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Li R, Wang Y, Wen X, Cheng B, Lv R, Chen R, Hu W, Wang Y, Liu J, Lin B, Zhang H, Zhang E, Tang X. A novel EIF3C-related CD8 + T-cell signature in predicting prognosis and immunotherapy response of nasopharyngeal carcinoma. J Cancer Res Clin Oncol 2024; 150:103. [PMID: 38400862 PMCID: PMC10894114 DOI: 10.1007/s00432-023-05552-x] [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: 09/17/2023] [Accepted: 11/09/2023] [Indexed: 02/26/2024]
Abstract
PURPOSE At present, dysfunctional CD8+ T-cells in the nasopharyngeal carcinoma (NPC) tumor immune microenvironment (TIME) have caused unsatisfactory immunotherapeutic effects, such as a low response rate of anti-PD-L1 therapy. Therefore, there is an urgent need to identify reliable markers capable of accurately predicting immunotherapy efficacy. METHODS Utilizing various algorithms for immune-infiltration evaluation, we explored the role of EIF3C in the TIME. We next found the influence of EIF3C expression on NPC based on functional analyses and RNA sequencing. By performing correlation and univariate Cox analyses of CD8+ Tcell markers from scRNA-seq data, we identified four signatures, which were then used in conjunction with the lasso algorithm to determine corresponding coefficients in the resulting EIF3C-related CD8+ T-cell signature (ETS). We subsequently evaluated the prognostic value of ETS using univariate and multivariate Cox regression analyses, Kaplan-Meier curves, and the area under the receiver operating characteristic curve (AUROC). RESULTS Our results demonstrate a significant relationship between low expression of EIF3C and high levels of CD8+ T-cell infiltration in the TIME, as well as a correlation between EIF3C expression and progression of NPC. Based on the expression levels of four EIF3C-related CD8+ T-cell marker genes, we constructed the ETS predictive model for NPC prognosis, which demonstrated success in validation. Notably, our model can also serve as an accurate indicator for detecting immunotherapy response. CONCLUSION Our findings suggest that EIF3C plays a significant role in NPC progression and immune modulation, particularly in CD8+ T-cell infiltration. Furthermore, the ETS model holds promise as both a prognostic predictor for NPC patients and a tool for adjusting individualized immunotherapy strategies.
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Affiliation(s)
- Rui Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Yikai Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Xin Wen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong Province, China
| | - Binglin Cheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Ruxue Lv
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Ruzhen Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Wen Hu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China
| | - Yinglei Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Jingwen Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Bingyi Lin
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Haixiang Zhang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - Enting Zhang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, Guangdong Province, China
| | - XinRan Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Avenue, Guangzhou, 510515, Guangdong Province, China.
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Qu H, Jiang J, Zhan X, Liang Y, Guo Q, Liu P, Lu L, Yang Y, Xu W, Zhang Y, Lan S, Chen Z, Lu Y, Ou Y, Qin Y. Integrating artificial intelligence in osteosarcoma prognosis: the prognostic significance of SERPINE2 and CPT1B biomarkers. Sci Rep 2024; 14:4318. [PMID: 38383657 PMCID: PMC10881519 DOI: 10.1038/s41598-024-54222-6] [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: 11/12/2023] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
The principal aim of this investigation is to identify pivotal biomarkers linked to the prognosis of osteosarcoma (OS) through the application of artificial intelligence (AI), with an ultimate goal to enhance prognostic prediction. Expression profiles from 88 OS cases and 396 normal samples were procured from accessible public databases. Prognostic models were established using univariate COX regression analysis and an array of AI methodologies including the XGB method, RF method, GLM method, SVM method, and LASSO regression analysis. Multivariate COX regression analysis was also employed. Immune cell variations in OS were examined using the CIBERSORT software, and a differential analysis was conducted. Routine blood data from 20,679 normal samples and 437 OS cases were analyzed to validate lymphocyte disparity. Histological assessments of the study's postulates were performed through immunohistochemistry and hematoxylin and eosin (HE) staining. AI facilitated the identification of differentially expressed genes, which were utilized to construct a prognostic model. This model discerned that the survival rate in the high-risk category was significantly inferior compared to the low-risk cohort (p < 0.05). SERPINE2 was found to be positively associated with memory B cells, while CPT1B correlated positively with CD8 T cells. Immunohistochemical assessments indicated that SERPINE2 was more prominently expressed in OS tissues relative to adjacent non-tumorous tissues. Conversely, CPT1B expression was elevated in the adjacent non-tumorous tissues compared to OS tissues. Lymphocyte counts from routine blood evaluations exhibited marked differences between normal and OS groups (p < 0.001). The study highlights SERPINE2 and CPT1B as crucial biomarkers for OS prognosis and suggests that dysregulation of lymphocytes plays a significant role in OS pathogenesis. Both SERPINE2 and CPT1B have potential utility as prognostic biomarkers for OS.
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Affiliation(s)
- Haishun Qu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jie Jiang
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning, China
| | - Xinli Zhan
- Department of Spine and Orthopedic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunxiao Liang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Quan Guo
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Peifeng Liu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Ling Lu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yanwei Yang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Weicheng Xu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yitian Zhang
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shaohang Lan
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zeshan Chen
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yuanhong Lu
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yufu Ou
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yijue Qin
- Guangxi Academy of Medical Sciences, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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103
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Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, Newell EW. Merkel cell polyomavirus-specific and CD39 +CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101390. [PMID: 38340724 PMCID: PMC10897544 DOI: 10.1016/j.xcrm.2023.101390] [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: 07/03/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39+CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells.
