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Kase N, Terashima M, Ohta A, Niwa A, Honda‐Ozaki F, Kawasaki Y, Nakahata T, Kanazawa N, Saito MK. Pluripotent stem cell-based screening identifies CUDC-907 as an effective compound for restoring the in vitro phenotype of Nakajo-Nishimura syndrome. Stem Cells Transl Med 2020; 10:455-464. [PMID: 33280267 PMCID: PMC7900583 DOI: 10.1002/sctm.20-0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/28/2020] [Accepted: 09/13/2020] [Indexed: 12/25/2022] Open
Abstract
Nakajo-Nishimura syndrome (NNS) is an autoinflammatory disorder caused by a homozygous mutations in the PSMB8 gene. The administration of systemic corticosteroids is partially effective, but continuous treatment causes severe side effects. We previously established a pluripotent stem cell (PSC)-derived NNS disease model that reproduces several inflammatory phenotypes, including the overproduction of monocyte chemoattractant protein-1 (MCP-1) and interferon gamma-induced protein-10 (IP-10). Here we performed high-throughput compound screening (HTS) using this PSC-derived NNS model to find potential therapeutic candidates and identified CUDC-907 as an effective inhibitor of the release of MCP-1 and IP-10. Short-term treatment of CUDC-907 did not induce cell death within therapeutic concentrations and was also effective on primary patient cells. Further analysis indicated that the inhibitory effect was post-transcriptional. These findings suggest that HTS with PSC-derived disease models is useful for finding drug candidates for autoinflammatory diseases.
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Affiliation(s)
- Naoya Kase
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Madoka Terashima
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Akira Ohta
- Department of Fundamental Cell TechnologyCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Akira Niwa
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Fumiko Honda‐Ozaki
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan,Department of Pediatrics and Developmental BiologyGraduate School of Medical and Dental Sciences, Tokyo Medical and Dental UniversityTokyoJapan
| | - Yuri Kawasaki
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Tatsutoshi Nakahata
- Department of Fundamental Cell TechnologyCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
| | - Nobuo Kanazawa
- Department of DermatologyWakayama Medical UniversityWakayamaJapan
| | - Megumu K. Saito
- Department of Clinical ApplicationCenter for iPS Cell Research and Application (CiRA), Kyoto UniversityKyotoJapan
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152
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The ubiquitin-proteasome system and its crosstalk with mitochondria as therapeutic targets in medicine. Pharmacol Res 2020; 163:105248. [PMID: 33065283 DOI: 10.1016/j.phrs.2020.105248] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
The ubiquitin-proteasome system constitutes a major pathway for protein degradation in the cell. Therefore the crosstalk of this pathway with mitochondria is a major topic with direct relevance to many mitochondrial diseases. Proteasome dysfunction triggers not only protein toxicity, but also mitochondrial dysfunction. The involvement of proteasomes in the regulation of protein transport into mitochondria contributes to an increase in mitochondrial function defects. On the other hand, mitochondrial impairment stimulates reactive oxygen species production, which increases protein damage, and protein misfolding and aggregation leading to proteasome overload. Concurrently, mitochondrial dysfunction compromises cellular ATP production leading to reduced protein ubiquitination and proteasome activity. In this review we discuss the complex relationship and interdependence of the ubiquitin-proteasome system and mitochondria. Furthermore, we describe pharmacological inhibition of proteasome activity as a novel strategy to treat a group of mitochondrial diseases.
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153
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Grimholt U, Fosse JH, Sundaram AYM. Selective Stimulation of Duplicated Atlantic Salmon MHC Pathway Genes by Interferon-Gamma. Front Immunol 2020; 11:571650. [PMID: 33123146 PMCID: PMC7573153 DOI: 10.3389/fimmu.2020.571650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Induction of cellular immune responses rely on Major histocompatibility complex (MHC) molecules presenting pathogenic peptides to T cells. Peptide processing, transport, loading and editing is a constitutive process in most cell types, but is accelerated upon infection. Recently, an unexpected complexity in the number of functional genes involved in MHC class I peptide cleavage, peptide transport, peptide loading and editing was found in teleosts, originating from the second and third whole genome duplication events. Salmonids have expanded upon this with functional duplicates also from a fourth unique salmonid whole genome duplication. However, little is known about how individual gene duplicates respond in the context of stimulation. Here we set out to investigate how interferon gamma (IFNg) regulates the transcription of immune genes in Atlantic salmon with particular focus on gene duplicates and MHC pathways. We identified a range of response patterns in Atlantic salmon gene duplicates, with upregulation of all duplicates for some genes, like interferon regulatory factor 1 (IRF1) and interferon induced protein 44-like (IFI44.L), but only induction of one or a few duplicates of other genes, such as TAPBP and ERAP2. A master regulator turned out to be the IRF1 and not the enhanceosome as seen in mammals. If IRF1 also collaborates with CIITA and possibly NLRC5 in regulating IFNg induction of MHCI and MHCII expression in Atlantic salmon, as in zebrafish, remains to be established. Altogether, our results show the importance of deciphering between gene duplicates, as they often respond very differently to stimulation and may have different biological functions.
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154
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Trash Talk: Mammalian Proteasome Regulation at the Transcriptional Level. Trends Genet 2020; 37:160-173. [PMID: 32988635 DOI: 10.1016/j.tig.2020.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 09/01/2020] [Indexed: 12/27/2022]
Abstract
The key to a healthy mammalian cell lies in properly functioning proteolytic machineries called proteasomes. The proteasomes are multisubunit complexes that catalyze the degradation of unwanted proteins and also control half-lives of key cellular regulatory factors. Aberrant proteasome activity is often associated with human diseases such as cancer and neurodegeneration, and so an in-depth understanding of how it is regulated has implications for potential disease interventions. Transcriptional regulation of the proteasome can dictate its abundance and also influence its function, assembly, and location. This ensures proper proteasomal activity in response to developmental cues and to physiological conditions such as starvation and oxidative stress. In this review, we highlight and discuss the roles of the transcription factors that are involved in the regulation of the mammalian proteasome.
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155
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Paes W, Leonov G, Partridge T, Nicastri A, Ternette N, Borrow P. Elucidation of the Signatures of Proteasome-Catalyzed Peptide Splicing. Front Immunol 2020; 11:563800. [PMID: 33072102 PMCID: PMC7541919 DOI: 10.3389/fimmu.2020.563800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
Proteasomes catalyze the degradation of endogenous proteins into oligopeptides, but can concurrently create spliced oligopeptides through ligation of previously non-contiguous peptide fragments. Recent studies have uncovered a formerly unappreciated role for proteasome-catalyzed peptide splicing (PCPS) in the generation of non-genomically templated human leukocyte antigen class I (HLA-I)-bound cis-spliced peptides that can be targeted by CD8+ T cells in cancer and infection. However, the mechanisms defining PCPS reactions are poorly understood. Here, we experimentally define the biochemical constraints of proteasome-catalyzed cis-splicing reactions by examination of in vitro proteasomal digests of a panel of viral- and self-derived polypeptide substrates using a tailored mass-spectrometry-based de novo sequencing workflow. We show that forward and reverse PCPS reactions display unique splicing signatures, defined by preferential fusion of distinct amino acid residues with stringent peptide length distributions, suggesting sequence- and size-dependent accessibility of splice reactants for proteasomal substrate binding pockets. Our data provide the basis for a more informed mechanistic understanding of PCPS that will facilitate future prediction of spliced peptides from protein sequences.
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Affiliation(s)
- Wayne Paes
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - German Leonov
- York Cross-Disciplinary Center for Systems Analysis, University of York, York, United Kingdom
| | - Thomas Partridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Annalisa Nicastri
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Clinical Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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156
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Kobayashi A. Roles of NRF3 in the Hallmarks of Cancer: Proteasomal Inactivation of Tumor Suppressors. Cancers (Basel) 2020; 12:cancers12092681. [PMID: 32962187 PMCID: PMC7563620 DOI: 10.3390/cancers12092681] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 01/18/2023] Open
Abstract
Simple Summary This review summarizes recent advances in our understanding of the physiological roles of the NFE2-related factor 2 (NRF2)-related transcription factor NRF3 in cancer. NRF3 confers cells with six so-called “hallmarks of cancer” through upregulating gene expression of specific target genes, leading to tumorigenesis and cancer malignancy. These driver gene-like functions of NRF3 in cancer are distinct from those of NRF2. Abstract The physiological roles of the NRF2-related transcription factor NRF3 (NFE2L3) have remained unknown for decades. The remarkable development of human cancer genome databases has led to strong suggestions that NRF3 has functional significance in cancer; specifically, high NRF3 mRNA levels are induced in many cancer types, such as colorectal cancer and pancreatic adenocarcinoma, and are associated with poor prognosis. On the basis of this information, the involvement of NRF3 in tumorigenesis and cancer malignancy has been recently proposed. NRF3 confers cancer cells with selective growth advantages by enhancing 20S proteasome assembly through induction of the chaperone gene proteasome maturation protein (POMP) and consequently promoting degradation of the tumor suppressors p53 and retinoblastoma (Rb) in a ubiquitin-independent manner. This new finding offers insight into the proteasomal but not the genetic inactivation mechanism of tumor suppressors. Moreover, NRF3 promotes cancer malignancy-related processes, including metastasis and angiogenesis. Finally, the molecular mechanisms underlying NRF3 activation have been elucidated, and this knowledge is expected to provide many insights that are useful for the development of anticancer drugs that attenuate NRF3 transcriptional activity. Collectively, the evidence indicates that NRF3 confers cells with six so-called “hallmarks of cancer”, implying that it exhibits cancer driver gene-like function. This review describes recent research advances regarding the newly discovered addiction of cancer cells to NRF3 compared to NRF2.
