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Ding L, Lu L, Zheng S, Zhang Z, Huang X, Ma R, Zhang M, Xu Z, Chen M, Guo Z, Zhu S, Gong J, Mao H, Zhang W, Xu P. Usp14 deficiency removes α-synuclein by regulating S100A8/A9 in Parkinson's disease. Cell Mol Life Sci 2024; 81:232. [PMID: 38780644 PMCID: PMC11116365 DOI: 10.1007/s00018-024-05246-8] [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: 02/15/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Ubiquitin-proteasome system dysfunction triggers α-synuclein aggregation, a hallmark of neurodegenerative diseases, such as Parkinson's disease (PD). However, the crosstalk between deubiquitinating enzyme (DUBs) and α-synuclein pathology remains unclear. In this study, we observed a decrease in the level of ubiquitin-specific protease 14 (USP14), a DUB, in the cerebrospinal fluid (CSF) of PD patients, particularly females. Moreover, CSF USP14 exhibited a dual correlation with α-synuclein in male and female PD patients. To investigate the impact of USP14 deficiency, we crossed USP14 heterozygous mouse (USP14+/-) with transgenic A53T PD mouse (A53T-Tg) or injected adeno-associated virus (AAV) carrying human α-synuclein (AAV-hα-Syn) in USP14+/- mice. We found that Usp14 deficiency improved the behavioral abnormities and pathological α-synuclein deposition in female A53T-Tg or AAV-hα-Syn mice. Additionally, Usp14 inactivation attenuates the pro-inflammatory response in female AAV-hα-Syn mice, whereas Usp14 inactivation demonstrated opposite effects in male AAV-hα-Syn mice. Mechanistically, the heterodimeric protein S100A8/A9 may be the downstream target of Usp14 deficiency in female mouse models of α-synucleinopathies. Furthermore, upregulated S100A8/A9 was responsible for α-synuclein degradation by autophagy and the suppression of the pro-inflammatory response in microglia after Usp14 knockdown. Consequently, our study suggests that USP14 could serve as a novel therapeutic target in PD.
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Affiliation(s)
- Liuyan Ding
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lin Lu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shaohui Zheng
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhiling Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingting Huang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Runfang Ma
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Mengran Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Zongtang Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Minshan Chen
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhimei Guo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Si Zhu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junwei Gong
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hengxu Mao
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenlong Zhang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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2
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Kandel R, Jung J, Neal S. Proteotoxic stress and the ubiquitin proteasome system. Semin Cell Dev Biol 2024; 156:107-120. [PMID: 37734998 PMCID: PMC10807858 DOI: 10.1016/j.semcdb.2023.08.002] [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: 04/18/2023] [Revised: 08/01/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.
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Affiliation(s)
- Rachel Kandel
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Jasmine Jung
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Sonya Neal
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, United States; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Kenny S, Lai CH, Chiang TS, Brown K, Hewitt CS, Krabill AD, Chang HT, Wang YS, Flaherty DP, Hsu STD, Das C. Altered Protein Dynamics and a More Reactive Catalytic Cysteine in a Neurodegeneration-associated UCHL1 Mutant. J Mol Biol 2024; 436:168438. [PMID: 38185323 DOI: 10.1016/j.jmb.2024.168438] [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: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
A mutant of ubiquitin C-terminal hydrolase L1 (UCHL1) detected in early-onset neurodegenerative patients, UCHL1R178Q, showed higher catalytic activity than wild-type UCHL1 (UCHL1WT). Lying within the active-site pocket, the arginine is part of an interaction network that holds the catalytic histidine in an inactive arrangement. However, the structural basis and mechanism of enzymatic activation upon glutamine substitution was not understood. We combined X-ray crystallography, protein nuclear magnetic resonance (NMR) analysis, enzyme kinetics, covalent inhibition analysis, and biophysical measurements to delineate activating factors in the mutant. While the crystal structure of UCHL1R178Q showed nearly the same arrangement of the catalytic residues and active-site pocket, the mutation caused extensive alteration in the chemical environment and dynamics of more than 30 residues, some as far as 15 Å away from the site of mutation. Significant broadening of backbone amide resonances in the HSQC spectra indicates considerable backbone dynamics changes in several residues, in agreement with solution small-angle X-ray scattering (SAXS) analyses which indicate an overall increase in protein flexibility. Enzyme kinetics show the activation is due to a kcat effect despite a slightly weakened substrate affinity. In line with this, the mutant shows a higher second-order rate constant (kinact/Ki) in a reaction with a substrate-derived irreversible inhibitor, Ub-VME, compared to the wild-type enzyme, an observation indicative of a more reactive catalytic cysteine in the mutant. Together, the observations underscore structural plasticity as a factor contributing to enzyme kinetic behavior which can be modulated through mutational effects.
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Affiliation(s)
- Sebastian Kenny
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Tsung-Sheng Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Kwame Brown
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chad S Hewitt
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Aaron D Krabill
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Hao-Ting Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States.
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Buneeva O, Medvedev A. Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson's Disease. Int J Mol Sci 2024; 25:1303. [PMID: 38279302 PMCID: PMC10816476 DOI: 10.3390/ijms25021303] [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: 12/25/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson's disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein-protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein-protein interactions, which still need better characterization.
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Affiliation(s)
| | - Alexei Medvedev
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia;
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5
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Thangavel R, Kaur H, Dubova I, Selvakumar GP, Ahmed ME, Raikwar SP, Govindarajan R, Kempuraj D. Parkinson's Disease Dementia Patients: Expression of Glia Maturation Factor in the Brain. Int J Mol Sci 2024; 25:1182. [PMID: 38256254 PMCID: PMC11154259 DOI: 10.3390/ijms25021182] [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: 12/09/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Parkinson's disease (PD) is the second most common progressive neurodegenerative disease characterized by the presence of dopaminergic neuronal loss and motor disorders. PD dementia (PDD) is a cognitive disorder that affects many PD patients. We have previously demonstrated the proinflammatory role of the glia maturation factor (GMF) in neuroinflammation and neurodegeneration in AD, PD, traumatic brain injury (TBI), and experimental autoimmune encephalomyelitis (EAE) in human brains and animal models. The purpose of this study was to investigate the expression of the GMF in the human PDD brain. We analyzed the expression pattern of the GMF protein in conjunction with amyloid plaques (APs) and neurofibrillary tangles (NFTs) in the substantia nigra (SN) and striatum of PDD brains using immunostaining. We detected a large number of GMF-positive glial fibrillary acidic protein (GFAP) reactive astrocytes, especially abundant in areas with degenerating dopaminergic neurons within the SN and striatum in PDD. Additionally, we observed excess levels of GMF in glial cells in the vicinity of APs, and NFTs in the SN and striatum of PDD and non-PDD patients. We found that the majority of GMF-positive immunoreactive glial cells were co-localized with GFAP-reactive astrocytes. Our findings suggest that the GMF may be involved in the pathogenesis of PDD.
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Lee D, Yoon E, Ham SJ, Lee K, Jang H, Woo D, Lee DH, Kim S, Choi S, Chung J. Diabetic sensory neuropathy and insulin resistance are induced by loss of UCHL1 in Drosophila. Nat Commun 2024; 15:468. [PMID: 38212312 PMCID: PMC10784524 DOI: 10.1038/s41467-024-44747-9] [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: 01/01/2023] [Accepted: 12/29/2023] [Indexed: 01/13/2024] Open
Abstract
Diabetic sensory neuropathy (DSN) is one of the most common complications of type 2 diabetes (T2D), however the molecular mechanistic association between T2D and DSN remains elusive. Here we identify ubiquitin C-terminal hydrolase L1 (UCHL1), a deubiquitinase highly expressed in neurons, as a key molecule underlying T2D and DSN. Genetic ablation of UCHL1 leads to neuronal insulin resistance and T2D-related symptoms in Drosophila. Furthermore, loss of UCHL1 induces DSN-like phenotypes, including numbness to external noxious stimuli and axonal degeneration of sensory neurons in flies' legs. Conversely, UCHL1 overexpression improves DSN-like defects of T2D model flies. UCHL1 governs insulin signaling by deubiquitinating insulin receptor substrate 1 (IRS1) and antagonizes an E3 ligase of IRS1, Cullin 1 (CUL1). Consistent with these results, genetic and pharmacological suppression of CUL1 activity rescues T2D- and DSN-associated phenotypes. Therefore, our findings suggest a complete set of genetic factors explaining T2D and DSN, together with potential remedies for the diseases.
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Affiliation(s)
- Daewon Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Eunju Yoon
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Su Jin Ham
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kunwoo Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Hansaem Jang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Daihn Woo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Da Hyun Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sehyeon Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sekyu Choi
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
| | - Jongkyeong Chung
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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7
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Peggion C, Barazzuol L, Poggio E, Calì T, Brini M. Ca 2+ signalling: A common language for organelles crosstalk in Parkinson's disease. Cell Calcium 2023; 115:102783. [PMID: 37597300 DOI: 10.1016/j.ceca.2023.102783] [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: 06/13/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/21/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease caused by multifactorial pathogenic mechanisms. Familial PD is linked with genetic mutations in genes whose products are either associated with mitochondrial function or endo-lysosomal pathways. Of note, mitochondria are essential to sustain high energy demanding synaptic activity of neurons and alterations in mitochondrial Ca2+ signaling have been proposed as causal events for neurodegenerative process, although the mechanisms responsible for the selective loss of specific neuronal populations in the different neurodegenerative diseases is still not clear. Here, we specifically discuss the importance of a correct mitochondrial communication with the other organelles occurring at regions where their membranes become in close contact. We discuss the nature and the role of contact sites that mitochondria establish with ER, lysosomes, and peroxisomes, and how PD related proteins participate in the regulation/dysregulation of the tethering complexes. Unravelling molecular details of mitochondria tethering could contribute to identify specific therapeutic targets and develop new strategies to counteract the progression of the disease.
