1
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Ducza L, Gaál B. The Neglected Sibling: NLRP2 Inflammasome in the Nervous System. Aging Dis 2024; 15:1006-1028. [PMID: 38722788 PMCID: PMC11081174 DOI: 10.14336/ad.2023.0926-1] [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: 08/01/2023] [Accepted: 09/26/2023] [Indexed: 05/13/2024] Open
Abstract
While classical NOD-like receptor pyrin domain containing protein 1 (NLRP1) and NLRP3 inflammasomal proteins have been extensively investigated, the contribution of NLRP2 is still ill-defined in the nervous system. Given the putative significance of NLRP2 in orchestrating neuroinflammation, further inquiry is needed to gain a better understanding of its connectome, hence its specific targeting may hold a promising therapeutic implication. Therefore, bioinformatical approach for extracting information, specifically in the context of neuropathologies, is also undoubtedly preferred. To the best of our knowledge, there is no review study selectively targeting only NLRP2. Increasing, but still fragmentary evidence should encourage researchers to thoroughly investigate this inflammasome in various animal- and human models. Taken together, herein we aimed to review the current literature focusing on the role of NLRP2 inflammasome in the nervous system and more importantly, we provide an algorithm-based protein network of human NLRP2 for elucidating potentially valuable molecular partnerships that can be the beginning of a new discourse and future therapeutic considerations.
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Affiliation(s)
- László Ducza
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Hungary, Hungary
| | - Botond Gaál
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, University of Debrecen, Hungary, Hungary
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2
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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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3
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Kaushik A, Parashar S, Ambasta RK, Kumar P. Ubiquitin E3 ligases assisted technologies in protein degradation: Sharing pathways in neurodegenerative disorders and cancer. Ageing Res Rev 2024; 96:102279. [PMID: 38521359 DOI: 10.1016/j.arr.2024.102279] [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: 01/10/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Abstract
E3 ligases, essential components of the ubiquitin-proteasome-mediated protein degradation system, play a critical role in cellular regulation. By covalently attaching ubiquitin (Ub) molecules to target proteins, these ligases mark them for degradation, influencing various bioprocesses. With over 600 E3 ligases identified, there is a growing realization of their potential as therapeutic candidates for addressing proteinopathies in cancer and neurodegenerative disorders (NDDs). Recent research has highlighted the need to delve deeper into the intricate roles of E3 ligases as nexus points in the pathogenesis of both cancer and NDDs. Their dysregulation is emerging as a common thread linking these seemingly disparate diseases, necessitating a comprehensive understanding of their molecular intricacies. Herein, we have discussed (i) the fundamental mechanisms through which different types of E3 ligases actively participate in selective protein degradation in cancer and NDDs, followed by an examination of common E3 ligases playing pivotal roles in both situations, emphasising common players. Moving to, (ii) the functional domains and motifs of E3 ligases involved in ubiquitination, we have explored their interactions with specific substrates in NDDs and cancer. Additionally, (iii) we have explored techniques like PROTAC, molecular glues, and other state-of-the-art methods for hijacking neurotoxic and oncoproteins. Lastly, (iv) we have provided insights into ongoing clinical trials, offering a glimpse into the evolving landscape of E3-based therapeutics for cancer and NDDs. Unravelling the intricate network of E3 ligase-mediated regulation holds the key to unlocking targeted therapies that address the specific molecular signatures of individual patients, heralding a new era in personalized medicines.
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Affiliation(s)
- Aastha Kaushik
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Somya Parashar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology and Microbiology, SRM University-Sonepat, Haryana, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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4
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Radmall KS, Shukla PK, Leng AM, Chandrasekharan MB. Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains. Sci Rep 2023; 13:16731. [PMID: 37794081 PMCID: PMC10550974 DOI: 10.1038/s41598-023-43969-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
Post-translational covalent conjugation of ubiquitin onto proteins or ubiquitination is important in nearly all cellular processes. Steady-state ubiquitination of individual proteins in vivo is maintained by two countering enzymatic activities: conjugation of ubiquitin by E1, E2 and E3 enzymes and removal by deubiquitinases. Here, we deleted one or more genes encoding deubiquitinases in yeast and evaluated the requirements for ubiquitin conjugation onto a target protein. Our proof-of-principle studies demonstrate that absence of relevant deubiquitinase(s) provides a facile and versatile method that can be used to study the nuances of ubiquitin conjugation and deubiquitination of target proteins in vivo. We verified our method using mutants lacking the deubiquitinases Ubp8 and/or Ubp10 that remove ubiquitin from histone H2B or PCNA. Our studies reveal that the C-terminal coiled-domain of the adapter protein Lge1 and the C-terminal acidic tail of Rad6 E2 contribute to monoubiquitination of histone H2BK123, whereas the distal acidic residues of helix-4 of Rad6, but not the acidic tail, is required for monoubiquitination of PCNA. Further, charged substitution at alanine-120 in the H2B C-terminal helix adversely affected histone H2BK123 monoubiquitination by inhibiting Rad6-Bre1-mediated ubiquitin conjugation and by promoting Ubp8/Ubp10-mediated deubiquitination. In summary, absence of yeast deubiquitinases UBP8 and/or UBP10 allows uncovering the regulation of and requirements for ubiquitin addition and removal from their physiological substrates such as histone H2B or PCNA in vivo.
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Affiliation(s)
- Kaitlin S Radmall
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Prakash K Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Andrew M Leng
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
- Huntsman Cancer Institute, University of Utah School of Medicine, 2000, Circle of Hope, Room 3715, Salt Lake City, UT, 84112, USA.
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5
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Radmall KS, Shukla PK, Leng AM, Chandrasekharan MB. Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.18.545485. [PMID: 37873190 PMCID: PMC10592830 DOI: 10.1101/2023.06.18.545485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Post-translational covalent conjugation of ubiquitin onto proteins or ubiquitination is important in nearly all cellular processes. Steady-state ubiquitination of individual proteins in vivo is maintained by two countering enzymatic activities: conjugation of ubiquitin by E1, E2 and E3 enzymes and removal by deubiquitinases. Here, we deleted one or more genes encoding deubiquitinases in yeast and evaluated the requirements for ubiquitin conjugation onto a target protein. Our proof-of-principle studies demonstrate that absence of relevant deubiquitinase(s) provides a facile and versatile method that can be used to study the nuances of ubiquitin conjugation and deubiquitination of target proteins in vivo . We verified our method using mutants lacking the deubiquitinases Ubp8 and/or Ubp10 that remove ubiquitin from histone H2B or PCNA. Our studies reveal that the C-terminal coiled-domain of the adapter protein Lge1 and the C-terminal acidic tail of Rad6 E2 contribute to monoubiquitination of histone H2BK123, whereas the distal acidic residues of helix-4 of Rad6, but not the acidic tail, is required for monoubiquitination of PCNA. Further, charged substitution at alanine-120 in the H2B C-terminal helix adversely affected histone H2BK123 monoubiquitination by inhibiting Rad6-Bre1-mediated ubiquitin conjugation and by promoting Ubp8/Ubp10-mediated deubiquitination. In summary, absence of yeast deubiquitinases UBP8 and/or UBP10 allows uncovering the regulation of and requirements for ubiquitin addition and removal from their physiological substrates such as histone H2B or PCNA in vivo .
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6
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Downregulation of UBE4B promotes CNS axon regrowth and functional recovery after stroke. iScience 2022; 26:105885. [PMID: 36654858 PMCID: PMC9840934 DOI: 10.1016/j.isci.2022.105885] [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: 06/23/2022] [Revised: 10/27/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The limited intrinsic regrowth capacity of corticospinal axons impedes functional recovery after cortical stroke. Although the mammalian target of rapamycin (mTOR) and p53 pathways have been identified as the key intrinsic pathways regulating CNS axon regrowth, little is known about the key upstream regulatory mechanism by which these two major pathways control CNS axon regrowth. By screening genes that regulate ubiquitin-mediated degradation of the p53 proteins in mice, we found that ubiquitination factor E4B (UBE4B) represses axonal regrowth in retinal ganglion cells and corticospinal neurons. We found that axonal regrowth induced by UBE4B depletion depended on the cooperative activation of p53 and mTOR. Importantly, overexpression of UbV.E4B, a competitive inhibitor of UBE4B, in corticospinal neurons promoted corticospinal axon sprouting and facilitated the recovery of corticospinal axon-dependent function in a cortical stroke model. Thus, our findings provide a translatable strategy for restoring corticospinal tract-dependent functions after cortical stroke.
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7
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Shukla PK, Sinha D, Leng AM, Bissell JE, Thatipamula S, Ganguly R, Radmall KS, Skalicky JJ, Shrieve DC, Chandrasekharan MB. Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 affect ubiquitination activity and decrease enzyme stability. J Biol Chem 2022; 298:102524. [PMID: 36162503 PMCID: PMC9630792 DOI: 10.1016/j.jbc.2022.102524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/28/2022] Open
Abstract
Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance, and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of helix-3 that causes defects in telomeric gene silencing, DNA repair, and protein degradation was reported over 2 decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6 in addition to disorganizing the global structure of the protein to decrease its stability in vivo. We also show that helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Providing insights into their ubiquitination defects, we determined helix-3 A126 mutations impair the initial ubiquitin charging and the final discharging steps during substrate ubiquitination by Rad6. In summary, our studies reveal that the conserved helix-3 is a crucial structural constituent that controls the organization of catalytic pockets, enzymatic activities, and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dhiraj Sinha
- IHU, Aix Marseille University, Marseille, France
| | - Andrew M Leng
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Shravya Thatipamula
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rajarshi Ganguly
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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8
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Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. eLife 2022; 11:72879. [PMID: 35737447 PMCID: PMC9225015 DOI: 10.7554/elife.72879] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/26/2022] [Indexed: 12/11/2022] Open
Abstract
Deubiquitinating enzymes (DUBs), ~100 of which are found in human cells, are proteases that remove ubiquitin conjugates from proteins, thereby regulating protein turnover. They are involved in a wide range of cellular activities and are emerging therapeutic targets for cancer and other diseases. Drugs targeting USP1 and USP30 are in clinical development for cancer and kidney disease respectively. However, the majority of substrates and pathways regulated by DUBs remain unknown, impeding efforts to prioritize specific enzymes for research and drug development. To assemble a knowledgebase of DUB activities, co-dependent genes, and substrates, we combined targeted experiments using CRISPR libraries and inhibitors with systematic mining of functional genomic databases. Analysis of the Dependency Map, Connectivity Map, Cancer Cell Line Encyclopedia, and multiple protein-protein interaction databases yielded specific hypotheses about DUB function, a subset of which were confirmed in follow-on experiments. The data in this paper are browsable online in a newly developed DUB Portal and promise to improve understanding of DUBs as a family as well as the activities of incompletely characterized DUBs (e.g. USPL1 and USP32) and those already targeted with investigational cancer therapeutics (e.g. USP14, UCHL5, and USP7).
