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Zheng H, Guan X, Meng X, Tong Y, Wang Y, Xie S, Guo L, Lu R. IFN-γ in ovarian tumor microenvironment upregulates HLA-E expression and predicts a poor prognosis. J Ovarian Res 2023; 16:229. [PMID: 38007483 PMCID: PMC10675946 DOI: 10.1186/s13048-023-01286-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/26/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Inflammation and immunity are two main characteristics of tumor microenvironment (TME). Interferon-gamma (IFN-γ) is generally considered as a pro-inflammatory cytokine which mediates anti-tumor immune response. Recently, IFN-γ was also reported to play a protumorigenic role. However, the mechanisms of tumor-promoting effect induced by IFN-γ remain unclear. METHODS The expression of leukocyte antigen-E (HLA-E), IFN-γ, CD3 and CD56 in clinical samples of ovarian cancer was detected by mutiplexed immunohistochemistry. The mechanism to induce HLA-E overexpression by IFN-γ was explored using human ovarian cancer cell lines through western blot and flow cytometry. We further clarify the role of overexpressed-HLA-E on natural killer (NK)-mediated cell lysis. RESULTS We found that IFN-γ could upregulate HLA-E protein expression through activating of JAK/STAT1 signaling pathway, and increase cell surface HLA-E level through enhancing proteasome activity. We also observed that only high levels of membrane HLA-E expression contributed to the inhibition of NK-mediated cytotoxicity. We showed that progression-free survival (PFS) of ovarian cancer patients was negatively correlated with IFN-γ expression in their tumor tissues, due to more tumor infiltrating NK cells compared with T lymphocytes. CONCLUSIONS Our study revealed the protumorigenic role of IFN-γ by upregulation of HLA-E expression and rendering tumors less susceptible to immune attack. We also provided a novel insight into the relationship between tumor microenvironment and immune evasion.
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Affiliation(s)
- Hui Zheng
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Xiaolin Guan
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, 200032, China
- Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Xin Meng
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ying Tong
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yanchun Wang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Suhong Xie
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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2
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Monittola F, Bianchi M, Nasoni MG, Luchetti F, Magnani M, Crinelli R. Gastric cancer cell types display distinct proteasome/immunoproteasome patterns associated with migration and resistance to proteasome inhibitors. J Cancer Res Clin Oncol 2023; 149:10085-10097. [PMID: 37261527 PMCID: PMC10423134 DOI: 10.1007/s00432-023-04948-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
PURPOSE Gastric cancers (GC) display histological and molecular differences. This heterogeneity has limited the development of new therapeutic strategies which requires the identification of the molecular players involved in GC pathogenesis and the investigation of their responsiveness to drugs. Several proteasome subunits have been identified as prognostic markers in GC and their role studied by gene knockdown. However, proteasomes are multi-subunit protein complexes co-existing in multiple forms with distinct activity/specificity and ability to change in response to inhibitors. Information on the role of different proteasome particles in cancer and their relevance as therapeutic targets is limited. METHODS Based on this evidence, subunit assembly into proteasome complexes and activity were investigated by native PAGE followed by immunoblotting, and by using fluorogenic substrates, respectively. RESULTS Here we show that GC cell lines with epithelial and/or diffuse Lauren's histotype express different levels of immunoproteasome subunits and equal amounts of constitutive counterparts. Immunoproteasome subunits were highly expressed and preferentially assembled into 19S capped complexes in diffuse-type cells, where most of the activity was catalyzed by the 26S and 30S particles. In epithelial cells, activity appeared equally distributed between 19S- and 11S-capped proteolytic particles. This proteasome pattern was associated with higher resistance of diffuse-type cells to proteasome inhibition. Immunoproteasome inhibition by ONX 0914 did not influence cell viability but affected metastatic cell migration. CONCLUSIONS These results suggest that pharmacological inhibition of the immunoproteasome may be useful in treating metastatic gastric cancers.
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Affiliation(s)
- Francesca Monittola
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| | - Marzia Bianchi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| | - Maria Gemma Nasoni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| | - Francesca Luchetti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy
| | - Rita Crinelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029, Urbino, PU, Italy.