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Affiliation(s)
| | | | - Elena Poggio
- Department of Biology (DIBIO), University of Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences (DSB), University of Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Italy; Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
| | - Marisa Brini
- Department of Biology (DIBIO), University of Padova, Italy; Study Center for Neurodegeneration (CESNE), University of Padova, Italy.
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Fishman-Jacob T, Youdim MBH. A sporadic Parkinson's disease model via silencing of the ubiquitin-proteasome/E3 ligase component, SKP1A. J Neural Transm (Vienna) 2023:10.1007/s00702-023-02687-6. [PMID: 37644186 DOI: 10.1007/s00702-023-02687-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Our and other's laboratory microarray-derived transcriptomic studies in human PD substantia nigra pars compacta (SNpc) samples have opened an avenue to concentrate on potential gene intersections or cross-talks along the dopaminergic (DAergic) neurodegenerative cascade in sporadic PD (SPD). One emerging gene candidate identified was SKP1A (p19, S-phase kinase-associated protein 1A), found significantly decreased in the SNpc as confirmed later at the protein level. SKP1 is part of the Skp1, Cullin 1, F-box protein (SCF) complex, the largest known class of sophisticated ubiquitin-proteasome/E3-ligases and was found to directly interact with FBXO7, a gene defective in PARK15-linked PD. This finding has led us to the hypothesis that a targeted site-specific reduction of Skp1 levels in DAergic neuronal cell culture and animal systems may result in a progressive loss of DAergic neurons and hopefully recreate motor disabilities in animals. The second premise considers the possibility that both intrinsic and extrinsic factors (e.g., manipulation of selected genes and mitochondria impairing toxins), alleged to play central roles in DAergic neurodegeneration in PD, may act in concert as modifiers of Skp1 deficiency-induced phenotype alterations ('dual-hit' hypothesis of neurodegeneration). To examine a possible role of Skp1 in DAergic phenotype, we have initially knocked down the expression of SKP1A gene in an embryonic mouse SN-derived cell line (SN4741) with short hairpin RNA (shRNA) lentiviruses (LVs). The deficiency of SKP1A closely recapitulated cardinal features of the DAergic pathology of human PD, such as decreased expression of DAergic phenotypic markers and cell cycle aberrations. Furthermore, the knocked down cells displayed a lethal phenotype when induced to differentiate exhibiting proteinaceous round inclusion structures, which were almost identical in composition to human Lewy bodies, a hallmark of PD. These findings support a role for Skp1 in neuronal phenotype, survival, and differentiation. The identification of Skp1 as a key player in DAergic neuron function suggested that a targeted site-specific reduction of Skp1 levels in mice SNpc may result in a progressive loss of DAergic neurons and terminal projections in the striatum. The injected LV SKP1shRNA to mouse SN resulted in decreased expression of Skp1 protein levels within DAergic neurons and loss of tyrosine hydroxylase immunoreactivity (TH-IR) in both SNpc and striatum that was accompanied by time-dependent motor disabilities. The reduction of the vertical movements, that is rearing, may be reminiscent of the early occurrence of hypokinesia and axial, postural instability in PD. According to the 'dual-hit' hypothesis of neurodegenerative diseases, it is predicted that gene-gene and/or gene-environmental factors would act in concert or sequentially to propagate the pathological process of PD. Our findings are compatible with this conjecture showing that the genetic vulnerability caused by knock down of SKP1A renders DAergic SN4741 cells especially sensitive to genetic reduction of Aldh1 and exposure to the external stressors MPP+ and DA, which have been implicated in PD pathology. Future consideration should be given in manipulation SKP1A expression as therapeutic window, via its induction genetically or pharmacological, to prevent degeneration of the nigra striatal dopamine neurons, since UPS is defective.
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Affiliation(s)
- Tali Fishman-Jacob
- Youdim Pharmaceutical Ltd, New Northern Industrial Park, 1 Ha- Tsmikha St, Stern Building, Fl-3, P. O. Box 72, 2069207, Yokneam, Israel
| | - Moussa B H Youdim
- Youdim Pharmaceutical Ltd, New Northern Industrial Park, 1 Ha- Tsmikha St, Stern Building, Fl-3, P. O. Box 72, 2069207, Yokneam, Israel.
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Chandran A, Oliver HJ, Rochet JC. Role of NFE2L1 in the Regulation of Proteostasis: Implications for Aging and Neurodegenerative Diseases. BIOLOGY 2023; 12:1169. [PMID: 37759569 PMCID: PMC10525699 DOI: 10.3390/biology12091169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
A hallmark of aging and neurodegenerative diseases is a disruption of proteome homeostasis ("proteostasis") that is caused to a considerable extent by a decrease in the efficiency of protein degradation systems. The ubiquitin proteasome system (UPS) is the major cellular pathway involved in the clearance of small, short-lived proteins, including amyloidogenic proteins that form aggregates in neurodegenerative diseases. Age-dependent decreases in proteasome subunit expression coupled with the inhibition of proteasome function by aggregated UPS substrates result in a feedforward loop that accelerates disease progression. Nuclear factor erythroid 2- like 1 (NFE2L1) is a transcription factor primarily responsible for the proteasome inhibitor-induced "bounce-back effect" regulating the expression of proteasome subunits. NFE2L1 is localized to the endoplasmic reticulum (ER), where it is rapidly degraded under basal conditions by the ER-associated degradation (ERAD) pathway. Under conditions leading to proteasome impairment, NFE2L1 is cleaved and transported to the nucleus, where it binds to antioxidant response elements (AREs) in the promoter region of proteasome subunit genes, thereby stimulating their transcription. In this review, we summarize the role of UPS impairment in aging and neurodegenerative disease etiology and consider the potential benefit of enhancing NFE2L1 function as a strategy to upregulate proteasome function and alleviate pathology in neurodegenerative diseases.
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Affiliation(s)
- Aswathy Chandran
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Haley Jane Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
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10
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Dovonou A, Bolduc C, Soto Linan V, Gora C, Peralta Iii MR, Lévesque M. Animal models of Parkinson's disease: bridging the gap between disease hallmarks and research questions. Transl Neurodegener 2023; 12:36. [PMID: 37468944 PMCID: PMC10354932 DOI: 10.1186/s40035-023-00368-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor and non-motor symptoms. More than 200 years after its first clinical description, PD remains a serious affliction that affects a growing proportion of the population. Prevailing treatments only alleviate symptoms; there is still neither a cure that targets the neurodegenerative processes nor therapies that modify the course of the disease. Over the past decades, several animal models have been developed to study PD. Although no model precisely recapitulates the pathology, they still provide valuable information that contributes to our understanding of the disease and the limitations of our treatment options. This review comprehensively summarizes the different animal models available for Parkinson's research, with a focus on those induced by drugs, neurotoxins, pesticides, genetic alterations, α-synuclein inoculation, and viral vector injections. We highlight their characteristics and ability to reproduce PD-like phenotypes. It is essential to realize that the strengths and weaknesses of each model and the induction technique at our disposal are determined by the research question being asked. Our review, therefore, seeks to better aid researchers by ensuring a concrete discernment of classical and novel animal models in PD research.
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Affiliation(s)
- Axelle Dovonou
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Cyril Bolduc
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Victoria Soto Linan
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Charles Gora
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Modesto R Peralta Iii
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada
| | - Martin Lévesque
- CERVO Brain Research Centre, 2601, Chemin de la Canardière, Québec, QC, G1J 2G3, Canada.
- Department of Psychiatry and Neurosciences, Faculty of Medicine, Université Laval, Québec, QC, Canada.
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11
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Mi Z, Graham SH. Role of UCHL1 in the pathogenesis of neurodegenerative diseases and brain injury. Ageing Res Rev 2023; 86:101856. [PMID: 36681249 PMCID: PMC9992267 DOI: 10.1016/j.arr.2023.101856] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
UCHL1 is a multifunctional protein expressed at high concentrations in neurons in the brain and spinal cord. UCHL1 plays important roles in regulating the level of cellular free ubiquitin and redox state as well as the degradation of select proteins. This review focuses on the potential role of UCHL1 in the pathogenesis of neurodegenerative diseases and brain injury and recovery. Subjects addressed in the review include 1) Normal physiological functions of UCHL1. 2) Posttranslational modification sites and splice variants that alter the function of UCHL1 and mouse models with mutations and deletions of UCHL1. 3) The hypothesized role and pathogenic mechanisms of UCHL1 in neurodegenerative diseases and brain injury. 4) Potential therapeutic strategies targeting UCHL1 in these disorders.
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Affiliation(s)
- Zhiping Mi
- Departments of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States; Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA 15213, United States.
| | - Steven H Graham
- Departments of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States; Geriatric Research Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA 15213, United States.
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12
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Lim SM, Nahm M, Kim SH. Proteostasis and Ribostasis Impairment as Common Cell Death Mechanisms in Neurodegenerative Diseases. J Clin Neurol 2023; 19:101-114. [PMID: 36854331 PMCID: PMC9982182 DOI: 10.3988/jcn.2022.0379] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 03/02/2023] Open
Abstract
The cellular homeostasis of proteins (proteostasis) and RNA metabolism (ribostasis) are essential for maintaining both the structure and function of the brain. However, aging, cellular stress conditions, and genetic contributions cause disturbances in proteostasis and ribostasis that lead to protein misfolding, insoluble aggregate deposition, and abnormal ribonucleoprotein granule dynamics. In addition to neurons being primarily postmitotic, nondividing cells, they are more susceptible to the persistent accumulation of abnormal aggregates. Indeed, defects associated with the failure to maintain proteostasis and ribostasis are common pathogenic components of age-related neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Furthermore, the neuronal deposition of misfolded and aggregated proteins can cause both increased toxicity and impaired physiological function, which lead to neuronal dysfunction and cell death. There is recent evidence that irreversible liquid-liquid phase separation (LLPS) is responsible for the pathogenic aggregate formation of disease-related proteins, including tau, α-synuclein, and RNA-binding proteins, including transactive response DNA-binding protein 43, fused in sarcoma, and heterogeneous nuclear ribonucleoprotein A1. Investigations of LLPS and its control therefore suggest that chaperone/disaggregase, which reverse protein aggregation, are valuable therapeutic targets for effective treatments for neurological diseases. Here we review and discuss recent studies to highlight the importance of understanding the common cell death mechanisms of proteostasis and ribostasis in neurodegenerative diseases.