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Affiliation(s)
- Akira Kobayashi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan; ; Tel.: +81-774-65-6273
- Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan
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157
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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158
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Majumder P, Baumeister W. Proteasomes: unfoldase-assisted protein degradation machines. Biol Chem 2020; 401:183-199. [PMID: 31665105 DOI: 10.1515/hsz-2019-0344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/02/2019] [Indexed: 01/05/2023]
Abstract
Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome - unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.
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Affiliation(s)
- Parijat Majumder
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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159
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Gan T, Li Y, Zhou XJ, Zhang H. Immunoproteasome in IgA Nephropathy: State-of-Art and Future Perspectives. Int J Biol Sci 2020; 16:2518-2526. [PMID: 32792854 PMCID: PMC7415421 DOI: 10.7150/ijbs.48330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
IgA nephropathy (IgAN) is a leading cause of chronic kidney disease and renal failure. The exact pathogenesis of IgAN is not well defined, but some genetic studies have led to a novel discovery that the immunoproteasome probably plays an important role in IgAN. The immunoproteasome is a proteasome variant that is expressed when cells are stressed or receive inflammatory signals. While immunoproteasome is suggested to be mainly involved in major histocompatibility complex-I (MHC-I) antigen presentation, recent studies indicate that it may assert broad functions in trafficking events that activate both innate and adaptive immunity. In this review, we first summarize new insights into its functions in immunity, and discuss how it underlies its associations with IgAN. We also highlight its potential as a therapeutic target for the future.
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Affiliation(s)
- Ting Gan
- Renal Division, Peking University First Hospital; Peking University Institute of Nephrology; Key Laboratory of Renal Disease, Ministry of Health of China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, 100034, People's Republic of China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Yang Li
- Renal Division, Peking University First Hospital; Peking University Institute of Nephrology; Key Laboratory of Renal Disease, Ministry of Health of China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, 100034, People's Republic of China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital; Peking University Institute of Nephrology; Key Laboratory of Renal Disease, Ministry of Health of China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, 100034, People's Republic of China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
| | - Hong Zhang
- Renal Division, Peking University First Hospital; Peking University Institute of Nephrology; Key Laboratory of Renal Disease, Ministry of Health of China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, 100034, People's Republic of China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences
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160
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Mondanelli G, Di Battista V, Pellanera F, Mammoli A, Macchiarulo A, Gargaro M, Mavridou E, Matteucci C, Ruggeri L, Orabona C, Volpi C, Grohmann U, Mecucci C. A novel mutation of indoleamine 2,3-dioxygenase 1 causes a rapid proteasomal degradation and compromises protein function. J Autoimmun 2020; 115:102509. [PMID: 32605792 DOI: 10.1016/j.jaut.2020.102509] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) - the enzyme catalyzing the rate-limiting step of tryptophan catabolism along the kynurenine pathway - belongs to the class of inhibitory immune checkpoint molecules. Such regulators of the immune system are crucial for maintaining self-tolerance and thus, when properly working, preventing autoimmunity. A dysfunctional IDO1 has recently been associated with a specific single nucleotide polymorphism (SNP) and with the occurrence of autoimmune diabetes and multiple sclerosis. Many genetic alterations of IDO1 have been proposed being related with dysimmune disorders. However, the molecular and functional meaning of variations in IDO1 exomes as well as the promoter region remains a poorly explored field. In the present study, we identified a rare missense variant (rs751360195) at the IDO1 gene in a patient affected by coeliac disease, thyroiditis, and selective immunoglobulin A deficiency. Molecular and functional studies demonstrated that the substitution of lysine (K) at position 257 with a glutamic acid (E) results in an altered IDO1 protein that undergoes a rapid protein turnover. This genotype-to-phenotype relation is produced by peripheral blood mononuclear cells (PBMCs) of the patient bearing this variation and is associated with a specific phenotype (i.e., impaired tryptophan catabolism and defective mechanisms of immune tolerance). Thus decoding functional mutations of the IDO1 exome may provide clinically relevant information exploitable to personalize therapeutic interventions.
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Affiliation(s)
| | | | | | - Andrea Mammoli
- Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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161
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Pfammatter S, Bonneil E, Lanoix J, Vincent K, Hardy MP, Courcelles M, Perreault C, Thibault P. Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling. Anal Chem 2020; 92:9194-9204. [DOI: 10.1021/acs.analchem.0c01545] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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162
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Hamazaki J, Murata S. ER-Resident Transcription Factor Nrf1 Regulates Proteasome Expression and Beyond. Int J Mol Sci 2020; 21:ijms21103683. [PMID: 32456207 PMCID: PMC7279161 DOI: 10.3390/ijms21103683] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Protein folding is a substantively error prone process, especially when it occurs in the endoplasmic reticulum (ER). The highly exquisite machinery in the ER controls secretory protein folding, recognizes aberrant folding states, and retrotranslocates permanently misfolded proteins from the ER back to the cytosol; these misfolded proteins are then degraded by the ubiquitin–proteasome system termed as the ER-associated degradation (ERAD). The 26S proteasome is a multisubunit protease complex that recognizes and degrades ubiquitinated proteins in an ATP-dependent manner. The complex structure of the 26S proteasome requires exquisite regulation at the transcription, translation, and molecular assembly levels. Nuclear factor erythroid-derived 2-related factor 1 (Nrf1; NFE2L1), an ER-resident transcription factor, has recently been shown to be responsible for the coordinated expression of all the proteasome subunit genes upon proteasome impairment in mammalian cells. In this review, we summarize the current knowledge regarding the transcriptional regulation of the proteasome, as well as recent findings concerning the regulation of Nrf1 transcription activity in ER homeostasis and metabolic processes.
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163
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Restricted Expression of the Thymoproteasome Is Required for Thymic Selection and Peripheral Homeostasis of CD8 + T Cells. Cell Rep 2020; 26:639-651.e2. [PMID: 30650357 DOI: 10.1016/j.celrep.2018.12.078] [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] [Received: 01/22/2018] [Revised: 10/10/2018] [Accepted: 12/17/2018] [Indexed: 11/21/2022] Open
Abstract
The thymoproteasome subunit β5t is specifically expressed in cortical thymic epithelial cells (TECs) and generates unique peptides to support positive selection. In this study, using a mouse model ubiquitously expressing β5t, we showed that aberrant expression of self-peptides generated by β5t affects CD8+ T cell homeostasis, including thymic selection and maintenance of the peripheral naive pool of CD8+ T cells. In mice in which β5t was expressed both in cortical and medullary TECs, the abundance of CD8+ lineage thymocytes was reduced, and extra-thymic expression of β5t caused accumulation of CD8+ T cells with the memory or exhausted phenotype and induced autoreactive T cell responses. We found that thymoproteasomes are essential for positive selection but that the subsequent change in peptide repertoire in the medulla is also crucial for thymic selection and that β5t-derived peptide must be confined to the thymus to avoid autoimmunity in peripheral tissues.
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164
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Colberg L, Cammann C, Greinacher A, Seifert U. Structure and function of the ubiquitin-proteasome system in platelets. J Thromb Haemost 2020; 18:771-780. [PMID: 31898400 DOI: 10.1111/jth.14730] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 12/16/2022]
Abstract
Platelets are small anucleate blood cells with a life span of 7 to 10 days. They are main regulators of hemostasis. Balanced platelet activity is crucial to prevent bleeding or occlusive thrombus formation. Growing evidence supports that platelets also participate in immune reactions, and interaction between platelets and leukocytes contributes to both thrombosis and inflammation. The ubiquitin-proteasome system (UPS) plays a key role in maintaining cellular protein homeostasis by its ability to degrade non-functional self-, foreign, or short-lived regulatory proteins. Platelets express standard and immunoproteasomes. Inhibition of the proteasome impairs platelet production and platelet function. Platelets also express major histocompatibility complex (MHC) class I molecules. Peptide fragments released by proteasomes can bind to MHC class I, which makes it also likely that platelets can activate epitope specific cytotoxic T lymphocytes (CTLs). In this review, we focus on current knowledge on the significance of the proteasome for the functions of platelets as critical regulators of hemostasis as well as modulators of the immune response.