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3
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Tabaei S, Haghshenas MR, Ariafar A, Gilany K, Stensballe A, Farjadian S, Ghaderi A. Comparative proteomics analysis in different stages of urothelial bladder cancer for identification of potential biomarkers: highlighted role for antioxidant activity. Clin Proteomics 2023; 20:28. [PMID: 37501157 PMCID: PMC10373361 DOI: 10.1186/s12014-023-09419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Non-muscle-invasive bladder cancer (NMIBC) has a high recurrence rate and muscle-invasive bladder cancer (MIBC) has unfavorable outcomes in urothelial bladder cancer (UBC) patients. Complex UBC-related protein biomarkers for outcome prediction may provide a more efficient management approach with an improved clinical outcome. The aim of this study is to recognize tumor-associated proteins, which are differentially expressed in different stages of UBC patients compared non-cancerous tissues. METHODS The proteome of tissue samples of 42 UBC patients (NMIBC n = 25 and MIBC n = 17) was subjected to two-dimensional electrophoresis (2-DE) combined with Liquid chromatography-mass spectrometry (LC-MS) system to identify differentially expressed proteins. The intensity of protein spots was quantified and compared with Prodigy SameSpots software. Functional, pathway, and interaction analyses of identified proteins were performed using geneontology (GO), PANTHER, Reactome, Gene MANIA, and STRING databases. RESULTS Twelve proteins identified by LC-MS showed differential expression (over 1.5-fold, p < 0.05) by LC-MS, including 9 up-regulated in NMIBC and 3 up-regulated in MIBC patients. Proteins involved in the detoxification of reactive oxygen species and cellular responses to oxidative stress showed the most significant changes in UBC patients. Additionally, the most potential functions related to these detected proteins were associated with peroxidase, oxidoreductase, and antioxidant activity. CONCLUSION We identified several alterations in protein expression involved in canonical pathways which were correlated with the clinical outcomes suggested might be useful as promising biomarkers for early detection, monitoring, and prognosis of UBC.
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Affiliation(s)
- Samira Tabaei
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Haghshenas
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Ariafar
- Department of Urology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Gistrup, 9260, Denmark
- Clinical Cancer Research Center, Aalborg University hospital, Gistrup, 9260, Denmark
| | - Shirin Farjadian
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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4
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Uribe-Herranz M, Beghi S, Ruella M, Parvathaneni K, Salaris S, Kostopoulos N, George SS, Pierini S, Krimitza E, Costabile F, Ghilardi G, Amelsberg KV, Lee YG, Pajarillo R, Markmann C, McGettigan-Croce B, Agarwal D, Frey N, Lacey SF, Scholler J, Gabunia K, Wu G, Chong E, Porter DL, June CH, Schuster SJ, Bhoj V, Facciabene A. Modulation of the gut microbiota engages antigen cross-presentation to enhance antitumor effects of CAR T cell immunotherapy. Mol Ther 2023; 31:686-700. [PMID: 36641624 PMCID: PMC10014349 DOI: 10.1016/j.ymthe.2023.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/20/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Several studies have shown the influence of commensal microbes on T cell function, specifically in the setting of checkpoint immunotherapy for cancer. In this study, we investigated how vancomycin-induced gut microbiota dysbiosis affects chimeric antigen receptor (CAR) T immunotherapy using multiple preclinical models as well as clinical correlates. In two murine tumor models, hematopoietic CD19+-A20 lymphoma and CD19+-B16 melanoma, mice receiving vancomycin in combination with CD19-directed CAR T cell (CART-19) therapy displayed increased tumor control and tumor-associated antigens (TAAs) cross-presentation compared with CART-19 alone. Fecal microbiota transplant from human healthy donors to pre-conditioned mice recapitulated the results obtained in naive gut microbiota mice. Last, B cell acute lymphoblastic leukemia patients treated with CART-19 and exposed to oral vancomycin showed higher CART-19 peak expansion compared with unexposed patients. These results substantiate the role of the gut microbiota on CAR T cell therapy and suggest that modulation of the gut microbiota using vancomycin may improve outcomes after CAR T cell therapy across tumor types.