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Affiliation(s)
- Su Min Lim
- Cell Therapy Center and Department of Neurology, College of Medicine, Hanyang University, Seoul, Korea
| | - Minyeop Nahm
- Dementia Research Group, Korea Brain Research Institute, Daegu, Korea
| | - Seung Hyun Kim
- Cell Therapy Center and Department of Neurology, College of Medicine, Hanyang University, Seoul, Korea.
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13
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Shadrina MI, Slominsky PA. Genetic Architecture of Parkinson's Disease. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:417-433. [PMID: 37076287 DOI: 10.1134/s0006297923030100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/28/2023]
Abstract
Year 2022 marks 25 years since the first mutation in familial autosomal dominant Parkinson's disease was identified. Over the years, our understanding of the role of genetic factors in the pathogenesis of familial and idiopathic forms of Parkinson's disease has expanded significantly - a number of genes for the familial form of the disease have been identified, and DNA markers for an increased risk of developing its sporadic form have been found. But, despite all the success achieved, we are far from an accurate assessment of the contribution of genetic and, even more so, epigenetic factors to the disease development. The review summarizes the information accumulated to date on the genetic architecture of Parkinson's disease and formulates issues that need to be addressed, which are primarily related to the assessment of epigenetic factors in the disease pathogenesis.
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Affiliation(s)
- Maria I Shadrina
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
| | - Petr A Slominsky
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
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14
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Role of Deubiquitinases in Parkinson's Disease-Therapeutic Perspectives. Cells 2023; 12:cells12040651. [PMID: 36831318 PMCID: PMC9954239 DOI: 10.3390/cells12040651] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that has been associated with mitochondrial dysfunction, oxidative stress, and defects in mitophagy as well as α-synuclein-positive inclusions, termed Lewy bodies (LBs), which are a common pathological hallmark in PD. Mitophagy is a process that maintains cellular health by eliminating dysfunctional mitochondria, and it is triggered by ubiquitination of mitochondrial-associated proteins-e.g., through the PINK1/Parkin pathway-which results in engulfment by the autophagosome and degradation in lysosomes. Deubiquitinating enzymes (DUBs) can regulate this process at several levels by deubiquitinating mitochondrial substrates and other targets in the mitophagic pathway, such as Parkin. Moreover, DUBs can affect α-synuclein aggregation through regulation of degradative pathways, deubiquitination of α-synuclein itself, and/or via co-localization with α-synuclein in inclusions. DUBs with a known association to PD are described in this paper, along with their function. Of interest, DUBs could be useful as novel therapeutic targets against PD through regulation of PD-associated defects.
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15
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Wang X, Zhang N, Li M, Hong T, Meng W, Ouyang T. Ubiquitin C‑terminal hydrolase‑L1: A new cancer marker and therapeutic target with dual effects (Review). Oncol Lett 2023; 25:123. [PMID: 36844618 PMCID: PMC9950345 DOI: 10.3892/ol.2023.13709] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/08/2022] [Indexed: 02/11/2023] Open
Abstract
Ubiquitin C-terminal hydrolase-L1 (UCH-L1), a member of the lesser-known deubiquitinating enzyme family, has deubiquitinase and ubiquitin (Ub) ligase activity and the role of stabilizing Ub. UCH-L1 was first discovered in the brain and is associated with regulating cell differentiation, proliferation, transcriptional regulation and numerous other biological processes. UCH-L1 is predominantly expressed in the brain and serves a role in tumor promotion or inhibition. There is still controversy about the effect of UCH-L1 dysregulation in cancer and its mechanisms are unknown. Extensive research to investigate the mechanism of UCH-L1 in different types of cancer is key for the future treatment of UCH-L1-associated cancer. The present review details the molecular structure and function of UCH-L1. The role of UCH-L1 in different types of cancer is also summarized and how novel treatment targets provide a theoretical foundation in cancer research is discussed.
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Affiliation(s)
- Xiaowei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China,Department of The Second Clinical Medical College of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Na Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Meihua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Wei Meng
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China,Correspondence to: Dr Wei Meng or Dr Taohui Ouyang, Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi 330006, P.R. China, E-mail:
| | - Taohui Ouyang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China,Correspondence to: Dr Wei Meng or Dr Taohui Ouyang, Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, 17 Yongwai Street, Nanchang, Jiangxi 330006, P.R. China, E-mail:
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16
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Richter F, Stanojlovic M, Käufer C, Gericke B, Feja M. A Mouse Model to Test Novel Therapeutics for Parkinson's Disease: an Update on the Thy1-aSyn ("line 61") Mice. Neurotherapeutics 2023; 20:97-116. [PMID: 36715870 PMCID: PMC10119371 DOI: 10.1007/s13311-022-01338-0] [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] [Accepted: 12/16/2022] [Indexed: 01/31/2023] Open
Abstract
Development of neuroprotective therapeutics for Parkinson's disease (PD) is facing a lack of translation from pre-clinical to clinical trials. One strategy for improvement is to increase predictive validity of pre-clinical studies by using extensively characterized animal models with a comprehensive set of validated pharmacodynamic readouts. Mice over-expressing full-length, human, wild-type alpha-synuclein under the Thy-1 promoter (Thy1-aSyn line 61) reproduce key features of sporadic PD, such as progressive loss of striatal dopamine, alpha-synuclein pathology, deficits in motor and non-motor functions, and elevation of inflammatory markers. Extensive work with this model by multiple laboratories over the past decade further increased confidence in its robustness and validity, especially for analyzing pathomechanisms of alpha-synuclein pathology and down-stream pathways, and for pre-clinical drug testing. Interestingly, while postnatal transgene expression is widespread in central and peripheral neurons, the extent and progression of down-stream pathology differs between brain regions, thereby replicating the characteristic selective vulnerability of neurodegenerative diseases. In-depth characterization of these readouts in conjunction with behavioral deficits has led to more informative endpoints for pre-clinical trials. Each drug tested in Thy1-aSyn line 61 enhances knowledge on how molecular targets, pathology, and functional behavioral readouts are interconnected, thereby further optimizing the platform towards predictive validity for clinical trials. Here, we present the current state of the art using Thy1-aSyn line 61 for drug target discovery, validation, and pre-clinical testing.
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Affiliation(s)
- Franziska Richter
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
- Center for Systems Neuroscience Hannover, Hannover, Germany.
| | - Milos Stanojlovic
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany
| | - Christopher Käufer
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany
| | - Birthe Gericke
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany
- Center for Systems Neuroscience Hannover, Hannover, Germany
| | - Malte Feja
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany
- Center for Systems Neuroscience Hannover, Hannover, Germany
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17
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Real CC, Binda KH, Thomsen MB, Lillethorup TP, Brooks DJ, Landau AM. Selecting the Best Animal Model of Parkinson's Disease for Your Research Purpose: Insight from in vivo PET Imaging Studies. Curr Neuropharmacol 2023; 21:1241-1272. [PMID: 36797611 PMCID: PMC10286593 DOI: 10.2174/1570159x21666230216101659] [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: 08/17/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 02/18/2023] Open
Abstract
Parkinson's disease (PD) is a debilitating neurodegenerative multisystem disorder leading to motor and non-motor symptoms in millions of individuals. Despite intense research, there is still no cure, and early disease biomarkers are lacking. Animal models of PD have been inspired by basic elements of its pathogenesis, such as dopamine dysfunction, alpha-synuclein accumulation, neuroinflammation and disruption of protein degradation, and these have been crucial for a deeper understanding of the mechanisms of pathology, the identification of biomarkers, and evaluation of novel therapies. Imaging biomarkers are non-invasive tools to assess disease progression and response to therapies; their discovery and validation have been an active field of translational research. Here, we highlight different considerations of animal models of PD that can be applied to future research, in terms of their suitability to answer different research questions. We provide the reader with important considerations of the best choice of model to use based on the disease features of each model, including issues related to different species. In addition, positron emission tomography studies conducted in PD animal models in the last 5 years are presented. With a variety of different species, interventions and genetic information, the choice of the most appropriate model to answer research questions can be daunting, especially since no single model recapitulates all aspects of this complex disorder. Appropriate animal models in conjunction with in vivo molecular imaging tools, if selected properly, can be a powerful combination for the assessment of novel therapies and developing tools for early diagnosis.
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Affiliation(s)
- Caroline Cristiano Real
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karina Henrique Binda
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Majken Borup Thomsen
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Thea Pinholt Lillethorup
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - David James Brooks
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Institute of Translational and Clinical Research, University of Newcastle, Upon Tyne, UK
| | - Anne Marlene Landau
- Department of Nuclear Medicine and PET Center, Aarhus University Hospital, Aarhus, Denmark
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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18
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Kang D, Baek Y, Lee JS. Mechanisms of RNA and Protein Quality Control and Their Roles in Cellular Senescence and Age-Related Diseases. Cells 2022; 11:cells11244062. [PMID: 36552825 PMCID: PMC9777292 DOI: 10.3390/cells11244062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cellular senescence, a hallmark of aging, is defined as irreversible cell cycle arrest in response to various stimuli. It plays both beneficial and detrimental roles in cellular homeostasis and diseases. Quality control (QC) is important for the proper maintenance of cellular homeostasis. The QC machineries regulate the integrity of RNA and protein by repairing or degrading them, and are dysregulated during cellular senescence. QC dysfunction also contributes to multiple age-related diseases, including cancers and neurodegenerative, muscle, and cardiovascular diseases. In this review, we describe the characters of cellular senescence, discuss the major mechanisms of RNA and protein QC in cellular senescence and aging, and comprehensively describe the involvement of these QC machineries in age-related diseases. There are many open questions regarding RNA and protein QC in cellular senescence and aging. We believe that a better understanding of these topics could propel the development of new strategies for addressing age-related diseases.
