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Identification of tumor antigens with immunopeptidomics. Nat Biotechnol 2021; 40:175-188. [PMID: 34635837 DOI: 10.1038/s41587-021-01038-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/29/2021] [Indexed: 12/18/2022]
Abstract
The identification of actionable tumor antigens is indispensable for the development of several cancer immunotherapies, including T cell receptor-transduced T cells and patient-specific mRNA or peptide vaccines. Most known tumor antigens have been identified through extensive molecular characterization and are considered canonical if they derive from protein-coding regions of the genome. By eluting human leukocyte antigen-bound peptides from tumors and subjecting these to mass spectrometry analysis, the peptides can be identified by matching the resulting spectra against reference databases. Recently, mass-spectrometry-based immunopeptidomics has enabled the discovery of noncanonical antigens-antigens derived from sequences outside protein-coding regions or generated by noncanonical antigen-processing mechanisms. Coupled with transcriptomics and ribosome profiling, this method enables the identification of thousands of noncanonical peptides, of which a substantial fraction may be detected exclusively in tumors. Spectral matching against the immense noncanonical reference may generate false positives. However, sensitive mass spectrometry, analytical validation and advanced bioinformatics solutions are expected to uncover the full landscape of presented antigens and clinically relevant targets.
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52
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Tundo GR, Sbardella D, Oddone F, Kudriaeva AA, Lacal PM, Belogurov AA, Graziani G, Marini S. At the Cutting Edge against Cancer: A Perspective on Immunoproteasome and Immune Checkpoints Modulation as a Potential Therapeutic Intervention. Cancers (Basel) 2021; 13:4852. [PMID: 34638337 PMCID: PMC8507813 DOI: 10.3390/cancers13194852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 01/22/2023] Open
Abstract
Immunoproteasome is a noncanonical form of proteasome with enzymological properties optimized for the generation of antigenic peptides presented in complex with class I MHC molecules. This enzymatic property makes the modulation of its activity a promising area of research. Nevertheless, immunotherapy has emerged as a front-line treatment of advanced/metastatic tumors providing outstanding improvement of life expectancy, even though not all patients achieve a long-lasting clinical benefit. To enhance the efficacy of the currently available immunotherapies and enable the development of new strategies, a broader knowledge of the dynamics of antigen repertoire processing by cancer cells is needed. Therefore, a better understanding of the role of immunoproteasome in antigen processing and of the therapeutic implication of its modulation is mandatory. Studies on the potential crosstalk between proteasome modulators and immune checkpoint inhibitors could provide novel perspectives and an unexplored treatment option for a variety of cancers.
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Affiliation(s)
| | | | | | - Anna A. Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.K.)
| | - Pedro M. Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, 00167 Rome, Italy;
| | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.K.)
- Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | - Grazia Graziani
- Laboratory of Molecular Oncology, IDI-IRCCS, 00167 Rome, Italy;
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Stefano Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, 00133 Rome, Italy;
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53
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Colberg L, Cammann C, Wesche J, Topfstedt E, Seifert U, Greinacher A. The platelet proteasome and immunoproteasome are stable in buffy-coat derived platelet concentrates for up to 7 days. Transfusion 2021; 61:2746-2755. [PMID: 34331776 DOI: 10.1111/trf.16605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 01/19/2023]
Abstract
OBJECTIVES Characterization of the proteasome and its stability in buffy-coat derived platelet concentrates (PCs) during storage. BACKGROUND The proteasome plays a key role in cell homeostasis by processing misfolded or abnormal proteins and regulating the levels and activities of a high number of proteins contributing to cell cycle, survival, and proliferation. Controversial data exist, whether inhibition of the proteasome affects platelet function. Little is known about function, expression, and stability of the proteasome in PCs during storage, and the potential role of the platelet proteasome in storage lesions. STUDY DESIGN AND METHODS PCs were produced by the buffy-coat method in additive solution and stored at room temperature under agitation. Platelet aggregation was monitored by light transmission aggregometry. Proteasome complexes were assessed by immunoprecipitation and immunoblotting, and proteasome activity was measured using fluorogenic substrates specific for the three different proteolytic activities over 7 days of storage. RESULTS Proteasome inhibition led to a decreased platelet aggregation response after activation with collagen, ADP, TRAP-6, and thrombin. There were no changes in the expression of the catalytic active subunits as well as the proteasome activity during storage of PCs, comparing baseline and day 7. DISCUSSION Platelet proteasome function is relevant for platelet aggregation in response to various agonists. The constitutive and stable expression of the active standard- and immunoproteasome in platelets makes it unlikely that loss of proteasome function is a relevant cause of storage lesions.
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Affiliation(s)
- Lisa Colberg
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany.,Friedrich Loeffler-Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Clemens Cammann
- Friedrich Loeffler-Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Jan Wesche
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Eylin Topfstedt
- Friedrich Loeffler-Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Ulrike Seifert
- Friedrich Loeffler-Institut für Medizinische Mikrobiologie-Virologie, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
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54
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Fidanza M, Gupta P, Sayana A, Shanker V, Pahlke SM, Vu B, Krantz F, Azameera A, Wong N, Anne N, Xia Y, Rong J, Anne A, Skirboll S, Lim M, Wong AJ. Enhancing proteasomal processing improves survival for a peptide vaccine used to treat glioblastoma. Sci Transl Med 2021; 13:13/598/eaax4100. [PMID: 34135109 DOI: 10.1126/scitranslmed.aax4100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/24/2020] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Despite its essential role in antigen presentation, enhancing proteasomal processing is an unexploited strategy for improving vaccines. pepVIII, an anticancer vaccine targeting EGFRvIII, has been tested in several trials for glioblastoma. We examined 20 peptides in silico and experimentally, which showed that a tyrosine substitution (Y6-pepVIII) maximizes proteasome cleavage and survival in a subcutaneous tumor model in mice. In an intracranial glioma model, Y6-pepVIII showed a 62 and 31% improvement in median survival compared to control animals and pepVIII-vaccinated mice. Y6-pepVIII vaccination altered tumor-infiltrating lymphocyte subsets and expression of PD-1 on intratumoral T cells. Combination with anti-PD-1 therapy cured 45% of the Y6-pepVIII-vaccinated mice but was ineffective for pepVIII-treated mice. Liquid chromatography-tandem mass spectrometry analysis of proteasome-digested pepVIII and Y6-pepVIII revealed that most fragments were similar but more abundant in Y6-pepVIII digests and 77% resulted from proteasome-catalyzed peptide splicing (PCPS). We identified 10 peptides that bound human and murine MHC class I. Nine were PCPS products and only one peptide was colinear with EGFRvIII, indicating that PCPS fragments may be a component of MHC class I recognition. Despite not being colinear with EGFRvIII, two of three PCPS products tested were capable of increasing survival when administered independently as vaccines. We hypothesize that the immune response to a vaccine represents the collective contribution from multiple PCPS and linear products. Our work suggests a strategy to increase proteasomal processing of a vaccine that results in an augmented immune response and enhanced survival in mice.
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Affiliation(s)
- Mario Fidanza
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Puja Gupta
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Anin Sayana
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Varun Shanker
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Svenja-Maria Pahlke
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Brandon Vu
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Fanny Krantz
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Aruna Azameera
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Nicollette Wong
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Navya Anne
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Yuanxuan Xia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiming Rong
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Avani Anne
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Stephen Skirboll
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Michael Lim
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Albert J Wong
- Department of Neurosurgery, Stanford University Medical Center, Stanford, CA 94305, USA. .,Cancer Biology Program, Stanford University Medical Center, Stanford, CA 94305, USA
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55
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Nagler A, Kalaora S, Barbolin C, Gangaev A, Ketelaars SLC, Alon M, Pai J, Benedek G, Yahalom-Ronen Y, Erez N, Greenberg P, Yagel G, Peri A, Levin Y, Satpathy AT, Bar-Haim E, Paran N, Kvistborg P, Samuels Y. Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics. Cell Rep 2021; 35:109305. [PMID: 34166618 PMCID: PMC8185308 DOI: 10.1016/j.celrep.2021.109305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
The human leukocyte antigen (HLA)-bound viral antigens serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of presented viral antigens. Using HLA peptidomics, we are able to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived peptides presented by highly prevalent HLA class I (HLA-I) molecules by using infected cells as well as overexpression of SARS-CoV-2 genes. We find 26 HLA-I peptides and 36 HLA class II (HLA-II) peptides. Among the identified peptides, some are shared between different cells and some are derived from out-of-frame open reading frames (ORFs). Seven of these peptides were previously shown to be immunogenic, and we identify two additional immunoreactive peptides by using HLA multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on presented viral-specific antigens that span several of the viral genes.
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Affiliation(s)
- Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chaya Barbolin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Steven L C Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joy Pai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Polina Greenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yagel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Pia Kvistborg
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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56
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Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
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Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
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57
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Immunoproteasome Function in Normal and Malignant Hematopoiesis. Cells 2021; 10:cells10071577. [PMID: 34206607 PMCID: PMC8305381 DOI: 10.3390/cells10071577] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/19/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is a central part of protein homeostasis, degrading not only misfolded or oxidized proteins but also proteins with essential functions. The fact that a healthy hematopoietic system relies on the regulation of protein homeostasis and that alterations in the UPS can lead to malignant transformation makes the UPS an attractive therapeutic target for the treatment of hematologic malignancies. Herein, inhibitors of the proteasome, the last and most important component of the UPS enzymatic cascade, have been approved for the treatment of these malignancies. However, their use has been associated with side effects, drug resistance, and relapse. Inhibitors of the immunoproteasome, a proteasomal variant constitutively expressed in the cells of hematopoietic origin, could potentially overcome the encountered problems of non-selective proteasome inhibition. Immunoproteasome inhibitors have demonstrated their efficacy and safety against inflammatory and autoimmune diseases, even though their development for the treatment of hematologic malignancies is still in the early phases. Various immunoproteasome inhibitors have shown promising preliminary results in pre-clinical studies, and one inhibitor is currently being investigated in clinical trials for the treatment of multiple myeloma. Here, we will review data on immunoproteasome function and inhibition in hematopoietic cells and hematologic cancers.