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Affiliation(s)
- Lisa Colberg
- Friedrich Loeffler Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Clemens Cammann
- Friedrich Loeffler Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Ulrike Seifert
- Friedrich Loeffler Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
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165
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Evaluating the immunoproteasome as a potential therapeutic target in cisplatin-resistant small cell and non-small cell lung cancer. Cancer Chemother Pharmacol 2020; 85:843-853. [PMID: 32232513 DOI: 10.1007/s00280-020-04061-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE We evaluated the expression of proteasome subunits to assess whether the proteasome could be a therapeutic target in cisplatin-resistant lung cancer cells. METHODS Cisplatin-resistant (CR) variants were established from three non-small cell lung cancer (NSCLC) cell lines (A549, H1299, and H1975) and two small cell lung cancer (SCLC) cell lines (SBC3 and SBC5). The expression of proteasome subunits, the sensitivity to immunoproteasome inhibitors, and 20S proteasomal proteolytic activity were examined in the CR variants of the lung cancer cell lines. RESULTS All five CR cell lines highly expressed one or both of the immunoproteasome subunit genes, PSMB8 and PSMB9, while no clear trend was observed in the expression of constitutive proteasome subunits. The CR cells expressed significantly higher levels of PSMB8 and PSMB9 proteins, as well. The CR variants of the H1299 and SBC3 cell lines were more sensitive to immunoproteasome inhibitors, and had significantly more proteasomal proteolytic activity than their parental counterparts. CONCLUSIONS The immunoproteasome may be an effective therapeutic target in a subset of CR lung cancers. Proteasomal proteolytic activity may be a predictive marker for the efficacy of immunoproteasome inhibitors in cisplatin-resistant SCLC and NSCLC.
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166
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Pawar A, Basler M, Goebel H, Alvarez Salinas GO, Groettrup M, Böttcher T. Competitive Metabolite Profiling of Natural Products Reveals Subunit Specific Inhibitors of the 20S Proteasome. ACS CENTRAL SCIENCE 2020; 6:241-246. [PMID: 32123742 PMCID: PMC7047272 DOI: 10.1021/acscentsci.9b01170] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Indexed: 05/11/2023]
Abstract
We have developed a syringolin-based chemical probe and explored its utility for the profiling of metabolite extracts as potent inhibitors of the 20S proteasome. Activity-guided fractionation by competitive labeling allowed us to isolate and identify glidobactin A and C as well as luminmycin A from a Burkholderiales strain. The natural products exhibited unique subunit specificities for the proteolytic subunits of human and mouse constitutive and immunoproteasome in the lower nanomolar range. In particular, glidobactin C displayed an unprecedented β2/β5 coinhibition profile with single-digit nanomolar potency in combination with sufficiently high cell permeability. These properties render glidobactin C a promising live cell proteasome inhibitor with potent activity against human breast cancer cell lines and comparably low immunotoxicity.
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Affiliation(s)
- Atul Pawar
- Department
of Chemistry, Zukunftskolleg, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Basler
- Division
of Immunology, Department of Biology, University
of Konstanz, 78457 Konstanz, Germany
- Biotechnology
Institute Thurgau, 8280 Kreuzlingen, Switzerland
| | - Heike Goebel
- Division
of Immunology, Department of Biology, University
of Konstanz, 78457 Konstanz, Germany
- Biotechnology
Institute Thurgau, 8280 Kreuzlingen, Switzerland
| | - Gerardo Omar Alvarez Salinas
- Division
of Immunology, Department of Biology, University
of Konstanz, 78457 Konstanz, Germany
- Biotechnology
Institute Thurgau, 8280 Kreuzlingen, Switzerland
| | - Marcus Groettrup
- Division
of Immunology, Department of Biology, University
of Konstanz, 78457 Konstanz, Germany
- Biotechnology
Institute Thurgau, 8280 Kreuzlingen, Switzerland
| | - Thomas Böttcher
- Department
of Chemistry, Zukunftskolleg, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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167
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Jenkins EC, Shah N, Gomez M, Casalena G, Zhao D, Kenny TC, Guariglia SR, Manfredi G, Germain D. Proteasome mapping reveals sexual dimorphism in tissue-specific sensitivity to protein aggregations. EMBO Rep 2020; 21:e48978. [PMID: 32090465 PMCID: PMC7132179 DOI: 10.15252/embr.201948978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
Defects in the proteasome can result in pathological proteinopathies. However, the pathogenic role of sex‐ and tissue‐specific sensitivity to proteotoxic stress remains elusive. Here, we map the proteasome activity across nine tissues, in male and female mice, and demonstrate strong sexual dimorphism in proteasome activity, where females have significantly higher activity in several tissues. Further, we report drastic differences in proteasome activity among tissues, independently of proteasome concentration, which are exacerbated under stress conditions. Sexual dimorphism in proteasome activity is confirmed in a SOD1 ALS mouse model, in which the spinal cord, a tissue with comparatively low proteasome activity, is severely affected. Our results offer mechanistic insight into tissue‐specific sensitivities to proteostasis stress and into sex differences in the progression of neurodegenerative proteinopathies.
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Affiliation(s)
- Edmund Charles Jenkins
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
| | - Nagma Shah
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
| | - Maria Gomez
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
| | - Gabriella Casalena
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Dazhi Zhao
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Timothy C Kenny
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
| | - Sara Rose Guariglia
- City University of New York, College of Staten Island, Staten Island, NY, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Doris Germain
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY, USA
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168
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Kondo H, Matsumura T, Kaneko M, Inoue K, Kosako H, Ikawa M, Takahama Y, Ohigashi I. PITHD1 is a proteasome-interacting protein essential for male fertilization. J Biol Chem 2020; 295:1658-1672. [PMID: 31915251 PMCID: PMC7008373 DOI: 10.1074/jbc.ra119.011144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 12/23/2019] [Indexed: 11/06/2022] Open
Abstract
The proteasome is a protein-degrading molecular complex that is necessary for protein homeostasis and various biological functions, including cell cycle regulation, signal transduction, and immune response. Proteasome activity is finely regulated by a variety of proteasome-interacting molecules. PITHD1 is a recently described molecule that has a domain putatively capable of interacting with the proteasome. However, it is unknown whether PITHD1 can actually bind to proteasomes and what it does in vivo Here we report that PITHD1 is detected specifically in the spermatids in the testis and the cortical thymic epithelium in the thymus. Interestingly, PITHD1 associates with immunoproteasomes in the testis, but not with thymoproteasomes in the thymus. Mice deficient in PITHD1 exhibit severe male infertility accompanied with morphological abnormalities and impaired motility of spermatozoa. Furthermore, PITHD1 deficiency reduces proteasome activity in the testis and alters the amount of proteins that are important for fertilization capability by the sperm. However, the PITHD1-deficient mice demonstrate no detectable defects in the thymus, including T cell development. Collectively, our results identify PITHD1 as a proteasome-interacting protein that plays a nonredundant role in the male reproductive system.
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Affiliation(s)
- Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Takafumi Matsumura
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Laboratory of Biopharmaceutical and Regenerative Sciences, Institute of Molecular Medicine and Life Science, Yokohama City University Association of Medical Science, Yokohama 236-0004, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan.
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169
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Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Molecules 2020; 25:molecules25030671. [PMID: 32033280 PMCID: PMC7037493 DOI: 10.3390/molecules25030671] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The proteasome is the central component of the main cellular protein degradation pathway. During the past four decades, the critical function of the proteasome in numerous physiological processes has been revealed, and proteasome activity has been linked to various human diseases. The proteasome prevents the accumulation of misfolded proteins, controls the cell cycle, and regulates the immune response, to name a few important roles for this macromolecular "machine." As a therapeutic target, proteasome inhibitors have been approved for the treatment of multiple myeloma and mantle cell lymphoma. However, inability to sufficiently inhibit proteasome activity at tolerated doses has hampered efforts to expand the scope of proteasome inhibitor-based therapies. With emerging new modalities in myeloma, it might seem challenging to develop additional proteasome-based therapies. However, the constant development of new applications for proteasome inhibitors and deeper insights into the intricacies of protein homeostasis suggest that proteasome inhibitors might have novel therapeutic applications. Herein, we summarize the latest advances in proteasome inhibitor development and discuss the future of proteasome inhibitors and other proteasome-based therapies in combating human diseases.
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170
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Kondo K, Ohigashi I, Takahama Y. Thymus machinery for T-cell selection. Int Immunol 2020; 31:119-125. [PMID: 30476234 DOI: 10.1093/intimm/dxy081] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/20/2018] [Indexed: 01/01/2023] Open
Abstract
An immunocompetent and self-tolerant pool of naive T cells is formed in the thymus through the process of repertoire selection. T cells that are potentially capable of responding to foreign antigens are positively selected in the thymic cortex and are further selected in the thymic medulla to help prevent self-reactivity. The affinity between T-cell antigen receptors expressed by newly generated T cells and self-peptide-major histocompatibility complexes displayed in the thymic microenvironments plays a key role in determining the fate of developing T cells during thymic selection. Recent advances in our knowledge of the biology of thymic epithelial cells have revealed unique machinery that contributes to positive and negative selection in the thymus. In this article, we summarize recent findings on thymic T-cell selection, focusing on the machinery unique to thymic epithelial cells.
