the Lys6 linked ubiquitin chains. USP30 plays an essential role in several cellular events, such as the PINK1/Parkin-mediated mitophagy, pexophagy, BAX/BAK-dependent apoptosis, and IKKβ–USP30–ACLY-regulated lipogenesis/tumorigenesis, and is tightly regulated by post-translational modification including phosphorylation and mono-ubiquitination. Dysregulation of USP30 is associated with a range of physiological disorders, such as neurodegenerative disease, hepatocellular carcinoma, pulmonary disorders, and peroxisome biogenesis disorders. Nowadays, scientists and many biopharmaceutical companies are making much effort to explore USP30 inhibitors including natural compounds, phenylalanine derivatives, N-cyano pyrrolidines, benzosulphonamide, and other compounds. For the treatment of pulmonary disorders, the study in Mission Therapeutics of USP30 inhibitor is already in the pre-clinical stage. In this review, we will summarize the current knowledge of the structure, regulation, emerging physiological role, and target inhibition of USP30, hoping to prompt further investigation and understanding of it.
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Bonam SR, Tranchant C, Muller S. Autophagy-Lysosomal Pathway as Potential Therapeutic Target in Parkinson's Disease. Cells 2021; 10:3547. [PMID: 34944054 PMCID: PMC8700067 DOI: 10.3390/cells10123547] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
Cellular quality control systems have gained much attention in recent decades. Among these, autophagy is a natural self-preservation mechanism that continuously eliminates toxic cellular components and acts as an anti-ageing process. It is vital for cell survival and to preserve homeostasis. Several cell-type-dependent canonical or non-canonical autophagy pathways have been reported showing varying degrees of selectivity with regard to the substrates targeted. Here, we provide an updated review of the autophagy machinery and discuss the role of various forms of autophagy in neurodegenerative diseases, with a particular focus on Parkinson's disease. We describe recent findings that have led to the proposal of therapeutic strategies targeting autophagy to alter the course of Parkinson's disease progression.
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Affiliation(s)
- Srinivasa Reddy Bonam
- Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Equipe-Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Christine Tranchant
- Service de Neurologie, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France;
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM-U964/CNRS-UMR7104/Université de Strasbourg, 67400 Illkirch, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67000 Strasbourg, France
| | - Sylviane Muller
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, 67000 Strasbourg, France
- CNRS and Strasbourg University, Unit Biotechnology and Cell Signaling/Strasbourg Drug Discovery and Development Institute (IMS), 67000 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), 67000 Strasbourg, France
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