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Affiliation(s)
- Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Korok Sarkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Candice D Church
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Nandita Kumar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Saumya Jani
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulla K Hansen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steven P Fling
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA.
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104
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Zhang M, Zhang S, Guo W, He Y. Novel molecular hepatocellular carcinoma subtypes and RiskScore utilizing apoptosis-related genes. Sci Rep 2024; 14:3913. [PMID: 38365931 PMCID: PMC10873508 DOI: 10.1038/s41598-024-54673-x] [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: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of global cancer-related deaths. Despite immunotherapy offering hope for patients with HCC, only some respond to it. However, it remains unclear how to pre-screen eligible patients. Our study aimed to address this issue. In this study, we identified 13 prognostic genes through univariate Cox regression analysis of 87 apoptosis-related genes. Subsequently, these 13 genes were analyzed using ConsensusClusterPlus, and patients were categorized into three molecular types: C1, C2, and C3. A prognostic model and RiskScore were constructed using Lasso regression analysis of 132 significant genes identified between C1 and C3. We utilized quantitative polymerase chain reaction to confirm the model's transcript level in Huh7 and THLE2 cell lines. Both molecular subtypes and RiskScores effectively predicted patients benefiting from immunotherapy. Cox regression analysis revealed RiskScore as the most significant prognosis factor, suggesting its clinical application potential and providing a foundation for future experimental research.
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Affiliation(s)
- Menggang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China.
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China.
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105
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Hummelink K, Tissier R, Bosch LJ, Krijgsman O, van den Heuvel MM, Theelen WS, Damotte D, Goldwasser F, Leroy K, Smit EF, Meijer GA, Thommen DS, Monkhorst K. A Dysfunctional T-cell Gene Signature for Predicting Nonresponse to PD-1 Blockade in Non-small Cell Lung Cancer That Is Suitable for Routine Clinical Diagnostics. Clin Cancer Res 2024; 30:814-823. [PMID: 38088895 PMCID: PMC10870113 DOI: 10.1158/1078-0432.ccr-23-1061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/17/2024]
Abstract
PURPOSE Because PD-1 blockade is only effective in a minority of patients with advanced-stage non-small cell lung cancer (NSCLC), biomarkers are needed to guide treatment decisions. Tumor infiltration by PD-1T tumor-infiltrating lymphocytes (TIL), a dysfunctional TIL pool with tumor-reactive capacity, can be detected by digital quantitative IHC and has been established as a novel predictive biomarker in NSCLC. To facilitate translation of this biomarker to the clinic, we aimed to develop a robust RNA signature reflecting a tumor's PD-1T TIL status. EXPERIMENTAL DESIGN mRNA expression analysis using the NanoString nCounter platform was performed in baseline tumor samples from 41 patients with advanced-stage NSCLC treated with nivolumab that were selected on the basis of PD-1T TIL infiltration by IHC. Samples were included as a training cohort (n = 41) to develop a predictive gene signature. This signature was independently validated in a second cohort (n = 42). Primary outcome was disease control at 12 months (DC 12 m), and secondary outcome was progression-free and overall survival. RESULTS Regularized regression analysis yielded a signature using 12 out of 56 differentially expressed genes between PD-1T IHC-high tumors from patients with DC 12 m and PD-1T IHC-low tumors from patients with progressive disease (PD). In the validation cohort, 6/6 (100%) patients with DC 12 m and 23/36 (64%) with PD were correctly classified with a negative predictive value (NPV) of 100% and a positive predictive value of 32%. CONCLUSIONS The PD-1T mRNA signature showed a similar high sensitivity and high NPV as the digital IHC quantification of PD-1T TIL. This finding provides a straightforward approach allowing for easy implementation in a routine diagnostic clinical setting.
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Affiliation(s)
- Karlijn Hummelink
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Renaud Tissier
- Biostatistics Unit, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Linda J.W. Bosch
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Michel M. van den Heuvel
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Willemijn S.M.E. Theelen
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Diane Damotte
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - François Goldwasser
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
| | - Karen Leroy
- Team Cancer, Immune Control and Escape, Cordeliers Research Center, UMRS 1138, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- University Paris Cité, Paris, France
- CERTIM, Medical Oncology, Hôpital Cochin, APHP, Paris, France
- Department of Biochemistry, Hôpital Cochin, Européen Georges Pompidou, APHP Centre, Paris, France
| | - Egbert F. Smit
- Department of Thoracic Oncology, Division of Medical Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daniela S. Thommen
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Division of Diagnostic Oncology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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106
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Wang Y, Zou L, Song M, Zong J, Wang S, Meng L, Jia Z, Zhao L, Han X, Lu M. Establishment of skin cutaneous melanoma prognosis model based on vascular mimicry risk score. Medicine (Baltimore) 2024; 103:e36679. [PMID: 38363903 PMCID: PMC10869071 DOI: 10.1097/md.0000000000036679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/24/2023] [Indexed: 02/18/2024] Open
Abstract
Studies have indicated that Vascular mimicry (VM) could contribute to the unfavorable prognosis of skin cutaneous melanoma (SKCM). Thus, the objective of this study was to identify therapeutic targets associated with VM in SKCM and develop a novel prognostic model. Gene expression data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) were utilized to identify differentially expressed genes (DEGs). By intersecting these DEGs with VM genes, we acquired VM-related DEGs specific to SKCM, and then identified prognostic-related VM genes. A VM risk score system was established based on these prognosis-associated VM genes, and patients were then categorized into high- and low-score groups using the median score. Subsequently, differences in clinical characteristics, gene set enrichment analysis (GSEA), and other analyses were further presented between the 2 groups of patients. Finally, a novel prognostic model for SKCM was established using the VM score and clinical characteristics. 26 VM-related DEGs were identified in SKCM, among the identified DEGs associated with VM in SKCM, 5 genes were found to be prognostic-related. The VM risk score system, comprised of these genes, is an independent prognostic risk factor. There were significant differences between the 2 patient groups in terms of age, pathological stage, and T stage. VM risk scores are associated with epithelial biological processes, angiogenesis, regulation of the SKCM immune microenvironment, and sensitivity to targeted drugs. The novel prognostic model demonstrates excellent predictive ability. Our study identified VM-related prognostic markers and therapeutic targets for SKCM, providing novel insights for clinical diagnosis and treatment.