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Affiliation(s)
- Kenta Kondo
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Kuramoto, Tokushima, Japan
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171
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Trowitzsch S, Tampé R. Multifunctional Chaperone and Quality Control Complexes in Adaptive Immunity. Annu Rev Biophys 2020; 49:135-161. [PMID: 32004089 DOI: 10.1146/annurev-biophys-121219-081643] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fundamental process of adaptive immunity relies on the differentiation of self from nonself. Nucleated cells are continuously monitored by effector cells of the immune system, which police the peptide status presented via cell surface molecules. Recent integrative structural approaches have provided insights toward our understanding of how sophisticated cellular machineries shape such hierarchical immune surveillance. Biophysical and structural achievements were invaluable for defining the interconnection of many key factors during antigen processing and presentation, and helped to solve several conundrums that persisted for many years. In this review, we illuminate the numerous quality control machineries involved in different steps during the maturation of major histocompatibility complex class I (MHC I) proteins, from their synthesis in the endoplasmic reticulum to folding and trafficking via the secretory pathway, optimization of antigenic cargo, final release to the cell surface, and engagement with their cognate receptors on cytotoxic T lymphocytes.
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Affiliation(s)
- Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
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172
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173
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Abstract
Proteasomes are large, multicatalytic protein complexes that cleave cellular proteins into peptides. There are many distinct forms of proteasomes that differ in catalytically active subunits, regulatory subunits, and associated proteins. Proteasome inhibitors are an important class of drugs for the treatment of multiple myeloma and mantle cell lymphoma, and they are being investigated for other diseases. Bortezomib (Velcade) was the first proteasome inhibitor to be approved by the US Food and Drug Administration. Carfilzomib (Kyprolis) and ixazomib (Ninlaro) have recently been approved, and more drugs are in development. While the primary mechanism of action is inhibition of the proteasome, the downstream events that lead to selective cell death are not entirely clear. Proteasome inhibitors have been found to affect protein turnover but at concentrations that are much higher than those achieved clinically, raising the possibility that some of the effects of proteasome inhibitors are mediated by other mechanisms.
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Affiliation(s)
- Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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174
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Finley D, Prado MA. The Proteasome and Its Network: Engineering for Adaptability. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033985. [PMID: 30833452 DOI: 10.1101/cshperspect.a033985] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proteasome, the most complex protease known, degrades proteins that have been conjugated to ubiquitin. It faces the unique challenge of acting enzymatically on hundreds and perhaps thousands of structurally diverse substrates, mechanically unfolding them from their native state and translocating them vectorially from one specialized compartment of the enzyme to another. Moreover, substrates are modified by ubiquitin in myriad configurations of chains. The many unusual design features of the proteasome may have evolved in part to endow this enzyme with a robust ability to process substrates regardless of their identity. The proteasome plays a major role in preserving protein homeostasis in the cell, which requires adaptation to a wide variety of stress conditions. Modulation of proteasome function is achieved through a large network of proteins that interact with it dynamically, modify it enzymatically, or fine-tune its levels. The resulting adaptability of the proteasome, which is unique among proteases, enables cells to control the output of the ubiquitin-proteasome pathway on a global scale.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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175
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Coux O, Zieba BA, Meiners S. The Proteasome System in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:55-100. [DOI: 10.1007/978-3-030-38266-7_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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176
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Saavedra-García P, Martini F, Auner HW. Proteasome inhibition in multiple myeloma: lessons for other cancers. Am J Physiol Cell Physiol 2019; 318:C451-C462. [PMID: 31875696 DOI: 10.1152/ajpcell.00286.2019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cellular protein homeostasis (proteostasis) depends on the controlled degradation of proteins that are damaged or no longer required by the ubiquitin-proteasome system (UPS). The 26S proteasome is the principal executer of substrate-specific proteolysis in eukaryotic cells and regulates a myriad of cellular functions. Proteasome inhibitors were initially developed as chemical tools to study proteasomal function but rapidly became widely used anticancer drugs that are now used at all stages of treatment for the bone marrow cancer multiple myeloma (MM). Here, we review the mechanisms of action of proteasome inhibitors that underlie their preferential toxicity to MM cells, focusing on endoplasmic reticulum stress, depletion of amino acids, and effects on glucose and lipid metabolism. We also discuss mechanisms of resistance to proteasome inhibition such as autophagy and metabolic rewiring and what lessons we may learn from the success and failure of proteasome inhibition in MM for treating other cancers with proteostasis-targeting drugs.
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Affiliation(s)
- Paula Saavedra-García
- Cancer Cell Metabolism Group, Hugh and Josseline Langmuir Centre for Myeloma Research, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Francesca Martini
- Department of Translational Research on New Technologies in Medicine and Surgery, Hematology Unit, Ospedale Santa Chiara, Pisa, Italy
| | - Holger W Auner
- Cancer Cell Metabolism Group, Hugh and Josseline Langmuir Centre for Myeloma Research, Faculty of Medicine, Imperial College London, London, United Kingdom
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177
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Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, Scalf M, Smith LM, Vierstra RD. Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis. J Biol Chem 2019; 294:17570-17592. [PMID: 31562246 PMCID: PMC6873196 DOI: 10.1074/jbc.ra119.010219] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/17/2019] [Indexed: 01/01/2023] Open
Abstract
The 26S proteasome is an essential protease that selectively eliminates dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this proteolytic machine in plants, we tagged either the core protease (CP) or the regulatory particle (RP) sub-complexes in Arabidopsis to enable rapid affinity purification followed by mass spectrometric analysis. Studies on proteasomes enriched from whole seedlings, with or without ATP needed to maintain the holo-proteasome complex, identified all known proteasome subunits but failed to detect isoform preferences, suggesting that Arabidopsis does not construct distinct proteasome sub-types. We also detected a suite of proteasome-interacting proteins, including likely orthologs of the yeast and mammalian chaperones Pba1, Pba2, Pba3, and Pba4 that assist in CP assembly; Ump1 that helps connect CP half-barrels; Nas2, Nas6, and Hsm3 that assist in RP assembly; and Ecm29 that promotes CP-RP association. Proteasomes from seedlings exposed to the proteasome inhibitor MG132 accumulated assembly intermediates, reflecting partially built proteasome sub-complexes associated with assembly chaperones, and the CP capped with the PA200/Blm10 regulator. Genetic analyses of Arabidopsis UMP1 revealed that, unlike in yeast, this chaperone is essential, with mutants lacking the major UMP1a and UMP1b isoforms displaying a strong gametophytic defect. Single ump1 mutants were hypersensitive to conditions that induce proteotoxic, salt and osmotic stress, and also accumulated several proteasome assembly intermediates, consistent with its importance for CP construction. Insights into the chaperones reported here should enable study of the assembly events that generate the 26S holo-proteasome in Arabidopsis from the collection of 64 or more subunits.
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Affiliation(s)
- David C Gemperline
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard S Marshall
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Kwang-Hee Lee
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Qingzhen Zhao
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
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178
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Pierce MR, Robinson RM, Ibarra-Rivera TR, Pirrung MC, Dolloff NG, Bachmann AS. Syrbactin proteasome inhibitor TIR-199 overcomes bortezomib chemoresistance and inhibits multiple myeloma tumor growth in vivo. Leuk Res 2019; 88:106271. [PMID: 31778912 DOI: 10.1016/j.leukres.2019.106271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 12/20/2022]
Abstract
Multiple myeloma (MM) and mantle cell lymphoma (MCL) are blood cancers that respond to proteasome inhibitors. Three FDA-approved drugs that block the proteasome are currently on the market, bortezomib, carfilzomib, and ixazomib. While these proteasome inhibitors have demonstrated clinical efficacy against refractory and relapsed MM and MCL, they are also associated with considerable adverse effects including peripheral neuropathy and cardiotoxicity, and tumor cells often acquire drug resistance. TIR-199 belongs to the syrbactin class, which constitutes a novel family of irreversible proteasome inhibitors. In this study, we compare TIR-199 head-to-head with three FDA-approved proteasome inhibitors. We demonstrate that TIR-199 selectively inhibits to varying degrees the sub-catalytic proteasomal activities (C-L/β1, T-L/β2, and CT-L/β5) in three actively dividing MM cell lines, with Ki50 (CT-L/β5) values of 14.61 ± 2.68 nM (ARD), 54.59 ± 10.4 nM (U266), and 26.8 ± 5.2 nM (MM.1R). In most instances, this range was comparable with the activity of ixazomib. However, TIR-199 was more effective than bortezomib, carfilzomib, and ixazomib in killing bortezomib-resistant MM and MCL cell lines, as judged by a low resistance index (RI) between 1.7 and 2.2, which implies that TIR-199 indiscriminately inhibits both bortezomib-sensitive and bortezomib-resistant MM and MCL cells at similar concentrations. Importantly, TIR-199 reduced the tumor burden in a MM mouse model (p < 0.01) confirming its potency in vivo. Given the fact that there is still no cure for MM, the further development of TIR-199 or similar molecules that belong to the syrbactin class of proteasome inhibitors is warranted.
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Affiliation(s)
- Marquicia R Pierce
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI 49503, USA
| | - Reeder M Robinson
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
| | | | - Michael C Pirrung
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA; Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, CA 92697, USA
| | - Nathan G Dolloff
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, 173 Ashley Ave, Charleston, SC 29425, USA
| | - André S Bachmann
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI 49503, USA.