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58
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Meinhardt A, Ramos PC, Dohmen RJ, Lucas N, Lee-Kirsch MA, Becker B, de Laffolie J, Cunha T, Niehues T, Salzer U, Yoshimi A, Erlacher M, Peters AMJ, Ehl S, Strahm B, Speckmann C. Curative Treatment of POMP-Related Autoinflammation and Immune Dysregulation (PRAID) by Hematopoietic Stem Cell Transplantation. J Clin Immunol 2021; 41:1664-1667. [PMID: 34131834 PMCID: PMC8452576 DOI: 10.1007/s10875-021-01067-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 11/27/2022]
Affiliation(s)
- Andrea Meinhardt
- Center for Pediatrics and Adolescent Medicine, Medical Center, University Hospital Giessen, Giessen, Germany
| | - Paula C Ramos
- Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - R Jürgen Dohmen
- Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Nadja Lucas
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Benjamin Becker
- Center for Pediatrics and Adolescent Medicine, Medical Center, University Hospital Giessen, Giessen, Germany
| | - Jan de Laffolie
- Center for Pediatrics and Adolescent Medicine, Medical Center, University Hospital Giessen, Giessen, Germany
| | - Tomás Cunha
- Center for Dermatology and Allergology, Medical Center, University Hospital Marburg, Marburg, Germany
| | - Tim Niehues
- Center for Pediatrics and Adolescent Medicine, Helios Hospital Krefeld, Krefeld, Germany
| | - Ulrich Salzer
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Ayami Yoshimi
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Miriam Erlacher
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Anke M J Peters
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Brigitte Strahm
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.
- Center for Pediatrics and Adolescent Medicine, Department of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.
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Direct Evidence for Viral Antigen Presentation during Latent Cytomegalovirus Infection. Pathogens 2021; 10:pathogens10060731. [PMID: 34200578 PMCID: PMC8229173 DOI: 10.3390/pathogens10060731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Murine models of cytomegalovirus (CMV) infection have revealed an immunological phenomenon known as “memory inflation” (MI). After a peak of a primary CD8+ T-cell response, the pool of epitope-specific cells contracts in parallel to the resolution of productive infection and the establishment of a latent infection, referred to as “latency.” CMV latency is associated with an increase in the number of cells specific for certain viral epitopes over time. The inflationary subset was identified as effector-memory T cells (iTEM) characterized by the cell surface phenotype KLRG1+CD127−CD62L−. As we have shown recently, latent viral genomes are not transcriptionally silent. Rather, viral genes are sporadically desilenced in a stochastic fashion. The current hypothesis proposes MI to be driven by presented viral antigenic peptides encoded by the corresponding, stochastically expressed viral genes. Although this mechanism suggests itself, independent evidence for antigen presentation during viral latency is pending. Here we fill this gap by showing that T cell-receptor transgenic OT-I cells that are specific for peptide SIINFEKL proliferate upon adoptive cell transfer in C57BL/6 recipients latently infected with murine CMV encoding SIINFEKL (mCMV-SIINFEKL), but not in those latently infected with mCMV-SIINFEKA, in which antigenicity is lost by mutation L8A of the C-terminal amino acid residue.
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60
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Komov L, Melamed Kadosh D, Barnea E, Admon A. The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides. Mol Cell Proteomics 2021; 20:100105. [PMID: 34087483 PMCID: PMC8724922 DOI: 10.1016/j.mcpro.2021.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Degradation products of surplus subunits are often presented as HLA peptides. Interferons increase degradation and presentation of such defective products. Dynamic SILAC facilitates identification of such HLA peptides. This cellular pathway provides alert to the immune system about viral infections.
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Affiliation(s)
- Liran Komov
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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61
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Blood Transcriptomics of Turbot Scophthalmus maximus: A Tool for Health Monitoring and Disease Studies. Animals (Basel) 2021; 11:ani11051296. [PMID: 33946507 PMCID: PMC8147184 DOI: 10.3390/ani11051296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The analysis of blood gene expression is emerging as a relevant source of information about the health status of an organism. While these investigations are increasingly performed in human and terrestrial animals, their potential is still underexplored in fish pathology. The aim of this work was to analyze the blood transcriptional profile of a commercially important flatfish species, turbot (Scophthalmus maximus), in healthy and diseased specimens. The analysis of the most expressed genes in healthy fish indicated that turbot red blood cells have important immunological functions. In diseased fish, parasitized by a myxozoan, the blood analysis reflected a broad inhibition of the immune response followed by intense inflammatory activation in heavy infections. The results showed that turbot response appears delayed, dysregulated and ineffective in stopping the infection. Particularly, a proper development of the adaptive immune response was lacking. This study points out that blood gene expression profiling is a reliable tool for health monitoring, as well as to advance in the knowledge of fish immunity and diseases. Abstract Blood transcriptomics is emerging as a relevant tool to monitor the status of the immune system and assist in diagnosis, prognosis, treatment and pathogenesis studies of diseases. In fish pathology, the potential of transcriptome profiling of blood is still poorly explored. Here, RNA sequencing was applied to analyze the blood transcriptional profile of turbot (Scophthalmus maximus), the most important farmed flatfish. The study was conducted in healthy specimens and specimens parasitized by the myxozoan Enteromyxum scophthalmi, which causes one of the most devastating diseases in turbot aquaculture. The blood of healthy turbot showed a transcriptomic profile mainly related to erythrocyte gas transportation function, but also to antigen processing and presentation. In moderately infected turbot, the blood reflected a broad inhibition of the immune response. Particularly, down-regulation of the B cell receptor signaling pathway was shared with heavily parasitized fish, which showed larger transcriptomic changes, including the activation of the inflammatory response. Turbot response to enteromyxosis proved to be delayed, dysregulated and ineffective in stopping the infection. The study evinces that blood transcriptomics can contribute to a better understanding of the teleost immune system and serve as a reliable tool to investigate the physiopathological status of fish.
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62
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Shi Y, Zhu C, Liu Y, Lu Y, Li X, Qin B, Luo Z, Luo L, Jiang M, Zhang J, Guan G, Zheng C, You J. A Vaccination with Boosted Cross Presentation by ER-Targeted Antigen Delivery for Anti-Tumor Immunotherapy. Adv Healthc Mater 2021; 10:e2001934. [PMID: 33502831 DOI: 10.1002/adhm.202001934] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/17/2020] [Indexed: 12/16/2022]
Abstract
Vaccination is a widely-accepted resort against the invasion or proliferation of bacteria, parasites, viruses, and even cancer, which accounts heavily on an active involvement of CD8+ T cells. As one of the pivotal strategies taken by dendritic cells (DCs) to promote the responsiveness of CD8+ T cells to exogenous antigens, cross presentation culminates in an elevated overall host defense against cancer or infection. However, the precise mechanisms regulating such a process remains elusive, and current attempts to fuel cross presentation usually fail to exert efficiency. Here, model antigen OVA-loaded, endoplasmic reticulum (ER)-targeting cationic liposome (OVA@lipoT) is developed and characterized with a booster effect on the activation and maturation of DCs. Moreover, OVA@lipoT pulsed DCs exhibit overwhelming superiority in triggering cytotoxic T lymphocyte response both in vivo and in vitro. Data reveal that lipoT alters the intracellular trafficking and presenting pathway of antigen, which promotes cross presentation and bears close relationship to the ER-associated degradation (ERAD). These results may drop a hint about the interconnectivity between cross presentation and ER-targeted antigen delivery, provide extra information to the understanding of ERAD-mediated cross priming, and even shed new light on the design and optimization of vaccines against currently intractable cancers or virus-infection.
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Affiliation(s)
- Yingying Shi
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Chunqi Zhu
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Yu Liu
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Yichao Lu
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Xiang Li
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Bing Qin
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Zhenyu Luo
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Lihua Luo
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Mengshi Jiang
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Junlei Zhang
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Guannan Guan
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
| | - Cheng Zheng
- Zhejiang Institute for Food and Drug Control Zhejiang 310058 P. R. China
| | - Jian You
- College of Pharmaceutical Sciences Zhejiang University Zhejiang 310058 P. R. China
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Fu Z, Yang R, Yu G, Ma Z. Tissue comparison of transcriptional response to acute acidification stress of barramundi Lates calcarifer in coastal and estuarine areas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100830. [PMID: 33812155 DOI: 10.1016/j.cbd.2021.100830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
In order to explore the common and unique physiological changes in tissues of juvenile barramundi Lates calcarifer in acidified water environment, RNA sequence analysis was used to analyze the molecular responses of liver, head kidney, and gill of juvenile barramundi in pH 7.4 and pH 8.1 seawater environment. The number of differential expression genes identified in liver, head kidney and gill were 860, 388 and 1792, respectively. Through functional enrichment analysis, the differential expression genes common to the three tissues were all related to immunity. Among the unique differential genes in the liver, pathways related to digestion, endocrine, and metabolism were enriched. Among the unique differential expression genes in gill, pathways related to genetic information processing, immunity and metabolism were enriched. The findings of the present study uncover the transcriptional changes in fish correspond to environmental pH change, and provide a better understanding on the biological process at molecular level to environmental pH adapting. This work highlights that assessments for the potential of estuarine fishes to cope with environmental pH change to develop the future conservation strategies.
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Affiliation(s)
- Zhengyi Fu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, PR China; Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China
| | - Rui Yang
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, PR China; Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China
| | - Gang Yu
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, PR China; Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China
| | - Zhenhua Ma
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, PR China; Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510300, PR China; Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China.
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64
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Tian W, Maresh ME, Trader DJ. Approaches to Evaluate the Impact of a Small-Molecule Binder to a Noncatalytic Site of the Proteasome. Chembiochem 2021; 22:1961-1965. [PMID: 33617657 DOI: 10.1002/cbic.202100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/11/2021] [Indexed: 11/11/2022]
Abstract
Proteasome activity is crucial for cell survival and proliferation. In recent years, small molecules have been discovered that can affect the catalytic activity of the proteasome. Rather than targeting the active sites of the proteasome, it might be possible to affect ubiquitin-dependent degradation of proteins by limiting the association of the 19S regulatory particle (19S RP) with the 20S core particle (20S CP) of the proteasome. We recently described the discovery of TXS-8, a peptoid that binds to Rpn-6. Rpn-6 is a proteasome-associated protein that makes critical contacts with the 19S RP and the 20S CP. Herein, we present a general workflow to evaluate the impact of a small-molecule binder on proteasome activity by using TXS-8 as an example. This workflow contains three steps in which specific probes or overexpressed proteins in cells are used to determine whether the hydrolysis activity of the proteasome is affected. Although, in our case, TXS-8 did not affect proteasome activity, our workflow is highly amenable to studying a variety of small-molecule-proteasome subunit interactions.
