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Cascio P. PA28γ, the ring that makes tumors invisible to the immune system? Biochimie 2024:S0300-9084(24)00078-6. [PMID: 38631454 DOI: 10.1016/j.biochi.2024.04.003] [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: 02/07/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
PA28γ is a proteasomal interactor whose main and most known function is to stimulate the hydrolytic activity of the 20 S proteasome independently of ubiquitin and ATP. Unlike its two paralogues, PA28α and PA28β, PA28γ is largely present in the nuclear compartment and plays pivotal functions in important pathways such as cellular division, apoptosis, neoplastic transformation, chromatin structure and organization, fertility, lipid metabolism, and DNA repair mechanisms. Although it is known that a substantial fraction of PA28γ is found in the cell in a free form (i.e. not associated with 20 S), almost all of the studies so far have focused on its ability to modulate proteasomal enzymatic activities. In this respect, the ability of PA28γ to strongly stimulate degradation of proteins, especially if intrinsically disordered and therefore devoid of three-dimensional tightly folded structure, appears to be the main molecular mechanism underlying its multiple biological effects. Initial studies, conducted more than 20 years ago, came to the conclusion that among the many biological functions of PA28γ, the immunological ones were rather limited and circumscribed. In this review, we focus on recent evidence showing that PA28γ fulfills significant functions in cell-mediated acquired immunity, with a particular role in attenuating MHC class I antigen presentation, especially in relation to neoplastic transformation and autoimmune diseases.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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2
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Ju L, Luo Y, Cui X, Zhang H, Chen L, Yao M. CircGPC3 promotes hepatocellular carcinoma progression and metastasis by sponging miR-578 and regulating RAB7A/PSME3 expression. Sci Rep 2024; 14:7632. [PMID: 38561366 PMCID: PMC10984923 DOI: 10.1038/s41598-024-58004-y] [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: 11/02/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
CircRNAs are a class of highly stable noncoding RNAs that play an important role in the progression of many diseases, especially cancer. In this study, high-throughput sequencing was used to screen for abnormally expressed circRNAs, and we found that circGPC3 was overexpressed in HCC tissues. However, the underlying mechanism of circGPC3 in the development and metastasis of hepatocellular carcinoma (HCC) remains unknown. In our study, we found that circGPC3 was significantly upregulated in HCC tissues and cells and that its overexpression was positively correlated with overall survival, TNM stage and lymph node metastasis. In vivo and in vitro experiments showed that circGPC3 knockdown repressed HCC cell migration, invasion and proliferation and promoted apoptosis. Mechanistically, circGPC3 promoted HCC proliferation and metastasis through the miR-578/RAB7A/PSME3 axis. Our results demonstrate that circGPC3 contributes to the progression of HCC and provides an intervention target for HCC.
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Affiliation(s)
- Linling Ju
- Medical School of Nantong University, Nantong University, Institute of Liver Diseases, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital,, 60 Middle Qingnian Road, Nantong, 226000, Jiangsu, China
| | - Yunfeng Luo
- Medical School of Nantong University, Nantong University, Institute of Liver Diseases, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital,, 60 Middle Qingnian Road, Nantong, 226000, Jiangsu, China
| | - Xiaohui Cui
- Medical School of Nantong University, Nantong University, Institute of Liver Diseases, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital,, 60 Middle Qingnian Road, Nantong, 226000, Jiangsu, China
| | - Hao Zhang
- Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, 41 Jianshe Road, Nantong, 226009, Jiangsu, China
| | - Lin Chen
- Medical School of Nantong University, Nantong University, Institute of Liver Diseases, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital,, 60 Middle Qingnian Road, Nantong, 226000, Jiangsu, China.
| | - Min Yao
- Medical School of Nantong University, Nantong University, Institute of Liver Diseases, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital,, 60 Middle Qingnian Road, Nantong, 226000, Jiangsu, China.