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179
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Zhan W, Hsu HC, Morgan T, Ouellette T, Burns-Huang K, Hara R, Wright AG, Imaeda T, Okamoto R, Sato K, Michino M, Ramjee M, Aso K, Meinke PT, Foley M, Nathan CF, Li H, Lin G. Selective Phenylimidazole-Based Inhibitors of the Mycobacterium tuberculosis Proteasome. J Med Chem 2019; 62:9246-9253. [PMID: 31560200 DOI: 10.1021/acs.jmedchem.9b01187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Hao-Chi Hsu
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Trevor Morgan
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Tierra Ouellette
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Kristin Burns-Huang
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Ryoma Hara
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Adrian G Wright
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Kenjiro Sato
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Manoj Ramjee
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Carl F Nathan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Huilin Li
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Gang Lin
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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180
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Merriman C, Fu D. Down-regulation of the islet-specific zinc transporter-8 (ZnT8) protects human insulinoma cells against inflammatory stress. J Biol Chem 2019; 294:16992-17006. [PMID: 31591269 DOI: 10.1074/jbc.ra119.010937] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/04/2019] [Indexed: 12/31/2022] Open
Abstract
Zinc transporter-8 (ZnT8) primarily functions as a zinc-sequestrating transporter in the insulin-secretory granules (ISGs) of pancreatic β-cells. Loss-of-function mutations in ZnT8 are associated with protection against type-2 diabetes (T2D), but the protective mechanism is unclear. Here, we developed an in-cell ZnT8 assay to track endogenous ZnT8 responses to metabolic and inflammatory stresses applied to human insulinoma EndoC-βH1 cells. Unexpectedly, high glucose and free fatty acids did not alter cellular ZnT8 levels, but proinflammatory cytokines acutely, reversibly, and gradually down-regulated ZnT8. Approximately 50% of the cellular ZnT8 was localized to the endoplasmic reticulum (ER), which was the primary target of the cytokine-mediated ZnT8 down-regulation. Transcriptome profiling of cytokine-exposed β-cells revealed an adaptive unfolded protein response (UPR) including a marked immunoproteasome activation that coordinately degraded ZnT8 and insulin over a 1,000-fold cytokine concentration range. RNAi-mediated ZnT8 knockdown protected cells against cytokine cytotoxicity, whereas inhibiting immunoproteasomes blocked cytokine-induced ZnT8 degradation and triggered a transition of the adaptive UPR to cell apoptosis. Hence, cytokine-induced down-regulation of the ER ZnT8 level promotes adaptive UPR, acting as a protective mechanism that decongests the ER burden of ZnT8 to protect β-cells from proapoptotic UPR during chronic low-grade inflammation.
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Affiliation(s)
- Chengfeng Merriman
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Dax Fu
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
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181
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Imai T, Suzue K, Ngo-Thanh H, Ono S, Orita W, Suzuki H, Shimokawa C, Olia A, Obi S, Taniguchi T, Ishida H, Van Kaer L, Murata S, Tanaka K, Hisaeda H. Fluctuations of Spleen Cytokine and Blood Lactate, Importance of Cellular Immunity in Host Defense Against Blood Stage Malaria Plasmodium yoelii. Front Immunol 2019; 10:2207. [PMID: 31608052 PMCID: PMC6773889 DOI: 10.3389/fimmu.2019.02207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/02/2019] [Indexed: 12/27/2022] Open
Abstract
Our previous studies of protective immunity and pathology against blood stage malaria parasites have shown that not only CD4+ T cells, but also CD8+ T cells and macrophages, are important for host defense against blood stage malaria infection. Furthermore, we found that Plasmodium yoelii 17XNL (PyNL) parasitizes erythroblasts, the red blood cell (RBC) precursor cells, which then express MHC class I molecules. In the present study, we analyzed spleen cytokine production. In CD8+ T cell-depleted mice, IL-10 production in early stage infection was increased over two-fold relative to infected control animals and IL-10+ CD3- cells were increased, whereas IFN-γ production in the late stage of infection was decreased. At day 16 after PyNL infection, CD8+ T cells produced more IFN-γ than CD4+ T cells. We evaluated the involvement of the immunoproteasome in induction of immune CD8+ T cells, and the role of Fas in protection against PyNL both of which are downstream of IFN-γ. In cell transfer experiments, at least the single molecules LMP7, LMP2, and PA28 are not essential for CD8+ T cell induction. The Fas mutant LPR mouse was weaker in resistance to PyNL infection than WT mice, and 20% of the animals died. LPR-derived parasitized erythroid cells exhibited less externalization of phosphatidylserine (PS), and phagocytosis by macrophages was impaired. Furthermore, we tried to identify the cause of death in malaria infection. Blood lactate concentration was increased in the CD8+ T cell-depleted PyNL-infected group at day 19 (around peak parasitemia) to similar levels as day 7 after infection with a lethal strain of Py. When we injected mice with lactate at day 4 and 6 of PyNL infection, all mice died at day 8 despite demonstrating low parasitemia, suggesting that hyperlactatemia is one of the causes of death in CD8+ T cell-depleted PyNL-infected mice. We conclude that CD8+ T cells might control cytokine production to some extent and regulate hyperparasitemia and hyperlactatemia in protection against blood stage malaria parasites.
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Affiliation(s)
- Takashi Imai
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan.,Department of Parasitology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazutomo Suzue
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Ha Ngo-Thanh
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Suguri Ono
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Wakako Orita
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Haruka Suzuki
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Chikako Shimokawa
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan.,Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Alex Olia
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan.,Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiji Obi
- Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tomoyo Taniguchi
- Center for Medical Education, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Hidekazu Ishida
- Department of Parasitology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hajime Hisaeda
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
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182
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Xi J, Zhuang R, Kong L, He R, Zhu H, Zhang J. Immunoproteasome-selective inhibitors: An overview of recent developments as potential drugs for hematologic malignancies and autoimmune diseases. Eur J Med Chem 2019; 182:111646. [PMID: 31521028 DOI: 10.1016/j.ejmech.2019.111646] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/24/2019] [Accepted: 08/25/2019] [Indexed: 12/23/2022]
Abstract
The immunoproteasome, a specialized form of proteasome, is mainly expressed in lymphocytes and monocytes of jawed vertebrates and responsible for the generation of antigenic peptides for cell-mediated immunity. Overexpression of immunoproteasome have been detected in a wide range of diseases including malignancies, autoimmune and inflammatory diseases. Following the successful approval of constitutive proteasome inhibitors bortezomib, carfilzomib and Ixazomib, and with the clarification of immunoproteasome crystal structure and functions, a variety of immunoproteasome inhibitors were discovered or rationally developed. Not only the inhibitory activities, the selectivities for immunoproteasome over constitutive proteasome are essential for the clinical potential of these analogues, which has been validated by the clinical evaluation of immunoproteasome-selective inhibitor KZR-616 for the treatment of systemic lupus erythematosus. In this review, structure, function as well as the current developments of various inhibitors against immunoproteasome are going to be summarized, which help to fully understand the target for drug discovery.
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Affiliation(s)
- Jianjun Xi
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Rangxiao Zhuang
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Limin Kong
- Department of Pharmacy, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, Zhejiang Province, China
| | - Ruoyu He
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, 310023, Zhejiang Province, China
| | - Huajian Zhu
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang Province, China
| | - Jiankang Zhang
- School of Medicine, Zhejiang University City College, Hangzhou, 310015, Zhejiang Province, China.