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Affiliation(s)
- Yubo Wang
- Dalian Medical University, Dalian, China
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital, Dalian, China
| | - Linxuan Zou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Mingzhi Song
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Junwei Zong
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shouyu Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lei Meng
- The First Affiliated Hospital of Nanhua Medical University, Hengyang, China
| | - Zhuqiang Jia
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Naqu People’s Hospital, Tibet, China
| | - Lin Zhao
- Department of Quality Management, Dalian Municipal Central Hospital, Dalian, China
| | - Xin Han
- Naqu People’s Hospital, Tibet, China
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ming Lu
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital, Dalian, China
- Department of Trauma and Tissue Repair Surgery, Dalian Municipal Central Hospital of Dalian Medical University, Dalian, China
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Wang M, Liu C, Wang Y, Jamil M, Alhomrani M, Alamri AS, Alsanie WF, Alsharif A, Ali M, Jabeen N. Bone morphogenetic protein 1: a prognostic indicator and potential biomarker in three cancer types. Am J Transl Res 2024; 16:400-414. [PMID: 38463598 PMCID: PMC10918118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/10/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Bone morphogenetic protein 1 (BMP1) is a metalloprotease that plays a role in activating both transforming growth factor-β (TGF-β) and BMP signaling pathways. TGF-β has been identified as a factor initiating and facilitating cancer development. Consequently, we propose the hypothesis that dysregulation of BMP1 could potentially contribute to the onset and advancement of human cancers. METHODS In this research, we aimed to analyze BMP1 expression level and the associated clinical outcomes across various cancers using online cancer OMICS databases, advanced Bioinformatics tools, and molecular analyses. RESULTS The outcomes of our web server-based expression analysis indicated an up-regulation of BMP1 in a majority of the human cancers examined. External validation using clinical samples also showed higher expression of BMP1. Moreover, heightened BMP1 expression exhibited a noteworthy correlation with reduced overall survival (OS) duration in Bladder Cancer (BLCA), Kidney Renal Clear Cell Carcinoma (KIRC), and Lung Adenocarcinoma (LUAD) patients. This suggests a substantial involvement of the BMP1 gene in the development and progression of these three types of cancers. The major signaling pathways related with BMP1 enriched genes were "ECM-receptor interaction, Amoebiasis, Focal adhesion, Protein digestion and absorption, progesterone-mediated, PI3K-Akt signaling pathway, and platelet activation". Moreover, we also explored some interesting correlations among BMP1 expression and its DNA promoter methylation level, CD8+ T immune cells level, and genetic variations. CONCLUSION In conclusion, our study has provided some solid basis for BMP1 to be used as a reliable common biomarker for BLCA, KIRC, and LUAD patients.
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Affiliation(s)
- Ming Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Chunmei Liu
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Yingjie Wang
- Department of Oncology, Hebei Yanda HospitalLangfang 065200, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CentreDera Ismail Khan 29050, Pakistan
| | - Majid Alhomrani
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulhakeem S Alamri
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Walaa F Alsanie
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Abdulaziz Alsharif
- College of Applied Medical Sciences, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif UniversityP.O. Box 11099, Taif 21944, Saudi Arabia
- Research Centre for Health Sciences, Taif UniversityTaif 26571, Saudi Arabia
| | - Mubarik Ali
- Animal Science Institute, National Agricultural Research CenterIslamabad 54000, Pakistan
| | - Norina Jabeen
- Department of Rural Sociology, University of Agriculture FaisalabadFaisalabad 38040, Punjab, Pakistan
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Zhao W, Kepecs B, Mahadevan NR, Segerstolpe A, Weirather JL, Besson NR, Giotti B, Soong BY, Li C, Vigneau S, Slyper M, Wakiro I, Jane-Valbuena J, Ashenberg O, Rotem A, Bueno R, Rozenblatt-Rosen O, Pfaff K, Rodig S, Hata AN, Regev A, Johnson BE, Tsankov AM. A cellular and spatial atlas of TP53 -associated tissue remodeling in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546977. [PMID: 37425718 PMCID: PMC10327017 DOI: 10.1101/2023.06.28.546977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
TP53 is the most frequently mutated gene across many cancers and is associated with shorter survival in lung adenocarcinoma (LUAD). To define how TP53 mutations affect the LUAD tumor microenvironment (TME), we constructed a multi-omic cellular and spatial tumor atlas of 23 treatment-naïve human lung tumors. We found that TP53 -mutant ( TP53 mut ) malignant cells lose alveolar identity and upregulate highly proliferative and entropic gene expression programs consistently across resectable LUAD patient tumors, genetically engineered mouse models, and cell lines harboring a wide spectrum of TP53 mutations. We further identified a multicellular tumor niche composed of SPP1 + macrophages and collagen-expressing fibroblasts that coincides with hypoxic, pro-metastatic expression programs in TP53 mut tumors. Spatially correlated angiostatic and immune checkpoint interactions, including CD274 - PDCD1 and PVR - TIGIT , are also enriched in TP53 mut LUAD tumors, which may influence response to checkpoint blockade therapy. Our methodology can be further applied to investigate mutation-specific TME changes in other cancers.