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3
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Li Y, Chen J, Xie M, Cao Y, Zhou Y, Zhang R. Identification of a circRNA-miRNA-mRNA network to explore the effects of circRNAs on renal injury in systemic lupus erythematosus. Autoimmunity 2023; 56:2193361. [PMID: 36967607 DOI: 10.1080/08916934.2023.2193361] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease. At present, the mechanism of non-coding RNA in renal injury in SLE patients is still unclear. A total of 64 DEcircRNAs, 75 DEmiRNAs, and 249 DEmRNAs were identified. We integrated 10 circRNAs, 10 miRNAs, and 88 target mRNAs into a circRNA-miRNA-mRNA network and obtained 9 hub genes (circ-0000006, miR-766-3p, miR-409-3p, miR-339-3p, miR-331-3p, miR-140-3p, miR-186-5p, miR-149-5p, PSME3). The ROC curve results showed that the diagnostic efficiency of 6 hub miRNA was higher than that of has_circ_0000006 and PSEME3. SsGSEA analysis revealed immune cell composition in SLE and control renal tissues, including 3 types of immune cells up-regulated (gamma delta T cell, effector memory CD4 T cell, central memory CD8 T cell) and 4 types down-regulated (memory B cell, mast cell, macrophage, immature dendritic cell, eosinophil) in SLE patients. In addition, PSME3 was negatively correlated with 3 up-regulated immune cells and positively correlated with 4 down-regulated immune cells in SLE patients. Our study provides a deeper understanding of the circRNA-related competing endogenous RNA regulatory mechanism in the renal injury of systemic lupus erythematosus.
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Affiliation(s)
- Ya Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Juan Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Min Xie
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yihui Cao
- Department of Acute Infectious Disease prevention and Control, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yan Zhou
- Department of Nephrology, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ruixian Zhang
- Department of Disease Control and Prevention, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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4
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Schmalen A, Kammerl IE, Meiners S, Noessner E, Deeg CA, Hauck SM. A Lysine Residue at the C-Terminus of MHC Class I Ligands Correlates with Low C-Terminal Proteasomal Cleavage Probability. Biomolecules 2023; 13:1300. [PMID: 37759700 PMCID: PMC10527444 DOI: 10.3390/biom13091300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The majority of peptides presented by MHC class I result from proteasomal protein turnover. The specialized immunoproteasome, which is induced during inflammation, plays a major role in antigenic peptide generation. However, other cellular proteases can, either alone or together with the proteasome, contribute peptides to MHC class I loading non-canonically. We used an immunopeptidomics workflow combined with prediction software for proteasomal cleavage probabilities to analyze how inflammatory conditions affect the proteasomal processing of immune epitopes presented by A549 cells. The treatment of A549 cells with IFNγ enhanced the proteasomal cleavage probability of MHC class I ligands for both the constitutive proteasome and the immunoproteasome. Furthermore, IFNγ alters the contribution of the different HLA allotypes to the immunopeptidome. When we calculated the HLA allotype-specific proteasomal cleavage probabilities for MHC class I ligands, the peptides presented by HLA-A*30:01 showed characteristics hinting at a reduced C-terminal proteasomal cleavage probability independently of the type of proteasome. This was confirmed by HLA-A*30:01 ligands from the immune epitope database, which also showed this effect. Furthermore, two additional HLA allotypes, namely, HLA-A*03:01 and HLA-A*11:01, presented peptides with a markedly reduced C-terminal proteasomal cleavage probability. The peptides eluted from all three HLA allotypes shared a peptide binding motif with a C-terminal lysine residue, suggesting that this lysine residue impairs proteasome-dependent HLA ligand production and might, in turn, favor peptide generation by other cellular proteases.
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Affiliation(s)
- Adrian Schmalen
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
| | - Ilona E. Kammerl
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians-University, Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), 81377 Munich, Germany
| | - Silke Meiners
- Research Center Borstel, Leibniz Lung Center, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), 23845 Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
| | - Elfriede Noessner
- Immunoanalytics Research Group—Tissue Control of Immunocytes, Helmholtz Center Munich, 81377 Munich, Germany
| | - Cornelia A. Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, Martinsried, 82152 Planegg, Germany
| | - Stefanie M. Hauck
- Core Facility—Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), 80939 Munich, Germany
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5
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Kallingal A, Olszewski M, Maciejewska N, Brankiewicz W, Baginski M. Cancer immune escape: the role of antigen presentation machinery. J Cancer Res Clin Oncol 2023; 149:8131-8141. [PMID: 37031434 PMCID: PMC10374767 DOI: 10.1007/s00432-023-04737-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
The mechanisms of antigen processing and presentation play a crucial role in the recognition and targeting of cancer cells by the immune system. Cancer cells can evade the immune system by downregulating or losing the expression of the proteins recognized by the immune cells as antigens, creating an immunosuppressive microenvironment, and altering their ability to process and present antigens. This review focuses on the mechanisms of cancer immune evasion with a specific emphasis on the role of antigen presentation machinery. The study of the immunopeptidome, or peptidomics, has provided insights into the mechanisms of cancer immune evasion and has potential applications in cancer diagnosis and treatment. Additionally, manipulating the epigenetic landscape of cancer cells plays a critical role in suppressing the immune response against cancer. Targeting these mechanisms through the use of HDACis, DNMTis, and combination therapies has the potential to improve the efficacy of cancer immunotherapy. However, further research is needed to fully understand the mechanisms of action and optimal use of these therapies in the clinical setting.
