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Liu T, Chen J, Wu J, Du Q, Liu J, Tan S, Pan Y, Yao S. Role of the tripartite motif (TRIM) family in female genital neoplasms. Pathol Res Pract 2023; 250:154811. [PMID: 37713735 DOI: 10.1016/j.prp.2023.154811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The tripartite motif proteins (TRIMs) family represents a class of highly conservative proteins which play a large regulatory role in molecular processes. Recently, increasing evidence has demonstrated a role of TRIMs in female genital neoplasms. Our review thereby aimed to provide an overview of the biological involvement of TRIMs in female genital neoplasms, to provide a better understanding of its role in the development and progression of such diseases, and emphasize its potential as targeted cancer therapy. Overall, our review highlighted that the wide-ranging roles of TRIMs, in not only target protein ubiquitination, tumor migration and/or invasion, epithelial-mesenchymal transition, stemness, cell adhesion, proliferation, cell cycle regulation, and apoptosis, but also in influencing estrogenic, and chemotherapy response.
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Affiliation(s)
- Tianyu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Jian Chen
- Department of Thyroid and Hernia Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jinjie Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Silu Tan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China.
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2
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Geiger KM, Manoharan M, Coombs R, Arana K, Park CS, Lee AY, Shastri N, Robey EA, Coscoy L. Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self. Cell Rep 2023; 42:112317. [PMID: 36995940 PMCID: PMC10539480 DOI: 10.1016/j.celrep.2023.112317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/02/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) plays a crucial role in shaping the peptide-major histocompatibility complex (MHC) class I repertoire and maintaining immune surveillance. While murine cytomegalovirus (MCMV) has multiple strategies for manipulating the antigen processing pathway to evade immune responses, the host has also developed ways to counter viral immune evasion. In this study, we find that MCMV modulates ERAAP and induces an interferon γ (IFN-γ)-producing CD8+ T cell effector response that targets uninfected ERAAP-deficient cells. We observe that ERAAP downregulation during infection leads to the presentation of the self-peptide FL9 on non-classical Qa-1b, thereby eliciting Qa-1b-restricted QFL T cells to proliferate in the liver and spleen of infected mice. QFL T cells upregulate effector markers upon MCMV infection and are sufficient to reduce viral load after transfer to immunodeficient mice. Our study highlights the consequences of ERAAP dysfunction during viral infection and provides potential targets for anti-viral therapies.
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Affiliation(s)
- Kristina M Geiger
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Manoharan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel Coombs
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathya Arana
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chan-Su Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angus Y Lee
- Cancer Research Lab, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ellen A Robey
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Laurent Coscoy
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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3
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Ryu HM, Islam SMS, Sayeed HM, Babita R, Seong JK, Lee H, Sohn S. Characterization of immune responses associated with ERAP-1 expression in HSV-induced Behçet's disease mouse model. Clin Immunol 2023; 250:109305. [PMID: 37003592 DOI: 10.1016/j.clim.2023.109305] [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: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023]
Abstract
Behçet's disease (BD) is a chronic multisystem inflammatory disorder. Endoplasmic reticulum aminopeptidase 1 (ERAP1) polymorphism has been reported as a risk factor for BD. However, the immunological role of ERAP1 in BD remains unclear. Therefore, the purpose of this study was to investigate the immunological role of ERAP1 in BD using a mouse model. ERAP1 incomplete expressing mice (ERAP1 hetero, +/-) were generated and inoculated with herpes simplex virus 1 to produce a BD mouse model. In these mice, dendritic cell activation markers and other immune response-related markers were analyzed. Among them, the factor showing a significant difference between ERAP+/- BD mice and WT BD mice was IL-17. In ERAP+/-, BD had significantly different expression levels of CD80, CD11b, Ly6G, RORγt, IFNγ, and IL-17 compared to asymptomatic controls. This study demonstrates ERAP1 defective expressions play an important role in BD development through inappropriate regulation of Th17.
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Affiliation(s)
- Hye-Myung Ryu
- Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - S M Shamsul Islam
- Department of Biomedical Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Hasan M Sayeed
- Department of Biomedical Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Rahar Babita
- Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 Plus Program for Advanced Veterinary Science and Research Institute for Veterinary Science, College of Veterinary Medicine, Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; Interdiscplinary Program for Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea; Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Ho Lee
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, Republic of Korea; Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi 10408, Republic of Korea
| | - Seonghyang Sohn
- Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea; Department of Biomedical Sciences, Ajou University, Suwon 16499, Republic of Korea.
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4
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Cruz FM, Chan A, Rock KL. Pathways of MHC I cross-presentation of exogenous antigens. Semin Immunol 2023; 66:101729. [PMID: 36804685 PMCID: PMC10023513 DOI: 10.1016/j.smim.2023.101729] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Phagocytes, particularly dendritic cells (DCs), generate peptide-major histocompatibility complex (MHC) I complexes from antigens they have collected from cells in tissues and report this information to CD8 T cells in a process called cross-presentation. This process allows CD8 T cells to detect, respond and eliminate abnormal cells, such as cancers or cells infected with viruses or intracellular microbes. In some settings, cross-presentation can help tolerize CD8 T cells to self-antigens. One of the principal ways that DCs acquire tissue antigens is by ingesting this material through phagocytosis. The resulting phagosomes are key hubs in the cross-presentation (XPT) process and in fact experimentally conferring the ability to phagocytize antigens can be sufficient to allow non-professional antigen presenting cells (APCs) to cross-present. Once in phagosomes, exogenous antigens can be cross-presented (XPTed) through three distinct pathways. There is a vacuolar pathway in which peptides are generated and then bind to MHC I molecules within the confines of the vacuole. Ingested exogenous antigens can also be exported from phagosomes to the cytosol upon vesicular rupture and/or possibly transport. Once in the cytosol, the antigen is degraded by the proteasome and the resulting oligopeptides can be transported to MHC I molecule in the endoplasmic reticulum (ER) (a phagosome-to-cytosol (P2C) pathway) or in phagosomes (a phagosome-to-cytosol-to-phagosome (P2C2P) pathway). Here we review how phagosomes acquire the necessary molecular components that support these three mechanisms and the contribution of these pathways. We describe what is known as well as the gaps in our understanding of these processes.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amanda Chan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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5
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Irie H, Morita K, Matsuda M, Koizumi M, Mochizuki S. Tyrosinase-Related Protein2 Peptide with Replacement of N-Terminus Residue by Cysteine Binds to H-2K b and Induces Antigen-Specific Cytotoxic T Lymphocytes after Conjugation with CpG-DNA. Bioconjug Chem 2023; 34:433-442. [PMID: 36708315 DOI: 10.1021/acs.bioconjchem.2c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Recent studies have shown the potent efficacy of peptide-based vaccines for cancer immunotherapy. Immunological performance is optimized through the co-delivery of adjuvant and antigenic peptide molecules to antigen-presenting cells simultaneously. In our previous study, we showed that a conjugate consisting of 40-mer CpG-DNA and an antigenic ovalbumin peptide through disulfide bonding could efficiently induce ovalbumin-specific cytotoxic T lymphocyte (CTL) responses in vivo. In this study, based on the conjugation design, we prepared a conjugate consisting of 30-mer CpG-DNA (CpG30) and a cancer antigenic peptide of Tyrosinase-related protein 2 (TRP2180-188) using a cysteine residue attached at the N-terminus of TRP2180-188. However, the immunization of mice with this conjugate did not induce efficient TRP2180-188-specific immune responses. It was thought that the resultant peptide (10-mer) cleaved from the conjugate might be too long to fit into the H-2Kb molecule because the optimal length for binding to it is 8-9 amino acids. We newly designed a conjugate consisting of CpG30 and the C-TRP2181-188 peptide (9-mer), in which the N-terminal serine residue of TRP2180-188 is replaced by a cysteine. By adjusting the peptide length, we succeeded in inducing strong TRP2180-188 peptide-specific CTL activity upon immunization with the CpG30-C-TRP2181-188 conjugate. Furthermore, various CpG30-C-TRP2181-188 conjugates having other CpG-DNA sequences or cysteine analogues also induced the same level of CTL activity. Therefore, CpG-C-peptide conjugates prepared by replacement of the amino acid residue at the N-terminus with a cysteine residue could be a new and effective platform for peptide vaccines for targeting specific antigens of cancers and infectious diseases.
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Affiliation(s)
- Hitomi Irie
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Koji Morita
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Miyu Matsuda
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
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6
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Sahu I, Sahoo MP, Kleifeld O, Glickman MH. Isolation of Proteasome-Trapped Peptides (PTPs) for Degradome Analysis. Methods Mol Biol 2023; 2602:229-241. [PMID: 36446979 DOI: 10.1007/978-1-0716-2859-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Analyzing intracellular peptides generated by proteasomes is highly informative to understand the spatiotemporal regulation of protein homeostasis. A large portion of eukaryotic proteins is proteolyzed within the 20S core particle of the 26S holoenzyme, where proteins are cleaved into peptides of varying lengths. A small percentage of these peptides are presented to the immune system as a representation of the proteome content of the cell. Therefore, understanding the rules that govern proteolytic specificity and product diversity is of relevance not only to biochemistry and proteostasis but also to physiology and immunology. One of the greatest challenges is to separate such proteasome-generated peptides from the total intracellular peptidome due to the susceptibility of short unstructured peptides to myriad proteases and peptidases that are activated upon cell lysis. Here, we describe a simple and rapid method to isolate peptides that are closely associated with proteasomes or trapped inside the core particle of proteasomes in eukaryotic cells. This approach termed PTPs, for proteasome-trapped peptides, requires a limited number of cells as starting materials compared to other published methods yet still provides sufficient yields for mass spectrometry-based proteomic analysis. A single sample obtained from cultured mammalian cells allowed the identification of 1000-2000 different PTPs following LC-MS analysis with high-resolution mass spectrometer.