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Affiliation(s)
- Mireia Uribe-Herranz
- Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Immunology Department, Hospital Clínic of Barcelona, Barcelona 08036, Spain
| | - Silvia Beghi
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Ruella
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kalpana Parvathaneni
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Silvano Salaris
- Unit of Biostatistics, Epidemiology and Public Health, University of Padova, Padova, Italy
| | - Nektarios Kostopoulos
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Subin S George
- Bioinformatics Core, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stefano Pierini
- Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; The Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elisavet Krimitza
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesca Costabile
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guido Ghilardi
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly V Amelsberg
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yong Gu Lee
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymone Pajarillo
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline Markmann
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bevin McGettigan-Croce
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Divyansh Agarwal
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Noelle Frey
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Simon F Lacey
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Scholler
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Khatuna Gabunia
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Gary Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elise Chong
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David L Porter
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carl H June
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Stephen J Schuster
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vijay Bhoj
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea Facciabene
- Center for Cellular Immunotherapies, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; Division of Radiation Oncology, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA; The Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Geoffroy K, Araripe Saraiva B, Viens M, Béland D, Bourgeois-Daigneault MC. Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers. Sci Rep 2023; 13:2129. [PMID: 36746983 PMCID: PMC9902398 DOI: 10.1038/s41598-023-28940-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023] Open
Abstract
Proteasome dependency is a feature of many cancers that can be targeted by proteasome inhibitors. For some cancer types, notably breast cancer and triple-negative breast cancer (TNBC), high mRNA expression of a modified form of the proteasome, called the immunoproteasome (ImP), correlates with better outcomes and higher expression of one ImP subunit was associated with slower tumor growth in a small patient cohort. While these findings are in line with an anti-tumoral role of the ImP in breast cancer, studies investigating ImP expression at the protein level in large patient cohorts are lacking. Furthermore, while ImPs can be found in both immune and non-immune cells, the cellular source is often ignored in correlative studies. In order to determine the impact of ImP expression on breast cancer outcomes, we assessed the protein expression and cellular source of the ImP subunits PSMB8 and PSMB9 in a cohort of 2070 patients. Our data show a clear correlation between high ImP expression and better outcomes, most notably for TNBC patients and when tumor cells rather than stromal or immune cells express PSMB8 or PSMB9. Our results therefore suggest that ImP expression by tumor cells could be used as prognostic markers of TNBC outcomes.
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Affiliation(s)
- Karen Geoffroy
- Cancer and Immunopathology Axes, CHUM Research Centre, Montreal, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada.,Institut du Cancer de Montréal, Montreal, Canada
| | - Bruna Araripe Saraiva
- Cancer and Immunopathology Axes, CHUM Research Centre, Montreal, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada.,Institut du Cancer de Montréal, Montreal, Canada
| | - Melissa Viens
- Cancer and Immunopathology Axes, CHUM Research Centre, Montreal, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada.,Institut du Cancer de Montréal, Montreal, Canada
| | - Delphine Béland
- Cancer and Immunopathology Axes, CHUM Research Centre, Montreal, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada.,Institut du Cancer de Montréal, Montreal, Canada
| | - Marie-Claude Bourgeois-Daigneault
- Cancer and Immunopathology Axes, CHUM Research Centre, Montreal, Canada. .,Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, University of Montreal, Montreal, Canada. .,Institut du Cancer de Montréal, Montreal, Canada.