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Kennedy PT, Saulters EL, Duckworth AD, Lim YJ, Woolley JF, Slupsky JR, Cragg MS, Ward FJ, Dahal LN. Soluble CTLA-4 attenuates T cell activation and modulates anti-tumor immunity. Mol Ther 2024; 32:457-468. [PMID: 38053333 PMCID: PMC10861965 DOI: 10.1016/j.ymthe.2023.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/12/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
CTLA-4 is a crucial immune checkpoint receptor involved in the maintenance of immune homeostasis, tolerance, and tumor control. Antibodies targeting CTLA-4 have been promising treatments for numerous cancers, but the mechanistic basis of their anti-tumoral immune-boosting effects is poorly understood. Although the ctla4 gene also encodes an alternatively spliced soluble variant (sCTLA-4), preclinical/clinical evaluation of anti-CTLA-4-based immunotherapies have not considered the contribution of this isoform. Here, we explore the functional properties of sCTLA-4 and evaluate the efficacy of isoform-specific anti-sCTLA-4 antibody targeting in a murine cancer model. We show that expression of sCTLA-4 by tumor cells suppresses CD8+ T cells in vitro and accelerates growth and experimental metastasis of murine tumors in vivo. These effects were accompanied by modification of the immune infiltrate, notably restraining CD8+ T cells in a non-cytotoxic state. sCTLA-4 blockade with isoform-specific antibody reversed this restraint, enhancing intratumoral CD8+ T cell activation and cytolytic potential, correlating with therapeutic efficacy and tumor control. This previously unappreciated role of sCTLA-4 suggests that the biology and function of multi-gene products of immune checkpoint receptors need to be fully elucidated for improved mechanistic understanding of cancer immunotherapies.
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Affiliation(s)
- Paul T Kennedy
- Department of Pharmacology and Therapeutics, University of Liverpool, L69 3GE Liverpool, UK
| | - Emma L Saulters
- Department of Pharmacology and Therapeutics, University of Liverpool, L69 3GE Liverpool, UK
| | - Andrew D Duckworth
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L69 3GE Liverpool, UK
| | - Yeong Jer Lim
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L69 3GE Liverpool, UK
| | - John F Woolley
- Department of Pharmacology and Therapeutics, University of Liverpool, L69 3GE Liverpool, UK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, L69 3GE Liverpool, UK
| | - Mark S Cragg
- Centre for Cancer Immunology, University of Southampton, SO16 6YD Southampton, UK
| | - Frank J Ward
- Department of Immunology, University of Aberdeen, AB25 2ZD Aberdeen, UK
| | - Lekh N Dahal
- Department of Pharmacology and Therapeutics, University of Liverpool, L69 3GE Liverpool, UK.
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110
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Joseph AM, Al Aiyan A, Al-Ramadi B, Singh SK, Kishore U. Innate and adaptive immune-directed tumour microenvironment in pancreatic ductal adenocarcinoma. Front Immunol 2024; 15:1323198. [PMID: 38384463 PMCID: PMC10879611 DOI: 10.3389/fimmu.2024.1323198] [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: 10/17/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
One of the most deadly and aggressive cancers in the world, pancreatic ductal adenocarcinoma (PDAC), typically manifests at an advanced stage. PDAC is becoming more common, and by the year 2030, it is expected to overtake lung cancer as the second greatest cause of cancer-related death. The poor prognosis can be attributed to a number of factors, including difficulties in early identification, a poor probability of curative radical resection, limited response to chemotherapy and radiotherapy, and its immunotherapy resistance. Furthermore, an extensive desmoplastic stroma that surrounds PDAC forms a mechanical barrier that prevents vascularization and promotes poor immune cell penetration. Phenotypic heterogeneity, drug resistance, and immunosuppressive tumor microenvironment are the main causes of PDAC aggressiveness. There is a complex and dynamic interaction between tumor cells in PDAC with stromal cells within the tumour immune microenvironment. The immune suppressive microenvironment that promotes PDAC aggressiveness is contributed by a range of cellular and humoral factors, which itself are modulated by the cancer. In this review, we describe the role of innate and adaptive immune cells, complex tumor microenvironment in PDAC, humoral factors, innate immune-mediated therapeutic advances, and recent clinical trials in PDAC.