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Affiliation(s)
- Indrajit Sahu
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
- Cancer Biology, Dana-Farber Cancer Institute, Massachusetts, Boston, US.
| | | | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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7
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Novel Class of Proteasome Inhibitors: In Silico and In Vitro Evaluation of Diverse Chloro(trifluoromethyl)aziridines. Int J Mol Sci 2022; 23:ijms232012363. [PMID: 36293216 PMCID: PMC9603864 DOI: 10.3390/ijms232012363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells. The role of proteasome inhibitors (PIs) as critical agents for regulating cancer cell death has been established. Aziridine derivatives are well-known alkylating agents employed against cancer. However, to the best of our knowledge, aziridine derivatives showing inhibitory activity towards proteasome have never been described before. Herein we report a new class of selective and nonPIs bearing an aziridine ring as a core structure. In vitro cell-based assays (two leukemia cell lines) also displayed anti-proliferative activity for some compounds. In silico studies indicated non-covalent binding mode and drug-likeness for these derivatives. Taken together, these results are promising for developing more potent PIs.
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8
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Liu M, Yang X, Zeng C, Zhao H, Li J, Hou Z, Wen H. Transcriptional Signatures of Immune, Neural, and Endocrine Functions in the Brain and Kidney of Rainbow Trout (Oncorhynchus mykiss) in Response to Aeromonas salmonicida Infection. Int J Mol Sci 2022; 23:ijms23031340. [PMID: 35163263 PMCID: PMC8835788 DOI: 10.3390/ijms23031340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
Rainbow trout (Oncorhynchus mykiss) serves as one of the most important commercial fish with an annual production of around 800,000 tonnes. However, infectious diseases, such as furunculosis caused by Aeromonas salmonicida infection, results in great economic loss in trout culture. The brain and kidney are two important organs associated with “sickness behaviors” and immunomodulation in response to disease. Therefore, we worked with 60 trout and investigated transcriptional responses and enrichment pathways between healthy and infected trout. We observed that furunculosis resulted in the activation of toll-like receptors with neuroinflammation and neural dysfunction in the brain, which might cause the “sickness behaviors” of infected trout including anorexia and lethargy. We also showed the salmonid-specific whole genome duplication contributed to duplicated colony stimulating factor 1 (csf-1) paralogs, which play an important role in modulating brain immunomodulation. Enrichment analyses of kidneys showed up-regulated immunomodulation and down-regulated neural functions, suggesting an immune-neural interaction between the brain and kidney. Moreover, the kidney endocrine network was activated in response to A. salmonicida infection, further convincing the communications between endocrine and immune systems in regulating internal homeostasis. Our study provided a foundation for pathophysiological responses of the brain and kidney in response to furunculosis and potentially offered a reference for generating disease-resistant trout strains.
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Affiliation(s)
| | | | | | | | | | - Zhishuai Hou
- Correspondence: (Z.H.); (H.W.); Tel.: +86-133-4524-7715 (Z.H.); +86-532-8203-1825 (H.W.)
| | - Haishen Wen
- Correspondence: (Z.H.); (H.W.); Tel.: +86-133-4524-7715 (Z.H.); +86-532-8203-1825 (H.W.)
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9
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Naik R, Peden K. Regulatory Considerations on the Development of mRNA Vaccines. Curr Top Microbiol Immunol 2022; 440:187-205. [PMID: 32638114 DOI: 10.1007/82_2020_220] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Developing traditional viral vaccines for infectious diseases usually takes years, as these are usually produced either by chemical inactivation of the virus or attenuation of the pathogen, processes that can take considerable time to validate and also require the live pathogen. With the advent of nucleic-acid vaccines (DNA and mRNA), the time to vaccine design and production is considerably shortened, since once the platform has been established, all that is required is the sequence of the antigen gene, its synthesis and insertion into an appropriate expression vector; importantly, no infectious virus is required. mRNA vaccines have some advantages over DNA vaccines, such as expression in non-dividing cells and the absence of the perceived risk of integration into host genome. Also, generally lower doses are required to induce the immune response. Based on experience in recent clinical trials, mRNA-based vaccines are a promising novel platform that might be useful for the development of vaccines against emerging pandemic infectious diseases. This chapter discusses some of the specific issues that mRNA vaccines raise with respect to production, quality, safety and efficacy, and how they have been addressed so as to allow their evaluation in clinical trials.
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Affiliation(s)
- Ramachandra Naik
- Division of Vaccines and Related Products Applications, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 71, Room 3045, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Keith Peden
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 52/72, Room 1220, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
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10
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Abstract
Proteasomes are compartmentalized, ATP-dependent, N-terminal nucleophile hydrolases that play essentials roles in intracellular protein turnover. They are present in all 3 kingdoms. Pharmacological inhibition of proteasomes is detrimental to cell viability. Proteasome inhibitor rugs revolutionize the treatment of multiple myeloma. Proteasomes in pathogenic microbes such as Mycobacterium tuberculosis (Mtb), Plasmodium falciparum (Pf), and other parasites and worms have been validated as therapeutic targets. Starting with Mtb proteasome, efforts in developing inhibitors selective for microbial proteasomes have made great progress lately. In this review, we describe the strategies and pharmacophores that have been used in developing proteasome inhibitors with potency and selectivity that spare human proteasomes and highlight the development of clinical proteasome inhibitor candidates for treatment of leishmaniasis and Chagas disease. Finally, we discuss the future challenges and therapeutical potentials of the microbial proteasome inhibitors.
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Affiliation(s)
- Hao Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, United States of America
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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11
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Boagni DA, Ravirala D, Zhang SX. Current strategies in engaging oncolytic viruses with antitumor immunity. Mol Ther Oncolytics 2021; 22:98-113. [PMID: 34514092 PMCID: PMC8411207 DOI: 10.1016/j.omto.2021.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Oncolytic virotherapy has produced promising yet limited results in preclinical and clinical studies. Besides direct oncolytic activity, a significant therapeutic mechanism of oncolytic virotherapy is the induction of tumor-specific immunity. Consequently, the efficacy of oncolytic viruses can be improved by the insertion of immune stimulator genes and rational combinatorial therapy with other immunotherapies. This article reviews recent efforts on arming oncolytic viruses with a variety of immune stimulator molecules, immune cell engagers, and other immune potentiating molecules. We outline what is known about the mechanisms of action and the corresponding results. The review also discusses recent preclinical and clinical studies of combining oncolytic virotherapy with immune-checkpoint inhibitors and the role of oncolytic virotherapy in changing the tumor microenvironment.
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Affiliation(s)
- Drew Ashton Boagni
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Divya Ravirala
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Shaun Xiaoliu Zhang
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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12
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Gatekeepers of the Gut: The Roles of Proteasomes at the Gastrointestinal Barrier. Biomolecules 2021; 11:biom11070989. [PMID: 34356615 PMCID: PMC8301830 DOI: 10.3390/biom11070989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022] Open
Abstract
The gut epithelial barrier provides the first line of defense protecting the internal milieu from the environment. To circumvent the exposure to constant challenges such as pathogenic infections and commensal bacteria, epithelial and immune cells at the gut barrier require rapid and efficient means to dynamically sense and respond to stimuli. Numerous studies have highlighted the importance of proteolysis in maintaining homeostasis and adapting to the dynamic changes of the conditions in the gut environment. Primarily, proteolytic activities that are involved in immune regulation and inflammation have been examined in the context of the lysosome and inflammasome activation. Yet, the key to cellular and tissue proteostasis is the ubiquitin–proteasome system, which tightly regulates fundamental aspects of inflammatory signaling and protein quality control to provide rapid responses and protect from the accumulation of proteotoxic damage. In this review, we discuss proteasome-dependent regulation of the gut and highlight the pathophysiological consequences of the disarray of proteasomal control in the gut, in the context of aberrant inflammatory disorders and tumorigenesis.
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13
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Jhunjhunwala S, Hammer C, Delamarre L. Antigen presentation in cancer: insights into tumour immunogenicity and immune evasion. Nat Rev Cancer 2021; 21:298-312. [PMID: 33750922 DOI: 10.1038/s41568-021-00339-z] [Citation(s) in RCA: 602] [Impact Index Per Article: 200.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/01/2021] [Indexed: 01/31/2023]
Abstract
Immune checkpoint blockade, which blocks inhibitory signals of T cell activation, has shown tremendous success in treating cancer, although success still remains limited to a fraction of patients. To date, clinically effective CD8+ T cell responses appear to target predominantly antigens derived from tumour-specific mutations that accumulate in cancer, also called neoantigens. Tumour antigens are displayed on the surface of cells by class I human leukocyte antigens (HLA-I). To elicit an effective antitumour response, antigen presentation has to be successful at two distinct events: first, cancer antigens have to be taken up by dendritic cells (DCs) and cross-presented for CD8+ T cell priming. Second, the antigens have to be directly presented by the tumour for recognition by primed CD8+ T cells and killing. Tumours exploit multiple escape mechanisms to evade immune recognition at both of these steps. Here, we review the tumour-derived factors modulating DC function, and we summarize evidence of immune evasion by means of quantitative modulation or qualitative alteration of the antigen repertoire presented on tumours. These mechanisms include modulation of antigen expression, HLA-I surface levels, alterations in the antigen processing and presentation machinery in tumour cells. Lastly, as complete abrogation of antigen presentation can lead to natural killer (NK) cell-mediated tumour killing, we also discuss how tumours can harbour antigen presentation defects and still evade NK cell recognition.
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14
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Shmueli MD, Sheban D, Eisenberg-Lerner A, Merbl Y. Histone degradation by the proteasome regulates chromatin and cellular plasticity. FEBS J 2021; 289:3304-3316. [PMID: 33914417 PMCID: PMC9292675 DOI: 10.1111/febs.15903] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/07/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Histones constitute the primary protein building blocks of the chromatin and play key roles in the dynamic control of chromatin compaction and epigenetic regulation. Histones are regulated by intricate mechanisms that alter their functionality and stability, thereby expanding the regulation of chromatin‐transacting processes. As such, histone degradation is tightly regulated to provide spatiotemporal control of cellular histone abundance. While several mechanisms have been implicated in controlling histone stability, here, we discuss proteasome‐dependent degradation of histones and the protein modifications that are associated with it. We then highlight specific cellular and physiological states that are associated with altered histone degradation by cellular proteasomes.