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Affiliation(s)
- Donghee Kang
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Yurim Baek
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Jae-Seon Lee
- Research Center for Controlling Intercellular Communication (RCIC), College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Republic of Korea
- Program in Biomedical Science & Engineering, Inha University, Incheon 22212, Republic of Korea
- Correspondence: ; Tel.: +82-32-860-9832; Fax: +82-32-885-8302
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19
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Törner R, Kupreichyk T, Hoyer W, Boisbouvier J. The role of heat shock proteins in preventing amyloid toxicity. Front Mol Biosci 2022; 9:1045616. [PMID: 36589244 PMCID: PMC9798239 DOI: 10.3389/fmolb.2022.1045616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The oligomerization of monomeric proteins into large, elongated, β-sheet-rich fibril structures (amyloid), which results in toxicity to impacted cells, is highly correlated to increased age. The concomitant decrease of the quality control system, composed of chaperones, ubiquitin-proteasome system and autophagy-lysosomal pathway, has been shown to play an important role in disease development. In the last years an increasing number of studies has been published which focus on chaperones, modulators of protein conformational states, and their effects on preventing amyloid toxicity. Here, we give a comprehensive overview of the current understanding of chaperones and amyloidogenic proteins and summarize the advances made in elucidating the impact of these two classes of proteins on each other, whilst also highlighting challenges and remaining open questions. The focus of this review is on structural and mechanistic studies and its aim is to bring novices of this field "up to speed" by providing insight into all the relevant processes and presenting seminal structural and functional investigations.
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Affiliation(s)
- Ricarda Törner
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
| | - Tatsiana Kupreichyk
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jerome Boisbouvier
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
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20
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Relevance of Fluorodopa PET Scan in Dopamine Responsive Dystonia and Juvenile Parkinsonism: A Systematic Review. Neurol Int 2022; 14:997-1006. [PMID: 36548184 PMCID: PMC9781753 DOI: 10.3390/neurolint14040079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Dopamine Responsive Dystonia (DRD) and Juvenile Parkinsonism (JP) are two diseases commonly presenting with parkinsonian symptoms in young patients. Current clinical guidelines offer a diagnostic approach based on molecular analysis. However, developing countries have limitations in terms of accessibility to these tests. We aimed to assess the utility of imaging equipment, usually more available worldwide, to help diagnose and improve patients' quality of life with these diseases. METHODS We performed a systematic literature review in English using the preferred reporting items for systematic reviews and meta-analyses (PRISMA) and meta-analysis of observational studies in epidemiology (MOOSE) protocols. We only used human clinical trials about dopamine responsive dystonia and juvenile parkinsonism patients in which a fluorodopa (FD) positron emission tomography (PET) scan was performed to identify its use in these diseases. RESULTS We included six studies that fulfilled our criteria. We found a clear pattern of decreased uptake in the putamen and caudate nucleus in JP cases. At the same time, the results in DRD were comparable to normal subjects, with only a slightly decreased marker uptake in the previously mentioned regions by the FD PET scan. CONCLUSIONS We found a distinctive pattern for each of these diseases. Identifying these findings with FD PET scans can shorten the delay in making a definitive diagnosis when genetic testing is unavailable, a common scenario in developing countries.
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21
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Khani M, Nafissi S, Shamshiri H, Moazzeni H, Taheri H, Sadeghi M, Salehi N, Chitsazian F, Elahi E. Identification of UBA1 as the causative gene of an X-linked non-Kennedy SBMA. Eur J Neurol 2022; 29:3556-3563. [PMID: 35996994 DOI: 10.1111/ene.15528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/18/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Spinal-bulbar muscular atrophy (SBMA; Kennedy's Disease) is a motor neuron disease (MND). Kennedy's Disease is nearly exclusively caused by mutations in the androgen receptor encoding gene (AR). We report results of studies aimed at identification of the genetic cause of a disease that best approximates SBMA in a pedigree (four patients) without mutations in AR. METHODS Clinical investigations included thorough neurologic and non-neurologic examinations and testings. Genetic analysis was performed by exome sequencing using standard protocols. UBA1 mutations were modeled on the crystal structure of UBA1. RESULTS The clinical features of the patients are described in detail. A missense mutation in UBA1 (c.T1499C; p.Ile500Thr) was identified as the probable cause of the non-Kennedy SBMA in the pedigree. Like AR, UBA1 is positioned on Chromosome X. UBA1 is a highly conserved gene. It encodes ubiquitin like modifier activating enzyme 1 (UBA1) which is the major E1 enzyme of the ubiquitin-proteasome system. Interestingly, UBA1 mutations can also cause infantile-onset X-linked spinal muscular atrophy (XL-SMA). The mutation identified here and the XL-SMA causative mutations were shown to affect amino acids positioned in the vicinity of UBA1's ATP binding site and to cause structural changes. CONCLUSION UBA1 was identified as a novel SBMA causative gene. The gene affects protein homeostasis which is one of most important components of the pathology of neurodegeneration. The contribution of this same gene to the etiology of XL-SMA is discussed.
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Affiliation(s)
- Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Tehran University of Medical Sciences, Tehran, Iran
| | - Hosein Shamshiri
- Department of Neurology, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Moazzeni
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Hanieh Taheri
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mehdi Sadeghi
- National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Najmeh Salehi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | | | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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22
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Panza E, Meyyazhagan A, Orlacchio A. Hereditary spastic paraplegia: Genetic heterogeneity and common pathways. Exp Neurol 2022; 357:114203. [PMID: 35970204 DOI: 10.1016/j.expneurol.2022.114203] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/11/2022] [Accepted: 08/09/2022] [Indexed: 02/07/2023]
Abstract
Hereditary Spastic Paraplegias (HSPs) are a heterogeneous group of disease, mainly characterized by progressive spasticity and weakness of the lower limbs resulting from distal degeneration of corticospinal tract axons. Although HSPs represent rare or ultra-rare conditions, with reported cases of mutated genes found in single families, overall, with 87 forms described, they are an important health and economic problem for society and patients. In fact, they are chronic and life-hindering conditions, still lacking a specific therapy. Notwithstanding the number of forms described, and 73 causative genes identified, overall, the molecular diagnostic rate varies among 29% to 61.8%, based on recent published analysis, suggesting that more genes are involved in HSP and/or that different molecular diagnostic approaches are necessary. The accumulating data in this field highlight several peculiar features of HSPs, such as genetic heterogeneity, the discovery that different mutations in a single gene can be transmitted in dominant and recessive trait in families and allelic heterogeneity, resulting in the involvement of HSP-genes in other conditions. Based on the observation of protein functions, the activity of many different proteins encoded by HSP-related genes converges into some distinct pathophysiological mechanisms. This suggests that common pathways could be a potential target for a therapy, possibly addressing several forms at once. Furthermore, the overlap of HSP genes with other neurological conditions can further expand this concept.
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Affiliation(s)
- Emanuele Panza
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, Bologna, Italy
| | - Arun Meyyazhagan
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy
| | - Antonio Orlacchio
- Dipartimento di Medicina e Chirurgia, Università di Perugia, Perugia, Italy; Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Fondazione Santa Lucia, Rome, Italy.
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23
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Sikander R, Arif M, Ghulam A, Worachartcheewan A, Thafar MA, Habib S. Identification of the ubiquitin–proteasome pathway domain by hyperparameter optimization based on a 2D convolutional neural network. Front Genet 2022; 13:851688. [PMID: 35937990 PMCID: PMC9355632 DOI: 10.3389/fgene.2022.851688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
The major mechanism of proteolysis in the cytosol and nucleus is the ubiquitin–proteasome pathway (UPP). The highly controlled UPP has an effect on a wide range of cellular processes and substrates, and flaws in the system can lead to the pathogenesis of a number of serious human diseases. Knowledge about UPPs provide useful hints to understand the cellular process and drug discovery. The exponential growth in next-generation sequencing wet lab approaches have accelerated the accumulation of unannotated data in online databases, making the UPP characterization/analysis task more challenging. Thus, computational methods are used as an alternative for fast and accurate identification of UPPs. Aiming this, we develop a novel deep learning-based predictor named “2DCNN-UPP” for identifying UPPs with low error rate. In the proposed method, we used proposed algorithm with a two-dimensional convolutional neural network with dipeptide deviation features. To avoid the over fitting problem, genetic algorithm is employed to select the optimal features. Finally, the optimized attribute set are fed as input to the 2D-CNN learning engine for building the model. Empirical evidence or outcomes demonstrates that the proposed predictor achieved an overall accuracy and AUC (ROC) value using 10-fold cross validation test. Superior performance compared to other state-of-the art methods for discrimination the relations UPPs classification. Both on and independent test respectively was trained on 10-fold cross validation method and then evaluated through independent test. In the case where experimentally validated ubiquitination sites emerged, we must devise a proteomics-based predictor of ubiquitination. Meanwhile, we also evaluated the generalization power of our trained modal via independent test, and obtained remarkable performance in term of 0.862 accuracy, 0.921 sensitivity, 0.803 specificity 0.803, and 0.730 Matthews correlation coefficient (MCC) respectively. Four approaches were used in the sequences, and the physical properties were calculated combined. When used a 10-fold cross-validation, 2D-CNN-UPP obtained an AUC (ROC) value of 0.862 predicted score. We analyzed the relationship between UPP protein and non-UPP protein predicted score. Last but not least, this research could effectively analyze the large scale relationship between UPP proteins and non-UPP proteins in particular and other protein problems in general and our research work might improve computational biological research. Therefore, we could utilize the latest features in our model framework and Dipeptide Deviation from Expected Mean (DDE) -based protein structure features for the prediction of protein structure, functions, and different molecules, such as DNA and RNA.