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Affiliation(s)
- Ann Mary Joseph
- Department of Veterinary Medicine (CAVM), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ahmad Al Aiyan
- Department of Veterinary Medicine (CAVM), United Arab Emirates University, Al Ain, United Arab Emirates
| | - Basel Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Shiv K. Singh
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Center, Goettingen, Germany
| | - Uday Kishore
- Department of Veterinary Medicine (CAVM), United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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111
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Delacher M, Schmidleithner L, Simon M, Stüve P, Sanderink L, Hotz-Wagenblatt A, Wuttke M, Schambeck K, Ruhland B, Hofmann V, Bittner S, Ritter U, Pant A, Helbich SS, Voss M, Lemmermann NA, Bessiri-Schake L, Bohn T, Eigenberger A, Menevse AN, Gebhard C, Strieder N, Abken H, Rehli M, Huehn J, Beckhove P, Hehlgans T, Junger H, Geissler EK, Prantl L, Werner JM, Schmidl C, Brors B, Imbusch CD, Feuerer M. The effector program of human CD8 T cells supports tissue remodeling. J Exp Med 2024; 221:e20230488. [PMID: 38226976 DOI: 10.1084/jem.20230488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
CD8 T lymphocytes are classically viewed as cytotoxic T cells. Whether human CD8 T cells can, in parallel, induce a tissue regeneration program is poorly understood. Here, antigen-specific assay systems revealed that human CD8 T cells not only mediated cytotoxicity but also promoted tissue remodeling. Activated CD8 T cells could produce the epidermal growth factor receptor (EGFR)-ligand amphiregulin (AREG) and sensitize epithelial cells for enhanced regeneration potential. Blocking the EGFR or the effector cytokines IFN-γ and TNF could inhibit tissue remodeling. This regenerative program enhanced tumor spheroid and stem cell-mediated organoid growth. Using single-cell gene expression analysis, we identified an AREG+, tissue-resident CD8 T cell population in skin and adipose tissue from patients undergoing abdominal wall or abdominoplasty surgery. These tissue-resident CD8 T cells showed a strong TCR clonal relation to blood PD1+TIGIT+ CD8 T cells with tissue remodeling abilities. These findings may help to understand the complex CD8 biology in tumors and could become relevant for the design of therapeutic T cell products.
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Affiliation(s)
- Michael Delacher
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
| | - Lisa Schmidleithner
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Malte Simon
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Faculty of Biosciences, Heidelberg University , Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Philipp Stüve
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Lieke Sanderink
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Agnes Hotz-Wagenblatt
- Core Facility Omics IT and Data Management, German Cancer Research Center , Heidelberg, Germany
| | - Marina Wuttke
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Kathrin Schambeck
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Brigitte Ruhland
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Veronika Hofmann
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Sebastian Bittner
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Uwe Ritter
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Asmita Pant
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Sara Salome Helbich
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
| | - Morten Voss
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
| | - Niels A Lemmermann
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
- Institute of Virology, University Medical Center Mainz , Mainz, Germany
- Institute of Virology, University of Bonn , Bonn, Germany
| | - Lisa Bessiri-Schake
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
| | - Toszka Bohn
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
| | - Andreas Eigenberger
- Department of Plastic, Hand- and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Ayse Nur Menevse
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Interventional Immunology, University Regensburg , Regensburg, Germany
| | | | | | - Hinrich Abken
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Genetic Immunotherapy, University Regensburg , Regensburg, Germany
| | - Michael Rehli
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Jochen Huehn
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Hannover Medical School , Hannover, Germany
- RESIST, Cluster of Excellence 2155, Hannover Medical School , Hannover, Germany
| | - Philipp Beckhove
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Interventional Immunology, University Regensburg , Regensburg, Germany
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Thomas Hehlgans
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
| | - Henrik Junger
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Edward K Geissler
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Lukas Prantl
- Department of Plastic, Hand- and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Jens M Werner
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | | | - Benedikt Brors
- Faculty of Biosciences, Heidelberg University , Heidelberg, Germany
- Faculty of Medicine Heidelberg, Heidelberg University , Heidelberg, Germany
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
- National Center for Tumor Diseases , Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center , Heidelberg, Germany
| | - Charles D Imbusch
- Institute of Immunology, University Medical Center Mainz , Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz , Mainz, Germany
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Markus Feuerer
- Leibniz Institute for Immunotherapy , Regensburg, Germany
- Chair for Immunology, University Regensburg , Regensburg, Germany
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112
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Ran X, Zheng J, Chen L, Xia Z, Wang Y, Sun C, Guo C, Lin P, Liu F, Wang C, Zhou J, Sun C, Liu Q, Ma J, Qin Z, Zhu X, Xie Q. Single-Cell Transcriptomics Reveals the Heterogeneity of the Immune Landscape of IDH-Wild-Type High-Grade Gliomas. Cancer Immunol Res 2024; 12:232-246. [PMID: 38091354 PMCID: PMC10835213 DOI: 10.1158/2326-6066.cir-23-0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/21/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
Isocitrate dehydrogenase (IDH)-wild-type (WT) high-grade gliomas, especially glioblastomas, are highly aggressive and have an immunosuppressive tumor microenvironment. Although tumor-infiltrating immune cells are known to play a critical role in glioma genesis, their heterogeneity and intercellular interactions remain poorly understood. In this study, we constructed a single-cell transcriptome landscape of immune cells from tumor tissue and matching peripheral blood mononuclear cells (PBMC) from IDH-WT high-grade glioma patients. Our analysis identified two subsets of tumor-associated macrophages (TAM) in tumors with the highest protumorigenesis signatures, highlighting their potential role in glioma progression. We also investigated the T-cell trajectory and identified the aryl hydrocarbon receptor (AHR) as a regulator of T-cell dysfunction, providing a potential target for glioma immunotherapy. We further demonstrated that knockout of AHR decreased chimeric antigen receptor (CAR) T-cell exhaustion and improved CAR T-cell antitumor efficacy both in vitro and in vivo. Finally, we explored intercellular communication mediated by ligand-receptor interactions within the tumor microenvironment and PBMCs and revealed the unique cellular interactions present in the tumor microenvironment. Taken together, our study provides a comprehensive immune landscape of IDH-WT high-grade gliomas and offers potential drug targets for glioma immunotherapy.