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Wang Q, Huang X, Zeng S, Zhou R, Wang D. Identification and validation of a TTN-associated immune prognostic model for skin cutaneous melanoma. Front Genet 2023; 13:1084937. [PMID: 36704353 PMCID: PMC9871619 DOI: 10.3389/fgene.2022.1084937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/27/2022] [Indexed: 01/12/2023] Open
Abstract
TTN is the most commonly mutated gene in skin cutaneous melanoma (SKCM). Tumor mutational burden (TMB) can generate new antigens that regulate the recognition of T cells, which will significantly affect the prognosis of patients. The TTN gene has a long coding sequence and a high number of mutant sites, which allows SKCM patients to produce higher TMB and may influence the immune response. It has been found that the overall survival (OS) of SKCM patients with TTN mutation was significantly higher than that of wild-type patients. However, the effect of TTN mutation on the immune microenvironment of SKCM has not been fully investigated. Here, we systematically explored the relationship and potential mechanisms between TTN mutation status and the immune response. We first revealed that TTN mutated SKCM were significantly associated with four immune-related biological processes. Next, 115 immune genes differentially expressed between TTN mutation and wild-type SKCM patients were found to significantly affect the OS of SKCM patients. Then, we screened four immune-related genes (CXCL9, PSMB9, CD274, and FCGR2A) using LASSO regression analysis and constructed a TTN mutation-associated immune prognostic model (TM-IPM) to distinguish the SKCM patients with a high or low risk of poor prognosis, independent of multiple clinical characteristics. SKCM in the low-risk group highly expressed a large number of immune-related genes, and functional enrichment analysis of these genes showed that this group was involved in multiple immune processes and pathways. Furthermore, the nomogram constructed by TM-IPM with other clinicopathological parameters can provide a predictive tool for clinicians. Moreover, we found that CD8+ T cells were significantly enriched in the low-risk group. The expression level of immune checkpoints was higher in the low-risk group than in the high-risk group. Additionally, the response to chemotherapeutic agents was higher in the low-risk group than in the high-risk group, which may be related to the long survival in the low-risk group. Collectively, we constructed and validated a TM-IPM using four immune-related genes and analyzed the potential mechanisms of TM-IPM to predict patient prognosis and response to immunotherapy from an immunological perspective.
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Affiliation(s)
- Qirui Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingtai Huang
- Shanghai Key Laboratory of Stomatology, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Orthodontics, College of Stomatology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siyi Zeng
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renpeng Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danru Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Danru Wang,
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7
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Xie T, Fan G, Huang L, Lou N, Han X, Xing P, Shi Y. Analysis on methylation and expression of PSMB8 and its correlation with immunity and immunotherapy in lung adenocarcinoma. Epigenomics 2022; 14:1427-1448. [PMID: 36683462 DOI: 10.2217/epi-2022-0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aim: To find biomarkers for immunity and immunotherapy in lung adenocarcinoma (LUAD) through multiomics analysis. Materials & methods: The multiomics data of patients with LUAD were downloaded from the TCGA and GEO databases. CIBERSORT, quanTIseq, ESTIMATEScore, k-means clustering, gene set enrichment analysis, gene set variation analysis, immunophenoscore and logistic regression were used in this study. Results: PSMB8 HypoMet-HighExp group patients have more active immune-related pathways, more antitumor immune cells, less protumor immune cells, higher immunophenoscore and longer progression-free survival of immune checkpoint inhibitor therapy than HyperMet-LowExp group. In multivariate analysis, PSMB8 showed an independent value. Conclusion: The combination of DNA methylation and mRNA expression of PSMB8 could independently distinguish types of tumor immune microenvironment and predict programmed cell death protein 1/programmed cell death-ligand 1 inhibitors' effects in patients with LUAD.
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Affiliation(s)
- Tongji Xie
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Guangyu Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Liling Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe & Rare Diseases, NMPA Key Laboratory for Clinical Research & Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Puyuan Xing
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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8
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The dichotomous role of immunoproteasome in cancer: Friend or foe? Acta Pharm Sin B 2022; 13:1976-1989. [DOI: 10.1016/j.apsb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022] Open
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9