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Affiliation(s)
- Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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15
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Kaur S, Mirza AH, Overgaard AJ, Pociot F, Størling J. A Dual Systems Genetics Approach Identifies Common Genes, Networks, and Pathways for Type 1 and 2 Diabetes in Human Islets. Front Genet 2021; 12:630109. [PMID: 33777101 PMCID: PMC7987941 DOI: 10.3389/fgene.2021.630109] [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: 11/16/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Type 1 and 2 diabetes (T1/2D) are complex metabolic diseases caused by absolute or relative loss of functional β-cell mass, respectively. Both diseases are influenced by multiple genetic loci that alter disease risk. For many of the disease-associated loci, the causal candidate genes remain to be identified. Remarkably, despite the partially shared phenotype of the two diabetes forms, the associated loci for T1D and T2D are almost completely separated. We hypothesized that some of the genes located in risk loci for T1D and T2D interact in common pancreatic islet networks to mutually regulate important islet functions which are disturbed by disease-associated variants leading to β-cell dysfunction. To address this, we took a dual systems genetics approach. All genes located in 57 T1D and 243 T2D established genome-wide association studies (GWAS) loci were extracted and filtered for genes expressed in human islets using RNA sequencing data, and then integrated with; (1) human islet expression quantitative trait locus (eQTL) signals in linkage disequilibrium (LD) with T1D- and T2D-associated variants; or (2) with genes transcriptionally regulated in human islets by pro-inflammatory cytokines or palmitate as in vitro models of T1D and T2D, respectively. Our in silico systems genetics approaches created two interaction networks consisting of densely-connected T1D and T2D loci genes. The "T1D-T2D islet eQTL interaction network" identified 9 genes (GSDMB, CARD9, DNLZ, ERAP1, PPIP5K2, TMEM69, SDCCAG3, PLEKHA1, and HEMK1) in common T1D and T2D loci that harbor islet eQTLs in LD with disease-associated variants. The "cytokine and palmitate islet interaction network" identified 4 genes (ASCC2, HIBADH, RASGRP1, and SRGAP2) in common T1D and T2D loci whose expression is mutually regulated by cytokines and palmitate. Functional annotation analyses of the islet networks revealed a number of significantly enriched pathways and molecular functions including cell cycle regulation, inositol phosphate metabolism, lipid metabolism, and cell death and survival. In summary, our study has identified a number of new plausible common candidate genes and pathways for T1D and T2D.
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Affiliation(s)
- Simranjeet Kaur
- Department of Translational T1D Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Aashiq H Mirza
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Anne J Overgaard
- Department of Translational T1D Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Flemming Pociot
- Department of Translational T1D Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark.,Pediatric Department E, University Hospital, Herlev, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Størling
- Department of Translational T1D Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Zhan W, Singh PK, Ban Y, Qing X, Ah Kioon MD, Fan H, Zhao Q, Wang R, Sukenick G, Salmon J, Warren JD, Ma X, Barrat FJ, Nathan CF, Lin G. Structure-Activity Relationships of Noncovalent Immunoproteasome β5i-Selective Dipeptides. J Med Chem 2020; 63:13103-13123. [PMID: 33095579 PMCID: PMC8086754 DOI: 10.1021/acs.jmedchem.0c01520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The immunoproteasome (i-20S) has emerged as a therapeutic target for autoimmune and inflammatory disorders and hematological malignancies. Inhibition of the chymotryptic β5i subunit of i-20S inhibits T cell activation, B cell proliferation, and dendritic cell differentiation in vitro and suppresses immune responses in animal models of autoimmune disorders and allograft rejection. However, cytotoxicity to immune cells has accompanied the use of covalently reactive β5i inhibitors, whose activity against the constitutive proteasome (c-20S) is cumulative with the time of exposure. Herein, we report a structure-activity relationship study of a class of noncovalent proteasome inhibitors with picomolar potencies and 1000-fold selectivity for i-20S over c-20S. Furthermore, these inhibitors are specific for β5i over the other five active subunits of i-20S and c-20S, providing useful tools to study the functions of β5i in immune responses. The potency of these compounds in inhibiting human T cell activation suggests that they may have therapeutic potential.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Pradeep K Singh
- Department of Biochemistry, Milstein Chemistry Core Facility
| | - Yi Ban
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Xiaoping Qing
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Marie Dominique Ah Kioon
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Hao Fan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Quanju Zhao
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Rong Wang
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center
| | - George Sukenick
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center
| | - Jane Salmon
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - J David Warren
- Department of Biochemistry, Milstein Chemistry Core Facility
| | - Xiaojing Ma
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Franck J. Barrat
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery, New York, NY 10065, USA
| | - Carl F. Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065
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17
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Irie H, Morita K, Koizumi M, Mochizuki S. Immune Responses and Antitumor Effect through Delivering to Antigen Presenting Cells by Optimized Conjugates Consisting of CpG-DNA and Antigenic Peptide. Bioconjug Chem 2020; 31:2585-2595. [PMID: 33151667 DOI: 10.1021/acs.bioconjchem.0c00523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Immunotherapy using antigen-specific cytotoxic T lymphocytes (CTLs) has become one of the most attractive strategies for cancer treatment. For the induction of antigen-specific CTLs in vivo, the co-delivery of CpG-DNAs and antigens to the same antigen-presenting cells (APCs) is a promising strategy. In this study, we prepared conjugates consisting of 40mer of CpG-DNA (CpG40) and antigenic peptide (OVA257-264), which have the following distinctive features: (1) multiple CpG motifs in a molecule; (2) cleavage in the cytosol because of the disulfide bonding via cysteine residue between peptide and CpG-DNA; (3) conjugation designed to induce antigen presentation on MHC class I molecules. Immunization with the conjugate CpG40-C-OVA257-264 at the mouse tail base induced strong CTL activity at a very low peptide dose of 20 ng/head. It was found that the conjugates were internalized into C-type mannose receptor 1 (MRC1)-expressing cells in inguinal lymph nodes, indicating that the CpG portion in the conjugate acts as not only an adjuvant for the activation of TLR9 but also a carrier to APCs expressing MRC1. In a tumor-bearing mice model, mice immunized with CpG40-C-OVA257-264 conjugates exhibited long delays in tumor growth compared with those treated with PBS, OVA257-264 alone, or a mixture of CpG40 and OVA257-264. Therefore, CpG-C-peptide conjugates could be a new and effective platform for peptide vaccine for the treatment of cancers and infectious diseases.
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Affiliation(s)
- Hitomi Irie
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Koji Morita
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Makoto Koizumi
- Modality Research Laboratories, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Shinichi Mochizuki
- Department of Chemistry and Biochemistry, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
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18
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Proteostasis Disturbances and Inflammation in Neurodegenerative Diseases. Cells 2020; 9:cells9102183. [PMID: 32998318 PMCID: PMC7601929 DOI: 10.3390/cells9102183] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis (proteostasis) disturbances and inflammation are evident in normal aging and some age-related neurodegenerative diseases. While the proteostasis network maintains the integrity of intracellular and extracellular functional proteins, inflammation is a biological response to harmful stimuli. Cellular stress conditions can cause protein damage, thus exacerbating protein misfolding and leading to an eventual overload of the degradation system. The regulation of proteostasis network is particularly important in postmitotic neurons due to their limited regenerative capacity. Therefore, maintaining balanced protein synthesis, handling unfolding, refolding, and degrading misfolded proteins are essential to preserve all cellular functions in the central nervous sysytem. Failing proteostasis may trigger inflammatory responses in glial cells, and the consequent release of inflammatory mediators may lead to disturbances in proteostasis. Here, we review the mechanisms of proteostasis and inflammatory response, emphasizing their role in the pathological hallmarks of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Furthermore, we discuss the interplay between proteostatic stress and excessive immune response that activates inflammation and leads to dysfunctional proteostasis.
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19
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Han XJ, Ma XL, Yang L, Wei YQ, Peng Y, Wei XW. Progress in Neoantigen Targeted Cancer Immunotherapies. Front Cell Dev Biol 2020; 8:728. [PMID: 32850843 PMCID: PMC7406675 DOI: 10.3389/fcell.2020.00728] [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: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 02/05/2023] Open
Abstract
Immunotherapies that harness the immune system to kill cancer cells have showed significant therapeutic efficacy in many human malignancies. A growing number of studies have highlighted the relevance of neoantigens in recognizing cancer cells by intrinsic T cells. Cancer neoantigens are a direct consequence of somatic mutations presenting on the surface of individual cancer cells. Neoantigens are fully cancer-specific and exempt from central tolerance. In addition, neoantigens are important targets for checkpoint blockade therapy. Recently, technological innovations have made neoantigen discovery possible in a variety of malignancies, thus providing an impetus to develop novel immunotherapies that selectively enhance T cell reactivity for the destruction of cancer cells while leaving normal tissues unharmed. In this review, we aim to introduce the methods of the identification of neoantigens, the mutational patterns of human cancers, related clinical trials, neoantigen burden and sensitivity to immune checkpoint blockade. Moreover, we focus on relevant challenges of targeting neoantigens for cancer treatment.
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20
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Litchfield K, Reading JL, Lim EL, Xu H, Liu P, Al-Bakir M, Wong YNS, Rowan A, Funt SA, Merghoub T, Perkins D, Lauss M, Svane IM, Jönsson G, Herrero J, Larkin J, Quezada SA, Hellmann MD, Turajlic S, Swanton C. Escape from nonsense-mediated decay associates with anti-tumor immunogenicity. Nat Commun 2020; 11:3800. [PMID: 32733040 PMCID: PMC7393139 DOI: 10.1038/s41467-020-17526-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 06/30/2020] [Indexed: 12/30/2022] Open
Abstract
Frameshift insertion/deletions (fs-indels) are an infrequent but highly immunogenic mutation subtype. Although fs-indels are degraded through the nonsense-mediated decay (NMD) pathway, we hypothesise that some fs-indels escape degradation and elicit anti-tumor immune responses. Using allele-specific expression analysis, expressed fs-indels are enriched in genomic positions predicted to escape NMD, and associated with higher protein expression, consistent with degradation escape (NMD-escape). Across four independent melanoma cohorts, NMD-escape mutations are significantly associated with clinical-benefit to checkpoint inhibitor (CPI) therapy (Pmeta = 0.0039). NMD-escape mutations are additionally found to associate with clinical-benefit in the low-TMB setting. Furthermore, in an adoptive cell therapy treated melanoma cohort, NMD-escape mutation count is the most significant biomarker associated with clinical-benefit. Analysis of functional T cell reactivity screens from personalized vaccine studies shows direct evidence of fs-indel derived neoantigens eliciting immune response, particularly those with highly elongated neo open reading frames. NMD-escape fs-indels represent an attractive target for biomarker optimisation and immunotherapy design.