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Affiliation(s)
- Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Marianne E Maresh
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907, USA
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Frantzeskakis M, Takahama Y, Ohigashi I. The Role of Proteasomes in the Thymus. Front Immunol 2021; 12:646209. [PMID: 33815406 PMCID: PMC8017227 DOI: 10.3389/fimmu.2021.646209] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/05/2021] [Indexed: 12/26/2022] Open
Abstract
The thymus provides a microenvironment that supports the generation and selection of T cells. Cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells (mTECs) are essential components of the thymic microenvironment and present MHC-associated self-antigens to developing thymocytes for the generation of immunocompetent and self-tolerant T cells. Proteasomes are multicomponent protease complexes that degrade ubiquitinated proteins and produce peptides that are destined to be associated with MHC class I molecules. cTECs specifically express thymoproteasomes that are essential for optimal positive selection of CD8+ T cells, whereas mTECs, which contribute to the establishment of self-tolerance in T cells, express immunoproteasomes. Immunoproteasomes are also detectable in dendritic cells and developing thymocytes, additionally contributing to T cell development in the thymus. In this review, we summarize the functions of proteasomes expressed in the thymus, focusing on recent findings pertaining to the functions of the thymoproteasomes and the immunoproteasomes.
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Affiliation(s)
- Melina Frantzeskakis
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, Bethesda, MD, United States
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, Bethesda, MD, United States
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
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A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny. PLoS Pathog 2021; 17:e1009403. [PMID: 33735221 PMCID: PMC7971519 DOI: 10.1371/journal.ppat.1009403] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Arteriviruses are enveloped positive-strand RNA viruses that assemble and egress using the host cell’s exocytic pathway. In previous studies, we demonstrated that most arteriviruses use a unique -2 ribosomal frameshifting mechanism to produce a C-terminally modified variant of their nonstructural protein 2 (nsp2). Like full-length nsp2, the N-terminal domain of this frameshift product, nsp2TF, contains a papain-like protease (PLP2) that has deubiquitinating (DUB) activity, in addition to its role in proteolytic processing of replicase polyproteins. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nsp2TF localizes to compartments of the exocytic pathway, specifically endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and Golgi complex. Here, we show that nsp2TF interacts with the two major viral envelope proteins, the GP5 glycoprotein and membrane (M) protein, which drive the key process of arterivirus assembly and budding. The PRRSV GP5 and M proteins were found to be poly-ubiquitinated, both in an expression system and in cells infected with an nsp2TF-deficient mutant virus. In contrast, ubiquitinated GP5 and M proteins did not accumulate in cells infected with the wild-type, nsp2TF-expressing virus. Further analysis implicated the DUB activity of the nsp2TF PLP2 domain in deconjugation of ubiquitin from GP5/M proteins, thus antagonizing proteasomal degradation of these key viral structural proteins. Our findings suggest that nsp2TF is targeted to the exocytic pathway to reduce proteasome-driven turnover of GP5/M proteins, thus promoting the formation of GP5-M dimers that are critical for arterivirus assembly. Arteriviruses are a rapidly expanding family of positive-stranded RNA viruses, which includes economically important veterinary pathogens like equine arteritis virus (EAV) and two species of porcine reproductive and respiratory syndrome virus (PRRSV-1 and PRRSV-2). In our previous studies, we uncovered an unprecedented arterivirus gene expression mechanism: a highly efficient -2 programmed ribosomal frameshift (PRF) that is controlled by an interaction of viral protein nsp1ß with specific RNA sequences and host poly(C) binding proteins. It is used by PRRSVs, and most other arteriviruses, to efficiently produce a previously unknown nonstructural protein variant, nsp2TF. In this study, we demonstrate that PRRSV nsp2TF interacts with the two major arteriviral envelope proteins, GP5 and M, whose heterodimerization in the secretory pathway is a key step in envelope protein trafficking and virus assembly. Our findings suggest that nsp2TF promotes arterivirus assembly by antagonizing the ubiquitination-dependent proteasomal degradation of GP5 and M proteins. This mechanism is based on the DUB activity of the PLP2 protease domain located within the N-terminal region of nsp2TF. To our knowledge, this is the first study to demonstrate that viruses can express a DUB that functions specifically to counteract the ubiquitination and degradation of key viral structural proteins.
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Leister H, Luu M, Staudenraus D, Lopez Krol A, Mollenkopf HJ, Sharma A, Schmerer N, Schulte LN, Bertrams W, Schmeck B, Bosmann M, Steinhoff U, Visekruna A. Pro- and Antitumorigenic Capacity of Immunoproteasomes in Shaping the Tumor Microenvironment. Cancer Immunol Res 2021; 9:682-692. [PMID: 33707310 DOI: 10.1158/2326-6066.cir-20-0492] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/14/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
Abstract
Apart from the constitutive proteasome, the immunoproteasome that comprises the three proteolytic subunits LMP2, MECL-1, and LMP7 is expressed in most immune cells. In this study, we describe opposing roles for immunoproteasomes in regulating the tumor microenvironment (TME). During chronic inflammation, immunoproteasomes modulated the expression of protumorigenic cytokines and chemokines and enhanced infiltration of innate immune cells, thus triggering the onset of colitis-associated carcinogenesis (CAC) in wild-type mice. Consequently, immunoproteasome-deficient animals (LMP2/MECL-1/LMP7-null mice) were almost completely resistant to CAC development. In patients with ulcerative colitis with high risk for CAC, immunoproteasome-induced protumorigenic mediators were upregulated. In melanoma tumors, the role of immunoproteasomes is relatively unknown. We found that high expression of immunoproteasomes in human melanoma was associated with better prognosis. Similarly, our data revealed that the immunoproteasome has antitumorigenic activity in a mouse model of melanoma. The antitumor immunity against melanoma was compromised in immunoproteasome-deficient mice because of the impaired activity of CD8+ CTLs, CD4+ Th1 cells, and antigen-presenting cells. These findings show that immunoproteasomes may exert opposing roles with either pro- or antitumoral properties in a context-dependent manner.
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Affiliation(s)
- Hanna Leister
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Maik Luu
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Daniel Staudenraus
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Aleksandra Lopez Krol
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Hans-Joachim Mollenkopf
- Max Planck Institute for Infection Biology, Core Facility Microarray/Genomics, Berlin, Germany
| | - Arjun Sharma
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Nils Schmerer
- Institute for Lung Research, UGMLC, Philipps-University Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, UGMLC, Philipps-University Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Wilhelm Bertrams
- Institute for Lung Research, UGMLC, Philipps-University Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, UGMLC, Philipps-University Marburg, Marburg, Germany.,German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Markus Bosmann
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.,Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany.
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68
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Mossallam GI, Fattah RA, Bokhary M, Moneer M, Mahmoud HK. LMP7 polymorphism may modify the presentation and clinical impact of minor histocompatibility antigens in matched related hematopoietic stem cell transplantation. Cell Immunol 2021; 364:104329. [PMID: 33798908 DOI: 10.1016/j.cellimm.2021.104329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Differential expression of minor histocompatibility antigens between the recipient and donor determines their disparity and can be modified by immunoproteasomes that regulate their processing and presentation. We examined the impact of HA-1 and HA-8 disparity, and immunoproteasome LMP7 polymorphism in 130 pairs. In multivariate analysis, HA-1 disparity showed a statistically significant association with an increased incidence of acute graft-versus-host disease (aGVHD) II-IV (p = 0.043, HR: 3.71, 95%CI = 1.04-13.26), while LMP7-Q/Q showed a trend toward increased incidence of aGVHD compared to LMP7-Q/K and K/K genotypes (p = 0.087, HR: 2.36, 95%CI = 0.88-6.31). All HA-1 and HA-8 disparate patients who developed aGVHD had the LMP7-Q/Q genotype. No significant association could be detected between HA-1, HA-8, or LMP7 and chronic GVHD, relapse-free survival (RFS), overall survival (OS), or transplant-related mortality (TRM). In conclusion, we suggested an association between the HA-1 disparity and the risk of developing aGVHD with a possible modifying effect of LMP7.
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Affiliation(s)
- Ghada I Mossallam
- Bone Marrow Transplantation Laboratory Unit, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Raafat Abdel Fattah
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt; Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
| | - Mahmoud Bokhary
- Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
| | - Manar Moneer
- Department of Epidemiology and Biostatistics, National Cancer Institute, Cairo University, Egypt
| | - Hossam K Mahmoud
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt; Bone Marrow Transplantation Unit, Nasser Institute Hospital for Research and Treatment, Cairo, Egypt
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69
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Shukla A, Cloutier M, Appiya Santharam M, Ramanathan S, Ilangumaran S. The MHC Class-I Transactivator NLRC5: Implications to Cancer Immunology and Potential Applications to Cancer Immunotherapy. Int J Mol Sci 2021; 22:ijms22041964. [PMID: 33671123 PMCID: PMC7922096 DOI: 10.3390/ijms22041964] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The immune system constantly monitors the emergence of cancerous cells and eliminates them. CD8+ cytotoxic T lymphocytes (CTLs), which kill tumor cells and provide antitumor immunity, select their targets by recognizing tumor antigenic peptides presented by MHC class-I (MHC-I) molecules. Cancer cells circumvent immune surveillance using diverse strategies. A key mechanism of cancer immune evasion is downregulation of MHC-I and key proteins of the antigen processing and presentation machinery (APM). Even though impaired MHC-I expression in cancers is well-known, reversing the MHC-I defects remains the least advanced area of tumor immunology. The discoveries that NLRC5 is the key transcriptional activator of MHC-I and APM genes, and genetic lesions and epigenetic modifications of NLRC5 are the most common cause of MHC-I defects in cancers, have raised the hopes for restoring MHC-I expression. Here, we provide an overview of cancer immunity mediated by CD8+ T cells and the functions of NLRC5 in MHC-I antigen presentation pathways. We describe the impressive advances made in understanding the regulation of NLRC5 expression, the data supporting the antitumor functions of NLRC5 and a few reports that argue for a pro-tumorigenic role. Finally, we explore the possible avenues of exploiting NLRC5 for cancer immunotherapy.