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Affiliation(s)
- Anoop Kallingal
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland.
| | - Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
| | - Wioletta Brankiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
- Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St 11/12, 80-233, Gdansk, Poland
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6
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Javitt A, Shmueli MD, Kramer MP, Kolodziejczyk AA, Cohen IJ, Radomir L, Sheban D, Kamer I, Litchfield K, Bab-Dinitz E, Zadok O, Neiens V, Ulman A, Wolf-Levy H, Eisenberg-Lerner A, Kacen A, Alon M, Rêgo AT, Stacher-Priehse E, Lindner M, Koch I, Bar J, Swanton C, Samuels Y, Levin Y, da Fonseca PCA, Elinav E, Friedman N, Meiners S, Merbl Y. The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC. NATURE CANCER 2023; 4:629-647. [PMID: 37217651 DOI: 10.1038/s43018-023-00557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 04/10/2023] [Indexed: 05/24/2023]
Abstract
Immunotherapy revolutionized treatment options in cancer, yet the mechanisms underlying resistance in many patients remain poorly understood. Cellular proteasomes have been implicated in modulating antitumor immunity by regulating antigen processing, antigen presentation, inflammatory signaling and immune cell activation. However, whether and how proteasome complex heterogeneity may affect tumor progression and the response to immunotherapy has not been systematically examined. Here, we show that proteasome complex composition varies substantially across cancers and impacts tumor-immune interactions and the tumor microenvironment. Through profiling of the degradation landscape of patient-derived non-small-cell lung carcinoma samples, we find that the proteasome regulator PSME4 is upregulated in tumors, alters proteasome activity, attenuates presented antigenic diversity and associates with lack of response to immunotherapy. Collectively, our approach affords a paradigm by which proteasome composition heterogeneity and function should be examined across cancer types and targeted in the context of precision oncology.
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Affiliation(s)
- Aaron Javitt
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav D Shmueli
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Matthias P Kramer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ivan J Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lihi Radomir
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Kevin Litchfield
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Oranit Zadok
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Vanessa Neiens
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Adi Ulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Wolf-Levy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Assaf Kacen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Ina Koch
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Asklepios Lung Clinic Munich-Gauting, Gauting, Germany
| | - Jair Bar
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Charles Swanton
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Yardena Samuels
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - 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
| | - Paula C A da Fonseca
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany
| | - Nir Friedman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Research Center Borstel, Borstel, Germany
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Yifat Merbl
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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7
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Targeting immunoproteasome in neurodegeneration: A glance to the future. Pharmacol Ther 2023; 241:108329. [PMID: 36526014 DOI: 10.1016/j.pharmthera.2022.108329] [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: 10/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
The immunoproteasome is a specialized form of proteasome equipped with modified catalytic subunits that was initially discovered to play a pivotal role in MHC class I antigen processing and immune system modulation. However, over the last years, this proteolytic complex has been uncovered to serve additional functions unrelated to antigen presentation. Accordingly, it has been proposed that immunoproteasome synergizes with canonical proteasome in different cell types of the nervous system, regulating neurotransmission, metabolic pathways and adaptation of the cells to redox or inflammatory insults. Hence, studying the alterations of immunoproteasome expression and activity is gaining research interest to define the dynamics of neuroinflammation as well as the early and late molecular events that are likely involved in the pathogenesis of a variety of neurological disorders. Furthermore, these novel functions foster the perspective of immunoproteasome as a potential therapeutic target for neurodegeneration. In this review, we provide a brain and retina-wide overview, trying to correlate present knowledge on structure-function relationships of immunoproteasome with the variety of observed neuro-modulatory functions.