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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK.
| | - James L Reading
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Po Liu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Maise Al-Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Yien Ning Sophia Wong
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Samuel A Funt
- Memorial Sloan Kettering Cancer Center, Division of Solid Tumor Oncology, Department of Medicine, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY, 10017, USA
| | - Taha Merghoub
- Memorial Sloan Kettering Cancer Center, Division of Solid Tumor Oncology, Department of Medicine, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY, 10017, USA
| | - David Perkins
- Mass Spectrometry Proteomics, The Francis Crick Institute, London, NW1 1AT, UK
| | - Martin Lauss
- Faculty of Medicine, Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Scheelegatan 2, Medicon Village, 22185, Lund, Sweden
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital Herlev, Borgmester Ib Juuls Vej 1, 2730, Herlev, Denmark
| | - Göran Jönsson
- Faculty of Medicine, Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Scheelegatan 2, Medicon Village, 22185, Lund, Sweden
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London, SW3 6JJ, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, Division of Solid Tumor Oncology, Department of Medicine, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY, 10017, USA
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden Hospital, London, SW3 6JJ, UK.
- Cancer Dynamics Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK.
- Department of Medical Oncology, University College London Hospitals, 235 Euston Rd, Fitzrovia, London, NW1 2BU, UK.
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21
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Kinetically distinct processing pathways diversify the CD8 + T cell response to a single viral epitope. Proc Natl Acad Sci U S A 2020; 117:19399-19407. [PMID: 32719124 DOI: 10.1073/pnas.2004372117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The source proteins from which CD8+ T cell-activating peptides are derived remain enigmatic. Glycoproteins are particularly challenging in this regard owing to several potential trafficking routes within the cell. By engineering a glycoprotein-derived epitope to contain an N-linked glycosylation site, we determined that optimal CD8+ T cell expansion and function were induced by the peptides that are rapidly produced from the exceedingly minor fraction of protein mislocalized to the cytosol. In contrast, peptides derived from the much larger fraction that undergoes translocation and quality control are produced with delayed kinetics and induce suboptimal CD8+ T cell responses. This dual system of peptide generation enhances CD8+ T cell participation in diversifying both antigenicity and the kinetics of peptide display.
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22
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Momtaz S, Memariani Z, El-Senduny FF, Sanadgol N, Golab F, Katebi M, Abdolghaffari AH, Farzaei MH, Abdollahi M. Targeting Ubiquitin-Proteasome Pathway by Natural Products: Novel Therapeutic Strategy for Treatment of Neurodegenerative Diseases. Front Physiol 2020; 11:361. [PMID: 32411012 PMCID: PMC7199656 DOI: 10.3389/fphys.2020.00361] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
Misfolded proteins are the main common feature of neurodegenerative diseases, thereby, normal proteostasis is an important mechanism to regulate the neural survival and the central nervous system functionality. The ubiquitin-proteasome system (UPS) is a non-lysosomal proteolytic pathway involved in numerous normal functions of the nervous system, modulation of neurotransmitter release, synaptic plasticity, and recycling of membrane receptors or degradation of damaged and regulatory intracellular proteins. Aberrant accumulation of intracellular ubiquitin-positive inclusions has been implicated to a variety of neurodegenerative disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington disease (HD), Amyotrophic Lateral Sclerosis (ALS), and Multiple Myeloma (MM). Genetic mutation in deubiquitinating enzyme could disrupt UPS and results in destructive effects on neuron survival. To date, various agents were characterized with proteasome-inhibitory potential. Proteins of the ubiquitin-proteasome system, and in particular, E3 ubiquitin ligases, may be promising molecular targets for neurodegenerative drug discovery. Phytochemicals, specifically polyphenols (PPs), were reported to act as proteasome-inhibitors or may modulate the proteasome activity. PPs modify the UPS by means of accumulation of ubiquitinated proteins, suppression of neuronal apoptosis, reduction of neurotoxicity, and improvement of synaptic plasticity and transmission. This is the first comprehensive review on the effect of PPs on UPS. Here, we review the recent findings describing various aspects of UPS dysregulation in neurodegenerative disorders. This review attempts to summarize the latest reports on the neuroprotective properties involved in the proper functioning of natural polyphenolic compounds with implication for targeting ubiquitin-proteasome pathway in the neurodegenerative diseases. We highlight the evidence suggesting that polyphenolic compounds have a dose and disorder dependent effects in improving neurological dysfunctions, and so their mechanism of action could stimulate the UPS, induce the protein degradation or inhibit UPS and reduce protein degradation. Future studies should focus on molecular mechanisms by which PPs can interfere this complex regulatory system at specific stages of the disease development and progression.
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Affiliation(s)
- Saeideh Momtaz
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran.,Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Gastrointestinal Pharmacology Interest Group, Universal Scientific Education and Research Network, Tehran, Iran
| | - Zahra Memariani
- Traditional Medicine and History of Medical Sciences Research Center, Health Research Center, Babol University of Medical Sciences, Babol, Iran
| | | | - Nima Sanadgol
- Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran.,Department of Biomolecular Sciences, School of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, Brazil
| | - Fereshteh Golab
- Cellular and Molecular Research Center, Iran University of Medical Science, Tehran, Iran
| | - Majid Katebi
- Department of Anatomy, Faculty of Medicine, Hormozgan University of Medical Sciences, Hormozgan, Iran
| | - Amir Hossein Abdolghaffari
- Medicinal Plants Research Center, Institute of Medicinal Plants, ACECR, Karaj, Iran.,Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Gastrointestinal Pharmacology Interest Group, Universal Scientific Education and Research Network, Tehran, Iran.,Department of Toxicology & Pharmacology, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Abdollahi
- Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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23
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Padariya M, Kalathiya U, Houston DR, Alfaro JA. Recognition Dynamics of Cancer Mutations on the ERp57-Tapasin Interface. Cancers (Basel) 2020; 12:cancers12030737. [PMID: 32244998 PMCID: PMC7140079 DOI: 10.3390/cancers12030737] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 01/16/2023] Open
Abstract
Down regulation of the major histocompatibility class (MHC) I pathway plays an important role in tumour development, and can be achieved by suppression of HLA expression or mutations in the MHC peptide-binding pocket. The peptide-loading complex (PLC) loads peptides on the MHC-I molecule in a dynamic multi-step assembly process. The effects of cancer variants on ERp57 and tapasin components from the MHC-I pathway is less known, and they could have an impact on antigen presentation. Applying computational approaches, we analysed whether the ERp57-tapasin binding might be altered by missense mutations. The variants H408R(ERp57) and P96L, D100A, G183R(tapasin) at the protein–protein interface improved protein stability (ΔΔG) during the initial screen of 14 different variants. The H408R(ERp57) and P96L(tapasin) variants, located close to disulphide bonds, were further studied by molecular dynamics (MD). Identifying intramolecular a-a’ domain interactions, MD revealed open and closed conformations of ERp57 in the presence and absence of tapasin. In wild-type and mutant ERp57-tapasin complexes, residues Val97, Ser98, Tyr100, Trp405, Gly407(ERp57) and Asn94, Cys95, Arg97, Asp100(tapasin) formed common H-bond interactions. Moreover, comparing the H-bond networks for P96L and H408R with each other, suggests that P96L(tapasin) improved ERp57-tapasin binding more than the H408R(ERp57) mutant. During MD, the C-terminus domain (that binds MHC-I) in tapasin from the ERp57(H408R)-tapasin complex moved away from the PLC, whereas in the ERp57-tapasin(P96L) system was oppositely displaced. These findings can have implications for the function of PLC and, ultimately, for the presentation of MHC-I peptide complex on the tumour cell surface.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Correspondence: (M.P.); (J.A.A.)
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
| | - Douglas R. Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, UK;
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH4 2XR, UK
- Correspondence: (M.P.); (J.A.A.)
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24
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Gewehr MCF, Silverio R, Rosa-Neto JC, Lira FS, Reckziegel P, Ferro ES. Peptides from Natural or Rationally Designed Sources Can Be Used in Overweight, Obesity, and Type 2 Diabetes Therapies. Molecules 2020; 25:E1093. [PMID: 32121443 PMCID: PMC7179135 DOI: 10.3390/molecules25051093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
Overweight and obesity are among the most prominent health problems in the modern world, mostly because they are either associated with or increase the risk of other diseases such as type 2 diabetes, hypertension, and/or cancer. Most professional organizations define overweight and obesity according to individual body-mass index (BMI, weight in kilograms divided by height squared in meters). Overweight is defined as individuals with BMI from 25 to 29, and obesity as individuals with BMI ≥30. Obesity is the result of genetic, behavioral, environmental, physiological, social, and cultural factors that result in energy imbalance and promote excessive fat deposition. Despite all the knowledge concerning the pathophysiology of obesity, which is considered a disease, none of the existing treatments alone or in combination can normalize blood glucose concentration and prevent debilitating complications from obesity. This review discusses some new perspectives for overweight and obesity treatments, including the use of the new orally active cannabinoid peptide Pep19, the advantage of which is the absence of undesired central nervous system effects usually experienced with other cannabinoids.