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Affiliation(s)
- Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Madanraj Appiya Santharam
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
- Correspondence: ; Tel.: +1-819-346-1110 (ext. 14834)
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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71
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Cascio P. PA28γ: New Insights on an Ancient Proteasome Activator. Biomolecules 2021; 11:228. [PMID: 33562807 PMCID: PMC7915322 DOI: 10.3390/biom11020228] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
PA28 (also known as 11S, REG or PSME) is a family of proteasome regulators whose members are widely present in many of the eukaryotic supergroups. In jawed vertebrates they are represented by three paralogs, PA28α, PA28β, and PA28γ, which assemble as heptameric hetero (PA28αβ) or homo (PA28γ) rings on one or both extremities of the 20S proteasome cylindrical structure. While they share high sequence and structural similarities, the three isoforms significantly differ in terms of their biochemical and biological properties. In fact, PA28α and PA28β seem to have appeared more recently and to have evolved very rapidly to perform new functions that are specifically aimed at optimizing the process of MHC class I antigen presentation. In line with this, PA28αβ favors release of peptide products by proteasomes and is particularly suited to support adaptive immune responses without, however, affecting hydrolysis rates of protein substrates. On the contrary, PA28γ seems to be a slow-evolving gene that is most similar to the common ancestor of the PA28 activators family, and very likely retains its original functions. Notably, PA28γ has a prevalent nuclear localization and is involved in the regulation of several essential cellular processes including cell growth and proliferation, apoptosis, chromatin structure and organization, and response to DNA damage. In striking contrast with the activity of PA28αβ, most of these diverse biological functions of PA28γ seem to depend on its ability to markedly enhance degradation rates of regulatory protein by 20S proteasome. The present review will focus on the molecular mechanisms and biochemical properties of PA28γ, which are likely to account for its various and complex biological functions and highlight the common features with the PA28αβ paralog.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy
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72
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Maresh ME, Salazar-Chaparro AF, Trader DJ. Methods for the discovery of small molecules to monitor and perturb the activity of the human proteasome. Future Med Chem 2021; 13:99-116. [PMID: 33275045 PMCID: PMC7857359 DOI: 10.4155/fmc-2020-0288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Regulating protein production and degradation is critical to maintaining cellular homeostasis. The proteasome is a key player in keeping proteins at the proper levels. However, proteasome activity can be altered in certain disease states, such as blood cancers and neurodegenerative diseases. Cancers often exhibit enhanced proteasomal activity, as protein synthesis is increased in these cells compared with normal cells. Conversely, neurodegenerative diseases are characterized by protein accumulation, leading to reduced proteasome activity. As a result, the proteasome has emerged as a target for therapeutic intervention. The potential of the proteasome as a therapeutic target has come from studies involving chemical stimulators and inhibitors, and the development of a suite of assays and probes that can be used to monitor proteasome activity with purified enzyme and in live cells.
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Affiliation(s)
- Marianne E Maresh
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN 47907, USA
| | - Andres F Salazar-Chaparro
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN 47907, USA
| | - Darci J Trader
- Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN 47907, USA
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73
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Gomez-Perosanz M, Ras-Carmona A, Lafuente EM, Reche PA. Identification of CD8 + T cell epitopes through proteasome cleavage site predictions. BMC Bioinformatics 2020; 21:484. [PMID: 33308150 PMCID: PMC7733697 DOI: 10.1186/s12859-020-03782-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 09/28/2020] [Indexed: 01/08/2023] Open
Abstract
Background We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8+ T cell epitopes. Results We first assembled an epitope dataset consisting of 844 unique virus-specific CD8+ T cell epitopes and their source proteins. We then analyzed cleavage predictions by PCPS immunoproteasome cleavage model on this dataset and compared them with those provided by a related method implemented by NetChop web server. PCPS was clearly superior to NetChop in term of sensitivity (0.89 vs. 0.79) but somewhat inferior with regard to specificity (0.55 vs. 0.60). Judging by the Mathew’s Correlation Coefficient, PCPS predictions were overall superior to those provided by NetChop (0.46 vs. 0.39). We next analyzed the power of C-terminal cleavage predictions provided by the same PCPS model to discriminate CD8+ T cell epitopes, finding that they could be discriminated from random peptides with an accuracy of 0.74. Following these results, we tuned the PCPS web server to predict CD8+ T cell epitopes and predicted the entire SARS-CoV-2 epitope space. Conclusions We report an improved version of PCPS named iPCPS for predicting proteasome cleavage sites and peptides with CD8+ T cell epitope features. iPCPS is available for free public use at https://imed.med.ucm.es/Tools/pcps/.
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Affiliation(s)
- Marta Gomez-Perosanz
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Alvaro Ras-Carmona
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Esther M Lafuente
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain
| | - Pedro A Reche
- Laboratory of Immunomedicine, Department of Immunology, Faculty of Medicine, Complutense University of Madrid, Pza Ramon y Cajal, s/n, 28040, Madrid, Spain.
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Wang Y, Yan K, Lin J, Liu Y, Wang J, Li X, Li X, Hua Z, Zheng Z, Shi J, Sun S, Bi J. CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer. Front Oncol 2020; 10:553399. [PMID: 33330025 PMCID: PMC7713665 DOI: 10.3389/fonc.2020.553399] [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: 04/18/2020] [Accepted: 10/20/2020] [Indexed: 01/05/2023] Open
Abstract
Purpose To identify immune-related co-expressed genes that promote CD8+ T cell infiltration in bladder cancer, and to explore the interactions among relevant genes in the tumor microenvironment. Method We obtained bladder cancer gene matrix and clinical information data from TCGA, GSE32894 and GSE48075. The “estimate” package was used to calculate tumor purity and immune score. The CIBERSORT algorithm was used to assess CD8+ T cell proportions. Weighted gene co-expression network analysis was used to identify the co-expression modules with CD8+ T cell proportions and bladder tumor purity. Subsequently, we performed correlation analysis among angiogenesis factors, angiogenesis inhibitors, immune inflammatory responses, and CD8+ T cell related genes in tumor microenvironment. Results A CD8+ T cell related co-expression network was identified. Eight co-expressed genes (PSMB8, PSMB9, PSMB10, PSME2, TAP1, IRF1, FBOX6, ETV7) were identified as CD8+ T cell-related genes that promoted infiltration of CD8+ T cells, and were enriched in the MHC class I tumor antigen presentation process. The proteins level encoded by these genes (PSMB10, PSMB9, PSMB8, TAP1, IRF1, and FBXO6) were lower in the high clinical grade patients, which suggested the clinical phenotype correlation both in mRNA and protein levels. These factors negatively correlated with angiogenesis factors and positively correlated with angiogenesis inhibitors. PD-1 and PD-L1 positively correlated with these genes which suggested PD-1 expression level positively correlated with the biological process composed by these co-expression genes. In the high expression group of these genes, inflammation and immune response were more intense, and the tumor purity was lower, suggesting that these genes were immune protective factors that improved the prognosis in patients with bladder cancer. Conclusion These co-expressed genes promote high levels of infiltration of CD8+ T cells in an immunoproteasome process involved in MHC class I molecules. The mechanism might provide new pathways for treatment of patients who are insensitive to PD-1 immunotherapy due to low degrees of CD8+ T cell infiltration.
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Affiliation(s)
- Yutao Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Kexin Yan
- Department of Dermatology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Jiaxing Lin
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Yang Liu
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Jianfeng Wang
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Xuejie Li
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Xinxin Li
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Zhixiong Hua
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Zhenhua Zheng
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Jianxiu Shi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Siqing Sun
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
| | - Jianbin Bi
- Department of Urology, China Medical University, The First Hospital of China Medical University, Shenyang, China
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Yang Y, Liu W, Hu D, Su R, Ji M, Huang Y, Shereen MA, Xu X, Luo Z, Zhang Q, Liu F, Wu K, Liu Y, Wu J. HIV-1 Nef Interacts with LMP7 To Attenuate Immunoproteasome Formation and Major Histocompatibility Complex Class I Antigen Presentation. mBio 2020; 11:e02221-19. [PMID: 33109760 PMCID: PMC7593969 DOI: 10.1128/mbio.02221-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/21/2020] [Indexed: 01/03/2023] Open
Abstract
The proteasome is a major protein degradation machinery with essential and diverse biological functions. Upon induction by cytokines, proteasome subunits β1, β2, and β5 are replaced by β1i/LMP2, β2i/MECL-1, and β5i/LMP7, resulting in the formation of an immunoproteasome (iProteasome). iProteasome-degraded products are loaded onto the major histocompatibility complex class I (MHC-I), regulating immune responses and inducing cytotoxic T lymphocytes (CTLs). Human immunodeficiency virus type 1 (HIV-1) is the causal agent of AIDS. HIV-1-specific CTLs represent a critical immune mechanism limiting viral replication. HIV-1 negative regulatory factor (Nef) counteracts host immunity, particularly the response involving MHC-I/CTL. This study identifies a distinct mechanism by which Nef facilitates immune evasion via suppressing the function of iProteasome and MHC-I. Nef interacts with LMP7 on the endoplasmic reticulum (ER), downregulating the incorporation of LMP7 into iProteasome and thereby attenuating its formation. Moreover, Nef represses the iProteasome function of protein degradation, MHC-I trafficking, and antigen presentation.IMPORTANCE The ubiquitin-proteasome system (UPS) is essential for the degradation of damaged proteins, which takes place in the proteasome. Upon activation by cytokines, the catalytic subunits of the proteasome are replaced by distinct isoforms resulting in the formation of an immunoproteasome (iProteasome). iProteasome generates peptides used by major histocompatibility complex class I (MHC-I) for antigen presentation and is essential for immune responses. HIV-1 is the causative agent of AIDS, and HIV-1-specific cytotoxic T lymphocytes (CTLs) provide immune responses limiting viral replication. This study identifies a distinct mechanism by which HIV-1 promotes immune evasion. The viral protein negative regulatory factor (Nef) interacts with a component of iProteasome, LMP7, attenuating iProteasome formation and protein degradation function, and thus repressing the MHC-I antigen presentation activity of MHC-I. Therefore, HIV-1 targets LMP7 to inhibit iProteasome activation, and LMP7 may be used as the target for the development of anti-HIV-1/AIDS therapy.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Weiyong Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Rui Su
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Man Ji
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuqing Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Muhammad Adnan Shereen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaodi Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Qi Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kailang Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yingle Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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Panagiotakopoulou V, Ivanyuk D, De Cicco S, Haq W, Arsić A, Yu C, Messelodi D, Oldrati M, Schöndorf DC, Perez MJ, Cassatella RP, Jakobi M, Schneiderhan-Marra N, Gasser T, Nikić-Spiegel I, Deleidi M. Interferon-γ signaling synergizes with LRRK2 in neurons and microglia derived from human induced pluripotent stem cells. Nat Commun 2020; 11:5163. [PMID: 33057020 PMCID: PMC7560616 DOI: 10.1038/s41467-020-18755-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease-associated kinase LRRK2 has been linked to IFN type II (IFN-γ) response in infections and to dopaminergic neuronal loss. However, whether and how LRRK2 synergizes with IFN-γ remains unclear. In this study, we employed dopaminergic neurons and microglia differentiated from patient-derived induced pluripotent stem cells carrying LRRK2 G2019S, the most common Parkinson's disease-associated mutation. We show that IFN-γ enhances the LRRK2 G2019S-dependent negative regulation of AKT phosphorylation and NFAT activation, thereby increasing neuronal vulnerability to immune challenge. Mechanistically, LRRK2 G2019S suppresses NFAT translocation via calcium signaling and possibly through microtubule reorganization. In microglia, LRRK2 modulates cytokine production and the glycolytic switch in response to IFN-γ in an NFAT-independent manner. Activated LRRK2 G2019S microglia cause neurite shortening, indicating that LRRK2-driven immunological changes can be neurotoxic. We propose that synergistic LRRK2/IFN-γ activation serves as a potential link between inflammation and neurodegeneration in Parkinson's disease.