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Ke CH, Chiu YH, Huang KC, Lin CS. Exposure of Immunogenic Tumor Antigens in Surrendered Immunity and the Significance of Autologous Tumor Cell-Based Vaccination in Precision Medicine. Int J Mol Sci 2022; 24:ijms24010147. [PMID: 36613591 PMCID: PMC9820296 DOI: 10.3390/ijms24010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The mechanisms by which immune systems identify and destroy tumors, known as immunosurveillance, have been discussed for decades. However, several factors that lead to tumor persistence and escape from the attack of immune cells in a normal immune system have been found. In the process known as immunoediting, tumors decrease their immunogenicity and evade immunosurveillance. Furthermore, tumors exploit factors such as regulatory T cells, myeloid-derived suppressive cells, and inhibitory cytokines that avoid cytotoxic T cell (CTL) recognition. Current immunotherapies targeting tumors and their surroundings have been proposed. One such immunotherapy is autologous cancer vaccines (ACVs), which are characterized by enriched tumor antigens that can escalate specific CTL responses. Unfortunately, ACVs usually fail to activate desirable therapeutic effects, and the low immunogenicity of ACVs still needs to be elucidated. This difficulty highlights the significance of immunogenic antigens in antitumor therapies. Previous studies have shown that defective host immunity triggers tumor development by reprogramming tumor antigenic expressions. This phenomenon sheds new light on ACVs and provides a potential cue to improve the effectiveness of ACVs. Furthermore, synergistically with the ACV treatment, combinational therapy, which can reverse the suppressive tumor microenvironments, has also been widely proposed. Thus, in this review, we focus on tumor immunogenicity sculpted by the immune systems and discuss the significance and application of restructuring tumor antigens in precision medicine.
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Affiliation(s)
- Chiao-Hsu Ke
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Han Chiu
- Department of Microbiology, Soochow University, Taipei 111002, Taiwan
| | - Kuo-Chin Huang
- Holistic Education Center, Mackay Medical College, New Taipei City 25245, Taiwan
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
- Correspondence: ; Tel.: +886-233-661-286
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9
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Atomic resolution Cryo-EM structure of human proteasome activator PA28γ. Int J Biol Macromol 2022; 219:500-507. [PMID: 35932807 DOI: 10.1016/j.ijbiomac.2022.07.246] [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: 05/15/2022] [Revised: 07/18/2022] [Accepted: 07/31/2022] [Indexed: 11/21/2022]
Abstract
The PA28 family proteasome activators play important roles in regulating proteasome activities. Though the three paralogs (PA28α, PA28β, and PA28γ) are similar in terms of primary sequence, they show significant difference in expression pattern, cellular localization and most importantly, biological functions. While PA28αβ is responsible for promoting peptidase activity of proteasome to facilitate MHC-I antigen processing, but unable to promote protein degradation, PA28γ is well-known to not only promote peptidase activity, but also proteolytic activity of proteasome. However, why this paralog has the unique function remains elusive. Previous structural studies have mainly focused on mammalian PA28α, PA28β and PA28αβ heptamers, while structural studies on mammalian PA28γ of atomic resolution are still absent to date. In the present work, we determined the Cryo-EM structure of the human PA28γ heptamer at atomic resolution, revealing interesting unique structural features that may hint our understanding the functional mechanisms of this proteasome activator.
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10
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Yu Z, Wei X, Liu L, Sun H, Fang T, Wang L, Li Y, Sui W, Wang K, He Y, Zhao Y, Huang W, An G, Meng F, Huang C, Yu T, Anderson KC, Cheng T, Qiu L, Hao M. Indirubin-3'-monoxime acts as proteasome inhibitor: Therapeutic application in multiple myeloma. EBioMedicine 2022; 78:103950. [PMID: 35344764 PMCID: PMC8958548 DOI: 10.1016/j.ebiom.2022.103950] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/26/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is still an incurable malignancy of plasma cells. Proteasome inhibitors (PIs) work as the backbone agent and have greatly improved the outcome in majority of newly diagnosed patients with myeloma. However, drug resistance remains the major obstacle causing treatment failure in clinical practice. Here, we investigated the effects of Indirubin-3'-monoxime (I3MO), one of the derivatives of Indirubin, in the treatment of MM. METHODS MM patient primary samples and human cell lines were examined. I3MO effects on myeloma treatment and the underling molecular mechanisms were investigated via in vivo and in vitro study. FINDINGS Our results demonstrated the anti-MM activity of I3MO in both drug- sensitive and -resistance MM cells. I3MO sensitizes MM cells to bortezomib-induced apoptosis. Mechanistically, I3MO acts as a multifaceted regulator of cell death, which induced DNA damage, cell cycle arrest, and abrogates NF-κB activation. I3MO efficiently down-regulated USP7 expression, promoted NEK2 degradation, and suppressed NF-κB signaling in MM. Our study reported that I3MO directly bound with and caused the down-regulation of PA28γ (PSME3), and PA200 (PSME4), the proteasome activators. Knockdown of PSME3 or PSME4 caused the inhibition of proteasome capacity and the overload of paraprotein, which sensitizes MM cells to bortezomib-mediated growth arrest. Clinical data demonstrated that PSME3 and PSME4 are over-expressed in relapsed/refractory MM (RRMM) and associated with inferior outcome. INTERPRETATION Altogether, our study indicates that I3MO is agent triggering proteasome inhibition and represents a promising therapeutic strategy to improve patient outcome in MM. FUNDINGS A full list of funding can be found in the acknowledgements.