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Affiliation(s)
- Laura M Doherty
- Harvard Medical School (HMS) Library of Integrated Network-based Cellular Signatures (LINCS) Center, Cambridge, United States.,Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Charles Tapley Hoyt
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Benjamin Gyori
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, United States.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, United States
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9
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van der Wal L, Bezstarosti K, Demmers JAA. A ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37. J Proteomics 2022; 262:104592. [PMID: 35489684 DOI: 10.1016/j.jprot.2022.104592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/05/2022] [Accepted: 04/17/2022] [Indexed: 12/12/2022]
Abstract
The removal of (poly)ubiquitin chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Three different deubiquitinating enzymes (DUBs) are associated to the human proteasome, PSMD14 (RPN11), USP14 and UCH37 (UCHL5). However, the functional roles and specificities of these proteasomal DUBs remain elusive. To reveal the specificities of proteasome associated DUBs, we used SILAC based quantitative ubiquitinomics to study the effects of CRISPR-Cas9 based knockout of each of these DUBs on the dynamic cellular ubiquitinome. We observed distinct effects on the global ubiquitinome upon removal of either USP14 or UCH37, while the simultaneous removal of both DUBs suggested less functional redundancy than previously anticipated. We also investigated whether the small molecule inhibitor b-AP15 has the potential to specifically target USP14 and UCH37 by comparing treatment of wild-type versus USP14/UCH37 double-knockout cells with this drug. Strikingly, broad and severe off-target effects were observed, questioning the alleged specificity of this inhibitor. In conclusion, this work presents novel insights into the function of proteasome associated DUBs and illustrates the power of in-depth ubiquitinomics for screening the activity of DUBs and of DUB modulating compounds. SIGNIFICANCE Introduction: The removal of (poly)ubiquitin chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Three different deubiquitinating enzymes (DUBs) are associated to the human proteasome, PSMD14/RPN11, USP14 and UCH37/UCHL5. However, the functional roles and specificities of these proteasomal DUBs remains elusive. MATERIALS & METHODS We have applied a SILAC based quantitative ubiquitinomics to study the effects of CRISPR-Cas9 based knockout of each of these DUBs on the dynamic cellular ubiquitinome. Also, we have studied the function of the small molecule inhibitor b-AP15, which has the potential to specifically target USP14 and UCH37. RESULTS We report distinct effects on the ubiquitinome and the ability of the proteasome to clear proteins upon removal of either USP14 or UCH37, while the simultaneous removal of both DUBs suggests less redundancy than previously anticipated. In addition, broad and severe off-target effects were observed for b-AP15, questioning the alleged specificity of this inhibitor. CONCLUSIONS This work presents novel insights into the function of proteasome associated DUBs and illustrates the power of in-depth ubiquitinomics for screening the activity of DUBs and of DUB modulating compounds.
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Affiliation(s)
- Lennart van der Wal
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands.
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10
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Martin RM, Bereman MS, Marsden KC. The Cyanotoxin 2,4-DAB Reduces Viability and Causes Behavioral and Molecular Dysfunctions Associated with Neurodegeneration in Larval Zebrafish. Neurotox Res 2022; 40:347-364. [PMID: 35029765 PMCID: PMC9035002 DOI: 10.1007/s12640-021-00465-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
Exposure to cyanotoxins has been linked to neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer's, and Parkinson's disease. While the cyanotoxin β-methylamino-L-alanine (BMAA) has received much attention, cyanobacteria produce many cyanotoxic compounds, several of which have been detected in nature alongside BMAA, including 2,4-diaminobutyric acid (2,4-DAB) and N-(2-aminoethyl)glycine (AEG). Thus, the question of whether 2,4-DAB and AEG also cause neurotoxic effects in vivo is of great interest, as is the question of whether they interact to enhance toxicity. Here, we evaluate the toxic and neurotoxic effects of these cyanotoxins alone or in combination by measuring zebrafish larval viability and behavior after exposure. 2,4-DAB was the most potent cyanotoxin as it decreased larval viability by approximately 50% at 6 days post fertilization, while BMAA and AEG decreased viability by just 16% and 8%, respectively. Although we only observed minor neurotoxic effects on spontaneous locomotion, BMAA and AEG enhanced acoustic startle sensitivity, and they interacted in an additive manner to exert their effects. 2,4-DAB; however, only modulated startle kinematics, an indication of motor dysfunction. To investigate the mechanisms of 2,4-DAB's effects, we analyzed the protein profile of larval zebrafish exposed to 500 µM 2,4-DAB at two time points and identified molecular signatures consistent with neurodegeneration, including disruption of metabolic pathways and downregulation of the ALS-associated genes SOD1 and UBQLN4. Together, our data demonstrate that BMAA and its isomers AEG and 2,4-DAB cause neurotoxic effects in vivo, with 2,4-DAB as the most potent of the three in the zebrafish model.
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Affiliation(s)
- Rubia M Martin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Kurt C Marsden
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
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11
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Cabrera SF, Muratore ME, Buijnsters P. The intriguing role of USP30 inhibitors as deubiquitinating enzymes from the patent literature since 2013. Expert Opin Ther Pat 2021; 32:523-559. [PMID: 34743664 DOI: 10.1080/13543776.2022.2003780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION : Ubiquitin specific peptidase 30 (USP30) is a mitochondrial deubiquitinase that antagonizes ubiquitination-mediated mitophagy of damaged or impaired mitochondria driven by the activity of PARK2/Parkin ubiquitin ligase and PINK1 protein kinase. Researchers have related low levels of USP30 to enhanced mitophagy and therefore have been pursuing mitophagy activation utilizing USP30 inhibitors as an alternative approach to target neurodegenerative disorders and other human diseases associated with defective mitophagy. AREAS COVERED : This review covers the research and patent literature on the discovery and development of USP30 inhibitors since 2013. EXPERT OPINION : Strategies towards mitophagy activation utilizing small-molecule inhibitors of USP30 have emerged as alternative pathways for the potential treatment of many human diseases. Research efforts have led to identifying good potent and selective small-molecule USP30 inhibitors. Most small-molecule USP30 inhibitors share a common N-cyano motif that binds covalently to the target. Non-covalently binding inhibitors have recently been disclosed as well. Lead compounds exhibit satisfactory inhibitory activities and are currently in preclinical development. Regrettably, complete pharmacological characterization and in vivo evaluation to validate and prove the therapeutic potential is lacking. Target validation could pave the way for discovering and developing USP30 inhibitors that could ultimately lead to marketed drugs.
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Affiliation(s)
- Sofia Ferrer Cabrera
- A Division of Janssen Pharmaceutica NV, Discovery Chemistry department, Discovery, Product Development & Supply, Janssen Research and Development, Beerse, Belgium
| | - Michael E Muratore
- A Division of Janssen Pharmaceutica NV, Discovery Chemistry department, Discovery, Product Development & Supply, Janssen Research and Development, Beerse, Belgium
| | - Peter Buijnsters
- A Division of Janssen Pharmaceutica NV, Discovery Chemistry department, Discovery, Product Development & Supply, Janssen Research and Development, Beerse, Belgium
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Atieh TB, Roth J, Yang X, Hoop CL, Baum J. DJ-1 Acts as a Scavenger of α-Synuclein Oligomers and Restores Monomeric Glycated α-Synuclein. Biomolecules 2021; 11:biom11101466. [PMID: 34680099 PMCID: PMC8533443 DOI: 10.3390/biom11101466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 12/03/2022] Open
Abstract
Glycation of α-synuclein (αSyn), as occurs with aging, has been linked to the progression of Parkinson’s disease (PD) through the promotion of advanced glycation end-products and the formation of toxic oligomers that cannot be properly cleared from neurons. DJ-1, an antioxidative protein that plays a critical role in PD pathology, has been proposed to repair glycation in proteins, yet a mechanism has not been elucidated. In this study, we integrate solution nuclear magnetic resonance (NMR) spectroscopy and liquid atomic force microscopy (AFM) techniques to characterize glycated N-terminally acetylated-αSyn (glyc-ac-αSyn) and its interaction with DJ-1. Glycation of ac-αSyn by methylglyoxal increases oligomer formation, as visualized by AFM in solution, resulting in decreased dynamics of the monomer amide backbone around the Lys residues, as measured using NMR. Upon addition of DJ-1, this NMR signature of glyc-ac-αSyn monomers reverts to a native ac-αSyn-like character. This phenomenon is reversible upon removal of DJ-1 from the solution. Using relaxation-based NMR, we have identified the binding site on DJ-1 for glycated and native ac-αSyn as the catalytic pocket and established that the oxidation state of the catalytic cysteine is imperative for binding. Based on our results, we propose a novel mechanism by which DJ-1 scavenges glyc-ac-αSyn oligomers without chemical deglycation, suppresses glyc-ac-αSyn monomer–oligomer interactions, and releases free glyc-ac-αSyn monomers in solution. The interference of DJ-1 with ac-αSyn oligomers may promote free ac-αSyn monomer in solution and suppress the propagation of toxic oligomer and fibril species. These results expand the understanding of the role of DJ-1 in PD pathology by acting as a scavenger for aggregated αSyn.
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13
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Nakamura T, Oh CK, Zhang X, Lipton SA. Protein S-nitrosylation and oxidation contribute to protein misfolding in neurodegeneration. Free Radic Biol Med 2021; 172:562-577. [PMID: 34224817 PMCID: PMC8579830 DOI: 10.1016/j.freeradbiomed.2021.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Neurodegenerative disorders like Alzheimer's disease and Parkinson's disease are characterized by progressive degeneration of synapses and neurons. Accumulation of misfolded/aggregated proteins represents a pathological hallmark of most neurodegenerative diseases, potentially contributing to synapse loss and neuronal damage. Emerging evidence suggests that misfolded proteins accumulate in the diseased brain at least in part as a consequence of excessively generated reactive oxygen species (ROS) and reactive nitrogen species (RNS). Mechanistically, not only disease-linked genetic mutations but also known risk factors for neurodegenerative diseases, such as aging and exposure to environmental toxins, can accelerate production of ROS/RNS, which contribute to protein misfolding - in many cases mimicking the effect of rare genetic mutations known to be linked to the disease. This review will focus on the role of RNS-dependent post-translational modifications, such as S-nitrosylation and tyrosine nitration, in protein misfolding and aggregation. Specifically, we will discuss molecular mechanisms whereby RNS disrupt the activity of the cellular protein quality control machinery, including molecular chaperones, autophagy/lysosomal pathways, and the ubiquitin-proteasome system (UPS). Because chronic accumulation of misfolded proteins can trigger mitochondrial dysfunction, synaptic damage, and neuronal demise, further characterization of RNS-mediated protein misfolding may establish these molecular events as therapeutic targets for intervention in neurodegenerative diseases.
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Affiliation(s)
- Tomohiro Nakamura
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Chang-Ki Oh
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xu Zhang
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Stuart A Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA; Department of Neurosciences, University of California San Diego, School of Medicine, La Jolla, CA, 92093, USA.
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14
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Signaling Pathways Regulated by UBR Box-Containing E3 Ligases. Int J Mol Sci 2021; 22:ijms22158323. [PMID: 34361089 PMCID: PMC8346999 DOI: 10.3390/ijms22158323] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular bases of their substrate recognition and the biological impact of the clearance of their substrates on cellular signaling pathways can provide valuable insights into the regulation of these pathways. This review provides an overview of the current knowledge of the binding mechanism of UBR box N-recognin/N-degron interactions and their roles in signaling pathways linked to G-protein-coupled receptors, apoptosis, mitochondrial quality control, inflammation, and DNA damage. The targeting of these UBR box N-recognins can provide potential therapies to treat diseases such as cancer and neurodegenerative diseases.