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Affiliation(s)
- Xiaojuan Ran
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Jian Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linchao Chen
- Department of Neurosurgery, Huashan Hospital Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen Xia
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Yin Wang
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Chengfang Sun
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Guo
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Peng Lin
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Fuyi Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chun Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianguo Zhou
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
| | - Chongran Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qichang Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianzhu Ma
- Institute of AI Industrial Research, Tsinghua University, Beijing, China
| | - Zhiyong Qin
- Department of Neurosurgery, Huashan Hospital Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiangdong Zhu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qi Xie
- Westlake Disease Modeling Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Basic Medical Sciences, Westlake Institute of Advanced Study, Hangzhou, Zhejiang, China
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113
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Zheng X, Chen J, Deng M, Ning K, Peng Y, Liu Z, Li X, Zhou Z, Tang H, Li Y, Kang T, Liu Z. G3BP1 and SLU7 Jointly Promote Immune Evasion by Downregulating MHC-I via PI3K/Akt Activation in Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305922. [PMID: 38084438 PMCID: PMC10870071 DOI: 10.1002/advs.202305922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/13/2023] [Indexed: 02/17/2024]
Abstract
Immune checkpoint inhibitors (ICIs) show promise as second-line treatment for advanced bladder cancer (BLCA); however, their responsiveness is limited by the immune evasion mechanisms in tumor cells. This study conduct a Cox regression analysis to screen mRNA-binding proteins and reveals an association between Ras GTPase-activating protein-binding protein 1 (G3BP1) and diminished effectiveness of ICI therapy in patients with advanced BLCA. Subsequent investigation demonstrates that G3BP1 enhances immune evasion in BLCA cells by downregulating major histocompatibility complex class I (MHC-I) through phosphoinositide 3-kinase (PI3K)/Akt signaling activation. Mechanistically, G3BP1 interacts with splicing factor synergistic lethal with U5 snRNA 7 (SLU7) to form a complex with poly(A)-binding protein cytoplasmic 1 and eukaryotic translation initiation factor 4 gamma 1. This complex stabilizes the closed-loop structure of the mRNAs of class IA PI3Ks and consequently facilitates their translation and stabilization, thereby activating PI3K/Akt signaling to downregulate MHC-I. Consistently, targeting G3BP1 with epigallocatechin gallate (EGCG) impedes immune evasion and sensitizes BLCA cells to anti-programmed cell death (PD)-1 antibodies in mice. Thus, G3BP1 and SLU7 collaboratively contribute to immune evasion in BLCA, indicating that EGCG is a precision therapeutic agent to enhance the effectiveness of anti-PD-1 therapy.
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Affiliation(s)
- Xianchong Zheng
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jiawei Chen
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of UrologyShunde HospitalSouthern Medical University (The First People's Hospital of Shunde Foshan)Foshan528000P. R. China
| | - Minhua Deng
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Kang Ning
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yulu Peng
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Zhenhua Liu
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Xiangdong Li
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Zhaohui Zhou
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Huancheng Tang
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Yaoying Li
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Zhuowei Liu
- Department of UrologySun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- State Key Laboratory of Oncology in South ChinaGuangdong Provincial Clinical Research Center for CancerSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of UrologySun Yat‐sen University Cancer Center Gansu HospitalLanzhou730000P. R. China
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114
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Romagnoli G, D'Alessandris QG, Capone I, Tavilla A, Canini I, Lapenta C, Buccarelli M, Giordano M, Tirelli V, Sanchez M, Fragale A, Giannetti S, Di Bonaventura R, Lauretti L, Biffoni M, Ricci-Vitiani L, Pallini R, Gabriele L. CD8+CD103+PD1+TIM3+ T cells in glioblastoma microenvironment correlate with prognosis. Immunology 2024; 171:198-211. [PMID: 37884280 DOI: 10.1111/imm.13710] [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: 07/27/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Glioblastoma, isocitrate dehydrogenase-wildtype (GB), is the most common and aggressive primary brain malignancy with poor outcome. Immune checkpoint inhibitors (ICIs) have been tested in GB and, despite disappointing results, the identification of a small subgroup of responders underlies the need to improve our understanding of the tumour microenvironment (TME) immunity. This study aimed to determine whether the expression of selected immune checkpoints on tissue-resident memory T cells (Trm) may predict patient outcome. We conducted a single cohort observational study. Tumour samples were collected from 45 patients with histologically confirmed GB (WHO grade 4) and processed to obtain single-cell suspensions. Patients were assessed for the correlation of Trm phenotype with overall survival (OS) or progression-free survival (PFS) using multiparametric flow cytometry and uni/multivariate analyses. Levels of Trm expressing programmed cell death protein 1 (PD1) and T cell immunoglobulin and mucin domain-containing protein 3 (TIM3) were found to be linked to clinical outcome. Low frequency of Trm expressing PD1 or TIM3 or both markers defined subgroups as independent positive prognostic factors for patient survival. On multivariate analysis, low CD8+CD103+PD1+TIM3+ Trm and Karnofsky performance status (KPS) ≥70 were confirmed to be the most predictive independent factors associated with longer OS (hazard ratios-HR [95%CI]: 0.14 [0.04-0.52] p < 0.001, 0.39 [0.16-0.96] p = 0.04, respectively). The CD8+CD103+ Trm subgroups were also age-related predictors for survival in GB.