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Affiliation(s)
- Vasiliki Panagiotakopoulou
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Dina Ivanyuk
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Silvia De Cicco
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Wadood Haq
- Centre for Ophthalmology, Institute for Ophthalmic Research University of Tübingen, University of Tübingen, Tübingen, 72076, Germany
| | - Aleksandra Arsić
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Cong Yu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Daria Messelodi
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Marvin Oldrati
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - David C Schöndorf
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Maria-Jose Perez
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Ruggiero Pio Cassatella
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Meike Jakobi
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Nicole Schneiderhan-Marra
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770, Reutlingen, Germany
| | - Thomas Gasser
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany
| | - Ivana Nikić-Spiegel
- Werner Reichardt Centre for Integrative Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Michela Deleidi
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, 72076, Germany.
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, 72076, Germany.
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Sabbatino F, Liguori L, Polcaro G, Salvato I, Caramori G, Salzano FA, Casolaro V, Stellato C, Dal Col J, Pepe S. Role of Human Leukocyte Antigen System as A Predictive Biomarker for Checkpoint-Based Immunotherapy in Cancer Patients. Int J Mol Sci 2020; 21:ijms21197295. [PMID: 33023239 PMCID: PMC7582904 DOI: 10.3390/ijms21197295] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Recent advances in cancer immunotherapy have clearly shown that checkpoint-based immunotherapy is effective in a small subgroup of cancer patients. However, no effective predictive biomarker has been identified so far. The major histocompatibility complex, better known in humans as human leukocyte antigen (HLA), is a very polymorphic gene complex consisting of more than 200 genes. It has a crucial role in activating an appropriate host immune response against pathogens and tumor cells by discriminating self and non-self peptides. Several lines of evidence have shown that down-regulation of expression of HLA class I antigen derived peptide complexes by cancer cells is a mechanism of tumor immune escape and is often associated to poor prognosis in cancer patients. In addition, it has also been shown that HLA class I and II antigen expression, as well as defects in the antigen processing machinery complex, may predict tumor responses in cancer immunotherapy. Nevertheless, the role of HLA in predicting tumor responses to checkpoint-based immunotherapy is still debated. In this review, firstly, we will describe the structure and function of the HLA system. Secondly, we will summarize the HLA defects and their clinical significance in cancer patients. Thirdly, we will review the potential role of the HLA as a predictive biomarker for checkpoint-based immunotherapy in cancer patients. Lastly, we will discuss the potential strategies that may restore HLA function to implement novel therapeutic strategies in cancer patients.
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Affiliation(s)
- Francesco Sabbatino
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Oncology Unit, AOU San Giovanni di Dio e Ruggi D’Aragona, 84131 Salerno, Italy
| | - Luigi Liguori
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Giovanna Polcaro
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Pulmonary Unit, Department of Biomedical Sciences, Dentistry, Morphological and Functional Imaging (BIOMORF), University of Messina, 98125 Messina, Italy;
| | - Gaetano Caramori
- Pulmonary Unit, Department of Biomedical Sciences, Dentistry, Morphological and Functional Imaging (BIOMORF), University of Messina, 98125 Messina, Italy;
| | - Francesco A. Salzano
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Correspondence: ; Tel.: +39-08996-5210
| | - Stefano Pepe
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Oncology Unit, AOU San Giovanni di Dio e Ruggi D’Aragona, 84131 Salerno, Italy
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Deviant proteome profile of equine granulocytes associates to latent activation status in organ specific autoimmune disease. J Proteomics 2020; 230:103989. [PMID: 32977044 DOI: 10.1016/j.jprot.2020.103989] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/26/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
Equine recurrent uveitis (ERU) is a spontaneous, remitting-relapsing autoimmune disease driven by the adaptive immune system. Although T cells are described as the main effector cells in pathogenesis, granulocytes have also emerged as possible disease mediators. To explore the role of these innate immune cells, we investigated the whole cell proteome of granulocytes from equine recurrent uveitis cases and healthy controls. Among the 2362 proteins identified by mass spectrometry, we found 96 proteins with significantly changed abundance between groups (p < 0.05, fold change >1.2), representing 4.1% of total granulocyte proteome. Within these differential identifications, calgranulin B, a protein associated with pathogenesis in other autoimmune diseases, showed highest abundance in equine recurrent uveitis (18 fold). For a better interpretation of the results from our hypothesis-generating approach, we added a threshold for biological significance (ratio ERU/controls >2: 36 proteins) to the proteins with increased abundance in equine recurrent uveitis and analyzed their allocation to the subsets within the Immune System superpathway. The 36 differentially abundant proteins predominantly associated to RAF/MAP kinase cascade, MHC-I-mediated antigen presentation and neutrophil degranulation, suggesting a latently activated phenotype of these innate immune cells in disease. Raw data are available via ProteomeXchange with identifier PXD013648. SIGNIFICANCE: Our study provides new insights into the protein repertoire of primary equine granulocytes and identifies protein abundance changes associated to equine recurrent uveitis (ERU), an organ specific, spontaneously occurring autoimmune disease. We show that granulocyte proteins with increased abundance in ERU strongly associate to RAF/MAP kinase signaling, MHC-I antigen presentation and neutrophil degranulation, pointing to a more activated state of these cells in ERU cases. Since cells were obtained in quiescent stage of disease, latent activation of granulocytes underlines the role of these innate immune cells in ERU. These findings are highly relevant for veterinary medicine, further establishing the importance of granulocytes in this T cell-driven autoimmune disease. Moreover, they have translational quality for autoimmune uveitis in man, due to strong similarity in disease occurrence, progression and pathogenesis.
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Singh VK, Kumar S, Tapryal S. Aggregation Propensities of Herpes Simplex Virus-1 Proteins and Derived Peptides: An In Silico and In Vitro Analysis. ACS OMEGA 2020; 5:12964-12973. [PMID: 32548480 PMCID: PMC7288601 DOI: 10.1021/acsomega.0c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/11/2020] [Indexed: 06/10/2023]
Abstract
Recurrent infections of neurotropic herpes simplex virus-1 (HSV-1) have been implicated in etiology and pathology of Alzheimer's disease (AD). Although protein and peptide aggregation events are at the center of the AD pathophysiology, except a single study where a peptide derived from glycoprotein B of HSV-1 was reported to form β-amyloid-like aggregates, similar investigations with the entire proteome of HSV-1 have not been attempted. In the current study, 70 HSV-1 proteins were screened using bioinformatics tools to identify aggregation-prone candidates. Thereafter, the 20S proteasome cleavage sites within the sequence of the selected proteins were determined using Pcleavage and NetChop algorithms, thereby mimicking a cellular proteasomal activity providing short peptides. Here, we report the biochemical characterization of a 28-residue-long peptide (HSV-1 gK208-235) derived from glycoprotein K of HSV-1. The peptide showed high aggregation propensity and homology to the C-terminus of Aβ1-42 peptide. The aggregates of gK208-235 peptide were characterized by the Congo red and Thioflavin T assays and Fourier transform infrared (FTIR) spectroscopy, and their spheroid oligomeric structure was established by atomic force microscopy (AFM). Furthermore, the aggregates demonstrated dose-dependent cytotoxicity to primary mouse splenocytes. The current findings hypothesize a mechanism by which HSV-1 may contribute to AD, which may be pursued further in the future.