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15
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Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons. Commun Biol 2021; 4:736. [PMID: 34127790 PMCID: PMC8203616 DOI: 10.1038/s42003-021-02272-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Aggregates of hyperphosphorylated tau protein are a pathological hallmark of more than 20 distinct neurodegenerative diseases, including Alzheimer’s disease, progressive supranuclear palsy, and frontotemporal dementia. While the exact mechanism of tau aggregation is unknown, the accumulation of aggregates correlates with disease progression. Here we report a genome-wide CRISPR screen to identify modulators of endogenous tau protein for the first time. Primary screens performed in SH-SY5Y cells, identified positive and negative regulators of tau protein levels. Hit validation of the top 43 candidate genes was performed using Ngn2-induced human cortical excitatory neurons. Using this approach, genes and pathways involved in modulation of endogenous tau levels were identified, including chromatin modifying enzymes, neddylation and ubiquitin pathway members, and components of the mTOR pathway. TSC1, a critical component of the mTOR pathway, was further validated in vivo, demonstrating the relevance of this screening strategy. These findings may have implications for treating neurodegenerative diseases in the future. Using an unbiased genome-wide CRISPR screen approach, Sanchez et al. identified modulators of endogenous tau protein. This study suggests that chromatin modifiers, neddylation, ubiquitination, and the mTOR pathways regulate overall levels of tau protein in neurons, which could help in future identification of therapeutics for neurodegenerative diseases.
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16
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Small molecules as tools for functional assessment of deubiquitinating enzyme function. Cell Chem Biol 2021; 28:1090-1100. [PMID: 34089649 DOI: 10.1016/j.chembiol.2021.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/05/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a largely understudied and untapped resource in the toolkit of protein degradation functionalities. They comprise a large repertoire of enzymes that remove ubiquitin from substrates in a variety of cellular and pathophysiological contexts, and have enormous potential for research and clinical use. It is only within the last 5 years that potent, selective, and well-characterized small-molecule inhibitors of DUBs have been described. These compounds are now being used to study the biological roles of DUBs. Here, we describe downstream applications of small-molecule inhibitors for studying DUBs and provide a framework for future studies. We highlight recent examples of using these inhibitors to confirm and explore the role of these enzymes in both normal and pathological contexts. These studies represent the first steps in the burgeoning field of pharmacological and chemoproteomic studies of DUBs, which will be critical for the continued advancement of DUB field.
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17
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Shrestha R, Das C. Crystal structure of the Thr316Ala mutant of a yeast JAMM deubiquitinase: implication of active-site loop dynamics in catalysis. Acta Crystallogr F Struct Biol Commun 2021; 77:163-170. [PMID: 34100774 PMCID: PMC8186415 DOI: 10.1107/s2053230x21005124] [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: 03/09/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
AMSH, an endosome-associated deubiquitinase (DUB) with a high specificity for Lys63-linked polyubiquitin chains, plays an important role in endosomal-lysosomal sorting and down-regulation of cell-surface receptors. AMSH belongs to the JAMM family of DUBs that contain two insertion segments, Ins-1 and Ins-2, in the catalytic domain relative to the JAMM core found in the archaebacterial AfJAMM. Structural analyses of the AMSH homologs human AMSH-LP and fission yeast Sst2 reveal a flap-like structure formed by Ins-2 near the active site that appears to open and close during its catalytic cycle. A conserved phenylalanine residue of the flap interacts with a conserved aspartate residue of the Ins-1 β-turn to form a closed `lid' over the active site in the substrate-bound state. Analyses of these two residues (Phe403 and Asp315) in Sst2 showed that their interaction plays an important role in controlling the flexibility of Ins-2. The Lys63-linked diubiquitin substrate-bound form of Sst2 showed that the conserved phenylalanine also interacts with Thr316 of Ins-1, which is substituted by tyrosine in other AMSH orthologs. Although Thr316 makes no direct interaction with the substrate, its mutation to alanine resulted in a significant loss of activity. In order to understand the contribution of Thr316 to catalysis, the crystal structure of this mutant was determined. In spite of the effect of the mutation on catalytic activity, the structure of the Sst2 Thr316Ala mutant did not reveal significant changes in either the overall structure or the active-site arrangement relative to the wild type. The Phe403-Thr316 van der Waals interaction is impaired by the Thr316Ala mutation, abrogating the adoption of the closed active-site conformation required for catalysis. Since van der Waals interactions with phenylalanine are conserved across substrate-bound forms of AMSH-LP and Sst2, these interactions may be critical for loop immobilization and the positioning of the isopeptide bond of Lys63-linked polyubiquitin-chain substrates.
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Affiliation(s)
- Rashmi Shrestha
- Chemistry Department, Berea College, CPO 2191, Berea, KY 40404, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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18
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Krabill AD, Chen H, Hussain S, Hewitt CS, Imhoff RD, Muli CS, Das C, Galardy PJ, Wendt MK, Flaherty DP. Optimization and Anti-Cancer Properties of Fluoromethylketones as Covalent Inhibitors for Ubiquitin C-Terminal Hydrolase L1. Molecules 2021; 26:1227. [PMID: 33668938 PMCID: PMC7956625 DOI: 10.3390/molecules26051227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
The deubiquitinating enzyme (DUB) UCHL1 is implicated in various disease states including neurodegenerative disease and cancer. However, there is a lack of quality probe molecules to gain a better understanding on UCHL1 biology. To this end a study was carried out to fully characterize and optimize the irreversible covalent UCHL1 inhibitor VAEFMK. Structure-activity relationship studies identified modifications to improve activity versus the target and a full cellular characterization was carried out for the first time with this scaffold. The studies produced a new inhibitor, 34, with an IC50 value of 7.7 µM against UCHL1 and no observable activity versus the closest related DUB UCHL3. The molecule was also capable of selectively inhibiting UCHL1 in cells and did not demonstrate any discernible off-target toxicity. Finally, the molecule was used for initial probe studies to assess the role of UCHL1 role in proliferation of myeloma cells and migration behavior in small cell lung cancer cells making 34 a new tool to be used in the biological evaluation of UCHL1.
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Affiliation(s)
- Aaron D. Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Sajjad Hussain
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA
| | - Chad S. Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Ryan D. Imhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Christine S. Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
| | - Chittaranjan Das
- Department of Chemistry, College of Science, 560 Oval Dr., West Lafayette, IN 47907, USA;
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
| | - Paul J. Galardy
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. Guggenheim 15, Rochester, MN 55905, USA; (S.H.); (P.J.G.)
| | - Michael K. Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
| | - Daniel P. Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, 575 Stadium Mall Dr., West Lafayette, IN 47907, USA; (A.D.K.); (H.C.); (C.S.H.); (R.D.I.); (C.S.M.); (M.K.W.)
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 University St., West Lafayette, IN 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Ln., West Lafayette, IN 47907, USA
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19
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Systematic characterization of mutations altering protein degradation in human cancers. Mol Cell 2021; 81:1292-1308.e11. [PMID: 33567269 PMCID: PMC9245451 DOI: 10.1016/j.molcel.2021.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/01/2020] [Accepted: 01/17/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitin-proteasome system (UPS) is the primary route for selective protein degradation in human cells. The UPS is an attractive target for novel cancer therapies, but the precise UPS genes and substrates important for cancer growth are incompletely understood. Leveraging multi-omics data across more than 9,000 human tumors and 33 cancer types, we found that over 19% of all cancer driver genes affect UPS function. We implicate transcription factors as important substrates and show that c-Myc stability is modulated by CUL3. Moreover, we developed a deep learning model (deepDegron) to identify mutations that result in degron loss and experimentally validated the prediction that gain-of-function truncating mutations in GATA3 and PPM1D result in increased protein stability. Last, we identified UPS driver genes associated with prognosis and the tumor microenvironment. This study demonstrates the important role of UPS dysregulation in human cancer and underscores the potential therapeutic utility of targeting the UPS.
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20
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Yang SY, Castellani CA, Longchamps RJ, Pillalamarri VK, O'Rourke B, Guallar E, Arking DE. Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. Genome Res 2021; 31:349-358. [PMID: 33441415 PMCID: PMC7919448 DOI: 10.1101/gr.269381.120] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA copy number (mtDNA-CN) is a proxy for mitochondrial function and is associated with aging-related diseases. However, it is unclear how mtDNA-CN measured in blood can reflect diseases that primarily manifest in other tissues. Using the Genotype-Tissue Expression Project, we interrogated relationships between mtDNA-CN measured in whole blood and gene expression from whole blood and 47 additional tissues in 419 individuals. mtDNA-CN was significantly associated with expression of 700 genes in whole blood, including nuclear genes required for mtDNA replication. Significant enrichment was observed for splicing and ubiquitin-mediated proteolysis pathways, as well as target genes for the mitochondrial transcription factor NRF1. In nonblood tissues, there were more significantly associated genes than expected in 30 tissues, suggesting that global gene expression in those tissues is correlated with blood-derived mtDNA-CN. Neurodegenerative disease pathways were significantly associated in multiple tissues, and in an independent data set, the UK Biobank, we observed that higher mtDNA-CN was significantly associated with lower rates of both prevalent (OR = 0.89, CI = 0.83; 0.96) and incident neurodegenerative disease (HR = 0.95, 95% CI = 0.91;0.98). The observation that mtDNA-CN measured in blood is associated with gene expression in other tissues suggests that blood-derived mtDNA-CN can reflect metabolic health across multiple tissues. Identification of key pathways including splicing, RNA binding, and catalysis reinforces the importance of mitochondria in maintaining cellular homeostasis. Finally, validation of the role of mtDNA CN in neurodegenerative disease in a large independent cohort study solidifies the link between blood-derived mtDNA-CN, altered gene expression in multiple tissues, and aging-related disease.
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Affiliation(s)
- Stephanie Y Yang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Christina A Castellani
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ryan J Longchamps
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Vamsee K Pillalamarri
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Brian O'Rourke
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Eliseo Guallar
- Departments of Epidemiology and Medicine, and Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Dan E Arking
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.,Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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21
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Maiti A, Saha N, Shukla A, Sarkar S, Sil AK. Cigarette smoke affects ESCRT-mediated vacuolar activity in Saccharomyces cerevisiae. Toxicol Lett 2020; 338:97-104. [PMID: 33309995 DOI: 10.1016/j.toxlet.2020.12.008] [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: 03/17/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 10/22/2022]
Abstract
Cigarette smoking is a risk factor for developing chronic obstructive pulmonary disease and protein aggresome formation is considered to be a hallmark event for the disease. Since dysfunction of lysosome-mediated protein degradation leads to enhanced accumulation of misfolded proteins and subsequent aggresome formation, we examined the effect of cigarette smoke extract (CSE) on ESCRT-mediated sorting in S. cerevisiae as this process is necessary for the functioning of the vacuole, the lysosomal equivalent in yeast. An operational ESCRT pathway is essential for ion homeostasis and our observation that exposure to CSE caused increased sensitivity to LiCl indicated CSE-induced impairment of ESCRT function. To confirm the inhibition of ESCRT function, the targeting of carboxypeptidase S (CPS), which reaches the vacuole lumen via the ESCRT pathway, was examined. Treatment with CSE resulted in the mislocalization of GFP-tagged CPS to the vacuolar membrane, instead of the vacuolar lumen, confirming defective functioning of the ESCRT machinery in CSE-treated cells. Further analysis revealed that CSE-treatment inhibited the recruitment of the ESCRT-0 component, Vps27, to the endosome surface, which is a key event is for the functioning of the ESCRT pathway. This lack of endosomal recruitment of Vps27 most likely results from a depletion of the endosomally-enriched lipid, phosphatidylinositol 3-phosphate (PI3-P), which is the target of Vps27. This is supported by our observation that the presence of excess leucine, a known activator of the lipid kinase responsible for the generation of PI3-P, Vps34, in the medium can rescue the CSE-induced ESCRT misfunctioning. Thus, the current study provides an insight into CSE-induced aggresome formation as it documents that CSE treatment compromises vacuolar degradation due to an impairment of the ESCRT pathway, which likely stems from the inhibition of Vps34. It also indicates that leucine has the potential to attenuate the CSE-induced accumulation of misfolded proteins.