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Affiliation(s)
- Giulia Romagnoli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Quintino Giorgio D'Alessandris
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Imerio Capone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Tavilla
- National Centre for Disease Prevention and Health Promotion, Istituto Superiore di Sanità, Rome, Italy
| | - Irene Canini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Caterina Lapenta
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Martina Giordano
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | | | - Alessandra Fragale
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Giannetti
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rina Di Bonaventura
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Liverana Lauretti
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Pallini
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Lucia Gabriele
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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Suma S, Suehara Y, Fujisawa M, Abe Y, Hattori K, Makishima K, Sakamoto T, Sawa A, Bando H, Kaji D, Sugio T, Kato K, Akashi K, Matsue K, Carreras J, Nakamura N, Suzuki A, Suzuki Y, Ito K, Shiiba H, Chiba S, Sakata-Yanagimoto M. Tumor heterogeneity and immune-evasive T follicular cell lymphoma phenotypes at single-cell resolution. Leukemia 2024; 38:340-350. [PMID: 38012392 PMCID: PMC10844096 DOI: 10.1038/s41375-023-02093-7] [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: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
T follicular helper (TFH) cell lymphomas (TFHLs) are characterized by TFH-like properties and accompanied by substantial immune-cell infiltration into tumor tissues. Nevertheless, the comprehensive understanding of tumor-cell heterogeneity and immune profiles of TFHL remains elusive. To address this, we conducted single-cell transcriptomic analysis on 9 lymph node (LN) and 16 peripheral blood (PB) samples from TFHL patients. Tumor cells were divided into 5 distinct subclusters, with significant heterogeneity observed in the expression levels of TFH markers. Copy number variation (CNV) and trajectory analyses indicated that the accumulation of CNVs, together with gene mutations, may drive the clonal evolution of tumor cells towards TFH-like and cell proliferation phenotypes. Additionally, we identified a novel tumor-cell-specific marker, PLS3. Notably, we found a significant increase in exhausted CD8+ T cells with oligoclonal expansion in TFHL LNs and PB, along with distinctive immune evasion characteristics exhibited by infiltrating regulatory T, myeloid, B, and natural killer cells. Finally, in-silico and spatial cell-cell interaction analyses revealed complex networking between tumor and immune cells, driving the formation of an immunosuppressive microenvironment. These findings highlight the remarkable tumor-cell heterogeneity and immunoevasion in TFHL beyond previous expectations, suggesting potential roles in treatment resistance.
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Affiliation(s)
- Sakurako Suma
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Yasuhito Suehara
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Manabu Fujisawa
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Yoshiaki Abe
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Keiichiro Hattori
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenichi Makishima
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Tatsuhiro Sakamoto
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Aya Sawa
- Department of Breast-Thyroid-Endocrine Surgery, University of Tsukuba Hospital, Tsukuba, Japan
| | - Hiroko Bando
- Department of Breast-Thyroid-Endocrine Surgery, University of Tsukuba Hospital, Tsukuba, Japan
| | - Daisuke Kaji
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Takeshi Sugio
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, USA
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Kosei Matsue
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Joaquim Carreras
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Naoya Nakamura
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, Kashiwa, Japan
| | - Ken Ito
- Oncology Business Unit, Eisai Co., Ltd., Tsukuba, Japan
| | - Hiroyuki Shiiba
- Oncology Department, Medical Head Quarters, Eisai Co., Ltd., Tokyo, Japan
| | - Shigeru Chiba
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mamiko Sakata-Yanagimoto
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan.
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan.
- Division of Advanced Hemato-Oncology, Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.