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Maia Falcão R, Kokaraki G, De Wispelaere W, Amant F, De Souza GA, de Souza JES, Carlson JW, Petta TB. The Expression of the Immunoproteasome Subunit PSMB9 Is Related to Distinct Molecular Subtypes of Uterine Leiomyosarcoma. Cancers (Basel) 2022; 14:cancers14205007. [PMID: 36291793 PMCID: PMC9600211 DOI: 10.3390/cancers14205007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Uterine leiomyosarcoma (uLMS) is a rare, aggressive, and highly heterogeneous tumor. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 develops spontaneous uLMS. In this study, we used molecular data from 3 non-related uLMS cohorts that were integrated and analyzed by proteotranscriptomics. We observed overexpression of the immunoproteasome pathway in uLMS, and then further classified the samples as low or high PSMB9 gene expression levels and we provide evidence that; (i) in the group high there is an enrichment of pathways related to the immune system and in the group low, the ECM formation; (ii) samples with high CD8+/PSMB9 ratio shows better OS; and (iii) the main regulator in the high group is IFNγ and in the low, the proto-oncogene SRC. These findings contribute to the understanding of potential therapeutic or prognostic markers in uLMS. Abstract Background: Uterine leiomyosarcoma (uLMS) are rare and malignant tumors that arise in the myometrium cells and whose diagnosis is based on histopathological features. Identifying diagnostic biomarkers for uLMS is a challenge due to molecular heterogeneity and the scarcity of samples. In vivo and in vitro models for uLMS are urgently needed. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 (MIM:177045) develop spontaneous uLMS. This study aimed to analyze the role of PSMB9 in uLMS tumorigenesis and patient outcome. Methods: Molecular data from 3 non-related uLMS cohorts were integrated and analyzed by proteotranscriptomic using gene expression and protein abundance levels in 68 normal adjacent myometrium (MM), 66 uterine leiomyoma (LM), and 67 uLMS. Results: the immunoproteasome pathway is upregulated and the gene PMSB9 shows heterogeneous expression values in uLMS. Quartile group analysis showed no significant difference between groups high and low PSMB9 expression groups at 3-years overall survival (OS). Using CYBERSORTx analysis we observed 9 out of 17 samples in the high group clustering together due to high M2 macrophages and CD4 memory resting, and high CD8+/PSMB9 ratio was associated with better OS. The main pathway regulated in the high group is IFNγ and in the low is the ECM pathway dependent on the proto-oncogene SRC. Conclusion: these findings suggest 2 subtypes of uLMS (immune-related and ECM-related) with different candidate mechanisms of malignancy.
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Affiliation(s)
- Raul Maia Falcão
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Georgia Kokaraki
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Wout De Wispelaere
- Department of Oncology, Leuven and Leuven Cancer Institute, Katholieke Universiteit, 3000 Leuven, Belgium
| | - Frédéric Amant
- Department of Oncology, Leuven and Leuven Cancer Institute, Katholieke Universiteit, 3000 Leuven, Belgium
- Department of Surgery, The Netherlands Cancer Institute, 1066 Amsterdam, The Netherlands
| | - Gustavo Antônio De Souza
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Jorge Estefano Santana de Souza
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Joseph Woodward Carlson
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
- K7 Onkologi-Patologi, Karolinska Institute, 17177 Stockholm, Sweden
| | - Tirzah Braz Petta
- Bioinformatics Graduate Program, Instituto Metropole Digital, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
- University of Southern California Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
- K7 Onkologi-Patologi, Karolinska Institute, 17177 Stockholm, Sweden
- Correspondence: ; Tel.: +1-323-442-1153
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Designing a novel E2-IFN-γ fusion protein against CSFV by immunoinformatics and structural vaccinology approaches. Appl Microbiol Biotechnol 2022; 106:3611-3623. [PMID: 35524776 DOI: 10.1007/s00253-022-11919-w] [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: 02/27/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Subunit vaccines with high purity and safety are gradually becoming a main trend in vaccinology. However, adjuvants such as interferon-gamma (IFN-γ) are required to enhance immune responses of subunit vaccines due to their poor immunogenicity. The conjugation of antigen with adjuvant can induce more potent immune responses compared to the mixture of antigen and adjuvant. At the same time, the selection of linker, indispensable in the construction of the stable and bioactive fusion proteins, is complicated and time-consuming. The development of immunoinformatics and structural vaccinology approaches provides a means to address the abovementioned problem. Therefore, in this study, a E2-IFN-γ fusion protein with an optimal linker (E2-R2-PIFN) was designed by bioinformatics approaches to improve the immunogenicity of the classical swine fever virus (CSFV) E2 subunit vaccine. Moreover, the E2-R2-PIFN fusion protein was expressed in HEK293T cells and the biological effects of IFN-γ in E2-R2-PIFN were confirmed in vitro via Western blotting. Here, an alternative method is utilized to simplify the design and validation of the antigen-adjuvant fusion protein, providing a potential subunit vaccine candidate against CSFV. KEY POINTS: • An effective and simple workflow of antigen-adjuvant fusion protein design and validation was established by immunoinformatics and structural vaccinology. • A novel E2-IFN-γ fusion protein with an optimal linker was designed as a potential CSFV vaccine. • The bioactivity of the newly designed fusion protein was preliminarily validated through in vitro experiments.
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