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Affiliation(s)
- Arnab Maiti
- Department of Microbiology, University of Calcutta, 35 B.C Road, Kolkata, 700019, India.
| | - Nabanita Saha
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme, VII M, Kolkata, 700054, India.
| | - Aditya Shukla
- Department of Microbiology, University of Calcutta, 35 B.C Road, Kolkata, 700019, India.
| | - Srimonti Sarkar
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme, VII M, Kolkata, 700054, India.
| | - Alok Kumar Sil
- Department of Microbiology, University of Calcutta, 35 B.C Road, Kolkata, 700019, India.
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22
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Pathak GA, Silzer TK, Sun J, Zhou Z, Daniel AA, Johnson L, O'Bryant S, Phillips NR, Barber RC. Genome-Wide Methylation of Mild Cognitive Impairment in Mexican Americans Highlights Genes Involved in Synaptic Transport, Alzheimer's Disease-Precursor Phenotypes, and Metabolic Morbidities. J Alzheimers Dis 2020; 72:733-749. [PMID: 31640099 DOI: 10.3233/jad-190634] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Mexican American population is among the fastest growing aging population and has a younger onset of cognitive decline. This group is also heavily burdened with metabolic conditions such as hypertension, diabetes, and obesity. Unfortunately, limited research has been conducted in this group. Understanding methylation alterations, which are influenced by both genetic and lifestyle factors, is key to identifying and addressing the root cause for mild cognitive impairment, a clinical precursor for dementia. We conducted an epigenome-wide association study on a community-based Mexican American population using the Illumina EPIC array. Following rigorous quality control measures, we identified 10 CpG sites to be differentially methylated between normal controls and individuals with mild cognitive impairment annotated to PKIB, KLHL29, SEPT9, OR2C3, CPLX3, BCL2L2-PABPN1, and CCNY. We found four regions to be differentially methylated in TMEM232, SLC17A8, ALOX12, and SEPT8. Functional gene-set analysis identified four gene-sets, RIN3, SPEG, CTSG, and UBE2L3, as significant. The gene ontology and pathway analyses point to neuronal cell death, metabolic dysfunction, and inflammatory processes. We found 1,450 processes to be enriched using empirical Bayes gene-set enrichment. In conclusion, the functional overlap of differentially methylated genes associated with cognitive impairment in Mexican Americans implies cross-talk between metabolically-instigated systemic inflammation and disruption of synaptic vesicular transport.
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Affiliation(s)
- Gita A Pathak
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Talisa K Silzer
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jie Sun
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Zhengyang Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Ann A Daniel
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Leigh Johnson
- Institute of Translational Medicine, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Pharmacology and Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Sid O'Bryant
- Institute of Translational Medicine, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA.,Department of Pharmacology and Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nicole R Phillips
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Robert C Barber
- Department of Pharmacology and Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
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23
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De Cesare V, Moran J, Traynor R, Knebel A, Ritorto MS, Trost M, McLauchlan H, Hastie CJ, Davies P. High-throughput matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry-based deubiquitylating enzyme assay for drug discovery. Nat Protoc 2020; 15:4034-4057. [PMID: 33139956 DOI: 10.1038/s41596-020-00405-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Deubiquitylating enzymes (DUBs) play a vital role in the ubiquitin pathway by editing or removing ubiquitin from their substrate. As breakthroughs within the ubiquitin field continue to highlight the potential of deubiquitylating enzymes as drug targets, there is increasing demand for versatile high-throughput (HT) tools for the identification of potent and selective DUB modulators. Here we present the HT adaptation of the previously published MALDI-TOF-based DUB assay method. In a MALDI-TOF DUB assay, we quantitate the amount of mono-ubiquitin generated by the in vitro cleavage of ubiquitin chains by DUBs. The method has been specifically developed for use with nanoliter-dispensing robotics to meet drug discovery requirements for the screening of large and diverse compound libraries. Contrary to the most common DUB screening technologies currently available, the MALDI-TOF DUB assay combines the use of physiological substrates with the sensitivity and reliability of the mass spectrometry-based readout.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
| | - Jennifer Moran
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Ryan Traynor
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.,Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, UK
| | - Hilary McLauchlan
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dundee, Scotland, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, Scotland, UK.
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24
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Tian T, McLean JW, Wilson JA, Wilson SM. Examination of genetic and pharmacological tools to study the proteasomal deubiquitinating enzyme ubiquitin-specific protease 14 in the nervous system. J Neurochem 2020; 156:309-323. [PMID: 32901953 DOI: 10.1111/jnc.15180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Strategies for enhancing protein degradation have been proposed for treating neurological diseases associated with a decline in proteasome activity. A proteasomal deubiquitinating enzyme that controls substrate entry into proteasomes, ubiquitin-specific protease 14 (USP14), is an attractive candidate for therapies that modulate proteasome activity. This report tests the validity of genetic and pharmacological tools to study USP14's role in regulating protein abundance. Although previous studies implicated USP14 in the degradation of microtubule associate protein tau, tar DNA binding protein, and prion protein, the levels of these proteins were similar in our neurons cultured from wild type and USP14-deficient mice. Neither loss nor over-expression of USP14 affected the levels of these proteins in mice, implying that modifying the amount of USP14 is not sufficient to alter their steady-state levels. However, neuronal over-expression of a catalytic mutant of USP14 showed that manipulating USP14's ubiquitin-hydrolase activity altered the levels of specific proteins in vivo. Although pharmacological inhibitors of USP14's ubiquitin-hydrolase activity reduced microtubule associate protein tau, tar DNA binding protein, and prion protein in culture, the effect was similar in wild type and USP14-deficient neurons, thus impacting their use for specifically evaluating USP14 in a therapeutic manner. While examining how targeting USP14 may affect other proteins in vivo, this report showed that fatty acid synthase, v-rel reticuloendotheliosis viral oncogene homolog, CTNNB1, and synaptosome associated protein 23 are reduced in USP14-deficient mice; however, loss of USP14 differentially altered the levels of these proteins in the liver and brain. As such, it is critical to more thoroughly examine how inhibiting USP14 alters protein abundance to determine if targeting USP14 will be a beneficial strategy for treating neurodegenerative diseases.
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Affiliation(s)
- Tina Tian
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John W McLean
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Julie A Wilson
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Scott M Wilson
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
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25
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Xie K, Kapetanou M, Sidiropoulou K, Bano D, Gonos ES, Djordjevic AM, Ehninger D. Signaling pathways of dietary energy restriction and metabolism on brain physiology and in age-related neurodegenerative diseases. Mech Ageing Dev 2020; 192:111364. [PMID: 32991920 DOI: 10.1016/j.mad.2020.111364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Several laboratory animal models have shown that dietary energy restriction (ER) can promote longevity and improve various health aspects in old age. However, whether the entire spectrum of ER-induced short- and long-term physiological and metabolic adaptions is translatable to humans remains to be determined. In this review article, we present recent evidence towards the elucidation of the impact of ER on brain physiology and in age-related neurodegenerative diseases. We also discuss modulatory influences of ER on metabolism and overall on human health, limitations of current experimental designs as well as future perspectives for ER trials in humans. Finally, we summarize signaling pathways and processes known to be affected by both aging and ER with a special emphasis on the link between ER and cellular proteostasis.
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Affiliation(s)
- Kan Xie
- Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany
| | - Marianna Kapetanou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | | | - Daniele Bano
- Aging and Neurodegeneration Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany
| | - Efstathios S Gonos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | - Aleksandra Mladenovic Djordjevic
- Department of Neurobiology, Institute for Biological Research 'Sinisa Stankovic', University of Belgrade, National Institute of Republic of Serbia, Boulevard Despota Stefana 142, 11000 Belgrade, Serbia
| | - Dan Ehninger
- Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany.
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26
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Ramesh N, Kour S, Anderson EN, Rajasundaram D, Pandey UB. RNA-recognition motif in Matrin-3 mediates neurodegeneration through interaction with hnRNPM. Acta Neuropathol Commun 2020; 8:138. [PMID: 32811564 PMCID: PMC7437177 DOI: 10.1186/s40478-020-01021-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is an adult-onset, fatal neurodegenerative disease characterized by progressive loss of upper and lower motor neurons. While pathogenic mutations in the DNA/RNA-binding protein Matrin-3 (MATR3) are linked to ALS and distal myopathy, the molecular mechanisms underlying MATR3-mediated neuromuscular degeneration remain unclear. Methods We generated Drosophila lines with transgenic insertion of human MATR3 wildtype, disease-associated variants F115C and S85C, and deletion variants in functional domains, ΔRRM1, ΔRRM2, ΔZNF1 and ΔZNF2. We utilized genetic, behavioral and biochemical tools for comprehensive characterization of our models in vivo and in vitro. Additionally, we employed in silico approaches to find transcriptomic targets of MATR3 and hnRNPM from publicly available eCLIP datasets. Results We found that targeted expression of MATR3 in Drosophila muscles or motor neurons shorten lifespan and produces progressive motor defects, muscle degeneration and atrophy. Strikingly, deletion of its RNA-recognition motif (RRM2) mitigates MATR3 toxicity. We identified rump, the Drosophila homolog of human RNA-binding protein hnRNPM, as a modifier of mutant MATR3 toxicity in vivo. Interestingly, hnRNPM physically and functionally interacts with MATR3 in an RNA-dependent manner in mammalian cells. Furthermore, common RNA targets of MATR3 and hnRNPM converge in biological processes important for neuronal health and survival. Conclusions We propose a model of MATR3-mediated neuromuscular degeneration governed by its RNA-binding domains and modulated by interaction with splicing factor hnRNPM. Electronic supplementary material The online version of this article (10.1186/s40478-020-01021-5) contains supplementary material, which is available to authorized users.