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Affiliation(s)
- Mayara C. F. Gewehr
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil;
| | - Renata Silverio
- Department of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina (UFSC), Florianópolis 88040-900, Brazil;
| | - José Cesar Rosa-Neto
- Department of Cell and Developmental Biology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil;
| | - Fabio S. Lira
- Department of Physical Education, São Paulo State University (UNESP), Presidente Prudente 19060-900, Brazil;
| | - Patrícia Reckziegel
- Department of Pharmacology, National Institute of Pharmacology and Molecular Biology (INFAR), Federal University of São Paulo (UNIFESP), São Paulo 05508-000, Brazil;
| | - Emer S. Ferro
- Department of Pharmacology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo 05508-000, Brazil;
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25
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Exploring long-range cooperativity in the 20S proteasome core particle from Thermoplasma acidophilum using methyl-TROSY-based NMR. Proc Natl Acad Sci U S A 2020; 117:5298-5309. [PMID: 32094174 DOI: 10.1073/pnas.1920770117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The 20S core particle (CP) proteasome is a molecular assembly catalyzing the degradation of misfolded proteins or proteins no longer required for function. It is composed of four stacked heptameric rings that form a barrel-like structure, sequestering proteolytic sites inside its lumen. Proteasome function is regulated by gates derived from the termini of α-rings and through binding of regulatory particles (RPs) to one or both ends of the barrel. The CP is dynamic, with an extensive allosteric pathway extending from one end of the molecule to catalytic sites in its center. Here, using methyl-transverse relaxation optimized spectroscopy (TROSY)-based NMR optimized for studies of high-molecular-weight complexes, we evaluate whether the pathway extends over the entire 150-Å length of the molecule. By exploiting a number of different labeling schemes, the two halves of the molecule can be distinguished, so that the effects of 11S RP binding, or the introduction of gate or allosteric pathway mutations at one end of the barrel can be evaluated at the distal end. Our results establish that while 11S binding and the introduction of key mutations affect each half of the CP allosterically, they do not further couple opposite ends of the molecule. This may have implications for the function of so-called "hybrid" proteasomes where each end of the CP is bound with a different regulator, allowing the CP to be responsive to both RPs simultaneously. The methodology presented introduces a general NMR strategy for dissecting pathways of communication in homo-oligomeric molecular machines.
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Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Molecules 2020; 25:molecules25030671. [PMID: 32033280 PMCID: PMC7037493 DOI: 10.3390/molecules25030671] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/25/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The proteasome is the central component of the main cellular protein degradation pathway. During the past four decades, the critical function of the proteasome in numerous physiological processes has been revealed, and proteasome activity has been linked to various human diseases. The proteasome prevents the accumulation of misfolded proteins, controls the cell cycle, and regulates the immune response, to name a few important roles for this macromolecular "machine." As a therapeutic target, proteasome inhibitors have been approved for the treatment of multiple myeloma and mantle cell lymphoma. However, inability to sufficiently inhibit proteasome activity at tolerated doses has hampered efforts to expand the scope of proteasome inhibitor-based therapies. With emerging new modalities in myeloma, it might seem challenging to develop additional proteasome-based therapies. However, the constant development of new applications for proteasome inhibitors and deeper insights into the intricacies of protein homeostasis suggest that proteasome inhibitors might have novel therapeutic applications. Herein, we summarize the latest advances in proteasome inhibitor development and discuss the future of proteasome inhibitors and other proteasome-based therapies in combating human diseases.
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Coux O, Zieba BA, Meiners S. The Proteasome System in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:55-100. [DOI: 10.1007/978-3-030-38266-7_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Huan X, Zhuo Z, Xiao Z, Ren EC. Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response. Sci Rep 2019; 9:16660. [PMID: 31723204 PMCID: PMC6853878 DOI: 10.1038/s41598-019-53201-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023] Open
Abstract
Peptides presented by Human leukocyte antigen (HLA) class-I molecules are generally 8-10 amino acids in length. However, the predominant pool of peptide fragments generated by proteasomes is less than 8 amino acids in length. Using the Epstein - Barr virus (EBV) Rta-epitope (ATIGTAMYK, residues 134-142) restricted by HLA-A*11:01 which generates a strong immunodominant response, we investigated the minimum length of a viral peptide that can constitute a viral epitope recognition by CD8 T cells. The results showed that Peripheral blood mononuclear cells (PBMCs) from healthy donors can be stimulated by a viral peptide fragment as short as 4-mer (AMYK), together with a 5-mer (ATIGT) to recapitulate the full length EBV Rta epitope. This was confirmed by generating crystals of the tetra-complex (2 peptides, HLA and β2-microglobulin). The solved crystal structure of HLA-A*11:01 in complex with these two short peptides revealed that they can bind in the same orientation similar to parental peptide (9-mer) and the free ends of two short peptides acquires a bulged conformation that is directed towards the T cell receptor. Our data shows that suboptimal length of 4-mer and 5-mer peptides can complement each other to form a stable peptide-MHC (pMHC) complex.
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Affiliation(s)
- Xuelu Huan
- Singapore Immunology Network, 8A Biomedical Grove, #03-06 Immunos, Singapore, 138648, Singapore
| | - Ziyi Zhuo
- Singapore Immunology Network, 8A Biomedical Grove, #03-06 Immunos, Singapore, 138648, Singapore
| | - Ziwei Xiao
- Singapore Immunology Network, 8A Biomedical Grove, #03-06 Immunos, Singapore, 138648, Singapore
| | - Ee Chee Ren
- Singapore Immunology Network, 8A Biomedical Grove, #03-06 Immunos, Singapore, 138648, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 119260, Singapore.
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Kirby L, Jin J, Cardona JG, Smith MD, Martin KA, Wang J, Strasburger H, Herbst L, Alexis M, Karnell J, Davidson T, Dutta R, Goverman J, Bergles D, Calabresi PA. Oligodendrocyte precursor cells present antigen and are cytotoxic targets in inflammatory demyelination. Nat Commun 2019; 10:3887. [PMID: 31467299 PMCID: PMC6715717 DOI: 10.1038/s41467-019-11638-3] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/24/2019] [Indexed: 01/09/2023] Open
Abstract
Oligodendrocyte precursor cells (OPCs) are abundant in the adult central nervous system, and have the capacity to regenerate oligodendrocytes and myelin. However, in inflammatory diseases such as multiple sclerosis (MS) remyelination is often incomplete. To investigate how neuroinflammation influences OPCs, we perform in vivo fate-tracing in an inflammatory demyelinating mouse model. Here we report that OPC differentiation is inhibited by both effector T cells and IFNγ overexpression by astrocytes. IFNγ also reduces the absolute number of OPCs and alters remaining OPCs by inducing the immunoproteasome and MHC class I. In vitro, OPCs exposed to IFNγ cross-present antigen to cytotoxic CD8 T cells, resulting in OPC death. In human demyelinated MS brain lesions, but not normal appearing white matter, oligodendroglia exhibit enhanced expression of the immunoproteasome subunit PSMB8. Therefore, OPCs may be co-opted by the immune system in MS to perpetuate the autoimmune response, suggesting that inhibiting immune activation of OPCs may facilitate remyelination.
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Affiliation(s)
- Leslie Kirby
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jing Jin
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Matthew D Smith
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kyle A Martin
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Hayley Strasburger
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Leyla Herbst
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Maya Alexis
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Joan Goverman
- Department of Immunology, University of Washington, Seattle, WA, USA
| | - Dwight Bergles
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Weinstein-Marom H, Hendel L, Laron EA, Sharabi-Nov A, Margalit A, Gross G. MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation. FASEB J 2019; 33:11458-11468. [PMID: 31343935 DOI: 10.1096/fj.201802717rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Among the earliest protein products of most cellular genes are those synthesized during the pioneer round of translation (PRT), a key step in nonsense-mediated mRNA decay (NMD) that allows scanning of new transcripts for the presence of a premature termination codon (PTC). It has been demonstrated that at least some PRT degradation products can be targeted to major histocompatibility (MHC)-I presentation. To gain new insight into this putative PRT-to-MHC-I route, we have assembled 2 pairs of reporter genes so that the 2 genes in each pair encode an identical fusion protein between a model antigenic peptide and enhanced green fluorescent protein (EGFP), one of which harbors a PTC. We expressed these genes in different mouse and human cell lines and confirmed enhanced NMD activity for the PTC(+) gene in each pair by monitoring the effect of cycloheximide on the level of the respective mRNA. We then exploited several strategies for establishing the ratio between level of peptide presentation and total amount of protein product. We consistently observed significantly higher ratios for the PTC(+) mRNAs compared with the PTC(-) ones, pointing to correlation between the turnover of otherwise identical proteins and the fate of their template mRNA. Using confocal microscopy, we showed a clear link between NMD, the presence of misfolded EGFP polypeptides, and enhanced MHC-I peptide presentation. Altogether, these findings imply that identical full-length gene products differing only in 3' noncoding sequences can be differentially degraded and targeted to the MHC-I presentation pathway, suggesting a more general role for the PRT in establishing the MHC-I peptidome.-Weinstein-Marom, H., Hendel, L., Laron, E. A., Sharabi-Nov, A., Margalit, A., Gross, G. MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation.