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Affiliation(s)
- Zhen Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Xiaojing Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lanting Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Hao Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Teng Fang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Ying Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Weiwei Sui
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Kefei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Yi He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Yaozhong Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Wenyang Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China
| | - Changjiang Huang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China
| | - Tengteng Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China.
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China.
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11
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Frayssinhes JYA, Cerruti F, Laulin J, Cattaneo A, Bachi A, Apcher S, Coux O, Cascio P. PA28γ-20S proteasome is a proteolytic complex committed to degrade unfolded proteins. Cell Mol Life Sci 2021; 79:45. [PMID: 34913092 PMCID: PMC11071804 DOI: 10.1007/s00018-021-04045-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023]
Abstract
PA28γ is a nuclear activator of the 20S proteasome that, unlike the 19S regulatory particle, stimulates hydrolysis of several substrates in an ATP- and ubiquitin-independent manner and whose exact biological functions and molecular mechanism of action still remain elusive. In an effort to shed light on these important issues, we investigated the stimulatory effect of PA28γ on the hydrolysis of different fluorogenic peptides and folded or denatured full-length proteins by the 20S proteasome. Importantly, PA28γ was found to dramatically enhance breakdown rates by 20S proteasomes of several naturally or artificially unstructured proteins, but not of their native, folded counterparts. Furthermore, these data were corroborated by experiments in cell lines with a nucleus-tagged myelin basic protein. Finally, mass spectrometry analysis of the products generated during proteasomal degradation of two proteins demonstrated that PA28γ does not increase, but rather decreases, the variability of peptides that are potentially suitable for MHC class I antigen presentation. These unexpected findings indicate that global stimulation of the degradation of unfolded proteins may represent a more general feature of PA28γ and suggests that this proteasomal activator might play a broader role in the pathway of protein degradation than previously believed.
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Affiliation(s)
| | - Fulvia Cerruti
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy
| | - Justine Laulin
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | | | - Angela Bachi
- The FIRC Institute of Molecular Oncology (IFOM), 20139, Milan, Italy
| | - Sebastien Apcher
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie Des Tumeurs et Immunothérapie, Villejuif, France
| | - Olivier Coux
- Centre de Recherche de Biologie Cellulaire de Montpellier (CRBM), CNRS UMR 5237, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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12
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Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
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Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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13
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Jia R, Sui Z, Zhang H, Yu Z. Identification and Validation of Immune-Related Gene Signature for Predicting Lymph Node Metastasis and Prognosis in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:679031. [PMID: 34109216 PMCID: PMC8182055 DOI: 10.3389/fmolb.2021.679031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is a serious malignancy, and lung adenocarcinoma (LUAD) is the most common pathological subtype. Immune-related factors play an important role in lymph node metastasis. In this study, we obtained gene expression profile data for LUAD and normal tissues from the TCGA database and analyzed their immune-related genes (IRGs), and observed that 459 IRGs were differentially expressed. Further analysis of the correlation between differentially expressed IRGs and lymph node metastasis revealed 18 lymph node metastasis-associated IRGs. In addition, we analyzed the mutations status, function and pathway enrichment of these IRGs, and regulatory networks established through TF genes. We then identified eight IRGs (IKBKB, LTBR, MIF, PPARD, PPIA, PSME3, S100A6, SEMA4B) as the best predictors by LASSO Logistic analysis and used these IRGs to construct a model to predict lymph node metastasis in patients with LUAD (AUC 0.75; 95% CI: 0.7064-0.7978), and survival analysis showed that the risk score independently affected patient survival. We validated the predictive effect of risk scores on lymph node metastasis and survival using the GEO database as a validation cohort and the results showed good agreement. In addition, the risk score was highly correlated with infiltration of immune cells (mast cells activated, macrophages M2, macrophages M0 and B cells naïve), immune and stromal scores, and immune checkpoint genes (LTBR, CD40LG, EDA2R, and TNFRSF19). We identified key IRGs associated with lymph node metastasis in LUAD and constructed a reliable risk score model, which may provide valuable biomarkers for LUAD patients and further reveal the mechanism of its occurrence.