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183
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Toste Rêgo A, da Fonseca PCA. Characterization of Fully Recombinant Human 20S and 20S-PA200 Proteasome Complexes. Mol Cell 2019; 76:138-147.e5. [PMID: 31473102 PMCID: PMC6863390 DOI: 10.1016/j.molcel.2019.07.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/27/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022]
Abstract
Proteasomes are essential in all eukaryotic cells. However, their function and regulation remain considerably elusive, particularly those of less abundant variants. We demonstrate the human 20S proteasome recombinant assembly and confirmed the recombinant complex integrity biochemically and with a 2.6 Å resolution cryo-EM map. To assess its competence to form higher-order assemblies, we prepared and analyzed recombinant human 20S-PA200, a poorly characterized nuclear complex. Its 3.0 Å resolution cryo-EM structure reveals the PA200 unique architecture; the details of its intricate interactions with the proteasome, resulting in unparalleled proteasome α ring rearrangements; and the molecular basis for PA200 allosteric modulation of the proteasome active sites. Non-protein cryo-EM densities could be assigned to PA200-bound inositol phosphates, and we speculate regarding their functional role. Here we open extensive opportunities to study the fundamental properties of the diverse and distinct eukaryotic proteasome variants and to improve proteasome targeting under different therapeutic conditions. Recombinant human 20S proteasomes and 20S-PA200 complexes are characterized Cryo-EM reveals intricate 20S-PA200 interactions and PA200-bound cofactors PA200 binding is allosterically communicated to the proteolytic active sites Basis to fully characterize the function and regulation of proteasome variants
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Affiliation(s)
- Ana Toste Rêgo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Paula C A da Fonseca
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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184
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Proteasome subunit α1 overexpression preferentially drives canonical proteasome biogenesis and enhances stress tolerance in yeast. Sci Rep 2019; 9:12418. [PMID: 31455793 PMCID: PMC6712033 DOI: 10.1038/s41598-019-48889-5] [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: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 02/04/2023] Open
Abstract
The 26S proteasome conducts the majority of regulated protein catabolism in eukaryotes. At the heart of the proteasome is the barrel-shaped 20S core particle (CP), which contains two β-rings sandwiched between two α-rings. Whereas canonical CPs contain α-rings with seven subunits arranged α1-α7, a non-canonical CP in which a second copy of the α4 subunit replaces the α3 subunit occurs in both yeast and humans. The mechanisms that control canonical versus non-canonical CP biogenesis remain poorly understood. Here, we have repurposed a split-protein reporter to identify genes that can enhance canonical proteasome assembly in mutant yeast producing non-canonical α4-α4 CPs. We identified the proteasome subunit α1 as an enhancer of α3 incorporation, and find that elevating α1 protein levels preferentially drives canonical CP assembly under conditions that normally favor α4-α4 CP formation. Further, we demonstrate that α1 is stoichiometrically limiting for α-ring assembly, and that enhancing α1 levels is sufficient to increase proteasome abundance and enhance stress tolerance in yeast. Together, our data indicate that the abundance of α1 exerts multiple impacts on proteasome assembly and composition, and we propose that the limited α1 levels observed in yeast may prime cells for alternative proteasome assembly following environmental stimuli.
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185
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Tundo GR, Sbardella D, Lacal PM, Graziani G, Marini S. On the Horizon: Targeting Next-Generation Immune Checkpoints for Cancer Treatment. Chemotherapy 2019; 64:62-80. [PMID: 31387102 DOI: 10.1159/000500902] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/11/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Immune checkpoints are critical regulatory pathways of the immune system which finely tune the response to biological threats. Among them, the CD-28/CTLA-4 and PD-1/PD-L1 axes play a key role in tumour immune escape and are well-established targets of cancer immunotherapy. SUMMARY The clinical experience accumulated to date provides unequivocal evidence that anti-CTLA-4, PD-1, or PD-L1 monoclonal antibodies, used as monotherapy or in combination regimes, are effective in a variety of advanced/metastatic types of cancer, with improved clinical outcomes compared to conventional chemotherapy. However, the therapeutic success is currently restricted to a limited subset of patients and reliable predictive biomarkers are still lacking. Key Message: The identification and characterization of additional co-inhibitory pathways as novel pharmacological targets to improve the clinical response in refractory patients has led to the development of different immune checkpoint inhibitors, the activities of which are currently under investigation. In this review, we discuss recent literature data concerning the mechanisms of action of next-generation monoclonal antibodies targeting LAG-3, TIM-3, and TIGIT co-inhibitory molecules that are being explored in clinical trials, as single agents or in combination with other immune-stimulating agents.
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Affiliation(s)
- Grazia R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy,
| | - Diego Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Pedro M Lacal
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy
| | - Grazia Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Stefano Marini
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata, IDI-IRCCS, Rome, Italy
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186
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Age-Dependent Effects of Immunoproteasome Deficiency on Mouse Adenovirus Type 1 Pathogenesis. J Virol 2019; 93:JVI.00569-19. [PMID: 31092582 DOI: 10.1128/jvi.00569-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/11/2019] [Indexed: 12/20/2022] Open
Abstract
Acute respiratory infection with mouse adenovirus type 1 (MAV-1) induces activity of the immunoproteasome, an inducible form of the proteasome that shapes CD8 T cell responses by enhancing peptide presentation by major histocompatibility complex (MHC) class I. We used mice deficient in all three immunoproteasome subunits (triple-knockout [TKO] mice) to determine whether immunoproteasome activity is essential for control of MAV-1 replication or inflammatory responses to acute infection. Complete immunoproteasome deficiency in adult TKO mice had no effect on MAV-1 replication, virus-induced lung inflammation, or adaptive immunity compared to C57BL/6 (B6) controls. In contrast, immunoproteasome deficiency in neonatal TKO mice was associated with decreased survival and decreased lung gamma interferon (IFN-γ) expression compared to B6 controls, although without substantial effects on viral replication, histological evidence of inflammation, or expression of the proinflammatory cytokines tumor necrosis factor alpha and interleukin-1β in lungs or other organs. T cell recruitment and IFN-γ production was similar in lungs of infected B6 and TKO mice. In lungs of uninfected B6 mice, we detected low levels of immunoproteasome subunit mRNA and protein that increased with age. Immunoproteasome subunit expression was lower in lungs of adult IFN-γ-deficient mice compared to B6 controls. Together, these results demonstrate developmental regulation of the immunoproteasome that is associated with age-dependent differences in MAV-1 pathogenesis.IMPORTANCE MAV-1 infection is a useful model to study the pathogenesis of an adenovirus in its natural host. Host factors that control MAV-1 replication and contribute to inflammation and disease are not fully understood. The immunoproteasome is an inducible component of the ubiquitin proteasome system that shapes the repertoire of peptides presented by MHC class I to CD8 T cells, influences other aspects of T cell survival and activation, and promotes production of proinflammatory cytokines. We found that immunoproteasome activity is dispensable in adult mice. However, immunoproteasome deficiency in neonatal mice increased mortality and impaired IFN-γ responses in the lungs. Baseline immunoproteasome subunit expression in lungs of uninfected mice increased with age. Our findings suggest the existence of developmental regulation of the immunoproteasome, like other aspects of host immune function, and indicate that immunoproteasome activity is a critical protective factor early in life.
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187
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Cellular Responses to Proteasome Inhibition: Molecular Mechanisms and Beyond. Int J Mol Sci 2019; 20:ijms20143379. [PMID: 31295808 PMCID: PMC6678303 DOI: 10.3390/ijms20143379] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023] Open
Abstract
Proteasome inhibitors have been actively tested as potential anticancer drugs and in the treatment of inflammatory and autoimmune diseases. Unfortunately, cells adapt to survive in the presence of proteasome inhibitors activating a variety of cell responses that explain why these therapies have not fulfilled their expected results. In addition, all proteasome inhibitors tested and approved by the FDA have caused a variety of side effects in humans. Here, we describe the different types of proteasome complexes found within cells and the variety of regulators proteins that can modulate their activities, including those that are upregulated in the context of inflammatory processes. We also summarize the adaptive cellular responses activated during proteasome inhibition with special emphasis on the activation of the Autophagic-Lysosomal Pathway (ALP), proteaphagy, p62/SQSTM1 enriched-inclusion bodies, and proteasome biogenesis dependent on Nrf1 and Nrf2 transcription factors. Moreover, we discuss the role of IRE1 and PERK sensors in ALP activation during ER stress and the involvement of two deubiquitinases, Rpn11 and USP14, in these processes. Finally, we discuss the aspects that should be currently considered in the development of novel strategies that use proteasome activity as a therapeutic target for the treatment of human diseases.
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188
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Lhuillier C, Rudqvist NP, Elemento O, Formenti SC, Demaria S. Radiation therapy and anti-tumor immunity: exposing immunogenic mutations to the immune system. Genome Med 2019; 11:40. [PMID: 31221199 PMCID: PMC6587285 DOI: 10.1186/s13073-019-0653-7] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The expression of antigens that are recognized by self-reactive T cells is essential for immune-mediated tumor rejection by immune checkpoint blockade (ICB) therapy. Growing evidence suggests that mutation-associated neoantigens drive ICB responses in tumors with high mutational burden. In most patients, only a few of the mutations in the cancer exome that are predicted to be immunogenic are recognized by T cells. One factor that limits this recognition is the level of expression of the mutated gene product in cancer cells. Substantial preclinical data show that radiation can convert the irradiated tumor into a site for priming of tumor-specific T cells, that is, an in situ vaccine, and can induce responses in otherwise ICB-resistant tumors. Critical for radiation-elicited T-cell activation is the induction of viral mimicry, which is mediated by the accumulation of cytosolic DNA in the irradiated cells, with consequent activation of the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon (IFN) genes (STING) pathway and downstream production of type I IFN and other pro-inflammatory cytokines. Recent data suggest that radiation can also enhance cancer cell antigenicity by upregulating the expression of a large number of genes that are involved in the response to DNA damage and cellular stress, thus potentially exposing immunogenic mutations to the immune system. Here, we discuss how the principles of antigen presentation favor the presentation of peptides that are derived from newly synthesized proteins in irradiated cells. These concepts support a model that incorporates the presence of immunogenic mutations in genes that are upregulated by radiation to predict which patients might benefit from treatment with combinations of radiotherapy and ICB.