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27
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Ko YU, Song HY, Kim WK, Yune TY, Yun N, Oh YJ. Calpain-mediated cleavage of Fbxw7 during excitotoxicity. Neurosci Lett 2020; 736:135265. [PMID: 32707070 DOI: 10.1016/j.neulet.2020.135265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022]
Abstract
Neuronal cell death induced by ischemic injury has been attributed to glutamate receptor-mediated excitotoxicity, which is known to be accompanied by Ca2+ overload in the cytoplasm with concomitant activation of calcium-dependent mechanisms. More specifically, the overactivation of calpains, calcium-dependent cysteine proteases, have been associated with neuronal cell death following glutamate treatment. Previously, we observed decreased expression levels of F-box/WD repeat domain-containing protein 7 (Fbxw7) after the hyperactivation of cyclin-dependent kinase 5 (Cdk5) in cortical neurons challenged with glutamate. As determined using in vitro calpain cleavage assays, we demonstrated that the cleavage of Fbxw7 was mediated by activated calpain and attenuated in the presence of the calpain inhibitor, calpeptin. Using the rat middle cerebral artery occlusion model, we confirmed that Fbxw7 was indeed cleaved by activated calpain in the ipsilateral cortex. Based on our data, we hypothesize that the negative regulation of Fbxw7 by calpain may contribute to neuronal cell death and that the preservation of Fbxw7 by the inhibition of calpain, Cdk5, or both composes a novel protective mechanism following excitotoxicity.
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Affiliation(s)
- Yeon Uk Ko
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 03722, South Korea
| | - Hwa Young Song
- Department of Neuroscience, College of Medicine, Korea University, Seoul 02841, South Korea
| | - Won-Ki Kim
- Department of Neuroscience, College of Medicine, Korea University, Seoul 02841, South Korea
| | - Tae Young Yune
- Age-Related and Brain Diseases Research Center, Kyung Hee University, Seoul 02447, South Korea
| | - Nuri Yun
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 03722, South Korea.
| | - Young J Oh
- Department of Systems Biology, Yonsei University College of Life Science and Biotechnology, Seoul 03722, South Korea.
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28
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Frydrýšková K, Mašek T, Pospíšek M. Changing faces of stress: Impact of heat and arsenite treatment on the composition of stress granules. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1596. [PMID: 32362075 DOI: 10.1002/wrna.1596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 11/07/2022]
Abstract
Stress granules (SGs), hallmarks of the cellular adaptation to stress, promote survival, conserve cellular energy, and are fully dissolved upon the cessation of stress treatment. Different stresses can initiate the assembly of SGs, but arsenite and heat are the best studied of these stresses. The composition of SGs and posttranslational modifications of SG proteins differ depending on the type and severity of the stress insult, methodology used, cell line, and presence of overexpressed and tagged proteins. A group of 18 proteins showing differential localization to SGs in heat- and arsenite-stressed mammalian cell lines is described. Upon severe and prolonged stress, physiological SGs transform into more solid protein aggregates that are no longer reversible and do not contain mRNA. Similar pathological inclusions are hallmarks of neurodegenerative diseases. SGs induced by heat stress are less dynamic than SGs induced by arsenite and contain a set of unique proteins and linkage-specific polyubiquitinated proteins. The same types of ubiquitin linkages have been found to contribute to the development of neurodegenerative disorders such as Parkinson disease, Alzheimer disease, and amyotrophic lateral sclerosis (ALS). We propose heat stress-induced SGs as a possible model of an intermediate stage along the transition from dynamic, fully reversible arsenite stress-induced SGs toward aberrant SGs, the hallmark of neurodegenerative diseases. Stress- and methodology-specific differences in the compositions of SGs and the transition of SGs to aberrant protein aggregates are discussed. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Martin Pospíšek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
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29
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Elmatboly AM, Sherif AM, Deeb DA, Benmelouka A, Bin-Jumah MN, Aleya L, Abdel-Daim MM. The impact of proteostasis dysfunction secondary to environmental and genetic causes on neurodegenerative diseases progression and potential therapeutic intervention. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11461-11483. [PMID: 32072427 DOI: 10.1007/s11356-020-07914-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
Aggregation of particular proteins in the form of inclusion bodies or plaques followed by neuronal death is a hallmark of neurodegenerative proteopathies such as primary Parkinsonism, Alzheimer's disease, Lou Gehrig's disease, and Huntington's chorea. Complex polygenic and environmental factors implicated in these proteopathies. Accumulation of proteins in these disorders indicates a substantial disruption in protein homeostasis (proteostasis). Proteostasis or cellular proteome homeostasis is attained by the synchronization of a group of cellular mechanisms called the proteostasis network (PN), which is responsible for the stability of the proteome and achieves the equilibrium between synthesis, folding, and degradation of proteins. In this review, we will discuss the different types of PN and the impact of PN component dysfunction on the four major neurodegenerative diseases mentioned earlier. Graphical abstract.
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Affiliation(s)
| | - Ahmed M Sherif
- Faculty of Medicine, Zagazig University, El-Sharkia, Egypt
| | - Dalia A Deeb
- Faculty of Medicine, Zagazig University, El-Sharkia, Egypt
| | - Amira Benmelouka
- Faculty of Medicine, University of Algiers, Sidi M'Hamed, Algeria
| | - May N Bin-Jumah
- Biology Department, College Of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon Cedex, France
| | - Mohamed M Abdel-Daim
- Department of Zoology, Science College, King Saud University, Riyadh, 11451, Saudi Arabia.
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt.
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30
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Thomas JM, Wang X, Guo G, Li T, Dai B, Nucifora LG, Nucifora FC, Liu Z, Xue F, Liu C, Ross CA, Smith WW. GTP-binding inhibitors increase LRRK2-linked ubiquitination and Lewy body-like inclusions. J Cell Physiol 2020; 235:7309-7320. [PMID: 32180220 DOI: 10.1002/jcp.29632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/30/2020] [Indexed: 01/05/2023]
Abstract
Parkinson's disease (PD) is one of the most common movement disorders with loss of dopaminergic neurons and the presence of Lewy bodies in certain brain areas. However, it is not clear how Lewy body (inclusion with protein aggregation) formation occurs. Mutations in leucine-rich repeat kinase 2 (LRRK2) can cause a genetic form of PD and contribute to sporadic PD with the typical Lewy body pathology. Here, we used our recently identified LRRK2 GTP-binding inhibitors as pharmacological probes to study the LRRK2-linked ubiquitination and protein aggregation. Pharmacological inhibition of GTP-binding by GTP-binding inhibitors (68 and Fx2149) increased LRRK2-linked ubiquitination predominantly via K27 linkage. Compound 68- or Fx2149 increased G2019S-LRRK2-linked ubiquitinated aggregates, which occurred through the atypical linkage types K27 and K63. Coexpression of K27R and K63R, which prevented ubiquitination via K27 and K63 linkages, reversed the effects of 68 and Fx2149. Moreover, 68 and Fx2149 also promoted G2019S-LRRK2-linked aggresome (Lewy body-like inclusion) formation via K27 and K63 linkages. These findings demonstrate that LRRK2 GTP-binding activity is critical in LRRK2-linked ubiquitination and aggregation formation. These studies provide novel insight into the LRRK2-linked Lewy body-like inclusion formation underlying PD pathogenesis.
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Affiliation(s)
- Joseph M Thomas
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Xiaobo Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Institute of Neuroscience, Soochow University School of Medicine, Suzhou, China
| | - Gongbo Guo
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tianxia Li
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bingling Dai
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leslie G Nucifora
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Frederick C Nucifora
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhaohui Liu
- Institute of Neuroscience, Soochow University School of Medicine, Suzhou, China
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Chunfeng Liu
- Institute of Neuroscience, Soochow University School of Medicine, Suzhou, China
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurology and Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pharmacology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wanli W Smith
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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31
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Krabill AD, Chen H, Hussain S, Feng C, Abdullah A, Das C, Aryal UK, Post CB, Wendt MK, Galardy PJ, Flaherty DP. Ubiquitin C-Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine-Based Inhibitor. Chembiochem 2020; 21:712-722. [PMID: 31449350 PMCID: PMC7042063 DOI: 10.1002/cbic.201900434] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Indexed: 11/09/2022]
Abstract
The deubiquitinase (DUB) ubiquitin C-terminal hydrolase L1 (UCHL1) is expressed primarily in the central nervous system under normal physiological conditions. However, UCHL1 is overexpressed in various aggressive forms of cancer with strong evidence supporting UCHL1 as an oncogene in lung, glioma, and blood cancers. In particular, the level of UCHL1 expression in these cancers correlates with increased invasiveness and metastatic behavior, as well as poor patient prognosis. Although UCHL1 is considered an oncogene with potential as a therapeutic target, there remains a significant lack of useful small-molecule probes to pharmacologically validate in vivo targeting of the enzyme. Herein, we describe the characterization of a new covalent cyanopyrrolidine-based UCHL1 inhibitory scaffold in biochemical and cellular studies to better understand the utility of this inhibitor in elucidating the role of UCHL1 in cancer biology.
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Affiliation(s)
- Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Hao Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Sajjad Hussain
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
| | - Chao Feng
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Ammara Abdullah
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, College of Science, Purdue University, 560 Oval, West Lafayette, IN, 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Biosciences Center, Purdue University, 1275 3rd St., West Lafayette, IN, 47907, USA
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, 915 W State St., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
| | - Paul J Galardy
- Division of Pediatric Hematology-Oncology, Mayo Clinic, 200 First St. SW, Guggenheim 15, Rochester, MN, 55905, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA
- Purdue Institute for Drug Discovery, 720 Clinic Dr., West Lafayette, IN, 47907, USA
- Purdue Center for Cancer Research, Hanson Life Sciences Research Building, 201 S University St., West Lafayette, IN, 47907, USA
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32
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Cha SJ, Choi HJ, Kim HJ, Choi EJ, Song KH, Im DS, Kim K. Parkin expression reverses mitochondrial dysfunction in fused in sarcoma-induced amyotrophic lateral sclerosis. INSECT MOLECULAR BIOLOGY 2020; 29:56-65. [PMID: 31290213 DOI: 10.1111/imb.12608] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/24/2019] [Accepted: 07/07/2019] [Indexed: 06/09/2023]
Abstract
Fused in sarcoma (FUS) is a DNA/RNA-binding protein associated with amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration. The exact molecular mechanisms by which FUS results in neurotoxicity have not yet been fully elucidated. Here, we found that parkin is a genetic suppressor of defective phenotypes induced by exogenous human wild type FUS in Drosophila. Although parkin overexpression did not modulate the FUS protein expression level, the locomotive defects in FUS-expressing larvae and adult flies were rescued by parkin expression. We found that FUS expression in muscle tissues resulted in a reduction of the levels and assembly of mitochondrial complex I and III subunits, as well as decreased ATP. Remarkably, expression of parkin suppressed these mitochondrial dysfunctions. Our results indicate parkin as a neuroprotective regulator of FUS-induced proteinopathy by recovering the protein levels of mitochondrial complexes I and III. Our findings on parkin-mediated neuroprotection may expand our understanding of FUS-induced ALS pathogenesis.