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Affiliation(s)
- Rahu Sikander
- School of Computer Science and Technology, Xidian University, Xi’an, China
- *Correspondence: Rahu Sikander, ; Apilak Worachartcheewan,
| | - Muhammad Arif
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Ali Ghulam
- Computerization and Network Section, Sindh Agriculture University, Tando Jam, Pakistan
| | - Apilak Worachartcheewan
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
- *Correspondence: Rahu Sikander, ; Apilak Worachartcheewan,
| | - Maha A. Thafar
- Department of Computer Science, Collage of Computer and Information Technology, Taif University, Taif, Saudi Arabia
| | - Shabana Habib
- Department of Information Technology, College of Computer, Qassim University, Buraydah, Saudi Arabia
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Zhao J, Guo J, Wang Y, Ma Q, Shi Y, Cheng F, Lu Q, Fu W, Ouyang G, Zhang J, Xu Q, Hu X. Research Progress of DUB Enzyme in Hepatocellular Carcinoma. Front Oncol 2022; 12:920287. [PMID: 35875077 PMCID: PMC9303014 DOI: 10.3389/fonc.2022.920287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
According to GLOBOCAN 2021 cancer incidence and mortality statistics compiled by the International Agency for Research on Cancer, hepatocellular carcinoma (HCC) is the most common malignancy in the human liver and one of the leading causes of cancer death worldwide. Although there have been great advances in the treatment of HCC, such as regofenib, sorafenib, and lomvatinib, which have been developed and approved for the clinical treatment of advanced or metastatic HCC. However, they only prolong survival by a few months, and patients with advanced liver cancer are susceptible to tumor invasion metastasis and drug resistance. Ubiquitination modification is a type of post-translational modification of proteins. It can affect the physiological activity of cells by regulating the localization, stability and activity of proteins, such as: gene transcription, DNA damage signaling and other pathways. The reversible process of ubiquitination is called de-ubiquitination: it is the process of re-releasing ubiquitinated substrates with the participation of de-ubiquitinases (DUBs) and other active substances. There is growing evidence that many dysregulations of DUBs are associated with tumorigenesis. Although dysregulation of deuquitinase function is often found in HCC and other cancers, The mechanisms of action of many DUBs in HCC have not been elucidated. In this review, we focused on several deubiquitinases (DUBs) associated with hepatocellular carcinoma, including their structure, function, and relationship to hepatocellular carcinoma. hepatocellular carcinoma was highlighted, as well as the latest research reports. Among them, we focus on the USP family and OTU family which are more studied in the HCC. In addition, we discussed the prospects and significance of targeting DUBs as a new strategy for the treatment of hepatocellular carcinoma. It also briefly summarizes the research progress of some DUB-related small molecule inhibitors and their clinical application significance as a treatment for HCC in the future.
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Affiliation(s)
- Jie Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yanan Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiancheng Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu Shi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Feng Cheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | | | - Ji Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
| | - Xiaoge Hu
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical CollegeHangzhou, China
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
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Behl T, Kumar S, Althafar ZM, Sehgal A, Singh S, Sharma N, Badavath VN, Yadav S, Bhatia S, Al-Harrasi A, Almoshari Y, Almikhlafi MA, Bungau S. Exploring the Role of Ubiquitin-Proteasome System in Parkinson's Disease. Mol Neurobiol 2022; 59:4257-4273. [PMID: 35505049 DOI: 10.1007/s12035-022-02851-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023]
Abstract
Over the last decade, researchers have discovered that a group of apparently unrelated neurodegenerative disorders, such as Parkinson's disease, have remarkable cellular and molecular biology similarities. Protein misfolding and aggregation are involved in all of the neurodegenerative conditions; as a result, inclusion bodies aggregation starts in the cells. Chaperone proteins and ubiquitin (26S proteasome's proteolysis signal), which aid in refolding misfolded proteins, are frequently found in these aggregates. The discovery of disease-causing gene alterations that code for multiple ubiquitin-proteasome pathway proteins in Parkinson's disease has strengthened the relationship between the ubiquitin-proteasome system and neurodegeneration. The specific molecular linkages between these systems and pathogenesis, on the other hand, are unknown and controversial. We outline the current level of knowledge in this article, focusing on important unanswered problems.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Sachin Kumar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Ziyad M Althafar
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences in Alquwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | | | - Shivam Yadav
- Yashraj Institute of Pharmacy, Uttar Pradesh, India
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.,School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Yosif Almoshari
- Department of Pharmaceutics, College of Pharmacy, Jazan University, Jazan, Saudi Arabia
| | - Mohannad A Almikhlafi
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibha University, Madinah, Saudi Arabia
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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Ubiquitin and Ubiquitin-like Proteins in Cancer, Neurodegenerative Disorders, and Heart Diseases. Int J Mol Sci 2022; 23:ijms23095053. [PMID: 35563444 PMCID: PMC9105348 DOI: 10.3390/ijms23095053] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/14/2023] Open
Abstract
Post-translational modification (PTM) is an essential mechanism for enhancing the functional diversity of proteins and adjusting their signaling networks. The reversible conjugation of ubiquitin (Ub) and ubiquitin-like proteins (Ubls) to cellular proteins is among the most prevalent PTM, which modulates various cellular and physiological processes by altering the activity, stability, localization, trafficking, or interaction networks of its target molecules. The Ub/Ubl modification is tightly regulated as a multi-step enzymatic process by enzymes specific to this family. There is growing evidence that the dysregulation of Ub/Ubl modifications is associated with various diseases, providing new targets for drug development. In this review, we summarize the recent progress in understanding the roles and therapeutic targets of the Ub and Ubl systems in the onset and progression of human diseases, including cancer, neurodegenerative disorders, and heart diseases.
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Ubiquitin Proteasome System and Microtubules Are Master Regulators of Central and Peripheral Nervous System Axon Degeneration. Cells 2022; 11:cells11081358. [PMID: 35456037 PMCID: PMC9033047 DOI: 10.3390/cells11081358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
Axonal degeneration is an active process that differs from neuronal death, and it is the hallmark of many disorders affecting the central and peripheral nervous system. Starting from the analyses of Wallerian degeneration, the simplest experimental model, here we describe how the long projecting neuronal populations affected in Parkinson’s disease and chemotherapy-induced peripheral neuropathies share commonalities in the mechanisms and molecular players driving the earliest phase of axon degeneration. Indeed, both dopaminergic and sensory neurons are particularly susceptible to alterations of microtubules and axonal transport as well as to dysfunctions of the ubiquitin proteasome system and protein quality control. Finally, we report an updated review on current knowledge of key molecules able to modulate these targets, blocking the on-going axonal degeneration and inducing neuronal regeneration. These molecules might represent good candidates for disease-modifying treatment, which might expand the window of intervention improving patients’ quality of life.
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Wu P, Li Y, Cai M, Ye B, Geng B, Li F, Zhu H, Liu J, Wang X. Ubiquitin Carboxyl-Terminal Hydrolase L1 of Cardiomyocytes Promotes Macroautophagy and Proteostasis and Protects Against Post-myocardial Infarction Cardiac Remodeling and Heart Failure. Front Cardiovasc Med 2022; 9:866901. [PMID: 35463782 PMCID: PMC9021418 DOI: 10.3389/fcvm.2022.866901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is a deubiquitinase known to play essential roles in the nervous tissue. Myocardial upregulation of UCHL1 was observed in human dilated cardiomyopathy and several animal models of heart disease, but the (patho)physiological significance of UCHL1 in cardiomyocytes remains undefined. Hence, we conducted this study to fill this critical gap. We produced cardiomyocyte-restricted Uchl1 knockout (CKO) by coupling the Uchl1-floxed allele with transgenic Myh6-Cre in C57B/6J inbred mice. Mice transgenic for Myh6-Cre were used as controls (CTL). Myocardial Uchl1 proteins were markedly reduced in CKO mice but they did not display discernible abnormal phenotype. Ten-week old CTL or CKO mice were subjected to left anterior descending artery ligation (myocardial infarction, MI) or sham surgery (Sham) and characterized at 7- and 28-day after surgery. Compared with Sham mice, significant increases in myocardial UCHL1 proteins were detected in CTL MI but not in CKO MI mice. MI-induced left ventricular (LV) chamber dilation, reduction of ejection fraction (EF) and fractional shortening (FS), and LV anterior wall thinning detected by echocardiography were comparable between the CTL MI and CKO MI groups 7-day post-MI. However, by 28-day post-MI, MI-induced LV chamber dilatation, EF and FS reduction, increases of myocardial ubiquitin conjugates, and increases in the heart weight to body weight ratio and the ventricular weight to body weight ratio were significantly more pronounced in CKO MI than CTL MI mice. As further revealed by LV pressure-volume relationship analyses, CKO MI mice but not CTL MI mice displayed significant decreases in stroke volume, cardiac output, and the maximum rates of LV pressure rising or declining and of LV volume declining, as well as significant increases in LV end-diastolic pressure and Tau, compared with their respective Sham controls. LC3-II flux assays reveal that autophagic flux is decreased in CKO mouse myocardium as well as in cultured Uchl1-deficient cardiomyocytes. In conclusion, UCHL1 of cardiomyocytes is dispensable for development but promotes macroautophagy in cardiomyocytes. Upregulation of UCHL1 in post-MI hearts occurs primarily in the cardiomyocytes and protects against post-MI cardiac remodeling and malfunction likely through supporting autophagic flux and proteostasis during a stress condition.