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Liu Q, Yu YY, Wang HY, Wang JF, He XJ. The IFN-γ-induced immunoproteasome is suppressed in highly pathogenic porcine reproductive and respiratory syndrome virus-infected alveolar macrophages. Vet Immunol Immunopathol 2020; 226:110069. [PMID: 32535163 DOI: 10.1016/j.vetimm.2020.110069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/19/2022]
Abstract
Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) evades cytotoxic T lymphocyte (CTL) responses through interactions between viral Nsp1α and Nsp4 and β2 M heavy and light chains, respectively, of swine leukocyte antigen class (SLA)-I. However, whether the immunoproteasome (i-proteasome) complex, which is an important component of the antigen delivery pathway that functions by mediating peptide production, is also affected by viral infection is unknown. In this study, we investigated the effects of HP-PRRSV (HuN4-F5) infection on IFN-γ-induced i-proteasome expression using a cell culture system (alveolar macrophages, AMs). We found that this virus inhibited the expression of IFN-γ-induced i-proteasome subunits LMP2, LMP7, and MECL-1 at the mRNA and protein level. In addition, expression levels of the i-proteasome regulatory subunits PSME1 and PSME2 in the HP-PRRSV HuN4-F5-infected group were also significantly decreased compared to those in the uninfected group. However, there was no significant difference in the expression of proteasome subunits PSMB5, PSMB6, and PSMB7 between HP-PRRSV HuN4-F5-infected and uninfected groups. This study provides insight into the mechanisms underlying immune regulation by HP-PRRSV; specifically, this virus affects the antigen-processing machinery by suppressing IFN-γ-induced i-proteasome expression in infected AMs.
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Affiliation(s)
- Qiang Liu
- Nanchong Key Laboratory of Disease Prevention, Control and Detection in Livestock and Poultry, Nanchong Vocational and Technical College, Nanchong 637131, China.
| | - Yue-Yang Yu
- Nanchong Key Laboratory of Disease Prevention, Control and Detection in Livestock and Poultry, Nanchong Vocational and Technical College, Nanchong 637131, China.
| | - Huai-Yu Wang
- Nanchong Key Laboratory of Disease Prevention, Control and Detection in Livestock and Poultry, Nanchong Vocational and Technical College, Nanchong 637131, China.
| | - Jing-Fei Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Xi-Jun He
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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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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82
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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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83
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Safari-Alighiarloo N, Taghizadeh M, Mohammad Tabatabaei S, Namaki S, Rezaei-Tavirani M. Identification of common key genes and pathways between type 1 diabetes and multiple sclerosis using transcriptome and interactome analysis. Endocrine 2020; 68:81-92. [PMID: 31912409 DOI: 10.1007/s12020-019-02181-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/27/2019] [Indexed: 01/24/2023]
Abstract
PURPOSE Type 1 diabetes (T1D) and multiple sclerosis (MS) are classified as T cell-mediated autoimmune diseases. Although convergent evidence proposed common genetic architecture for autoimmune diseases, it remains a challenge to identify them. This study aimed to determine common gene signature and pathways in T1D and MS via systems biology approach. METHODS Gene expression profiles of peripheral blood mononuclear cells (PBMCs) and pancreatic-β cells in T1D as well as PBMCs and cerebrospinal fluid (CSF) in MS were analyzed in our previous published data, and differential expressed genes were integrated with protein-protein interactions data to construct Query-Query PPI (QQPPI) networks. In this study, QQPPI networks were further analyzed to investigate more central genes, functional modules and complexes shared in T1D and MS progression. Lastly, the interaction of common genes with drugs was also explored. RESULTS Several cytokines such as IL-23A, IL-32, IL-34, and IL-37 tend to be differentially expressed in both diseases. In addition, PSMA1, MYC, SRPK1, YBX1, HNRNPM, NF-κB2, IKBKE, RAC1, FN1, ARRB2, ESR1, HSP90AB1, and PPP1CA were common high central genes in QQPPI networks corresponding to each disease. Proteasome, spliceosome, immune responses, apoptosis, cellular communication/signaling transduction mechanism, interaction with environment, and activity of intercellular mediators were shared biological processes in T1D and MS. Finally, azathioprine, melatonin, resveratrol, and geldanamycin identified as prioritized drugs for the treatment of patients with T1D and MS. CONCLUSIONS This study represented novel key genes and pathways shared between T1D and MS, which may facilitate the identification of potential therapeutic targets in these diseases.
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Affiliation(s)
- Nahid Safari-Alighiarloo
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran, Iran
| | - Seyyed Mohammad Tabatabaei
- Medical Informatics Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeed Namaki
- Immunology Department, Faculty of Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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84
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Proteostasis Failure in Neurodegenerative Diseases: Focus on Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:5497046. [PMID: 32308803 PMCID: PMC7140146 DOI: 10.1155/2020/5497046] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Protein homeostasis or proteostasis is an essential balance of cellular protein levels mediated through an extensive network of biochemical pathways that regulate different steps of the protein quality control, from the synthesis to the degradation. All proteins in a cell continuously turn over, contributing to development, differentiation, and aging. Due to the multiple interactions and connections of proteostasis pathways, exposure to stress conditions may cause various types of protein damage, altering cellular homeostasis and disrupting the entire network with additional cellular stress. Furthermore, protein misfolding and/or alterations during protein synthesis results in inactive or toxic proteins, which may overload the degradation mechanisms. The maintenance of a balanced proteome, preventing the formation of impaired proteins, is accomplished by two major catabolic routes: the ubiquitin proteasomal system (UPS) and the autophagy-lysosomal system. The proteostasis network is particularly important in nondividing, long-lived cells, such as neurons, as its failure is implicated with the development of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. These neurological disorders share common risk factors such as aging, oxidative stress, environmental stress, and protein dysfunction, all of which alter cellular proteostasis, suggesting that general mechanisms controlling proteostasis may underlay the etiology of these diseases. In this review, we describe the major pathways of cellular proteostasis and discuss how their disruption contributes to the onset and progression of neurodegenerative diseases, focusing on the role of oxidative stress.
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85
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Lynn GM, Sedlik C, Baharom F, Zhu Y, Ramirez-Valdez RA, Coble VL, Tobin K, Nichols SR, Itzkowitz Y, Zaidi N, Gammon JM, Blobel NJ, Denizeau J, de la Rochere P, Francica BJ, Decker B, Maciejewski M, Cheung J, Yamane H, Smelkinson MG, Francica JR, Laga R, Bernstock JD, Seymour LW, Drake CG, Jewell CM, Lantz O, Piaggio E, Ishizuka AS, Seder RA. Peptide-TLR-7/8a conjugate vaccines chemically programmed for nanoparticle self-assembly enhance CD8 T-cell immunity to tumor antigens. Nat Biotechnol 2020; 38:320-332. [PMID: 31932728 PMCID: PMC7065950 DOI: 10.1038/s41587-019-0390-x] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/10/2019] [Indexed: 12/16/2022]
Abstract
Personalized cancer vaccines targeting patient-specific neoantigens are a promising cancer treatment modality; however, neoantigen physicochemical variability can present challenges to manufacturing personalized cancer vaccines in an optimal format for inducing anticancer T cells. Here, we developed a vaccine platform (SNP-7/8a) based on charge-modified peptide-TLR-7/8a conjugates that are chemically programmed to self-assemble into nanoparticles of uniform size (~20 nm) irrespective of the peptide antigen composition. This approach provided precise loading of diverse peptide neoantigens linked to TLR-7/8a (adjuvant) in nanoparticles, which increased uptake by and activation of antigen-presenting cells that promote T-cell immunity. Vaccination of mice with SNP-7/8a using predicted neoantigens (n = 179) from three tumor models induced CD8 T cells against ~50% of neoantigens with high predicted MHC-I binding affinity and led to enhanced tumor clearance. SNP-7/8a delivering in silico-designed mock neoantigens also induced CD8 T cells in nonhuman primates. Altogether, SNP-7/8a is a generalizable approach for codelivering peptide antigens and adjuvants in nanoparticles for inducing anticancer T-cell immunity.
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Affiliation(s)
- Geoffrey M Lynn
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
- Avidea Technologies, Inc, Baltimore, MD, USA.
| | - Christine Sedlik
- Institut Curie, PSL Research University, Paris, France
- Centre d'Investigation Clinique Biothérapie, Institut Curie, Paris, France
| | - Faezzah Baharom
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yaling Zhu
- Avidea Technologies, Inc, Baltimore, MD, USA
| | - Ramiro A Ramirez-Valdez
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Kennedy Tobin
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | | | - Neeha Zaidi
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Joshua M Gammon
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Nicolas J Blobel
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jordan Denizeau
- Institut Curie, PSL Research University, Paris, France
- Centre d'Investigation Clinique Biothérapie, Institut Curie, Paris, France
| | - Philippe de la Rochere
- Institut Curie, PSL Research University, Paris, France
- Centre d'Investigation Clinique Biothérapie, Institut Curie, Paris, France
| | - Brian J Francica
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Tempest Therapeutics, San Francisco, CA, USA
| | | | | | - Justin Cheung
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hidehiro Yamane
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Margery G Smelkinson
- Biological Imaging Section, Research Technologies Branch, NIAID, NIH, Bethesda, MD, USA
| | - Joseph R Francica
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Richard Laga
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Joshua D Bernstock
- Avidea Technologies, Inc, Baltimore, MD, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard University, Boston, MA, USA
| | | | - Charles G Drake
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Christopher M Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Olivier Lantz
- Institut Curie, PSL Research University, Paris, France
- Centre d'Investigation Clinique Biothérapie, Institut Curie, Paris, France
| | - Eliane Piaggio
- Institut Curie, PSL Research University, Paris, France
- Centre d'Investigation Clinique Biothérapie, Institut Curie, Paris, France
| | - Andrew S Ishizuka
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Avidea Technologies, Inc, Baltimore, MD, USA
| | - Robert A Seder
- Vaccine Research Center (VRC), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.