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Affiliation(s)
- S J Cha
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, South Korea
| | - H-J Choi
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, South Korea
| | - H-J Kim
- Department of Neural Development and Disease, Korea Brain Research Institute (KBRI), Daegu, South Korea
| | - E J Choi
- Department of Neurology, Ulsan University Hospital, Ulsan University College of Medicine, Ulsan, South Korea
| | - K-H Song
- Department of Pharmaceutical Engineering, Soonchunhyang University, Asan, South Korea
| | - D S Im
- Department of Chemistry, Soonchunhyang University, Asan, South Korea
| | - K Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, South Korea
- Department of Medical Biotechnology, Soonchunhyang University, Asan, South Korea
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33
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Itoh Y. Drug Discovery Researches on Modulators of Lysine-Modifying Enzymes Based on Strategic Chemistry Approaches. Chem Pharm Bull (Tokyo) 2020; 68:34-45. [DOI: 10.1248/cpb.c19-00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
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34
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Oeckl P, Weydt P, Thal DR, Weishaupt JH, Ludolph AC, Otto M. Proteomics in cerebrospinal fluid and spinal cord suggests UCHL1, MAP2 and GPNMB as biomarkers and underpins importance of transcriptional pathways in amyotrophic lateral sclerosis. Acta Neuropathol 2020; 139:119-134. [PMID: 31701227 DOI: 10.1007/s00401-019-02093-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/11/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease and the proteins and pathways involved in the pathophysiology are not fully understood. Even less is known about the preclinical disease phase. To uncover new ALS-related proteins and pathways, we performed a comparative proteomic analysis in cerebrospinal fluid (CSF) of asymptomatic (n = 14) and symptomatic (n = 14) ALS mutation carriers and sporadic ALS patients (n = 12) as well as post-mortem human spinal cord tissue (controls: n = 7, ALS, n = 8). Using a CSF-optimized proteomic workflow, we identified novel (e.g., UCHL1, MAP2, CAPG, GPNMB, HIST1H4A, HIST1H2B) and well-described (e.g., NEFL, NEFH, NEFM, CHIT1, CHI3L1) protein level changes in CSF of sporadic and genetic ALS patients with enrichment of proteins related to transcription, cell cycle and lipoprotein remodeling (total protein IDs: 2303). No significant alteration was observed in asymptomatic ALS mutation carriers representing the prodromal disease phase. We confirmed UCHL1, MAP2, CAPG and GPNMB as novel biomarker candidates for ALS in an independent validation cohort of patients (n = 117) using multiple reaction monitoring. In spinal cord tissue, 292 out of 6810 identified proteins were significantly changed in ALS with enrichment of proteins involved in mRNA splicing and of the neurofilament compartment. In conclusion, our proteomic data in asymptomatic ALS mutation carriers support the hypothesis of a sudden disease onset instead of a long preclinical phase. Both CSF and tissue proteomic data indicate transcriptional pathways to be amongst the most affected. UCHL1, MAP2 and GPNMB are promising ALS biomarker candidates which might provide additional value to the established neurofilaments in patient follow-up and clinical trials.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Patrick Weydt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Dietmar R Thal
- Laboratory of Neuropathology, Institute of Pathology, Ulm University, Ulm, Germany
- Department of Imaging and Pathology, KU Leuven and Department of Pathology, UZ Leuven, Louvain, Belgium
| | - Jochen H Weishaupt
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Albert C Ludolph
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital, Oberer Eselsberg 45, 89081, Ulm, Germany.
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35
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Schauer NJ, Magin RS, Liu X, Doherty LM, Buhrlage SJ. Advances in Discovering Deubiquitinating Enzyme (DUB) Inhibitors. J Med Chem 2019; 63:2731-2750. [DOI: 10.1021/acs.jmedchem.9b01138] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nathan J. Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Robert S. Magin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Laura M. Doherty
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sara J. Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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36
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Kolber P, Krüger R. Gene-environment interaction and Mendelian randomisation. Rev Neurol (Paris) 2019; 175:597-603. [PMID: 31543362 DOI: 10.1016/j.neurol.2019.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 04/20/2019] [Indexed: 12/11/2022]
Abstract
Genetic factors only account for up to a third of the cases of Parkinson's disease (PD), while the remaining cases are of unknown aetiology. Environmental exposures (such as pesticides or heavy metals) and the interaction with genetic susceptibility factors (summarized in the concept of impaired xenobiotic metabolism) are believed to play a major role in the mechanisms of neurodegeneration. Beside of the classical association studies (e.g. genome-wide association studies), a novel approach to investigate environmental risk factors are Mendelian randomisation studies. This review explores the gene-environment interaction and the gain of Mendelian randomisation studies in assessing causalities of modifiable risk factors for PD.
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Affiliation(s)
- P Kolber
- Luxembourg Centre for Systems Biomedicine, Clinical and Experimental Neuroscience, University of Luxembourg, 4362 Belval, Esch-sur-Alzette, Luxembourg; Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - R Krüger
- Luxembourg Centre for Systems Biomedicine, Clinical and Experimental Neuroscience, University of Luxembourg, 4362 Belval, Esch-sur-Alzette, Luxembourg; Neurology, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg; Luxembourg Institute of Health, Luxembourg, Luxembourg.
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37
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Abstract
Protein homeostasis is essential for the survival of cells. It is closely related to the functioning of the ubiquitin-proteasome system, which utilizes the small protein ubiquitin as a posttranslational modifier (PTM). Clinically, the modification is of great importance as its disruption is the cause of many diseases. Unlike other PTMs, ubiquitin can encode several cellular signals by being attached as a single molecule or as a chain of several ubiquitins in various conformations. Thus, ubiquitin signaling is dependent not only on the site of attachment but also on the chain type, the so-called ubiquitin chain topology.The most reliable quantification method for the chain topology uses a bottom-up targeted mass spectrometry-based proteomics technique. While similar to other targeted proteomics techniques, the measurement of ubiquitination chain topology is complicated. First, the ubiquitin chains in the sample have to be biochemically stabilized. Second, the selection of peptides for the analysis is restricted to a given set harboring the PTMs and does not allow for optimization for amenability to mass spectrometry-based quantification. Instead, the topology-characteristic peptides are fixed. We here present such a methodology, including notes for a successful application.
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Huang H, Arighi CN, Ross KE, Ren J, Li G, Chen SC, Wang Q, Cowart J, Vijay-Shanker K, Wu CH. iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res 2019; 46:D542-D550. [PMID: 29145615 PMCID: PMC5753337 DOI: 10.1093/nar/gkx1104] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/24/2017] [Indexed: 12/19/2022] Open
Abstract
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach—combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.
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Affiliation(s)
- Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Cecilia N Arighi
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Karen E Ross
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Jia Ren
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Gang Li
- Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Sheng-Chih Chen
- Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Qinghua Wang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Julie Cowart
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - K Vijay-Shanker
- Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.,Department of Computer & Information Sciences, University of Delaware, Newark, DE 19711, USA.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
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39
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Site-specific phosphorylation of Fbxw7 by Cdk5/p25 and its resulting decreased stability are linked to glutamate-induced excitotoxicity. Cell Death Dis 2019; 10:579. [PMID: 31371703 PMCID: PMC6675790 DOI: 10.1038/s41419-019-1818-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022]
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a serine/threonine protein kinase that regulates brain development and neurodegeneration. Cdk5 is activated by p25 that is generated from calpain-dependent cleavage of p35. The generation of p25 is responsible for the aberrant hyper-activation of Cdk5, which causes neurodegeneration. Using in vitro assays, we discovered that F-box/WD repeat-containing protein 7 (Fbxw7) is a new substrate of Cdk5. Additionally, Cdk5-dependent phosphorylation of Fbxw7 was detected in the presence of p25, and two amino acid residues (S349 and S372) were determined to be major phosphorylation sites. This phosphorylation was eventually linked to decreased stability of Fbxw7. Using a culture model of cortical neurons challenged with glutamate, we confirmed that decreased stability of Fbxw7 was indeed Cdk5-dependent. Furthermore, diminished levels of Fbxw7 led to increased levels of transcription factor AP-1 (c-Jun), a known substrate of Fbxw7. Given that previous reports demonstrate that c-Jun plays a role in accelerating neuronal apoptosis in these pathological models, our data support the concepts of a molecular cascade in which Cdk5-mediated phosphorylation of Fbxw7 negatively regulates Fbxw7 expression, thereby contributing to neuronal cell death following glutamate-mediated excitotoxicity.
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Antfolk D, Antila C, Kemppainen K, Landor SKJ, Sahlgren C. Decoding the PTM-switchboard of Notch. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118507. [PMID: 31301363 PMCID: PMC7116576 DOI: 10.1016/j.bbamcr.2019.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/03/2019] [Accepted: 07/06/2019] [Indexed: 01/08/2023]
Abstract
The developmentally indispensable Notch pathway exhibits a high grade of pleiotropism in its biological output. Emerging evidence supports the notion of post-translational modifications (PTMs) as a modus operandi controlling dynamic fine-tuning of Notch activity. Although, the intricacy of Notch post-translational regulation, as well as how these modifications lead to multiples of divergent Notch phenotypes is still largely unknown, numerous studies show a correlation between the site of modification and the output. These include glycosylation of the extracellular domain of Notch modulating ligand binding, and phosphorylation of the PEST domain controlling half-life of the intracellular domain of Notch. Furthermore, several reports show that multiple PTMs can act in concert, or compete for the same sites to drive opposite outputs. However, further investigation of the complex PTM crosstalk is required for a complete understanding of the PTM-mediated Notch switchboard. In this review, we aim to provide a consistent and up-to-date summary of the currently known PTMs acting on the Notch signaling pathway, their functions in different contexts, as well as explore their implications in physiology and disease. Furthermore, we give an overview of the present state of PTM research methodology, and allude to a future with PTM-targeted Notch therapeutics.
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Affiliation(s)
- Daniel Antfolk
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Christian Antila
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Kati Kemppainen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Sebastian K-J Landor
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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41
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Non-Proteasomal UbL-UbA Family of Proteins in Neurodegeneration. Int J Mol Sci 2019; 20:ijms20081893. [PMID: 30999567 PMCID: PMC6514573 DOI: 10.3390/ijms20081893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin-like/ubiquitin-associated proteins (UbL-UbA) are a well-studied family of non-proteasomal ubiquitin receptors that are evolutionarily conserved across species. Members of this non-homogenous family facilitate and support proteasomal activity by promoting different effects on proteostasis but exhibit diverse extra-proteasomal activities. Dysfunctional UbL-UbA proteins render cells, particularly neurons, more susceptible to stressors or aging and may cause earlier neurodegeneration. In this review, we summarized the properties and functions of UbL-UbA family members identified to date, with an emphasis on new findings obtained using Drosophila models showing a direct or indirect role in some neurodegenerative diseases.