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Affiliation(s)
- Penglong Wu
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, United States
- Department of Cardiology, Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yifan Li
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, United States
| | - Mingqi Cai
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, United States
| | - Bo Ye
- Lillehei Heart Institute and the Department of Medicine, University of Minnesota College of Medicine, Minneapolis, MN, United States
| | - Bingchuan Geng
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Faqian Li
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Hua Zhu
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Jinbao Liu
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xuejun Wang
- Division of Basic Biomedical Sciences, University of South Dakota Sanford School of Medicine, Vermillion, SD, United States
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Chaperone-Mediated Autophagy in Neurodegenerative Diseases and Acute Neurological Insults in the Central Nervous System. Cells 2022; 11:cells11071205. [PMID: 35406769 PMCID: PMC8997510 DOI: 10.3390/cells11071205] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an important function that mediates the degradation of intracellular proteins and organelles. Chaperone-mediated autophagy (CMA) degrades selected proteins and has a crucial role in cellular proteostasis under various physiological and pathological conditions. CMA dysfunction leads to the accumulation of toxic protein aggregates in the central nervous system (CNS) and is involved in the pathogenic process of neurodegenerative diseases, including Parkinson’s disease and Alzheimer’s disease. Previous studies have suggested that the activation of CMA to degrade aberrant proteins can provide a neuroprotective effect in the CNS. Recent studies have shown that CMA activity is upregulated in damaged neural tissue following acute neurological insults, such as cerebral infarction, traumatic brain injury, and spinal cord injury. It has been also suggested that various protein degradation mechanisms are important for removing toxic aberrant proteins associated with secondary damage after acute neurological insults in the CNS. Therefore, enhancing the CMA pathway may induce neuroprotective effects not only in neurogenerative diseases but also in acute neurological insults. We herein review current knowledge concerning the biological mechanisms involved in CMA and highlight the role of CMA in neurodegenerative diseases and acute neurological insults. We also discuss the possibility of developing CMA-targeted therapeutic strategies for effective treatments.
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Atypical Ubiquitination and Parkinson's Disease. Int J Mol Sci 2022; 23:ijms23073705. [PMID: 35409068 PMCID: PMC8998352 DOI: 10.3390/ijms23073705] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Ubiquitination (the covalent attachment of ubiquitin molecules to target proteins) is one of the main post-translational modifications of proteins. Historically, the type of polyubiquitination, which involves K48 lysine residues of the monomeric ubiquitin, was the first studied type of ubiquitination. It usually targets proteins for their subsequent proteasomal degradation. All the other types of ubiquitination, including monoubiquitination; multi-monoubiquitination; and polyubiquitination involving lysine residues K6, K11, K27, K29, K33, and K63 and N-terminal methionine, were defined as atypical ubiquitination (AU). Good evidence now exists that AUs, participating in the regulation of various cellular processes, are crucial for the development of Parkinson's disease (PD). These AUs target various proteins involved in PD pathogenesis. The K6-, K27-, K29-, and K33-linked polyubiquitination of alpha-synuclein, the main component of Lewy bodies, and DJ-1 (another PD-associated protein) is involved in the formation of insoluble aggregates. Multifunctional protein kinase LRRK2 essential for PD is subjected to K63- and K27-linked ubiquitination. Mitophagy mediated by the ubiquitin ligase parkin is accompanied by K63-linked autoubiquitination of parkin itself and monoubiquitination and polyubiquitination of mitochondrial proteins with the formation of both classical K48-linked ubiquitin chains and atypical K6-, K11-, K27-, and K63-linked polyubiquitin chains. The ubiquitin-specific proteases USP30, USP33, USP8, and USP15, removing predominantly K6-, K11-, and K63-linked ubiquitin conjugates, antagonize parkin-mediated mitophagy.
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α-Synuclein at the Presynaptic Axon Terminal as a Double-Edged Sword. Biomolecules 2022; 12:biom12040507. [PMID: 35454096 PMCID: PMC9029495 DOI: 10.3390/biom12040507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
α-synuclein (α-syn) is a presynaptic, lipid-binding protein strongly associated with the neuropathology observed in Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and Alzheimer’s Disease (AD). In normal physiology, α-syn plays a pivotal role in facilitating endocytosis and exocytosis. Interestingly, mutations and modifications of precise α-syn domains interfere with α-syn oligomerization and nucleation that negatively affect presynaptic vesicular dynamics, protein expressions, and mitochondrial profiles. Furthermore, the integration of the α-syn oligomers into the presynaptic membrane results in pore formations, ion influx, and excitotoxicity. Targeted therapies against specific domains of α-syn, including the use of small organic molecules, monoclonal antibodies, and synthetic peptides, are being screened and developed. However, the prospect of an effective α-syn targeted therapy is still plagued by low permeability across the blood–brain barrier (BBB), and poor entry into the presynaptic axon terminals. The present review proposes a modification of current strategies, which includes the use of novel encapsulation technology, such as lipid nanoparticles, to bypass the BBB and deliver such agents into the brain.
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Liu S, Xu J, Xing Y, Yan T, Yu S, Sun H, Liu J. Nanozymes as efficient tools for catalytic therapeutics. VIEW 2022. [DOI: 10.1002/viw.20200147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Shengda Liu
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
| | - Jiayun Xu
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
| | - Yunpeng Xing
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry Jilin University Changchun P. R. China
| | - Tengfei Yan
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
| | - Shuangjiang Yu
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
| | - Hongcheng Sun
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
| | - Junqiu Liu
- College of Material Chemistry and Chemical Engineering Hangzhou Normal University Hangzhou P. R. China
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Liu F, Morderer D, Wren MC, Vettleson-Trutza SA, Wang Y, Rabichow BE, Salemi MR, Phinney BS, Oskarsson B, Dickson DW, Rossoll W. Proximity proteomics of C9orf72 dipeptide repeat proteins identifies molecular chaperones as modifiers of poly-GA aggregation. Acta Neuropathol Commun 2022; 10:22. [PMID: 35164882 PMCID: PMC8842533 DOI: 10.1186/s40478-022-01322-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
The most common inherited cause of two genetically and clinico-pathologically overlapping neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), is the presence of expanded GGGGCC intronic hexanucleotide repeats in the C9orf72 gene. Aside from haploinsufficiency and toxic RNA foci, another non-exclusive disease mechanism is the non-canonical translation of the repeat RNA into five different dipeptide repeat proteins (DPRs), which form neuronal inclusions in affected patient brains. While evidence from cellular and animal models supports a toxic gain-of-function of pathologic poly-GA, poly-GR, and poly-PR aggregates in promoting deposition of TDP-43 pathology and neurodegeneration in affected brain areas, the relative contribution of DPRs to the disease process in c9FTD/ALS patients remains unclear. Here we have used the proximity-dependent biotin identification (BioID) proximity proteomics approach to investigate the formation and collective composition of DPR aggregates using cellular models. While interactomes of arginine rich poly-GR and poly-PR aggregates overlapped and were enriched for nucleolar and ribosomal proteins, poly-GA aggregates demonstrated a distinct association with proteasomal components, molecular chaperones (HSPA1A/HSP70, HSPA8/HSC70, VCP/p97), co-chaperones (BAG3, DNAJA1A) and other factors that regulate protein folding and degradation (SQSTM1/p62, CALR, CHIP/STUB1). Experiments in cellular models of poly-GA pathology show that molecular chaperones and co-chaperones are sequestered to the periphery of dense cytoplasmic aggregates, causing depletion from their typical cellular localization. Their involvement in the pathologic process is confirmed in autopsy brain tissue, where HSPA8, BAG3, VCP, and its adapter protein UBXN6 show a close association with poly-GA aggregates in the frontal cortex, temporal cortex, and hippocampus of c9FTLD and c9ALS cases. The association of heat shock proteins and co-chaperones with poly-GA led us to investigate their potential role in reducing its aggregation. We identified HSP40 co-chaperones of the DNAJB family as potent modifiers that increased the solubility of poly-GA, highlighting a possible novel therapeutic avenue and a central role of molecular chaperones in the pathogenesis of human C9orf72-linked diseases.
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [PMID: 34973458 DOI: 10.1016/j.arr.2021.101554] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a common motor disorder that has become increasingly prevalent in the ageing population. Recent works have suggested that circadian rhythms disruption is a common event in PD patients. Clock genes regulate the circadian rhythm of biological processes in eukaryotic organisms, but their roles in PD remain unclear. Despite this, several lines of evidence point to the possibility that clock genes may have a significant impact on the development and progression of the disease. This review aims to consolidate recent understanding of the roles of clock genes in PD. We first summarized the findings of clock gene expression and epigenetic analyses in PD patients and animal models. We also discussed the potential contributory role of clock gene variants in the development of PD and/or its symptoms. We further reviewed the mechanisms by which clock genes affect mitochondrial dynamics as well as the rhythmic synthesis and secretion of endocrine hormones, the impairment of which may contribute to the development of PD. Finally, we discussed the limitations of the currently available studies, and suggested future potential studies to deepen our understanding of the roles of clock genes in PD pathogenesis.
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Affiliation(s)
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Mai Abdelgawad
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef 62511, Egypt
| | - Hitesh Chopra
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
| | - Muhammad Bilal
- College of Pharmacy, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | | | | | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Peterlee Place NSW2700, Australia; AFNP Med, Haidingergasse 29, 1030 Wien, Austria
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022; 74:101554. [DOI: https:/doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Shkodina AD, Tan SC, Hasan MM, Abdelgawad M, Chopra H, Bilal M, Boiko DI, Tarianyk KA, Alexiou A. Roles of clock genes in the pathogenesis of Parkinson's disease. Ageing Res Rev 2022. [DOI: https://doi.org/10.1016/j.arr.2021.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Huang Y, Wei J, Cooper A, Morris MJ. Parkinson's Disease: From Genetics to Molecular Dysfunction and Targeted Therapeutic Approaches. Genes Dis 2022. [DOI: 10.1016/j.gendis.2021.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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38
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Deubiquitinating enzymes (DUBs): decipher underlying basis of neurodegenerative diseases. Mol Psychiatry 2022; 27:259-268. [PMID: 34285347 DOI: 10.1038/s41380-021-01233-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Neurodegenerative diseases (NDs) are characterized by the aggregation of neurotoxic proteins in the central nervous system. Aberrant protein accumulation in NDs is largely caused by the dysfunction of the two principal protein catabolism pathways, the ubiquitin-proteasome system (UPS), and the autophagy-lysosomal pathway (ALP). The two protein quality control pathways are bridged by ubiquitination, a post-translational modification that can induce protein degradation via both the UPS and the ALP. Perturbed ubiquitination leads to the formation of toxic aggregates and inclusion bodies that are deleterious to neurons. Ubiquitination is promoted by a cascade of ubiquitinating enzymes and counter-regulated by deubiquitinating enzymes (DUBs). As fine-tuning regulators of ubiquitination and protein degradation, DUBs modulate the stability of ND-associated pathogenic proteins including amyloid β protein, Tau, and α-synuclein. Besides, DUBs also influence ND-associated mitophagy, protein secretion, and neuroinflammation. Given the various and critical functions of DUBs in NDs, DUBs may become potential therapeutic targets for NDs.