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Affiliation(s)
- Hadas Weinstein-Marom
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel.,Inter-Faculty Biotechnology Program, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liron Hendel
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | - Efrat Avigad Laron
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | | | - Alon Margalit
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | - Gideon Gross
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
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Chen S, Dong Z, Ren X, Zhao D, Zhang Y, Tang M, Han J, Ye L, Zhao P. Proteomic Identification of Immune-Related Silkworm Proteins Involved in the Response to Bacterial Infection. JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:5538637. [PMID: 31343690 PMCID: PMC6657664 DOI: 10.1093/jisesa/iez056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Indexed: 05/03/2023]
Abstract
Bombyx mori (Lepidoptera: Bombycidae) is an important economic insect and a classic Lepidopteran model system. Although immune-related genes have been identified at a genome-wide scale in the silkworm, proteins involved in immune defense of the silkworm have not been comprehensively characterized. In this study, two types of bacteria were injected into the silkworm larvae, Gram-negative Escherichia coli (Enterobacteriales: Enterobacteriaceae), or Gram-positive Staphylococcus aureus (Bacillales: Staphylococcaceae). After injection, proteomic analyses of hemolymph were performed by liquid chromatography-tandem mass spectrometry. In total, 514 proteins were identified in the uninduced control group, 540 were identified in the E. coli-induced group, and 537 were identified in the S. aureus-induced group. Based on Uniprot annotations, 32 immunological recognition proteins, 28 immunological signaling proteins, and 21 immunological effector proteins were identified. We found that 127 proteins showed significant upregulation, including 10 immunological recognition proteins, 4 immunological signaling proteins, 11 immunological effector proteins, and 102 other proteins. Using real-time quantitative polymerase chain reaction in the fat body, we verified that immunological recognition proteins, signaling proteins, and effector proteins also showed significant increases at the transcriptional level after infection with E. coli and S. aureus. Five newly identified proteins showed upregulation at both protein and transcription levels after infection, including 30K protein, yellow-d protein, chemosensory protein, and two uncharacterized proteins. This study identified many new immune-related proteins, deepening our understanding of the immune defense system in B. mori. The data have been deposited to the iProX with identifier IPX0001337000.
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Affiliation(s)
- Shiyi Chen
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Zhaoming Dong
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Xiu Ren
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Dongchao Zhao
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Yan Zhang
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
- College of Biotechnology, Southwest University, Chongqing, China
| | - Muya Tang
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Jiaxuan Han
- College of Biotechnology, Southwest University, Chongqing, China
| | - Lin Ye
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Sericulture, Southwest University, Chongqing, China
- Corresponding author, e-mail:
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Effect of Protein Denaturation and Enzyme Inhibitors on Proteasomal-Mediated Production of Peptides in Human Embryonic Kidney Cells. Biomolecules 2019; 9:biom9060207. [PMID: 31142026 PMCID: PMC6627375 DOI: 10.3390/biom9060207] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022] Open
Abstract
Peptides produced by the proteasome have been proposed to function as signaling molecules that regulate a number of biological processes. In the current study, we used quantitative peptidomics to test whether conditions that affect protein stability, synthesis, or turnover cause changes in the levels of peptides in Human Embryonic Kidney 293T (HEK293T) cells. Mild heat shock (42 °C for 1 h) or treatment with the deubiquitinase inhibitor b-AP15 led to higher levels of ubiquitinated proteins but did not significantly increase the levels of intracellular peptides. Treatment with cycloheximide, an inhibitor of protein translation, did not substantially alter the levels of intracellular peptides identified herein. Cells treated with a combination of epoxomicin and bortezomib showed large increases in the levels of most peptides, relative to the levels in cells treated with either compound alone. Taken together with previous studies, these results support a mechanism in which the proteasome cleaves proteins into peptides that are readily detected in our assays (i.e., 6–37 amino acids) and then further degrades many of these peptides into smaller fragments.
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33
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New strategies and perspectives on managing IgA nephropathy. Clin Exp Nephrol 2019; 23:577-588. [PMID: 30756248 PMCID: PMC6469670 DOI: 10.1007/s10157-019-01700-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/17/2019] [Indexed: 12/23/2022]
Abstract
IgA nephropathy is an inflammatory renal disease characterised by the deposition of IgA in the glomerular mesangium and is the most commonly reported primary glomerulonephritis worldwide. Thirty to forty percent of patients with the disease develop progressive renal function decline, requiring renal replacement therapy within two decades of diagnosis. Despite this, accurate individual risk stratification at diagnosis and predicting treatment response remains a challenge. Furthermore, there are currently no disease specific treatments currently licensed to treat the condition due to long standing challenges in the nature and prevalence of the disease. Despite this, there have been exciting recent advances in the field that may represent paradigm shifts in the way IgA nephropathy is managed in the near future. In this review, we explore the evidence base informing current approaches to management and explore new strategies and future directions in the diagnosis and management of IgA nephropathy.
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Proteasome Inhibition in Multiple Myeloma: Head-to-Head Comparison of Currently Available Proteasome Inhibitors. Cell Chem Biol 2019; 26:340-351.e3. [PMID: 30612952 DOI: 10.1016/j.chembiol.2018.11.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/18/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022]
Abstract
Proteasome inhibitors (PIs) are a backbone of multiple myeloma (MM) therapy. The proteasome harbors six proteolytically active subunits (β1, β2, β5), while β5 was identified as rate-limiting and is a primary target of clinically available PIs. The most effective pattern of subunit inhibition provided by these PIs for cytotoxic activity in MM is unknown. A head-to-head comparison of clinically available PIs shows that in the clinically relevant setting only the co-inhibition of β1 or β2 with β5 activity achieves meaningful functional proteasome inhibition and cytotoxicity, while the selective β2/β5 inhibition of both constitutive and immunoproteasome is the most cytotoxic. In the long-term setting, selective inhibition of β5 subunit is sufficient to induce cytotoxicity in PI-sensitive, but not in PI-resistant MM, and the β5/β2 co-inhibition is the most cytotoxic in PI-resistant MM. These results give a rational basis for selecting individual PIs for the treatment of MM.
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35
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Jensen SM, Potts GK, Ready DB, Patterson MJ. Specific MHC-I Peptides Are Induced Using PROTACs. Front Immunol 2018; 9:2697. [PMID: 30524438 PMCID: PMC6262898 DOI: 10.3389/fimmu.2018.02697] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/01/2018] [Indexed: 01/10/2023] Open
Abstract
Peptides presented by the class-I major histocompatibility complex (MHC-I) are important targets for immunotherapy. The identification of these peptide targets greatly facilitates the generation of T-cell-based therapeutics. Herein, we report the capability of proteolysis targeting chimera (PROTAC) compounds to induce the presentation of specific MHC class-I peptides derived from endogenous cellular proteins. Using LC-MS/MS, we identified several BET-derived MHC-I peptides induced by treatment with three BET-directed PROTAC compounds. To understand our ability to tune this process, we measured the relative rate of presentation of these peptides under varying treatment conditions using label-free mass spectrometry quantification. We found that the rate of peptide presentation reflected the rate of protein degradation, indicating a direct relationship between PROTAC treatment and peptide presentation. We additionally analyzed the effect of PROTAC treatment on the entire immunopeptidome and found many new peptides that were displayed in a PROTAC-specific fashion: we determined that these identifications map to the BET pathway, as well as, potential off-target or unique-to-PROTAC pathways. This work represents the first evidence of the use of PROTAC compounds to induce the presentation of MHC-I peptides from endogenous cellular proteins, highlighting the capability of PROTAC compounds for the discovery and generation of new targets for immunotherapy.
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Affiliation(s)
- Stephanie M Jensen
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Gregory K Potts
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
| | - Damien B Ready
- Discovery Chemistry and Technology, AbbVie North Chicago, IL, United States
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36
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Wolf-Levy H, Javitt A, Eisenberg-Lerner A, Kacen A, Ulman A, Sheban D, Dassa B, Fishbain-Yoskovitz V, Carmona-Rivera C, Kramer MP, Nudel N, Regev I, Zahavi L, Elinger D, Kaplan MJ, Morgenstern D, Levin Y, Merbl Y. Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides. Nat Biotechnol 2018; 36:nbt.4279. [PMID: 30346940 PMCID: PMC8897557 DOI: 10.1038/nbt.4279] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/21/2018] [Indexed: 12/18/2022]
Abstract
Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows for capture, isolation and analysis of proteasome-cleaved peptides. Application of MAPP to cancer cell lines as well as primary immune cells revealed dynamic modulation of the cellular degradome in response to various stimuli, such as proinflammatory signals. Further, we performed analysis of minute amounts of clinical samples by studying cells from the peripheral blood of patients with systemic lupus erythematosus (SLE). We found increased degradation of histones in patient immune cells, thereby suggesting a role of aberrant proteasomal degradation in the pathophysiology of SLE. Thus, MAPP offers a broadly applicable method to facilitate the study of the cellular-degradation landscape in various cellular conditions and diseases involving changes in proteasomal degradation, including protein aggregation diseases, autoimmunity and cancer.
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Affiliation(s)
- Hila Wolf-Levy
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Aaron Javitt
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Ulman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - Matthias P. Kramer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Nudel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ifat Regev
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Liron Zahavi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dalia Elinger
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Mariana J. Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - David Morgenstern
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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Roeten MSF, Cloos J, Jansen G. Positioning of proteasome inhibitors in therapy of solid malignancies. Cancer Chemother Pharmacol 2018; 81:227-243. [PMID: 29184971 PMCID: PMC5778165 DOI: 10.1007/s00280-017-3489-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/13/2022]
Abstract
Targeting of the protein degradation pathway, in particular, the ubiquitin-proteasome system, has emerged as an attractive novel cancer chemotherapeutic modality. Although proteasome inhibitors have been most successfully applied in the treatment of hematological malignancies, they also received continuing interest for the treatment of solid tumors. In this review, we summarize the current positioning of proteasome inhibitors in the treatment of common solid malignancies (e.g., lung, colon, pancreas, breast, and head and neck cancer), addressing topics of their mechanism(s) of action, predictive factors and molecular mechanisms of resistance.
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Affiliation(s)
- Margot S F Roeten
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands.
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Gerrit Jansen
- Amsterdam Rheumatology and Immunology Center, Location VUmc, VU University Medical Center, Amsterdam, The Netherlands
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38
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Manches O, Muniz LR, Bhardwaj N. Dendritic Cell Biology. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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39
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Iyer SP, Hunt CR, Pandita TK. Cross Talk between Radiation and Immunotherapy: The Twain Shall Meet. Radiat Res 2017; 189:219-224. [PMID: 29261410 DOI: 10.1667/rr14941.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
There has been increased interest in the immune stimulatory properties of ionizing radiation based on several preclinical models and recently completed clinical studies performed in combination with checkpoint inhibitors. This is a paradigm shift in that it considers the role of radiation beyond its direct cytotoxic effects, however, the factors that promote or limit radiation-induced immunogenicity are still unclear. Here we review the role of radiation in modulating the various aspects of the tumor immune microenvironment and discuss in particular the direct effects of radiation on the DNA damage response and its immediate consequences to neighboring cells. The latter "danger response" in particular can enhance recruitment of dendritic and macrophage cells to the tumor microenvironment, which in turn can activate or diminish subsequent T-cell priming. Identification of the critical factors that modulate the interaction between radiation-induced cell damage and the immune system will allow for rational combinational therapy design and the development of biomarkers that predict effective immune responses.