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Affiliation(s)
- Claire Lhuillier
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA
| | - Nils-Petter Rudqvist
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th Street, New York, NY, 10021, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.,Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY, 10021, USA
| | - Silvia C Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, Stich Radiation Oncology Center, 525 East 68th Street, New York, NY, 10065, USA. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA. .,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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189
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Marshall RS, Vierstra RD. Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation. Front Mol Biosci 2019; 6:40. [PMID: 31231659 PMCID: PMC6568242 DOI: 10.3389/fmolb.2019.00040] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
All eukaryotes rely on selective proteolysis to control the abundance of key regulatory proteins and maintain a healthy and properly functioning proteome. Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine. Proteasomes recognize and degrade proteins first marked with one or more chains of poly-ubiquitin, the addition of which is actuated by hundreds of ligases that individually identify appropriate substrates for ubiquitylation. Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans. Importantly, dysfunction of 26S proteasomes is associated with numerous human pathologies and profoundly impacts crop performance, thus making an understanding of proteasome dynamics critically relevant to almost all facets of human health and nutrition. Given this widespread significance, it is not surprising that sophisticated mechanisms have evolved to tightly regulate 26S proteasome assembly, abundance and activity in response to demand, organismal development and stress. These include controls on transcription and chaperone-mediated assembly, influences on proteasome localization and activity by an assortment of binding proteins and post-translational modifications, and ultimately the removal of excess or damaged particles via autophagy. Intriguingly, the autophagic clearance of damaged 26S proteasomes first involves their modification with ubiquitin, thus connecting ubiquitylation and autophagy as key regulatory events in proteasome quality control. This turnover is also influenced by two distinct biomolecular condensates that coalesce in the cytoplasm, one attracting damaged proteasomes for autophagy, and the other reversibly storing proteasomes during carbon starvation to protect them from autophagic clearance. In this review, we describe the current state of knowledge regarding the dynamic regulation of 26S proteasomes at all stages of their life cycle, illustrating how protein degradation through this proteolytic machine is tightly controlled to ensure optimal growth, development and longevity.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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190
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Portilho LG, Duarte BCD, Queiroz FR, Ribeiro THC, Jeremias WDJ, Babá EH, Coelho PMZ, Morais ER, Cabral FJ, Caldeira RL, Gomes MDS. Genome-wide identification, characterisation and expression profiling of the ubiquitin-proteasome genes in Biomphalaria glabrata. Mem Inst Oswaldo Cruz 2019; 114:e190052. [PMID: 31166481 PMCID: PMC6548493 DOI: 10.1590/0074-02760190052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/02/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Biomphalaria glabrata is the major species used for the
study of schistosomiasis-related parasite-host relationships, and
understanding its gene regulation may aid in this endeavor. The
ubiquitin-proteasome system (UPS) performs post-translational regulation in
order to maintain cellular protein homeostasis and is related to several
mechanisms, including immune responses. OBJECTIVE The aims of this work were to identify and characterise the putative genes
and proteins involved in UPS using bioinformatic tools and also their
expression on different tissues of B. glabrata. METHODS The putative genes and proteins of UPS in B. glabrata were
predicted using BLASTp and as queries reference proteins from model
organism. We characterised these putative proteins using PFAM and CDD
software describing the conserved domains and active sites. The phylogenetic
analysis was performed using ClustalX2 and MEGA5.2. Expression evaluation
was performed from 12 snail tissues using RPKM. FINDINGS 119 sequences involved in the UPS in B. glabrata were
identified, which 86 have been related to the ubiquitination pathway and 33
to proteasome. In addition, the conserved domains found were associated with
the ubiquitin family, UQ_con, HECT, U-box and proteasome. The main active
sites were lysine and cysteine residues. Lysines are responsible and the
starting point for the formation of polyubiquitin chains, while the cysteine
residues of the enzymes are responsible for binding to ubiquitin. The
phylogenetic analysis showed an organised distribution between the organisms
and the clades of the sequences, corresponding to the tree of life of the
animals, for all groups of sequences analysed. The ubiquitin sequence was
the only one with a high expression profile found in all libraries,
inferring its wide range of performance. MAIN CONCLUSIONS Our results show the presence, conservation and expression profile of the UPS
in this mollusk, providing a basis and new knowledge for other studies
involving this system. Due to the importance of the UPS and B.
glabrata, this work may influence the search for new
methodologies for the control of schistosomiasis.
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Affiliation(s)
- Laysa Gomes Portilho
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil
| | - Bruna Custódio Dias Duarte
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil
| | - Fábio Ribeiro Queiroz
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Thales Henrique Cherubino Ribeiro
- Universidade Federal de Lavras, Departamento de Biologia, Seção de Fisiologia de Plantas, Laboratório de Fisiologia Molecular de Plantas, Lavras, MG, Brasil
| | - Wander de Jesus Jeremias
- Universidade Federal de Ouro Preto, Departamento de Farmácia/Escola de Farmácia, Ouro Preto, MG, Brasil
| | - Elio Hideo Babá
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Paulo Marcos Zech Coelho
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Biologia do Schistosoma mansoni e sua Interação com o Hospedeiro, Belo Horizonte, MG, Brasil
| | - Enyara Rezende Morais
- Universidade Federal de Uberlândia, Laboratório de Bioquímica e Biologia Molecular, Patos de Minas, MG, Brasil
| | - Fernanda Janku Cabral
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Animal, Campinas, SP, Brasil
| | - Roberta Lima Caldeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto René Rachou, Grupo de Pesquisa em Helmintologia e Malacologia Médica, Belo Horizonte, MG, Brasil
| | - Matheus de Souza Gomes
- Universidade Federal de Uberlândia, Laboratório de Bioinformática e Análises Moleculares, Patos de Minas, MG, Brasil
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191
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Effect of Protein Denaturation and Enzyme Inhibitors on Proteasomal-Mediated Production of Peptides in Human Embryonic Kidney Cells. Biomolecules 2019; 9:biom9060207. [PMID: 31142026 PMCID: PMC6627375 DOI: 10.3390/biom9060207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Peptides produced by the proteasome have been proposed to function as signaling molecules that regulate a number of biological processes. In the current study, we used quantitative peptidomics to test whether conditions that affect protein stability, synthesis, or turnover cause changes in the levels of peptides in Human Embryonic Kidney 293T (HEK293T) cells. Mild heat shock (42 °C for 1 h) or treatment with the deubiquitinase inhibitor b-AP15 led to higher levels of ubiquitinated proteins but did not significantly increase the levels of intracellular peptides. Treatment with cycloheximide, an inhibitor of protein translation, did not substantially alter the levels of intracellular peptides identified herein. Cells treated with a combination of epoxomicin and bortezomib showed large increases in the levels of most peptides, relative to the levels in cells treated with either compound alone. Taken together with previous studies, these results support a mechanism in which the proteasome cleaves proteins into peptides that are readily detected in our assays (i.e., 6–37 amino acids) and then further degrades many of these peptides into smaller fragments.
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192
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Motosugi R, Murata S. Dynamic Regulation of Proteasome Expression. Front Mol Biosci 2019; 6:30. [PMID: 31119134 PMCID: PMC6504791 DOI: 10.3389/fmolb.2019.00030] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/15/2019] [Indexed: 12/14/2022] Open
Abstract
The 26S proteasome is a multisubunit complex that catalyzes the degradation of ubiquitinated proteins. The proteasome comprises 33 distinct subunits, all of which are essential for its function and structure. Proteasomes are necessary for various biological processes in cells; therefore, precise regulation of proteasome expression and activity is essential for maintaining cellular health and function. Two decades of research revealed that transcription factors such as Rpn4 and Nrf1 control expression of proteasomes. In this review, we focus on the current understanding and recent findings on the mechanisms underlying the regulation of proteasome expression, as well as the translational regulation of proteasomes.
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Affiliation(s)
- Ryo Motosugi
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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193
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194
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Major Histocompatibility Complex (MHC) Genes and Disease Resistance in Fish. Cells 2019; 8:cells8040378. [PMID: 31027287 PMCID: PMC6523485 DOI: 10.3390/cells8040378] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/12/2019] [Accepted: 04/23/2019] [Indexed: 12/20/2022] Open
Abstract
Fascinating about classical major histocompatibility complex (MHC) molecules is their polymorphism. The present study is a review and discussion of the fish MHC situation. The basic pattern of MHC variation in fish is similar to mammals, with MHC class I versus class II, and polymorphic classical versus nonpolymorphic nonclassical. However, in many or all teleost fishes, important differences with mammalian or human MHC were observed: (1) The allelic/haplotype diversification levels of classical MHC class I tend to be much higher than in mammals and involve structural positions within but also outside the peptide binding groove; (2) Teleost fish classical MHC class I and class II loci are not linked. The present article summarizes previous studies that performed quantitative trait loci (QTL) analysis for mapping differences in teleost fish disease resistance, and discusses them from MHC point of view. Overall, those QTL studies suggest the possible importance of genomic regions including classical MHC class II and nonclassical MHC class I genes, whereas similar observations were not made for the genomic regions with the highly diversified classical MHC class I alleles. It must be concluded that despite decades of knowing MHC polymorphism in jawed vertebrate species including fish, firm conclusions (as opposed to appealing hypotheses) on the reasons for MHC polymorphism cannot be made, and that the types of polymorphism observed in fish may not be explained by disease-resistance models alone.