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86
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Tian W, Trader DJ. Discovery of a Small Molecule Probe of Rpn-6, an Essential Subunit of the 26S Proteasome. ACS Chem Biol 2020; 15:554-561. [PMID: 31877015 DOI: 10.1021/acschembio.9b01019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A considerable number of essential cellular proteins have no catalytic activity and serve instead as structural components to aid in assembling protein complexes. For example, the assembly and function of the 26S proteasome, the major enzymatic complex necessary for ubiquitin-dependent protein degradation, require a number of essential protein contacts to associate the 19S regulatory particle with the 20S core particle. Previously, small molecule inhibitors of the active sites of the 20S core particle have been developed, but the activity of the 26S proteasome could also be altered via the disruption of its assembly. We were interested in discovering a small molecule binder of Rpn-6, as it is among several essential proteins that facilitate 26S assembly, which could be used to further our understanding of the association of the 19S regulatory particle with the 20S core particle. Additionally, we were interested in whether a small molecule-Rpn-6 interaction could potentially be cytotoxic to cancer cells that rely heavily on proteasome activity for survival. A workflow for utilizing a one-bead, one-compound library and a thermal shift assay was developed to discover such a molecule. TXS-8, our lead hit, was discovered to have a low micromolar binding affinity for Rpn-6 as well as very limited binding to other proteins. The cytotoxicity of TXS-8 was evaluated in several cell lines, revealing increased cytotoxicity to hematological cancers. Discovery of this peptoid binder of Rpn-6 provides the initial evidence that Rpn-6 could be a druggable target to affect protein degradation and serves as a primary scaffold from which to design more potent binders. We suspect that Rpn-6 could have additional essential roles beyond that of a molecular clamp of the proteasome to help hematological cancer cells survive and that TXS-8 can serve as a useful tool for further elucidating its roles.
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Affiliation(s)
- Wenzhi Tian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Darci J. Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, Indiana 47907, United States
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87
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Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma. Nat Commun 2020; 11:896. [PMID: 32060274 PMCID: PMC7021791 DOI: 10.1038/s41467-020-14639-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Predicting the outcome of immunotherapy treatment in melanoma patients is challenging. Alterations in genes involved in antigen presentation and the interferon gamma (IFNγ) pathway play an important role in the immune response to tumors. We describe here that the overexpression of PSMB8 and PSMB9, two major components of the immunoproteasome, is predictive of better survival and improved response to immune-checkpoint inhibitors of melanoma patients. We study the mechanism underlying this connection by analyzing the antigenic peptide repertoire of cells that overexpress these subunits using HLA peptidomics. We find a higher response of patient-matched tumor infiltrating lymphocytes against antigens diferentially presented after immunoproteasome overexpression. Importantly, we find that PSMB8 and PSMB9 expression levels are much stronger predictors of melanoma patientsʼ immune response to checkpoint inhibitors than the tumors’ mutational burden. These results suggest that PSMB8 and PSMB9 expression levels can serve as important biomarkers for stratifying melanoma patients for immune-checkpoint treatment. The response to immunotherapy of melanoma patients is heterogeneous. Here, the authors demonstrate that a high expression of the two major components of the immunoproteasome, PSMB8 and PSMB9, modulates the production of HLA peptides and it is predictive of better survival and improved response to immune-checkpoint inhibitors of melanoma patients.
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88
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Imai J, Ohashi S, Sakai T. Endoplasmic Reticulum-Associated Degradation-Dependent Processing in Cross-Presentation and Its Potential for Dendritic Cell Vaccinations: A Review. Pharmaceutics 2020; 12:pharmaceutics12020153. [PMID: 32070016 PMCID: PMC7076524 DOI: 10.3390/pharmaceutics12020153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 01/14/2023] Open
Abstract
While the success of dendritic cell (DC) vaccination largely depends on cross-presentation (CP) efficiency, the precise molecular mechanism of CP is not yet characterized. Recent research revealed that endoplasmic reticulum (ER)-associated degradation (ERAD), which was first identified as part of the protein quality control system in the ER, plays a pivotal role in the processing of extracellular proteins in CP. The discovery of ERAD-dependent processing strongly suggests that the properties of extracellular antigens are one of the keys to effective DC vaccination, in addition to DC subsets and the maturation of these cells. In this review, we address recent advances in CP, focusing on the molecular mechanisms of the ERAD-dependent processing of extracellular proteins. As ERAD itself and the ERAD-dependent processing in CP share cellular machinery, enhancing the recognition of extracellular proteins, such as the ERAD substrate, by ex vivo methods may serve to improve the efficacy of DC vaccination.
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Affiliation(s)
- Jun Imai
- Correspondence: ; Tel.: +81-27-352-1180
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89
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Woodle E, Tremblay S, Brailey P, Girnita A, Alloway R, Aronow B, Dasgupta N, Ebstein F, Kloetzel P, Lee M, Kim K, Singh H, Driscoll J. Proteasomal adaptations underlying carfilzomib-resistance in human bone marrow plasma cells. Am J Transplant 2020; 20:399-410. [PMID: 31595669 PMCID: PMC6984988 DOI: 10.1111/ajt.15634] [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: 08/30/2018] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 01/25/2023]
Abstract
Donor-specific antibodies (DSAs) have a deleterious effect on allografts and remain a major immunologic barrier in transplantation. Current therapies to eliminate DSAs are ineffective in highly HLA-sensitized patients. Proteasome inhibitors have been employed as a strategy to target bone marrow plasma cells (BMPCs), the source of long-term antibody production; however, their efficacy has been limited by poorly defined drug-resistance mechanisms. Here, we performed transcriptomic profiling of CD138+ BMPCs that survived in vivo desensitization therapy with the proteasome inhibitor carfilzomib to identify mechanisms of drug resistance. The results revealed a genomic signature that included increased expression of the immunoproteasome, a highly specialized proteasomal variant. Western blotting and functional studies demonstrated that catalytically active immunoproteasomes and the immunoproteasome activator PA28 were upregulated in carfilzomib-resistant BMPCs. Carfilzomib-resistant BMPCs displayed reduced sensitivity to the proteasome inhibitors carfilzomib, bortezomib, and ixazomib, but enhanced sensitivity to an immunoproteasome-specific inhibitor ONX-0914. Finally, in vitro carfilzomib treatment of BMPCs from HLA-sensitized patients increased levels of the immunoproteasome β5i (PSMB8) catalytic subunit suggesting that carfilzomib therapy directly induces an adaptive immunoproteasome response. Taken together, our results indicate that carfilzomib induces structural changes in proteasomes and immunoproteasome formation.
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Affiliation(s)
- E.S. Woodle
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Corresponding authors: E. Steve Woodle, MD; James J. Driscoll, MD, PhD; driscojs@ UCMAIL.UC.EDU
| | - S. Tremblay
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Department of Environmental Health, Division of Epidemiology, Cincinnati, OH, 45229, USA
| | - P. Brailey
- Hoxworth Blood Center, Transplant Immunology Division, Cincinnati, OH, 45229, USA
| | - A. Girnita
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Hoxworth Blood Center, Transplant Immunology Division, Cincinnati, OH, 45229, USA
| | - R.R. Alloway
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA
| | - B. Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - N. Dasgupta
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - F. Ebstein
- Institute for Biochemistry, Charité - University Medicine Berlin, Berlin, Germany
| | - P.M. Kloetzel
- Institute for Biochemistry, Charité - University Medicine Berlin, Berlin, Germany
| | - M.J. Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - K.B. Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - H. Singh
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - J.J. Driscoll
- Department of Internal Medicine, Division of Hematology and Oncology, Cincinnati, OH, 45267, USA,University of Cincinnati Cancer Institute, Cincinnati, OH, 45267, USA,Corresponding authors: E. Steve Woodle, MD; James J. Driscoll, MD, PhD; driscojs@ UCMAIL.UC.EDU
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90
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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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91
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Xin BT, Espinal C, de Bruin G, Filippov DV, van der Marel GA, Florea BI, Overkleeft HS. Two-Step Bioorthogonal Activity-Based Protein Profiling of Individual Human Proteasome Catalytic Sites. Chembiochem 2020; 21:248-255. [PMID: 31597011 DOI: 10.1002/cbic.201900551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Indexed: 12/12/2022]
Abstract
Bioorthogonal chemistry allows the selective modification of biomolecules in complex biological samples. One application of this methodology is in two-step activity-based protein profiling (ABPP), a methodology that is particularly attractive where direct ABPP using fluorescent or biotinylated probes is ineffective. Herein we describe a set of norbornene-modified, mechanism-based proteasome inhibitors aimed to be selective for each of the six catalytic sites of human constitutive proteasomes and immunoproteasomes. The probes developed for β1i, β2i, β5c, and β5i proved to be useful two-step ABPs that effectively label their developed proteasome subunits in both Raji cell extracts and living Raji cells through inverse-electron-demand Diels-Alder (iEDDA) ligation. The compound developed for β1c proved incapable of penetrating the cell membrane, but effectively labels β1c in vitro. The compound developed for β2c proved not selective, but its azide-containing analogue LU-002c proved effective in labeling of β2c via azide-alkyne click ligation chemistry both in vitro and in situ. In total, our results contribute to the growing list of proteasome activity tools to include five subunit-selective activity-based proteasome probes, four of which report on proteasome activities in living cells.
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Affiliation(s)
- Bo-Tao Xin
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Christofer Espinal
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gerjan de Bruin
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.,Present address, Acerta Pharma B.V., Industrielaan 63, 5349 AE, Oss, The Netherlands
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bogdan I Florea
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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92
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Kwon D, Kim SM, Correia MA. Cytochrome P450 endoplasmic reticulum-associated degradation (ERAD): therapeutic and pathophysiological implications. Acta Pharm Sin B 2020; 10:42-60. [PMID: 31993306 PMCID: PMC6976991 DOI: 10.1016/j.apsb.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
The hepatic endoplasmic reticulum (ER)-anchored cytochromes P450 (P450s) are mixed-function oxidases engaged in the biotransformation of physiologically relevant endobiotics as well as of myriad xenobiotics of therapeutic and environmental relevance. P450 ER-content and hence function is regulated by their coordinated hemoprotein syntheses and proteolytic turnover. Such P450 proteolytic turnover occurs through a process known as ER-associated degradation (ERAD) that involves ubiquitin-dependent proteasomal degradation (UPD) and/or autophagic-lysosomal degradation (ALD). Herein, on the basis of available literature reports and our own recent findings of in vitro as well as in vivo experimental studies, we discuss the therapeutic and pathophysiological implications of altered P450 ERAD and its plausible clinical relevance. We specifically (i) describe the P450 ERAD-machinery and how it may be repurposed for the generation of antigenic P450 peptides involved in P450 autoantibody pathogenesis in drug-induced acute hypersensitivity reactions and liver injury, or viral hepatitis; (ii) discuss the relevance of accelerated or disrupted P450-ERAD to the pharmacological and/or toxicological effects of clinically relevant P450 drug substrates; and (iii) detail the pathophysiological consequences of disrupted P450 ERAD, contributing to non-alcoholic fatty liver disease (NAFLD)/non-alcoholic steatohepatitis (NASH) under certain synergistic cellular conditions.