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42
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Ju UH, Liu FC, Lin CS, Huang WY, Lin TY, Shen CH, Chou YC, Lin CL, Lin KT, Kao CH, Chen CH, Yang TY. Risk of Parkinson disease in Sjögren syndrome administered ineffective immunosuppressant therapies: A nationwide population-based study. Medicine (Baltimore) 2019; 98:e14984. [PMID: 30946325 PMCID: PMC6455855 DOI: 10.1097/md.0000000000014984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To determine the incidence and risk of Parkinson disease (PD) in patients with Sjögren syndrome (SS) according to a nationwide population-based database.In total, 12,640 patients in the SS cohort and 50,560 in the non-SS cohort were enrolled from Taiwan's National Health Insurance Research Database from 2000 to 2010. We used the Cox multivariable proportional hazards model to determine the risk factors for PD in the SS cohort.We observed an increased incidence of PD in patients with SS, with a crude hazard ratio (HR) of 1.40 and an adjusted HR (aHR) of 1.23. The cumulative incidence of PD was 1.95% higher in the SS cohort than in the non-SS cohort. The SS cohort had an elevated HR under medication use, namely cevimeline and pilocarpine (crude HR, 1.28), hydroxychloroquine (crude HR, 1.43; aHR, 1.46), and methylprednisolone (crude HR, 2.21; aHR, 1.49). Patients receiving other non-hydroxychloroquine immunosuppressant therapies had a lower risk (aHR, 0.86) of PD. Furthermore, patients with SS aged 20 to 49 years had a 1.93-fold higher risk of PD than did those without SS (aHR, 1.93). The risk of PD was higher (aHR, 2.20) in patients with SS without comorbidities than in those with comorbidities. The aHR of PD significantly increased when the follow-up period exceeded 9 years (aHR, 1.93).We determined an increased risk of PD in patients with SS. Further investigation is warranted to determine the possible underlying mechanisms and the potential role of non-hydroxychloroquine immunosuppressants in ameliorating PD.
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Affiliation(s)
- Uei-Han Ju
- Division of Rheumatology/Immunology and Allergy
| | | | | | | | - Te-Yu Lin
- Department of Radiation Oncology
- Division of Infectious disease, Department of Internal Medicine
| | - Chih-Hao Shen
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei
| | - Yu-Ching Chou
- School of Public Health, National Defense Medical Center, Taipei
| | - Cheng-Li Lin
- College of Medicine, China Medical University
- Management Office for Health Data, China Medical University Hospital
| | | | - Chia-Hung Kao
- Department of Nuclear Medicine and PET Center, China Medical University Hospital
- Graduate Institute of Clinical Medical Science and School of Medicine, College of Medicine, China Medical University
- Department of Bioinformatics and Medical Engineering, Asia University
| | - Chao-Hsien Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung
| | - Tse-Yen Yang
- Department of Medical Research, China Medical University HsinChu Hospital, HsinChu County, China Medical University
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung
- Molecular and Genomic Epidemiology Center, China Medical University Hospital, Taichung, Taiwan
- Division of Nephrology, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
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43
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Cao J, Zhong MB, Toro CA, Zhang L, Cai D. Endo-lysosomal pathway and ubiquitin-proteasome system dysfunction in Alzheimer's disease pathogenesis. Neurosci Lett 2019; 703:68-78. [PMID: 30890471 DOI: 10.1016/j.neulet.2019.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/19/2019] [Accepted: 03/11/2019] [Indexed: 01/04/2023]
Abstract
Several lines of evidence have shown that defects in the endo-lysosomal autophagy degradation pathway and the ubiquitin-proteasome system play a role in Alzheimer's Disease (AD) pathogenesis and pathophysiology. Early pathological changes, such as marked enlargement of endosomal compartments, gradual accumulation of autophagic vacuoles (AVs) and lysosome dyshomeostasis, are well-recognized in AD. In addition to these pathological indicators, many genetic variants of key regulators in the endo-lysosomal autophagy networks and the ubiquitin-proteasome system have been found to be associated with AD. Furthermore, altered expression levels of key proteins in these pathways have been found in AD human brain tissues, primary cells and AD mouse models. In this review, we discuss potential disease mechanisms underlying the dysregulation of protein homeostasis governing systems. While the importance of two major protein degradation pathways in AD pathogenesis has been highlighted, targeted therapy at key components of these pathways has great potential in developing novel therapeutic interventions for AD. Future investigations are needed to define molecular mechanisms by which these complex regulatory systems become malfunctional at specific stages of AD development and progression, which will facilitate future development of novel therapeutic interventions. It is also critical to investigate all key components of the protein degradation pathways, both upstream and downstream, to improve our abilities to manipulate transport pathways with higher efficacy and less side effects.
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Affiliation(s)
- Jiqing Cao
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; The Central Hospital of The Hua Zhong University of Science and Technology, Wuhan, China.
| | - Margaret B Zhong
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Barnard College of Columbia University, New York, NY 10027, United States.
| | - Carlos A Toro
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; National Center for the Medical Consequences of Spinal Cord Injury, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Larry Zhang
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Dongming Cai
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Neurology Section, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; The Central Hospital of The Hua Zhong University of Science and Technology, Wuhan, China.
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44
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Chen ZS, Wong AKY, Cheng TC, Koon AC, Chan HYE. FipoQ/FBXO33, a Cullin-1-based ubiquitin ligase complex component modulates ubiquitination and solubility of polyglutamine disease protein. J Neurochem 2019; 149:781-798. [PMID: 30685895 DOI: 10.1111/jnc.14669] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/17/2018] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Polyglutamine (polyQ) diseases describe a group of progressive neurodegenerative disorders caused by the CAG triplet repeat expansion in the coding region of the disease genes. To date, nine such diseases, including spinocerebellar ataxia type 3 (SCA3), have been reported. The formation of SDS-insoluble protein aggregates in neurons causes cellular dysfunctions, such as impairment of the ubiquitin-proteasome system, and contributes to polyQ pathologies. Recently, the E3 ubiquitin ligases, which govern substrate specificity of the ubiquitin-proteasome system, have been implicated in polyQ pathogenesis. The Cullin (Cul) proteins are major components of Cullin-RING ubiquitin ligases (CRLs) complexes that are evolutionarily conserved in the Drosophila genome. In this study, we examined the effect of individual Culs on SCA3 pathogenesis and found that the knockdown of Cul1 expression enhances SCA3-induced neurodegeneration and reduces the solubility of expanded SCA3-polyQ proteins. The F-box proteins are substrate receptors of Cul1-based CRL. We further performed a genetic modifier screen of the 19 Drosophila F-box genes and identified F-box involved in polyQ pathogenesis (FipoQ) as a genetic modifier of SCA3 degeneration that modulates the ubiquitination and solubility of expanded SCA3-polyQ proteins. In the human SK-N-MC cell model, we identified that F-box only protein 33 (FBXO33) exerts similar functions as FipoQ in modulating the ubiquitination and solubility of expanded SCA3-polyQ proteins. Taken together, our study demonstrates that Cul1-based CRL and its associated F-box protein, FipoQ/FBXO33, modify SCA3 protein toxicity. These findings will lead to a better understanding of the disease mechanism of SCA3 and provide insights for developing treatments against SCA3. Cover Image for this issue: doi: 10.1111/jnc.14510.
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Affiliation(s)
- Zhefan Stephen Chen
- Laboratory of Drosophila Research, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Biochemistry Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Azaria Kam Yan Wong
- Laboratory of Drosophila Research, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Molecular Biotechnology Programme, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Tat Cheung Cheng
- Laboratory of Drosophila Research, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Biochemistry Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Alex Chun Koon
- Laboratory of Drosophila Research, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Molecular Biotechnology Programme, Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Biochemistry Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China.,Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Shatin N.T., Hong Kong SAR, China
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45
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Cartier E, Garcia-Olivares J, Janezic E, Viana J, Moore M, Lin ML, Caplan JL, Torres G, Kim YH. The SUMO-Conjugase Ubc9 Prevents the Degradation of the Dopamine Transporter, Enhancing Its Cell Surface Level and Dopamine Uptake. Front Cell Neurosci 2019; 13:35. [PMID: 30828290 PMCID: PMC6386010 DOI: 10.3389/fncel.2019.00035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/23/2019] [Indexed: 12/12/2022] Open
Abstract
The dopamine transporter (DAT) is a plasma membrane protein responsible for the uptake of released dopamine back to the presynaptic terminal and ending dopamine neurotransmission. The DAT is the molecular target for cocaine and amphetamine as well as a number of pathological conditions including autism spectrum disorders, attention-deficit hyperactivity disorder (ADHD), dopamine transporter deficiency syndrome (DTDS), and Parkinson’s disease. The DAT uptake capacity is dependent on its level in the plasma membrane. In vitro studies show that DAT functional expression is regulated by a balance of endocytosis, recycling, and lysosomal degradation. However, recent reports suggest that DAT regulation by endocytosis in neurons is less significant than previously reported. Therefore, additional mechanisms appear to determine DAT steady-state level and functional expression in the neuronal plasma membrane. Here, we hypothesize that the ubiquitin-like protein small ubiquitin-like modifier 1 (SUMO1) increases the DAT steady-state level in the plasma membrane. In confocal microscopy, fluorescent resonance energy transfer (FRET), and Western blot analyses, we demonstrate that DAT is associated with SUMO1 in the rat dopaminergic N27 and DAT overexpressing Human Embryonic Kidney cells (HEK)-293 cells. The overexpression of SUMO1 and the Ubc9 SUMO-conjugase induces DAT SUMOylation, reduces DAT ubiquitination and degradation, enhancing DAT steady-state level. In addition, the Ubc9 knock-down by interference RNA (RNAi) increases DAT degradation and reduces DAT steady-state level. Remarkably, the Ubc9-mediated SUMOylation increases the expression of DAT in the plasma membrane and dopamine uptake capacity. Our results strongly suggest that SUMOylation is a novel mechanism that plays a central role in regulating DAT proteostasis, dopamine uptake, and dopamine signaling in neurons. For that reason, the SUMO pathway including SUMO1, SUMO2, Ubc9, and DAT SUMOylation, can be critical therapeutic targets in regulating DAT stability and dopamine clearance in health and pathological states.
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Affiliation(s)
- Etienne Cartier
- Department of Biological Sciences, Delaware State University, Dover, DE, United States
| | | | - Eric Janezic
- Department of Biological Sciences, Delaware State University, Dover, DE, United States
| | - Juan Viana
- Department of Biological Sciences, Delaware State University, Dover, DE, United States
| | - Michael Moore
- Imaging Core, Delaware State University, Dover, DE, United States
| | - Min Landon Lin
- Department of Neuroscience and Department of Pharmacology, University of Florida, Gainesville, FL, United States
| | - Jeffrey L Caplan
- BioImaging Center, University of Delaware, Newark, DE, United States
| | - Gonzalo Torres
- Department of Neuroscience and Department of Pharmacology, University of Florida, Gainesville, FL, United States
| | - Yong-Hwan Kim
- Department of Biological Sciences, Delaware State University, Dover, DE, United States
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46
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Proteasome inhibition by MG-132 protects against deltamethrin-induced apoptosis in rat hippocampus. Life Sci 2019; 220:76-83. [PMID: 30695709 DOI: 10.1016/j.lfs.2019.01.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/06/2019] [Accepted: 01/25/2019] [Indexed: 11/21/2022]
Abstract
AIMS Deltamethrin (DM), a type II synthetic pyrethroid insecticide, is widely used in agriculture and home pest control. The evaluation of their toxic effects is of major concern to public health. However, the molecular mechanism of DM-induced neurodegenerative disease is still far from clear. This study was designed to investigate the potential role of ubiquitin proteasome system (UPS) in DM-induced neurotoxicity where the proteasome inhibitor MG-132 could mitigate the neurotoxic effects. MAIN METHODS Male Sprague-Dawley rats were divided into two batches. The first batch of rats was administrated with a single dose of DM (12.5 mg/kg) by intraperitoneal injections (i.p.) and the animals were then euthanized at 5, 24, and 48 h post injection. The second batch was treated as follow: control group, DM (12.5 mg/kg) groups for 24 h, MG-132 (0.5 mg/kg, i.p.) 2 h plus DM 24 h group, and MG-132 alone group. Ubiqutinatied proteins, DNA damage and apoptosis were investigated. KEY FINDINGS DM treatment induced the ubiquitinated proteins expression with the peaks at 5 h. Moreover, DM increased DNA damage, early apoptotic rate, the expression level of Cleaved Caspase-3, caspase-3 activity and decreased the expression level of Bcl-2 at DM 24 h group. Compared to DM 24 h group, MG-132 pretreatment significantly down-regulated ubiquitinated proteins, lowered the DNA damage and apoptosis by decreasing Caspase-3 and increasing Bcl-2 expression. SIGNIFICANCE These results indicate that MG-132 effectively alleviates DM-induced DNA damage and apoptosis by inhibiting ubiquitinated proteins. UPS may play a role in DM-induced neurodegenerative disorders.