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Affiliation(s)
- Swaminathan P Iyer
- a Department of Hematology, Houston Methodist Cancer Center, Weil Cornell Medical College, Houston Texas 77030
| | - Clayton R Hunt
- b Department of Radiation Oncology, The Houston Methodist Research Institute, Weil Cornell Medical College, Houston Texas 77030
| | - Tej K Pandita
- b Department of Radiation Oncology, The Houston Methodist Research Institute, Weil Cornell Medical College, Houston Texas 77030
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Gaczynska M, Osmulski PA. Targeting Protein-Protein Interactions in the Ubiquitin-Proteasome Pathway. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:123-165. [PMID: 29412995 DOI: 10.1016/bs.apcsb.2017.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is a major venue for controlled intracellular protein degradation in Eukaryota. The machinery of several hundred proteins is involved in recognizing, tagging, transporting, and cleaving proteins, all in a highly regulated manner. Short-lived transcription factors, misfolded translation products, stress-damaged polypeptides, or worn-out long-lived proteins, all can be found among the substrates of UPP. Carefully choreographed protein-protein interactions (PPI) are involved in each step of the pathway. For many of the steps small-molecule inhibitors have been identified and often they directly or indirectly target PPI. The inhibitors may destabilize intracellular proteostasis and trigger apoptosis. So far this is the most explored option used as an anticancer strategy. Alternatively, substrate-specific polyubiquitination may be regulated for a precise intervention aimed at a particular metabolic pathway. This very attractive opportunity is moving close to clinical application. The best known drug target in UPP is the proteasome: the end point of the journey of a protein destined for degradation. The proteasome alone is a perfect object to study the mechanisms and roles of PPI on many levels. This giant protease is built from multisubunit modules and additionally utilizes a service from transient protein ligands, for example, delivering substrates. An elaborate set of PPI within the highest-order proteasome assembly is involved in substrate recognition and processing. Below we will outline PPI involved in the UPP and discuss the growing prospects for their utilization in pharmacological interventions.
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Affiliation(s)
- Maria Gaczynska
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.
| | - Pawel A Osmulski
- Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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Erokhov PA, Lyupina YV, Radchenko AS, Kolacheva AA, Nikishina YO, Sharova NP. Detection of active proteasome structures in brain extracts: proteasome features of August rat brain with violations in monoamine metabolism. Oncotarget 2017; 8:70941-70957. [PMID: 29050334 PMCID: PMC5642609 DOI: 10.18632/oncotarget.20208] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/23/2017] [Indexed: 12/15/2022] Open
Abstract
The aim of this work was to detect changes in proteasome pools of brain parts of August rats with monoamine metabolism violations in comparison with that of control Wistar rats. To reveal active proteasome structures, a method of native electrophoresis for the analysis of crude tissue fractions was developed. By means of this method and following Western blotting, the most pronounced changes in reorganization of proteasome structures were detected in proteasome pool of the brain cortex of August rats. Main findings are the enhanced expression of immune proteasome subtypes containing proteolytic subunit LMP2 and activator PA28αβ as well as immune proteasome subtypes containing proteolytic subunit LMP7 and activator PA700 and simultaneously decreased expression of subtypes with subunit LMP2 and activator PA700 in the brain cortex of August rats compared to that of Wistar rats. These results were indirectly confirmed by SDS PAGE method followed by Western blotting, which showed the increased quantities of immune subunits and proteasome activators in the brain cortex of August rats compared to that of Wistar rats. Immune proteasomes were revealed by immunohistochemistry in neurons, but not in glial cells of August and Wistar rat cortex. The detected reorganization of proteasome pools is likely to be important for production of special peptides to provide the steady interaction between neurons and adaptation of central nervous system to conditions caused by monoamine metabolism deviations.
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Affiliation(s)
- Pavel A. Erokhov
- Laboratory of Biochemistry of Ontogenesis Processes, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Yulia V. Lyupina
- Laboratory of Biochemistry of Ontogenesis Processes, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Alexandra S. Radchenko
- Laboratory of Biochemistry of Ontogenesis Processes, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Anna A. Kolacheva
- Laboratory of Neural and Neuroendocrine Regulations, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Yulia O. Nikishina
- Laboratory of Neural and Neuroendocrine Regulations, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Natalia P. Sharova
- Laboratory of Biochemistry of Ontogenesis Processes, N.K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
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Singh R, Williams J, Vince R. Puromycin based inhibitors of aminopeptidases for the potential treatment of hematologic malignancies. Eur J Med Chem 2017; 139:325-336. [PMID: 28803047 DOI: 10.1016/j.ejmech.2017.07.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 07/14/2017] [Accepted: 07/22/2017] [Indexed: 02/01/2023]
Abstract
Substantial progress has been described in the study of puromycin and its analogs for antibiotic properties. However, the peptidase inhibitory activity of related analogs has not been explored as extensively. Specifically, inhibiting aminopeptidases for achieving antitumor effect has been sparsely investigated. Herein, we address this challenge by reporting the synthesis of a series of analogs based on the structural template of puromycin. We also present exhaustive biochemical and in vitro analyses in support of our thesis. Analyzing the structure-activity relationship revealed a steric requirement for maximum potency. Effective inhibitors of Puromycin-Sensitive Aminopeptidase (PSA) are disclosed here. These potential therapeutic agents display superior in vitro antitumor potency against two leukemic cell lines, as compared to known inhibitors of aminopeptidases.
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Affiliation(s)
- Rohit Singh
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jessica Williams
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert Vince
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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Starck SR, Shastri N. Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance. Immunol Rev 2017; 272:8-16. [PMID: 27319338 DOI: 10.1111/imr.12434] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Effective immune surveillance by CD8(+) cytotoxic T cells of intracellular microbes and cancer depends on the antigen presentation pathway. This pathway produces an optimal peptide repertoire for presentation by major histocompatibility (MHC) class I molecules (pMHCs I) on the cell surface. We have known for years that the pMHC I repertoire is a reflection of the intracellular protein pool. However, many studies have revealed that pMHCs I present peptides not only from precursors encoded in open-reading frames of mRNA transcripts but also cryptic peptides encoded in apparently 'untranslated' regions. These sources vastly increase the availability of peptides for presentation and immune evasion. Here, we review studies on the composition of the cryptic pMHC I repertoire, the immunological significance of these pMHC I, and the novel translational mechanisms that generate cryptic peptides from unusual sources.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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Different Polyubiquitinated Bodies in Human Dendritic Cells: IL-4 Causes PaCS During Differentiation while LPS or IFNα Induces DALIS During Maturation. Sci Rep 2017; 7:1844. [PMID: 28500302 PMCID: PMC5431999 DOI: 10.1038/s41598-017-02090-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/05/2017] [Indexed: 01/08/2023] Open
Abstract
Two types of polyubiquitin-reactive cytoplasmic bodies, particulate cytoplasmic structures (PaCS) and dendritic cell (DC) aggresome-like induced structures (DALIS), were analyzed by electron microscopy, immunocytochemistry, immunoblotting, and flow cytometry in DC obtained from human blood monocytes incubated with GM-CSF plus IL-4 (IL4-DC), GM-CSF plus IFNα (IFN-DC), or GM-CSF alone (GM-DC), with or without LPS maturation. PaCS developed as monomorphic aggregates of proteasome-reactive barrel-like particles only in ribosomes-rich cytoplasmic areas of differentiating IL4-DC. In contrast, DALIS formed as vesicular bodies storing K63-linked ubiquitinated proteins by coalescence of increased endosomal structures, in IFN-DC or after LPS maturation of GM-DC. DALIS-forming cells showed incomplete morphological and functional DC-type differentiation when compared to PaCS-forming IL4-DC. PaCS and DALIS may have different function as well as different origin and cytochemistry. DALIS may be a transient accumulation site of potentially antigenic polyubiquitinated proteins during their processing and presentation. PaCS are found under physiologic or pathologic conditions associated with increased/deranged protein synthesis and increased ubiquitin-proteasome activity. Given its high heat-shock protein content PaCS may work as a quality control structure for newly synthesized, cytosolic proteins. This comparative analysis suggests that PaCS and DALIS have distinctive roles in DC.
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45
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Capietto AH, Jhunjhunwala S, Delamarre L. Characterizing neoantigens for personalized cancer immunotherapy. Curr Opin Immunol 2017; 46:58-65. [PMID: 28478383 DOI: 10.1016/j.coi.2017.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
Abstract
Somatic mutations can generate neoantigens that are presented on MHC molecules and drive effective T cells responses against cancer. Mutation load in cancer patients predicts response to immune checkpoint blockade therapy. Additionally, vaccination targeting neoantigens controls established tumor growth in preclinical models. These recent findings led to a renewed interest in the field of cancer vaccines and the development of antigen-targeted cancer immunotherapies. However, targeting neoantigens is challenging, as most mutations are unique to each cancer patient. In addition, only a small fraction of the mutations are immunogenic and therefore their accurate prediction is critical. In this review, we discuss the properties of neoantigens that influence their immunogenicity, along with questions that remain to be addressed in order to improve prediction algorithms.