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Key Words
- 3MA, 3-methyladenine
- AAA, ATPases associated with various cellular activities
- ACC1, acetyl-CoA carboxylase 1
- ACC2, acetyl-CoA carboxylase 2
- ACHE, acetylcholinesterase
- ACOX1, acyl-CoA oxidase 1
- ALD, autophagic-lysosomal degradation
- AMPK1
- AP-1, activator protein 1
- ASK1, apoptosis signal-regulating kinase
- ATF2, activating transcription factor 2
- AdipoR1, gene of adiponectin receptor 1
- Atg14, autophagy-related 14
- CBZ, carbamazepine
- CHIP E3 ubiquitin ligase
- CHIP, carboxy-terminus of Hsc70-interacting protein
- Cytochromes P450
- Endoplasmic reticulum-associated degradation
- FOXO, forkhead box O
- Fas, fatty acid synthase
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- INH, isoniazid
- IRS1, insulin receptor substrate 1
- Il-1β, interleukin 1 β
- Il-6, interleukin 6
- Insig1, insulin-induced gene 1
- JNK1
- Lpl, lipoprotein lipase
- Mcp1, chemokine (C–C motif) ligand 1
- Non-alcoholic fatty liver disease
- Non-alcoholic steatohepatitis
- Pgc1, peroxisome proliferator-activated receptor coactivator 1
- SREBP1c, sterol regulatory element binding transcription factor 1c
- Scd1, stearoyl-coenzyme A desaturase
- Tnf, tumor necrosis factor
- UPD, ubiquitin (Ub)-dependent proteasomal degradation
- Ub, ubiquitin
- gp78/AMFR E3 ubiquitin ligase
- gp78/AMFR, autocrine motility factor receptor
- shRNAi, shRNA interference
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Abstract
The proteasome complex is mainly responsible for proteolytic degradation of cytosolic proteins, generating the C-terminus of MHC I-restricted peptide ligands and CD8 T cell epitopes. Therefore, prediction of proteasomal cleavage sites is relevant for anticipating CD8 T-cell epitopes. There are two different proteasomes, the constitutive proteasome, expressed in all types of cells, and the immunoproteasome, constitutively expressed in dendritic cells. Although both proteasome forms generate peptides for presentation by MHC I molecules, the immunoproteasome is the main form involved in providing peptide fragments for priming CD8 T cells. On the contrary, the proteasome provides peptides for presentation by MHC I molecules that can be targeted by already primed CD8 T cells. Proteasome cleavage prediction server (PCPS) is a server for predicting cleavage sites generated by both the constitutive proteasome and the immunoproteasome. Here, we illustrate the usage of PCPS to predict proteasome and immunoproteasome cleavage sites and compare the results with those provided by NetChop, a related tool available online. PCPS is implemented for free public use available online at http://imed.med.ucm.es/Tools/pcps/ .
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94
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Amon L, Lehmann CHK, Baranska A, Schoen J, Heger L, Dudziak D. Transcriptional control of dendritic cell development and functions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 349:55-151. [PMID: 31759434 DOI: 10.1016/bs.ircmb.2019.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dendritic cells (DCs) are major regulators of adaptive immunity, as they are not only capable to induce efficient immune responses, but are also crucial to maintain peripheral tolerance and thereby inhibit autoimmune reactions. DCs bridge the innate and the adaptive immune system by presenting peptides of self and foreign antigens as peptide MHC complexes to T cells. These properties render DCs as interesting target cells for immunomodulatory therapies in cancer, but also autoimmune diseases. Several subsets of DCs with special properties and functions have been described. Recent achievements in understanding transcriptional programs on single cell level, together with the generation of new murine models targeting specific DC subsets, advanced our current understanding of DC development and function. Thus, DCs arise from precursor cells in the bone marrow with distinct progenitor cell populations splitting the monocyte populations and macrophage populations from the DC lineage, which upon lineage commitment can be separated into conventional cDC1, cDC2, and plasmacytoid DCs (pDCs). The DC populations harbor intrinsic programs enabling them to react for specific pathogens in dependency on the DC subset, and thereby orchestrate T cell immune responses. Similarities, but also varieties, between human and murine DC subpopulations are challenging, and will require further investigation of human specimens under consideration of the influence of the tissue micromilieu and DC subset localization in the future.
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Affiliation(s)
- Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Baranska
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Janina Schoen
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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95
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Imai J, Otani M, Sakai T. Distinct Subcellular Compartments of Dendritic Cells Used for Cross-Presentation. Int J Mol Sci 2019; 20:ijms20225606. [PMID: 31717517 PMCID: PMC6888166 DOI: 10.3390/ijms20225606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/29/2019] [Accepted: 11/06/2019] [Indexed: 02/06/2023] Open
Abstract
Dendritic cells (DCs) present exogenous protein-derived peptides on major histocompatibility complex class I molecules to prime naïve CD8+ T cells. This DC specific ability, called cross-presentation (CP), is important for the activation of cell-mediated immunity and the induction of self-tolerance. Recent research revealed that endoplasmic reticulum-associated degradation (ERAD), which was first identified as a part of the unfolded protein response—a quality control system in the ER—plays a pivotal role in the processing of exogenous proteins in CP. Moreover, DCs express a variety of immuno-modulatory molecules and cytokines to regulate T cell activation in response to the environment. Although both CP and immuno-modulation are indispensable, contrasting ER conditions are required for their correct activity. Since ERAD substrates are unfolded proteins, their accumulation may result in ER stress, impaired cell homeostasis, and eventually apoptosis. In contrast, activation of the unfolded protein response should be inhibited for DCs to express immuno-modulatory molecules and cytokines. Here, we review recent advances on antigen CP, focusing on intracellular transport routes for exogenous antigens and distinctive subcellular compartments involved in ERAD.
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Affiliation(s)
- Jun Imai
- Correspondence: ; Tel.: +81-27-352-1180
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96
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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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97
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Kors S, Geijtenbeek K, Reits E, Schipper-Krom S. Regulation of Proteasome Activity by (Post-)transcriptional Mechanisms. Front Mol Biosci 2019; 6:48. [PMID: 31380390 PMCID: PMC6646590 DOI: 10.3389/fmolb.2019.00048] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/11/2019] [Indexed: 12/23/2022] Open
Abstract
Intracellular protein synthesis, folding, and degradation are tightly controlled processes to ensure proper protein homeostasis. The proteasome is responsible for the degradation of the majority of intracellular proteins, which are often targeted for degradation via polyubiquitination. However, the degradation rate of proteins is also affected by the capacity of proteasomes to recognize and degrade these substrate proteins. This capacity is regulated by a variety of proteasome modulations including (1) changes in complex composition, (2) post-translational modifications, and (3) altered transcription of proteasomal subunits and activators. Various diseases are linked to proteasome modulation and altered proteasome function. A better understanding of these modulations may offer new perspectives for therapeutic intervention. Here we present an overview of these three proteasome modulating mechanisms to give better insight into the diversity of proteasomes.
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Affiliation(s)
- Suzan Kors
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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98
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Ganser-Pornillos BK, Pornillos O. Restriction of HIV-1 and other retroviruses by TRIM5. Nat Rev Microbiol 2019; 17:546-556. [PMID: 31312031 DOI: 10.1038/s41579-019-0225-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
Mammalian cells express a variety of innate immune proteins - known as restriction factors - which defend against invading retroviruses such as HIV-1. Two members of the tripartite motif protein family - TRIM5α and TRIMCyp - were identified in 2004 as restriction factors that recognize and inactivate the capsid shell that surrounds and protects the incoming retroviral core. Research on these TRIM5 proteins has uncovered a novel mode of non-self recognition that protects against cross-species transmission of retroviruses. Our developing understanding of the mechanism of TRIM5 restriction underscores the concept that core uncoating and reverse transcription of the viral genome are coordinated processes rather than discrete steps of the post-entry pathway of retrovirus replication. In this Review, we provide an overview of the current state of knowledge of the molecular mechanism of TRIM5-mediated restriction, highlight recent advances and discuss implications for the development of capsid-targeted antiviral therapeutics.
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Affiliation(s)
- Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
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99
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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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100
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Han Z, Xue W, Tao L, Lou Y, Qiu Y, Zhu F. Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. Brief Bioinform 2019; 21:1023-1037. [PMID: 31323688 DOI: 10.1093/bib/bbz036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/29/2022] Open
Abstract
Abstract
The pathogenesis of multiple sclerosis (MS) is significantly regulated by long noncoding RNAs (lncRNAs), the expression of which is substantially influenced by a number of MS-associated risk single nucleotide polymorphisms (SNPs). It is thus hypothesized that the dysregulation of lncRNA induced by genomic variants may be one of the key molecular mechanisms for the pathology of MS. However, due to the lack of sufficient data on lncRNA expression and SNP genotypes of the same MS patients, such molecular mechanisms underlying the pathology of MS remain elusive. In this study, a bioinformatics strategy was applied to obtain lncRNA expression and SNP genotype data simultaneously from 142 samples (51 MS patients and 91 controls) based on RNA-seq data, and an expression quantitative trait loci (eQTL) analysis was conducted. In total, 2383 differentially expressed lncRNAs were identified as specifically expressing in brain-related tissues, and 517 of them were affected by SNPs. Then, the functional characterization, secondary structure changes and tissue and disease specificity of the cis-eQTL SNPs and lncRNA were assessed. The cis-eQTL SNPs were substantially and specifically enriched in neurological disease and intergenic region, and the secondary structure was altered in 17.6% of all lncRNAs in MS. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate how the influence of SNPs on lncRNAs contributed to the pathogenesis of MS. As a result, the regulation of lncRNAs by SNPs was found to mainly influence the antigen processing/presentation and mitogen-activated protein kinases (MAPK) signaling pathway in MS. These results revealed the effectiveness of the strategy proposed in this study and give insight into the mechanism (SNP-mediated modulation of lncRNAs) underlying the pathology of MS.
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Affiliation(s)
- Zhijie Han
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Zhu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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