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47
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Rahman MR, Islam T, Turanli B, Zaman T, Faruquee HM, Rahman MM, Mollah MNH, Nanda RK, Arga KY, Gov E, Moni MA. Network-based approach to identify molecular signatures and therapeutic agents in Alzheimer's disease. Comput Biol Chem 2018; 78:431-439. [PMID: 30606694 DOI: 10.1016/j.compbiolchem.2018.12.011] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/25/2018] [Indexed: 01/15/2023]
Abstract
Alzheimer's disease (AD) is a dynamic degeneration of the brain with progressive dementia. Considering the uncertainties in its molecular mechanism, in the present study, we employed network-based integrative analyses, and aimed to explore the key molecules and their associations with small drugs to identify potential biomarkers and therapeutic agents for the AD. First of all, we studied a transcriptome dataset and identified 1521 differentially expressed genes (DEGs). Integration of transcriptome data with protein-protein and transcriptional regulatory interactions resulted with central (hub) proteins (UBA52, RAC1, CREBBP, AR, RPS11, SMAD3, RPS6, RPL12, RPL15, and UBC), regulatory transcription factors (FOXC1, GATA2, YY1, FOXL1, NFIC, E2F1, USF2, SRF, PPARG, and JUN) and microRNAs (mir-335-5p, mir-26b-5p, mir-93-5p, mir-124-3p, mir-17-5p, mir-16-5p, mir-20a-5p, mir-92a-3p, mir-106b-5p, and mir-192-5p) as key signaling and regulatory molecules associated with transcriptional changes for the AD. Considering these key molecules as potential therapeutic targets and Connectivity Map (CMap) architecture, candidate small molecular agents (such as STOCK1N-35696) were identified as novel potential therapeutics for the AD. This study presents molecular signatures at RNA and protein levels which might be useful in increasing discernment of the molecular mechanisms, and potential drug targets and therapeutics to design effective treatment strategies for the AD.
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Affiliation(s)
- Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh; Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj, Bangladesh
| | - Tania Islam
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Beste Turanli
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey; Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Toyfiquz Zaman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj, Bangladesh
| | - Hossain Md Faruquee
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh; Translational Health, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Md Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Ranjan Kumar Nanda
- Translational Health, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - Esra Gov
- Department of Bioengineering, Adana Science and Technology University, Adana, Turkey.
| | - Mohammad Ali Moni
- The University of Sydney, Sydney Medical School, School of Medical Sciences, Discipline of Biomedical Science, Sydney, New South Wales, Australia.
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48
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Mejia Maza A, Carmen-Orozco RP, Carter ES, Dávila-Villacorta DG, Castillo G, Morales JD, Mamani J, Gavídia CM, Alroy J, Sterling CR, Gonzalez AE, García HH, Woltjer RL, Verástegui MR, Gilman RH. Axonal swellings and spheroids: a new insight into the pathology of neurocysticercosis. Brain Pathol 2018; 29:425-436. [PMID: 30368965 DOI: 10.1111/bpa.12669] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/21/2018] [Indexed: 12/13/2022] Open
Abstract
Neurocysticercosis is a parasitic brain disease caused by the larval form (Cysticercus cellulosae) of Taenia solium and is the leading cause of preventable epilepsy worldwide. However, the pathophysiology and relation to the wide range of clinical features remains poorly understood. Axonal swelling is emerging as an important early pathological finding in multiple neurodegenerative diseases and as a cause of brain injury, but has not been well described in neurocysticercosis. Histological analysis was performed on human, rat and porcine NCC brain specimens to identify axonal pathology. Rat infection was successfully carried out via two routes of inoculation: direct intracranial injection and oral feeding. Extensive axonal swellings, in the form of spheroids, were observed in both humans and rats and to a lesser extent in pigs with NCC. Spheroids demonstrated increased immunoreactivity to amyloid precursor protein and neurofilament indicating probable impairment of axonal transport. These novel findings demonstrate that spheroids are present in NCC which is conserved across species. Not only is this an important contribution toward understanding the pathogenesis of NCC, but it also provides a model to analyze the association of spheroids with specific clinical features and to investigate the reversibility of spheroid formation with antihelminthic treatment.
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Affiliation(s)
- Alan Mejia Maza
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Rogger P Carmen-Orozco
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Emma S Carter
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Danitza G Dávila-Villacorta
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Gino Castillo
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jemina D Morales
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Javier Mamani
- Faculty of Veterinary Medicine and Animal Husbandry, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cesar M Gavídia
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Joseph Alroy
- Department of Pathology, Tufts University School of Medicine and Tufts-New England Medical Center, Boston, MA
| | - Charles R Sterling
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ
| | - Armando E Gonzalez
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Héctor H García
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú.,Cysticercosis Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Randy L Woltjer
- Department of Pathology, Layton Aging & Alzheimer's Disease Center, Oregon Health & Science University, Portland, OR
| | - Manuela R Verástegui
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H Gilman
- Infectious Diseases Laboratory Research-LID, Faculty of Science and Philosophy, Alberto Cazorla Talleri, Universidad Peruana Cayetano Heredia, Lima, Perú.,The Department of International Health, Bloomberg School of Hygiene and Public Health, Johns Hopkins University, Baltimore, MD.,Asociación Benéfica PRISMA, Lima, Perú
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49
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Proteomic analysis of protein homeostasis and aggregation. J Proteomics 2018; 198:98-112. [PMID: 30529741 DOI: 10.1016/j.jprot.2018.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/24/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022]
Abstract
Protein homeostasis (proteostasis) refers to the ability of cells to preserve the correct balance between protein synthesis, folding and degradation. Proteostasis is essential for optimal cell growth and survival under stressful conditions. Various extracellular and intracellular stresses including heat shock, oxidative stress, proteasome malfunction, mutations and aging-related modifications can result in disturbed proteostasis manifested by enhanced misfolding and aggregation of proteins. To limit protein misfolding and aggregation cells have evolved various strategies including molecular chaperones, proteasome system and autophagy. Molecular chaperones assist folding of proteins, protect them from denaturation and facilitate renaturation of the misfolded polypeptides, whereas proteasomes and autophagosomes remove the irreversibly damaged proteins. The impairment of proteostasis results in protein aggregation that is a major pathological hallmark of numerous age-related disorders, such as cataract, Alzheimer's, Parkinson's, Huntington's, and prion diseases. To discover protein markers and speed up diagnosis of neurodegenerative diseases accompanied by protein aggregation, proteomic tools have increasingly been used in recent years. Systematic and exhaustive analysis of the changes that occur in the proteomes of affected tissues and biofluids in humans or in model organisms is one of the most promising approaches to reveal mechanisms underlying protein aggregation diseases, improve their diagnosis and develop therapeutic strategies. Significance: In this review we outline the elements responsible for maintaining cellular proteostasis and present the overview of proteomic studies focused on protein-aggregation diseases. These studies provide insights into the mechanisms responsible for age-related disorders and reveal new potential biomarkers for Alzheimer's, Parkinson's, Huntigton's and prion diseases.
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50
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Lee YC, Huang WC, Lin JH, Kao TJ, Lin HC, Lee KH, Lin HC, Shen CKJ, Chang WC, Huang CC. Znf179 E3 ligase-mediated TDP-43 polyubiquitination is involved in TDP-43- ubiquitinated inclusions (UBI) (+)-related neurodegenerative pathology. J Biomed Sci 2018; 25:76. [PMID: 30404641 PMCID: PMC6223059 DOI: 10.1186/s12929-018-0479-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background The brain predominantly expressed RING finger protein, Znf179, is known to be important for embryonic neuronal differentiation during brain development. Downregulation of Znf179 has been observed in motor neurons of adult mouse models for amyotrophic lateral sclerosis (ALS), yet the molecular function of Znf179 in neurodegeneration has never been previously described. Znf179 contains the classical C3HC4 RING finger domain, and numerous proteins containing C3HC4 RING finger domain act as E3 ubiquitin ligases. Hence, we are interested to identify whether Znf179 possesses E3 ligase activity and its role in ALS neuropathy. Methods We used in vivo and in vitro ubiquitination assay to examine the E3 ligase autoubiquitination activity of Znf179 and its effect on 26S proteasome activity. To search for the candidate substrates of Znf179, we immunoprecipitated Znf179 and subjected to mass spectrometry (MS) analysis to identify its interacting proteins. We found that ALS/ FTLD-U (frontotemporal lobar degeneration (FTLD) with ubiquitin inclusions)-related neurodegenerative TDP-43 protein is the E3 ligase substrate of Znf179. To further clarify the role of E3 ubiquitin ligase Znf179 in neurodegenerative TDP-43-UBI (ubiquitinated inclusions) (+) proteinopathy, the effect of Znf179-mediated TDP-43 polyubiquitination on TDP-43 protein stability, aggregate formation and nucleus/cytoplasm mislocalization were evaluated in vitro cell culture system and in vivo animal model. Results Here we report that Znf179 is a RING E3 ubiquitin ligase which possesses autoubiquitination feature and regulates 26S proteasome activity through modulating the protein expression levels of 19S/20S proteasome subunits. Our immunoprecipitation assay and MS analysis results revealed that the neuropathological TDP-43 protein is one of its E3 ligase substrate. Znf179 interactes with TDP-43 protein and mediates polyubiquitination of TDP-43 in vitro and in vivo. In neurodegenerative TDP-43 proteinopathy, we found that Znf179-mediated polyubiquitination of TDP-43 accelerates its protein turnover rate and attenuates insoluble pathologic TDP-43 aggregates, while knockout of Znf179 in mouse brain results in accumulation of insoluble TDP-43 and cytosolic TDP-43 inclusions in cortex, hippocampus and midbrain regions. Conclusions Here we unveil the important role for the novel E3 ligase Znf179 in TDP-43-mediated neuropathy, and provide a potential therapeutic strategy for combating ALS/ FTLD-U neurodegenerative pathologies. Electronic supplementary material The online version of this article (10.1186/s12929-018-0479-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Chao Lee
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan
| | - Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Jiann-Her Lin
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan.,Department of Neurosurgery, Taipei Medical University, Taipei, Taiwan.,Division of Neurosurgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Jen Kao
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan
| | - Hui-Ching Lin
- Institute and Department of Physiology, School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 115, Taiwan
| | - Hsin-Chuan Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | | | - Wen-Chang Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Chi-Chen Huang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan.
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