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Guasp P, Barnea E, González-Escribano MF, Jiménez-Reinoso A, Regueiro JR, Admon A, López de Castro JA. The Behçet's disease-associated variant of the aminopeptidase ERAP1 shapes a low-affinity HLA-B*51 peptidome by differential subpeptidome processing. J Biol Chem 2017; 292:9680-9689. [PMID: 28446606 DOI: 10.1074/jbc.m117.789180] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/21/2017] [Indexed: 01/05/2023] Open
Abstract
A low-activity variant of endoplasmic reticulum aminopeptidase 1 (ERAP1), Hap10, is associated with the autoinflammatory disorder Behçet's disease (BD) in epistasis with HLA-B*51, which is the main risk factor for this disorder. The role of Hap10 in BD pathogenesis is unknown. We sought to define the effects of Hap10 on the HLA-B*51 peptidome and to distinguish these effects from those due to HLA-B*51 polymorphisms unrelated to disease. The peptidome of the BD-associated HLA-B*51:08 subtype expressed in a Hap10-positive cell line was isolated, characterized by mass spectrometry, and compared with the HLA-B*51:01 peptidome from cells expressing more active ERAP1 allotypes. We additionally performed synthetic peptide digestions with recombinant ERAP1 variants and estimated peptide-binding affinity with standard algorithms. In the BD-associated ERAP1 context of B*51:08, longer peptides were generated; of the two major HLA-B*51 subpeptidomes with Pro-2 and Ala-2, the former one was significantly reduced, and the latter was increased and showed more ERAP1-susceptible N-terminal residues. These effects were readily explained by the low activity of Hap10 and the differential susceptibility of X-Pro and X-Ala bonds to ERAP1 trimming and together resulted in a significantly altered peptidome with lower affinity. The differences due to ERAP1 were clearly distinguished from those due to HLA-B*51 subtype polymorphism, which affected residue frequencies at internal positions of the peptide ligands. The alterations in the nature and affinity of HLA-B*51·peptide complexes probably affect T-cell and natural killer cell recognition, providing a sound basis for the joint association of ERAP1 and HLA-B*51 with BD.
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Affiliation(s)
- Pablo Guasp
- From the Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), 28049 Madrid, Spain
| | - Eilon Barnea
- the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | | | - Anaïs Jiménez-Reinoso
- the Department of Immunology, Hospital 12 de Octubre Health Research Institute (imas12), Complutense University School of Medicine, 28040 Madrid, Spain
| | - José R Regueiro
- the Department of Immunology, Hospital 12 de Octubre Health Research Institute (imas12), Complutense University School of Medicine, 28040 Madrid, Spain
| | - Arie Admon
- the Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - José A López de Castro
- From the Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), 28049 Madrid, Spain,
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Chhabra S. Novel Proteasome Inhibitors and Histone Deacetylase Inhibitors: Progress in Myeloma Therapeutics. Pharmaceuticals (Basel) 2017; 10:E40. [PMID: 28398261 PMCID: PMC5490397 DOI: 10.3390/ph10020040] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/28/2017] [Accepted: 04/04/2017] [Indexed: 01/01/2023] Open
Abstract
The unfolded protein response is responsible for the detection of misfolded proteins and the coordination of their disposal and is necessary to maintain the cellular homoeostasis. Multiple myeloma cells secrete large amounts of immunoglobulins, proteins that need to be correctly folded by the chaperone system. If this process fails, the misfolded proteins have to be eliminated by the two main garbage-disposal systems of the cell: proteasome and aggresome. The blockade of either of these systems will result in accumulation of immunoglobulins and other toxic proteins in the cytoplasm and cell death. The simultaneous inhibition of the proteasome, by proteasome inhibitors (PIs) and the aggresome, by histone deacetylase inhibitors (HDACi) results in a synergistic increase in cytotoxicity in myeloma cell lines. This review provides an overview of mechanisms of action of second-generation PIs and HDACi in multiple myeloma (MM), the clinical results currently observed with these agents and assesses the potential therapeutic impact of the different agents in the two classes. The second-generation PIs offer benefits in terms of increased efficacy, reduced neurotoxicity as off-target effect and may overcome resistance to bortezomib because of their different chemical structure, mechanism of action and biological properties. HDACi with anti-myeloma activity in clinical development discussed in this review include vorinostat, panobinostat and selective HDAC6 inhibitor, ricolinostat.
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Affiliation(s)
- Saurabh Chhabra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, 9200 W Wisconsin Ave, Milwaukee, WI 53226, USA.
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48
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Ubiquitinated proteins promote the association of proteasomes with the deubiquitinating enzyme Usp14 and the ubiquitin ligase Ube3c. Proc Natl Acad Sci U S A 2017; 114:E3404-E3413. [PMID: 28396413 DOI: 10.1073/pnas.1701734114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In mammalian cells, the 26S proteasomes vary in composition. In addition to the standard 28 subunits in the 20S core particle and 19 subunits in each 19S regulatory particle, a small fraction (about 10-20% in our preparations) also contains the deubiquitinating enzyme Usp14/Ubp6, which regulates proteasome activity, and the ubiquitin ligase, Ube3c/Hul5, which enhances proteasomal processivity. When degradation of ubiquitinated proteins in cells was inhibited, levels of Usp14 and Ube3c on proteasomes increased within minutes. Conversely, when protein ubiquitination was prevented, or when purified proteasomes hydrolyzed the associated ubiquitin conjugates, Usp14 and Ube3c dissociated rapidly (unlike other 26S subunits), but the inhibitor ubiquitin aldehyde slowed their dissociation. Recombinant Usp14 associated with purified proteasomes preferentially if they contained ubiquitin conjugates. In cells or extracts, adding Usp14 inhibitors (IU-1 or ubiquitin aldehyde) enhanced Usp14 and Ube3c binding further. Thus, in the substrate- or the inhibitor-bound conformations, Usp14 showed higher affinity for proteasomes and surprisingly enhanced Ube3c binding. Moreover, adding ubiquitinated proteins to cell extracts stimulated proteasome binding of both enzymes. Thus, Usp14 and Ube3c cycle together on and off proteasomes, and the presence of ubiquitinated substrates promotes their association. This mechanism enables proteasome activity to adapt to the supply of substrates.
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49
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Meng L, Tong J, Wang H, Tao C, Wang Q, Niu C, Zhang X, Gao Q. PPE38 Protein of Mycobacterium tuberculosis Inhibits Macrophage MHC Class I Expression and Dampens CD8 + T Cell Responses. Front Cell Infect Microbiol 2017; 7:68. [PMID: 28348981 PMCID: PMC5346565 DOI: 10.3389/fcimb.2017.00068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/22/2017] [Indexed: 12/23/2022] Open
Abstract
Suppression of CD8+ T cell activation is a critical mechanism used by Mycobacterium tuberculosis (MTB) to escape protective host immune responses. PPE38 belongs to the unique PPE family of MTB and in our previous study, PPE38 protein was speculated to participate in manipulating macrophage MHC class I pathway. To test this hypothesis, the function of mycobacterial PPE38 protein was assessed here using macrophage and mouse infection models. Decreased amount of MHC class I was observed on the surface of macrophages infected with PPE38-expressing mycobacteria. The transcript of genes encoding MHC class I was also inhibited by PPE38. After infection of C57BL/6 mice with Mycobacterium smegmatis expressing PPE38 (Msmeg-PPE38), decreased number of CD8+ T cells was found in spleen, liver, and lungs through immunohistochemical analysis, comparing to the control strain harboring empty vector (Msmeg-V). Consistently, flow cytometry assay showed that fewer effector/memory CD8+ T cells (CD44highCD62Llow) were activated in spleen from Msmeg-PPE38 infected mice. Moreover, Msmeg-PPE38 confers a growth advantage over Msmeg-V in C57BL/6 mice, indicating an effect of PPE38 to favor mycobacterial persistence in vivo. Overall, this study shows a unique biological function of PPE38 protein to facilitate mycobacteria to escape host immunity, and provides hints for TB vaccine development.
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Affiliation(s)
- Lu Meng
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan University Shanghai, China
| | - Jingfeng Tong
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan University Shanghai, China
| | - Hui Wang
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan UniversityShanghai, China; The State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, School of Medicine, Shenzhen UniversityGuangdong, China
| | - Chengwu Tao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences Shanghai, China
| | - Qinglan Wang
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan University Shanghai, China
| | - Chen Niu
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan University Shanghai, China
| | - Xiaoming Zhang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences Shanghai, China
| | - Qian Gao
- Key laboratory of Medical Molecular Virology, Institute of Biomedical Sciences and Institute of Medical Microbiology, Shanghai Medical College, Fudan University Shanghai, China
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Kaplan GS, Torcun CC, Grune T, Ozer NK, Karademir B. Proteasome inhibitors in cancer therapy: Treatment regimen and peripheral neuropathy as a side effect. Free Radic Biol Med 2017; 103:1-13. [PMID: 27940347 DOI: 10.1016/j.freeradbiomed.2016.12.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/22/2016] [Accepted: 12/04/2016] [Indexed: 01/10/2023]
Abstract
Proteasomal system plays an important role in protein turnover, which is essential for homeostasis of cells. Besides degradation of oxidized proteins, it is involved in the regulation of many different signaling pathways. These pathways include mainly cell differentiation, proliferation, apoptosis, transcriptional activation and angiogenesis. Thus, proteasomal system is a crucial target for treatment of several diseases including neurodegenerative diseases, cystic fibrosis, atherosclerosis, autoimmune diseases, diabetes and cancer. Over the last fifteen years, proteasome inhibitors have been tested to highlight their mechanisms of action and used in the clinic to treat different types of cancer. Proteasome inhibitors are mainly used in combinational therapy along with classical chemo-radiotherapy. Several studies have proved their significant effects but serious side effects such as peripheral neuropathy, limits their use in required effective doses. Recent studies focus on peripheral neuropathy as the primary side effect of proteasome inhibitors. Therefore, it is important to delineate the underlying mechanisms of peripheral neuropathy and develop new inhibitors according to obtained data. This review will detail the role of proteasome inhibition in cancer therapy and development of peripheral neuropathy as a side effect. Additionally, new approaches to prevent treatment-limiting side effects will be discussed in order to help researchers in developing effective strategies to overcome side effects of proteasome inhibitors.
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Affiliation(s)
- Gulce Sari Kaplan
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Ceyda Corek Torcun
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Tilman Grune
- Department for Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Nesrin Kartal Ozer
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey.
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