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195
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de Araujo CB, Heimann AS, Remer RA, Russo LC, Colquhoun A, Forti FL, Ferro ES. Intracellular Peptides in Cell Biology and Pharmacology. Biomolecules 2019; 9:biom9040150. [PMID: 30995799 PMCID: PMC6523763 DOI: 10.3390/biom9040150] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 12/11/2022] Open
Abstract
Intracellular peptides are produced by proteasomes following degradation of nuclear, cytosolic, and mitochondrial proteins, and can be further processed by additional peptidases generating a larger pool of peptides within cells. Thousands of intracellular peptides have been sequenced in plants, yeast, zebrafish, rodents, and in human cells and tissues. Relative levels of intracellular peptides undergo changes in human diseases and also when cells are stimulated, corroborating their biological function. However, only a few intracellular peptides have been pharmacologically characterized and their biological significance and mechanism of action remains elusive. Here, some historical and general aspects on intracellular peptides' biology and pharmacology are presented. Hemopressin and Pep19 are examples of intracellular peptides pharmacologically characterized as inverse agonists to cannabinoid type 1 G-protein coupled receptors (CB1R), and hemopressin fragment NFKF is shown herein to attenuate the symptoms of pilocarpine-induced epileptic seizures. Intracellular peptides EL28 (derived from proteasome 26S protease regulatory subunit 4; Rpt2), PepH (derived from Histone H2B type 1-H), and Pep5 (derived from G1/S-specific cyclin D2) are examples of peptides that function intracellularly. Intracellular peptides are suggested as biological functional molecules, and are also promising prototypes for new drug development.
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Affiliation(s)
- Christiane B de Araujo
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signaling - CeTICS, Butantan Institute, São Paulo SP 05503-900, Brazil.
| | | | | | - Lilian C Russo
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Alison Colquhoun
- Department of Cell and Developmental Biology, University of São Paulo (USP), São Paulo 05508-000, Brazil.
| | - Fábio L Forti
- Department of Biochemistry, Chemistry Institute, University of São Paulo 1111, São Paulo 05508-000, Brazil.
| | - Emer S Ferro
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil.
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Fuchs ACD, Hartmann MD. On the Origins of Symmetry and Modularity in the Proteasome Family. Bioessays 2019; 41:e1800237. [DOI: 10.1002/bies.201800237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Adrian C. D. Fuchs
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingen Germany
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingen Germany
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197
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Menneteau T, Fabre B, Garrigues L, Stella A, Zivkovic D, Roux-Dalvai F, Mouton-Barbosa E, Beau M, Renoud ML, Amalric F, Sensébé L, Gonzalez-de-Peredo A, Ader I, Burlet-Schiltz O, Bousquet MP. Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Human Adipose-derived Mesenchymal Stromal/Stem Cells. Mol Cell Proteomics 2019; 18:744-759. [PMID: 30700495 PMCID: PMC6442357 DOI: 10.1074/mcp.ra118.000958] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/21/2019] [Indexed: 01/18/2023] Open
Abstract
The proteasome controls a multitude of cellular processes through protein degradation and has been identified as a therapeutic target in oncology. However, our understanding of its function and the development of specific modulators are hampered by the lack of a straightforward method to determine the overall proteasome status in biological samples. Here, we present a method to determine the absolute quantity and stoichiometry of ubiquitous and tissue-specific human 20S proteasome subtypes based on a robust, absolute SILAC-based multiplexed LC-Selected Reaction Monitoring (SRM) quantitative mass spectrometry assay with high precision, accuracy, and sensitivity. The method was initially optimized and validated by comparison with a reference ELISA assay and by analyzing the dynamics of catalytic subunits in HeLa cells following IFNγ-treatment and in range of human tissues. It was then successfully applied to reveal IFNγ- and O2-dependent variations of proteasome status during primary culture of Adipose-derived-mesenchymal Stromal/Stem Cells (ADSCs). The results show the critical importance of controlling the culture conditions during cell expansion for future therapeutic use in humans. We hypothesize that a shift from the standard proteasome to the immunoproteasome could serve as a predictor of immunosuppressive and differentiation capacities of ADSCs and, consequently, that quality control should include proteasomal quantification in addition to examining other essential cell parameters. The method presented also provides a new powerful tool to conduct more individualized protocols in cancer or inflammatory diseases where selective inhibition of the immunoproteasome has been shown to reduce side effects.
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Affiliation(s)
- Thomas Menneteau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;; §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Bertrand Fabre
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Garrigues
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Alexandre Stella
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Dusan Zivkovic
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Florence Roux-Dalvai
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Mathilde Beau
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Marie-Laure Renoud
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - François Amalric
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Luc Sensébé
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France
| | - Isabelle Ader
- §STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
| | - Marie-Pierre Bousquet
- From the ‡Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS UMR 5089, UPS, Toulouse, France;.
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198
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Xiao Y, Zhu H, Li L, Gao S, Liu D, Dai B, Li Q, Duan H, Yang H, Li Q, Zhang H, Luo H, Zuo X. Global analysis of protein expression in muscle tissues of dermatomyositis/polymyosisits patients demonstrated an association between dysferlin and human leucocyte antigen A. Rheumatology (Oxford) 2019; 58:kez085. [PMID: 30907425 DOI: 10.1093/rheumatology/kez085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/04/2019] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES DM and PM are characterized by myofibre damage with inflammatory cell infiltration due to the strong expressions of MHC class I HLA-A and monocyte chemoattractant protein-1 (MCP-1). Dysferlin (DYSF) is a transmembrane glycoprotein that anchors in the sarcolemma of myofibres. DYSF mutation is closely associated with inherited myopathies. This study aimed to determine the role of DYSF in the development of DM/PM. METHODS Mass spectrometry was performed in muscle tissues from DM/PM patients and controls. The DYSF levels in muscle tissue, peripheral blood cells and serum were detected by Western blotting, IF, flow cytometry or ELISA. Double IF and co-immunoprecipitation were used to investigate the relationship between DYSF and HLA-A. RESULTS Mass spectrometry and bioinformatics analysis findings suggested the dysregulated proteins in DM/PM patients participated in common biological processes and pathways, such as the generation of precursor metabolites and energy. DYSF was upregulated in the muscle tissue and serum of DM/PM patients. DYSF was mainly expressed in myofibres and co-localized with HLA-A and MCP-1. DYSF and HLA-A expressions were elevated in myocytes and endothelial cells after being stimulated by patient serum and IFN-β. However, no direct interactions were found between DYSF and HLA-A by co-immunoprecipitation. CONCLUSION Our study revealed the dysregulated proteins involved in common and specific biological processes in DM/PM patient samples. DYSF is upregulated and exhibits a potential role along with that of HLA-A and MCP-1 in inflammatory cell infiltration and muscle damage during the development of DM/PM.
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Affiliation(s)
- Yizhi Xiao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Liya Li
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Siming Gao
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Di Liu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Bingying Dai
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Qiuxiang Li
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Huiqian Duan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Huan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Quanzhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huali Zhang
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Hui Luo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Rheumatology and Immunology, Central South University, Changsha, China
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199
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Kasahara M, Flajnik MF. Origin and evolution of the specialized forms of proteasomes involved in antigen presentation. Immunogenetics 2019; 71:251-261. [PMID: 30675634 DOI: 10.1007/s00251-019-01105-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 01/10/2023]
Abstract
Proteasomes are a multi-subunit protease complex that produces peptides bound by major histocompatibility complex (MHC) class I molecules. Phylogenetic studies indicate that two specialized forms of proteasomes, immunoproteasomes and thymoproteasomes, and the proteasome activator PA28αβ emerged in a common ancestor of jawed vertebrates which acquired adaptive immunity based on the MHC, T cell receptors, and B cell receptors ~ 500 million years ago. Comparative genomics studies now provide strong evidence that the genes coding for the immunoproteasome subunits emerged by genome-wide duplication. On the other hand, the gene encoding the thymoproteasome subunit β5t emerged by tandem duplication from the gene coding for the β5 subunit. Strikingly, birds lack immunoproteasomes, thymoproteasomes, and the proteasome activator PA28αβ, raising an interesting question of whether they have evolved any compensatory mechanisms.
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Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan.
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Abstract
Positive selection of T cells in the thymus is induced by low-affinity TCR recognition of self-peptide-MHC complexes expressed by cortical thymic epithelial cells (cTECs). cTECs express a specialized type of proteasomes, the thymoproteasome, which generates a unique spectrum of MHC class I-associated peptides and plays a critical role in thymic positive selection of CD8+ T cells. However, it remains unclear how the thymoproteasome contributes to the thymic positive selection. More than 30 years ago, the "peptidic self" hypothesis proposed that TCRs recognize MHC-presented peptides only, without interacting with MHC molecules, which turned out to be incorrect. Interestingly, however, by implying that a set of MHC-associated peptides forms immunological self, this hypothesis also predicted that positive selection in the thymus is the primary immune response to "foreign epitope" peptides during T cell development. The thymoproteasome-dependent unique self-peptides may create those foreign epitope peptides displayed in the thymus for positive selection of T cells.
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