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Long S, Yang L, Dang W, Xin S, Jiang M, Zhang W, Li J, Wang Y, Zhang S, Lu J. Cellular Deubiquitylating Enzyme: A Regulatory Factor of Antiviral Innate Immunity. Front Microbiol 2021; 12:805223. [PMID: 34966378 PMCID: PMC8710732 DOI: 10.3389/fmicb.2021.805223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Deubiquitylating enzymes (DUBs) are proteases that crack the ubiquitin code from ubiquitylated substrates to reverse the fate of substrate proteins. Recently, DUBs have been found to mediate various cellular biological functions, including antiviral innate immune response mediated by pattern-recognition receptors (PRRs) and NLR Family pyrin domain containing 3 (NLRP3) inflammasomes. So far, many DUBs have been identified to exert a distinct function in fine-tuning antiviral innate immunity and are utilized by viruses for immune evasion. Here, the recent advances in the regulation of antiviral responses by DUBs are reviewed. We also discussed the DUBs-mediated interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and antiviral innate immunity. The understanding of the mechanisms on antiviral innate immunity regulated by DUBs may provide therapeutic opportunities for viral infection.
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Affiliation(s)
- Sijing Long
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Li Yang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wei Dang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Mingjuan Jiang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wentao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jing Li
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Senmiao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Identification and validation of selective deubiquitinase inhibitors. Cell Chem Biol 2021; 28:1758-1771.e13. [PMID: 34129829 PMCID: PMC9473745 DOI: 10.1016/j.chembiol.2021.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a class of isopeptidases that regulate ubiquitin dynamics through catalytic cleavage of ubiquitin from protein substrates and ubiquitin precursors. Despite growing interest in DUB biological function and potential as therapeutic targets, few selective small-molecule inhibitors and no approved drugs currently exist. To identify chemical scaffolds targeting specific DUBs and establish a broader framework for future inhibitor development across the gene family, we performed high-throughput screening of a chemically diverse small-molecule library against eight different DUBs, spanning three well-characterized DUB families. Promising hit compounds were validated in a series of counter-screens and orthogonal assays, as well as further assessed for selectivity across expanded panels of DUBs. Through these efforts, we have identified multiple highly selective DUB inhibitors and developed a roadmap for rapidly identifying and validating selective inhibitors of related enzymes.
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Affiliation(s)
- Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dominick Casalena
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Douglas Auld
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Nag S, Jahan M, Tóth M, Nakao R, Varrone A, Halldin C. PET Imaging of VMAT2 with the Novel Radioligand [ 18F]FE-DTBZ-d4 in Nonhuman Primates: Comparison with [ 11C]DTBZ and [ 18F]FE-DTBZ. ACS Chem Neurosci 2021; 12:4580-4586. [PMID: 34813272 PMCID: PMC8678981 DOI: 10.1021/acschemneuro.1c00651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
![]()
The vesicular monoamine
transporter type 2 (VMAT2) is believed
to be responsible for the uptake of monoamines into the vesicles of
the synaptic terminals. Two VMAT2 radioligands [11C]DTBZ
and [18F]FP-DTBZ have been used to assess the degree of
nigrostriatal deficit in Parkinson’s disease (PD) using positron
emission tomography (PET). [18F]FE-DTBZ-d4, the nondeuterated
analogue of [18F]FE-DTBZ showed similar imaging properties
with better stability against defluorination. Therefore, [18F]FE-DTBZ-d4 draws attention to be investigated as an imaging marker
for VMAT2 in the brain. The aim of this study was to investigate the
brain kinetics and quantification of [18F]FE-DTBZ-d4 in
nonhuman primates (NHPs), with comparison to [11C]DTBZ
and [18F]FE-DTBZ. Radiolabeling was successfully achieved
either by one-step 11C-methylation or by a two-step fluorine-18
nucleophilic substitution reaction. The stability and radiochemical
yield were analyzed with high-performance liquid chromatography (HPLC).
Three female cynomolgus monkeys were included in the study and underwent
a total of 12 positron emission tomography (PET) measurements. Each
monkey was examined with each tracer. In addition, two pretreatment
and one displacement PET measurements with tetrabenazine (2.0 mg/kg)
were performed for [18F]FE-DTBZ-d4. All PET measurements
were conducted using a high-resolution research tomograph (HRRT) system.
Radiometabolites were measured in monkey plasma using gradient radio-HPLC.
[18F]FE-DTBZ-d4 (SUV: 4.28 ± 1.01) displayed higher
brain uptake compared to both [18F]FE-DTBZ (SUV: 3.43 ±
0.54) and [11C]DTBZ (SUV: 3.06 ± 0.32) and faster
washout. Binding potential (BPND) values of [18F]FE-DTBZ-d4 in different brain regions (putamen: 5.5 ± 1.4;
caudate: 4.4 ± 1.1; midbrain: 1.4 ± 0.4) were higher than
those of [11C]DTBZ and [18F]FE-DTBZ. [18F]FE-DTBZ showed faster radiometabolism in plasma compared to [11C]DTBZ and [18F]FE-DTBZ-d4. [18F]FE-DTBZ-d4
is a suitable radioligand for quantification of VMAT2 in the nonhuman
primate brain, with better imaging properties than [11C]DTBZ
and [18F]FE-DTBZ. A preliminary comparison suggests that
[18F]FE-DTBZ-d4 has increased stability against defluorination
compared to the nondeuterated analogue.
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Affiliation(s)
- Sangram Nag
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Mahabuba Jahan
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Miklós Tóth
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Ryuji Nakao
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Andrea Varrone
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Christer Halldin
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
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Danilenko V, Devyatkin A, Marsova M, Shibilova M, Ilyasov R, Shmyrev V. Common Inflammatory Mechanisms in COVID-19 and Parkinson's Diseases: The Role of Microbiome, Pharmabiotics and Postbiotics in Their Prevention. J Inflamm Res 2021; 14:6349-6381. [PMID: 34876830 PMCID: PMC8643201 DOI: 10.2147/jir.s333887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
In the last decade, metagenomic studies have shown the key role of the gut microbiome in maintaining immune and neuroendocrine systems. Malfunction of the gut microbiome can induce inflammatory processes, oxidative stress, and cytokine storm. Dysfunction of the gut microbiome can be caused by short-term (virus infection and other infectious diseases) or long-term (environment, nutrition, and stress) factors. Here, we reviewed the inflammation and oxidative stress in neurodegenerative diseases and coronavirus infection (COVID-19). Here, we reviewed the renin-angiotensin-aldosterone system (RAAS) involved in the processes of formation of oxidative stress and inflammation in viral and neurodegenerative diseases. Moreover, the coronavirus uses ACE2 receptors of the RAAS to penetrate human cells. The coronavirus infection can be the trigger for neurodegenerative diseases by dysfunction of the RAAS. Pharmabiotics, postbiotics, and next-generation probiotics, are considered as a means to prevent oxidative stress, inflammatory processes, neurodegenerative and viral diseases through gut microbiome regulation.
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Affiliation(s)
- Valery Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Devyatkin
- Central Clinical Hospital with a Polyclinic CMP RF, Moscow, Russia
| | - Mariya Marsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Rustem Ilyasov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens. Genes (Basel) 2021; 12:genes12121857. [PMID: 34946806 PMCID: PMC8701255 DOI: 10.3390/genes12121857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.