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Affiliation(s)
- Ran Jia
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China.,Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, China
| | - Zhilin Sui
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
| | - Hongdian Zhang
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
| | - Zhentao Yu
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China.,Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, China
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14
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Cascio P. PA28γ: New Insights on an Ancient Proteasome Activator. Biomolecules 2021; 11:228. [PMID: 33562807 PMCID: PMC7915322 DOI: 10.3390/biom11020228] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
PA28 (also known as 11S, REG or PSME) is a family of proteasome regulators whose members are widely present in many of the eukaryotic supergroups. In jawed vertebrates they are represented by three paralogs, PA28α, PA28β, and PA28γ, which assemble as heptameric hetero (PA28αβ) or homo (PA28γ) rings on one or both extremities of the 20S proteasome cylindrical structure. While they share high sequence and structural similarities, the three isoforms significantly differ in terms of their biochemical and biological properties. In fact, PA28α and PA28β seem to have appeared more recently and to have evolved very rapidly to perform new functions that are specifically aimed at optimizing the process of MHC class I antigen presentation. In line with this, PA28αβ favors release of peptide products by proteasomes and is particularly suited to support adaptive immune responses without, however, affecting hydrolysis rates of protein substrates. On the contrary, PA28γ seems to be a slow-evolving gene that is most similar to the common ancestor of the PA28 activators family, and very likely retains its original functions. Notably, PA28γ has a prevalent nuclear localization and is involved in the regulation of several essential cellular processes including cell growth and proliferation, apoptosis, chromatin structure and organization, and response to DNA damage. In striking contrast with the activity of PA28αβ, most of these diverse biological functions of PA28γ seem to depend on its ability to markedly enhance degradation rates of regulatory protein by 20S proteasome. The present review will focus on the molecular mechanisms and biochemical properties of PA28γ, which are likely to account for its various and complex biological functions and highlight the common features with the PA28αβ paralog.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy
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15
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Jia R, Sui Z, Zhang H, Yu Z. Identification and Validation of Immune-Related Gene Signature for Predicting Lymph Node Metastasis and Prognosis in Lung Adenocarcinoma. Front Mol Biosci 2021. [PMID: 34109216 DOI: 10.3389/fmolb.2020.585245/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
Lung cancer is a serious malignancy, and lung adenocarcinoma (LUAD) is the most common pathological subtype. Immune-related factors play an important role in lymph node metastasis. In this study, we obtained gene expression profile data for LUAD and normal tissues from the TCGA database and analyzed their immune-related genes (IRGs), and observed that 459 IRGs were differentially expressed. Further analysis of the correlation between differentially expressed IRGs and lymph node metastasis revealed 18 lymph node metastasis-associated IRGs. In addition, we analyzed the mutations status, function and pathway enrichment of these IRGs, and regulatory networks established through TF genes. We then identified eight IRGs (IKBKB, LTBR, MIF, PPARD, PPIA, PSME3, S100A6, SEMA4B) as the best predictors by LASSO Logistic analysis and used these IRGs to construct a model to predict lymph node metastasis in patients with LUAD (AUC 0.75; 95% CI: 0.7064-0.7978), and survival analysis showed that the risk score independently affected patient survival. We validated the predictive effect of risk scores on lymph node metastasis and survival using the GEO database as a validation cohort and the results showed good agreement. In addition, the risk score was highly correlated with infiltration of immune cells (mast cells activated, macrophages M2, macrophages M0 and B cells naïve), immune and stromal scores, and immune checkpoint genes (LTBR, CD40LG, EDA2R, and TNFRSF19). We identified key IRGs associated with lymph node metastasis in LUAD and constructed a reliable risk score model, which may provide valuable biomarkers for LUAD patients and further reveal the mechanism of its occurrence.
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Affiliation(s)
- Ran Jia
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
- Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, China
| | - Zhilin Sui
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
| | - Hongdian Zhang
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
| | - Zhentao Yu
- Department of Esophageal Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center of Cancer, Tianjin, China
- Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, China
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