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Tyagi A, Haq S, Ramakrishna S. Redox regulation of DUBs and its therapeutic implications in cancer. Redox Biol 2021; 48:102194. [PMID: 34814083 PMCID: PMC8608616 DOI: 10.1016/j.redox.2021.102194] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) act as a double-edged sword in cancer, where low levels of ROS are beneficial but excessive accumulation leads to cancer progression. Elevated levels of ROS in cancer are counteracted by the antioxidant defense system. An imbalance between ROS generation and the antioxidant system alters gene expression and cellular signaling, leading to cancer progression or death. Post-translational modifications, such as ubiquitination, phosphorylation, and SUMOylation, play a critical role in the maintenance of ROS homeostasis by controlling ROS production and clearance. Recent evidence suggests that deubiquitinating enzymes (DUBs)-mediated ubiquitin removal from substrates is regulated by ROS. ROS-mediated oxidation of the catalytic cysteine (Cys) of DUBs, leading to their reversible inactivation, has emerged as a key mechanism regulating DUB-controlled cellular events. A better understanding of the mechanism by which DUBs are susceptible to ROS and exploring the ways to utilize ROS to pharmacologically modulate DUB-mediated signaling pathways might provide new insight for anticancer therapeutics. This review assesses the recent findings regarding ROS-mediated signaling in cancers, emphasizes DUB regulation by oxidation, highlights the relevant recent findings, and proposes directions of future research based on the ROS-induced modifications of DUB activity.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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45
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Yoo D, Lee W, Lee SJ, Sung JJ, Jeon GS, Ban JJ, Shin C, Kim J, Kim HS, Ahn TB. A Novel TFG Mutation in a Korean Family with α-Synucleinopathy and Amyotrophic Lateral Sclerosis. Mov Disord 2021; 37:384-391. [PMID: 34779525 DOI: 10.1002/mds.28857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Tropomyosin-receptor kinase fused gene (TFG) functions as a regulator of intracellular protein packaging and trafficking at the endoplasmic reticulum exit sites. TFG has recently been proposed as a cause of multisystem proteinopathy. OBJECTIVES Here, we describe a Korean family presenting with Parkinson's disease or amyotrophic lateral sclerosis caused by a novel variant of TFG (c.1148 G > A, p.Arg383His). METHODS We collected clinical, genetic, dopamine transporter imaging, nerve conduction, and electromyography data from the seven subjects. To verify the pathogenicity of the R383H variant, we studied cell viability and the abnormal aggregation of α-synuclein and TAR DNA-binding protein 43 (TDP-43) in HeLa cells expressing R383H-TFG. RESULTS The clinical phenotypes of the R383H-TFG mutation varied; of the five family members, one had Parkinson's disease, three had subclinical parkinsonism, and one (the proband) had amyotrophic lateral sclerosis. The individual with multiple system atrophy was the proband's paternal cousin, but the TFG genotype was not confirmed due to unavailability of samples. Our in vitro studies showed that R383H-TFG overexpression impaired cell viability. In cells co-expressing R383H-TFG and α-synuclein, insoluble α-synuclein aggregates increased in concentration and were secreted from the cells and co-localized with R383H-TFG. The levels of cytoplasmic insoluble aggregates of TDP-43 increased in HeLa cells expressing R383H-TFG and co-localized with R383H-TFG. CONCLUSIONS Clinical and in vitro studies have supported the pathogenic role of the novel TFG mutation in α-synucleinopathy and TDP-43 proteinopathy. These findings expand the phenotypic spectrum of TFG and suggest a pivotal role of endoplasmic reticulum dysfunction during neurodegeneration. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Dallah Yoo
- Department of Neurology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Wonjae Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, and Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Neuramedy Co., Ltd, Seoul, Republic of Korea
| | - Seung-Jae Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, and Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung-Joon Sung
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Gye Sun Jeon
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Jun Ban
- Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chaewon Shin
- Department of Neurology, Neuroscience Center, Chungnam National University Sejong Hospital, Chungnam National University College of Medicine, Sejong-si, Republic of Korea
| | - Jungho Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Hyo Sun Kim
- Laboratory of Molecular and Cellular Biology, Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Tae-Beom Ahn
- Department of Neurology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
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Mambourg K, Tumanov N, Henon G, Lanners S, Garcia-Ladona J, Wouters J. Crystal structures of two alanylpiperidine analogues. Acta Crystallogr E Crystallogr Commun 2021; 77:1095-1098. [PMID: 34868643 PMCID: PMC8587977 DOI: 10.1107/s2056989021010392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 11/25/2022]
Abstract
The crystal structures of ethyl 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylate and 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylic acid, two analogues studied as potentiators of Ubiquitin C-terminal hydrolase-L1 (UCH-L1), have been determined. Despite being analogues, different crystal packings are observed. A polymorph risk assessment was carried out to study interactions in the second compound. The structure of ethyl 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylate, C19H28N2O5S, I, a compound of interest as activator of Ubiquitin C-terminal Hydrolase-L1 (UCH-L1), was determined by single-crystal X-ray diffraction (SCXRD) analysis. In order to find new activators, a derivative of compound I, namely, 1-[N-(4-methylphenyl)-N-(methylsulfonyl)alanyl]piperidine-4-carboxylic acid, C17H24N2O5S, II, was studied. The synthesis and crystal structure are also reported. Despite being analogues, different crystal packings are observed. Compound II bears a carboxylic group, which favors a strong hydrogen bond. A polymorph risk assessment was carried out to study interactions in compound II.
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47
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Hommen F, Bilican S, Vilchez D. Protein clearance strategies for disease intervention. J Neural Transm (Vienna) 2021; 129:141-172. [PMID: 34689261 PMCID: PMC8541819 DOI: 10.1007/s00702-021-02431-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/10/2021] [Indexed: 02/06/2023]
Abstract
Protein homeostasis, or proteostasis, is essential for cell function and viability. Unwanted, damaged, misfolded and aggregated proteins are degraded by the ubiquitin–proteasome system (UPS) and the autophagy-lysosome pathway. Growing evidence indicates that alterations in these major proteolytic mechanisms lead to a demise in proteostasis, contributing to the onset and development of distinct diseases. Indeed, dysregulation of the UPS or autophagy is linked to several neurodegenerative, infectious and inflammatory disorders as well as cancer. Thus, modulation of protein clearance pathways is a promising approach for therapeutics. In this review, we discuss recent findings and open questions on how targeting proteolytic mechanisms could be applied for disease intervention.
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Affiliation(s)
- Franziska Hommen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Saygın Bilican
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. .,Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
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48
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Wang X, Li Y, He M, Kong X, Jiang P, Liu X, Diao L, Zhang X, Li H, Ling X, Xia S, Liu Z, Liu Y, Cui CP, Wang Y, Tang L, Zhang L, He F, Li D. UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. Nucleic Acids Res 2021; 50:D719-D728. [PMID: 34669962 PMCID: PMC8728189 DOI: 10.1093/nar/gkab962] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
As an important post-translational modification, ubiquitination mediates ∼80% of protein degradation in eukaryotes. The degree of protein ubiquitination is tightly determined by the delicate balance between specific ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase-mediated deubiquitination. In 2017, we developed UbiBrowser 1.0, which is an integrated database for predicted human proteome-wide E3-substrate interactions. Here, to meet the urgent requirement of proteome-wide E3/deubiquitinase-substrate interactions (ESIs/DSIs) in multiple organisms, we updated UbiBrowser to version 2.0 (http://ubibrowser.ncpsb.org.cn). Using an improved protocol, we collected 4068/967 known ESIs/DSIs by manual curation, and we predicted about 2.2 million highly confident ESIs/DSIs in 39 organisms, with >210-fold increase in total data volume. In addition, we made several new features in the updated version: (i) it allows exploring proteins' upstream E3 ligases and deubiquitinases simultaneously; (ii) it has significantly increased species coverage; (iii) it presents a uniform confidence scoring system to rank predicted ESIs/DSIs. To facilitate the usage of UbiBrowser 2.0, we also redesigned the web interface for exploring these known and predicted ESIs/DSIs, and added functions of 'Browse', 'Download' and 'Application Programming Interface'. We believe that UbiBrowser 2.0, as a discovery tool, will contribute to the study of protein ubiquitination and the development of drug targets for complex diseases.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mengqi He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiangren Kong
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Peng Jiang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Xi Liu
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Lihong Diao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xinlei Zhang
- Beijing Geneworks Technology Co.,Ltd., Beijing 100101, China
| | - Honglei Li
- Beijing Geneworks Technology Co.,Ltd., Beijing 100101, China
| | - Xinping Ling
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Simin Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Zhongyang Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yuan Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Chun-Ping Cui
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Liujun Tang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,College of Life Sciences, Hebei University, Baoding 071002, China.,School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
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49
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Pradhan N, Singh C, Singh A. Coenzyme Q10 a mitochondrial restorer for various brain disorders. Naunyn Schmiedebergs Arch Pharmacol 2021; 394:2197-2222. [PMID: 34596729 DOI: 10.1007/s00210-021-02161-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Coenzyme Q10 (ubiquinone or CoQ10) is a lipid molecule that acts as an electron mobile carrier of the electron transport chain and also contains antioxidant properties. Supplementation of CoQ10 has been very useful to treat mitochondrial diseases. CoQ10 along with its synthetic analogue, idebenone, is used largely to treat various neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, Huntington's disease, Amyotrophic lateral sclerosis, and Friedreich's ataxia and additional brain disease condition like autism, multiple sclerosis, epilepsy, depression, and bipolar disorder, which are related to mitochondrial impairment. In this article, we have reviewed numerous physiological functions of CoQ10 and the rationale for its use in clinical practice in different brain disorders.
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Affiliation(s)
- Nilima Pradhan
- Department of Pharmacology, ISF College of Pharmacy, Moga, 142001, Punjab, India
- Affiliated to IK Gujral Punjab Technical University, Jalandhar, 144603, Punjab, India
| | - Charan Singh
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, 142001, Punjab, India
- Affiliated to IK Gujral Punjab Technical University, Jalandhar, 144603, Punjab, India
| | - Arti Singh
- Department of Pharmacology, ISF College of Pharmacy, Moga, 142001, Punjab, India.
- Affiliated to IK Gujral Punjab Technical University, Jalandhar, 144603, Punjab, India.
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50
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Ebstein F, Küry S, Papendorf JJ, Krüger E. Neurodevelopmental Disorders (NDD) Caused by Genomic Alterations of the Ubiquitin-Proteasome System (UPS): the Possible Contribution of Immune Dysregulation to Disease Pathogenesis. Front Mol Neurosci 2021; 14:733012. [PMID: 34566579 PMCID: PMC8455891 DOI: 10.3389/fnmol.2021.733012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over thirty years have passed since the first description of ubiquitin-positive structures in the brain of patients suffering from Alzheimer’s disease. Meanwhile, the intracellular accumulation of ubiquitin-modified insoluble protein aggregates has become an indisputable hallmark of neurodegeneration. However, the role of ubiquitin and a fortiori the ubiquitin-proteasome system (UPS) in the pathogenesis of neurodevelopmental disorders (NDD) is much less described. In this article, we review all reported monogenic forms of NDD caused by lesions in genes coding for any component of the UPS including ubiquitin-activating (E1), -conjugating (E2) enzymes, ubiquitin ligases (E3), ubiquitin hydrolases, and ubiquitin-like modifiers as well as proteasome subunits. Strikingly, our analysis revealed that a vast majority of these proteins have a described function in the negative regulation of the innate immune response. In this work, we hypothesize a possible involvement of autoinflammation in NDD pathogenesis. Herein, we discuss the parallels between immune dysregulation and neurodevelopment with the aim at improving our understanding the biology of NDD and providing knowledge required for the design of novel therapeutic strategies.
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Affiliation(s)
- Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'Institut du Thorax, CNRS, INSERM, CHU Nantes, Université de Nantes, Nantes, France
| | - Jonas Johannes Papendorf
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
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