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116
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Gao H, Sun H, He A, Liu H, Zhang Z, Li D, Mao W, Qian J. Single-cell combined bioinformatics analysis: construction of immune cluster and risk prognostic model in kidney renal clear cells based on CD8 + T cell-associated genes. Eur J Med Res 2024; 29:89. [PMID: 38291496 PMCID: PMC10825992 DOI: 10.1186/s40001-024-01689-8] [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: 12/03/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Kidney cancer is an immunogenic solid tumor, characterized by high tumor burden and infiltration of CD8+ T cells. Although immunotherapy targeting the PD1/CTLA-4 axis has demonstrated excellent clinical efficacy, clinical outcomes in most patients are poor. METHODS We used the RNA sequencing data from the GEO database for KIRC GSE121636 and normal kidney tissue GSE131685, and performed single-cell analysis for cluster identification, pathway enrichment, and CD8+ T cell-associated gene identification. Subsequently, the significance of different CD8+ T-cell associated gene subtypes was elucidated by consensus clustering, pathway analysis, mutated gene analysis, and KIRC immune microenvironment analysis in the TCGA-KIRC disease cohort. Single gene analysis identified LAG3 as the most critical CD8+ T-cell-associated gene and its function was verified by cell phenotype and immunohistochemistry in KIRC. RESULTS In the present study, CD8+ T-cell associated genes in KIRC were screened, including GZMK, CD27, CCL4L2, FXYD2, LAG3, RGS1, CST7, DUSP4, CD8A, and TRBV20-1 and an immunological risk prognostic model was constructed (risk score = - 0.291858656434841*GZMK - 0.192758342489394*FXYD2 + 0.625023643446193*LAG3 + 0.161324477181591*RGS1 - 0.380169045328895*DUSP4 - 0.107221347575037*TRBV20-1). LAG3 was identified and proved as the most critical CD8+ T cell-associated gene in KIRC. CONCLUSION We proposed and constructed an immunological risk prognostic model for CD8+ T cell-associated genes and identified LAG3 as a pivotal gene for KIRC progression and CD8+ T-cell infiltration. The model comprehensively explained the immune microenvironment and provided novel immune-related therapeutic targets and biomarkers in KIRC.
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Affiliation(s)
- Haifeng Gao
- Department of Urology, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hang Sun
- Department of Urology, Binhai County People's Hospital, Yancheng, 224000, China
| | - Aifeng He
- Department of Emergency, Binhai County People's Hospital, Yancheng, 224000, China
| | - Hui Liu
- Department of Urology, Binhai County People's Hospital, Yancheng, 224000, China
| | - Zihang Zhang
- Department of Pathology, Binhai County People's Hospital, Yancheng, 224000, China
| | - Dongling Li
- Department of Nephrology, Binhai County People's Hospital, Yancheng, 224000, China
| | - Weipu Mao
- Department of Urology, Zhongda Hospital Southeast University, 87 Dingjia Bridge Hunan Road, Nanjing, 210009, China.
| | - Jinke Qian
- Department of Urology, Binhai County People's Hospital, Yancheng, 224000, China.
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117
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Andreatta M, Hérault L, Gueguen P, Gfeller D, Berenstein AJ, Carmona SJ. Semi-supervised integration of single-cell transcriptomics data. Nat Commun 2024; 15:872. [PMID: 38287014 PMCID: PMC10825117 DOI: 10.1038/s41467-024-45240-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: 07/25/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Batch effects in single-cell RNA-seq data pose a significant challenge for comparative analyses across samples, individuals, and conditions. Although batch effect correction methods are routinely applied, data integration often leads to overcorrection and can result in the loss of biological variability. In this work we present STACAS, a batch correction method for scRNA-seq that leverages prior knowledge on cell types to preserve biological variability upon integration. Through an open-source benchmark, we show that semi-supervised STACAS outperforms state-of-the-art unsupervised methods, as well as supervised methods such as scANVI and scGen. STACAS scales well to large datasets and is robust to incomplete and imprecise input cell type labels, which are commonly encountered in real-life integration tasks. We argue that the incorporation of prior cell type information should be a common practice in single-cell data integration, and we provide a flexible framework for semi-supervised batch effect correction.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Léonard Hérault
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Paul Gueguen
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ariel J Berenstein
- Laboratorio de Biología Molecular, División Patología, Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Buenos Aires, C1425EFD, Argentina
| | - Santiago J Carmona
- Department of Oncology, Lausanne Branch, Ludwig Institute for Cancer Research, CHUV and University of Lausanne, 1011, Lausanne, Switzerland.
- AGORA Cancer Research Center, 1005, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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118
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Yamakawa M, Rexach JE. Cell States and Interactions of CD8 T Cells and Disease-Enriched Microglia in Human Brains with Alzheimer's Disease. Biomedicines 2024; 12:308. [PMID: 38397909 PMCID: PMC10886701 DOI: 10.3390/biomedicines12020308] [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: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
Alzheimer's disease (AD) is a multi-stage neurodegenerative disorder characterized by beta-amyloid accumulation, hyperphosphorylated Tau deposits, neurodegeneration, neuroinflammation, and cognitive impairment. Recent studies implicate CD8 T cells as neuroimmune responders to the accumulation of AD pathology in the brain and potential contributors to toxic neuroinflammation. However, more evidence is needed to understand lymphocytes in disease, including their functional states, molecular mediators, and interacting cell types in diseased brain tissue. The scarcity of lymphocytes in brain tissue samples has limited the unbiased profiling of disease-associated cell types, cell states, drug targets, and relationships to common AD genetic risk variants based on transcriptomic analyses. However, using recent large-scale, high-quality single-nuclear sequencing datasets from over 84 Alzheimer's disease and control cases, we leverage single-nuclear RNAseq data from 800 lymphocytes collected from 70 individuals to complete unbiased molecular profiling. We demonstrate that effector memory CD8 T cells are the major lymphocyte subclass enriched in the brain tissues of individuals with AD dementia. We define disease-enriched interactions involving CD8 T cells and multiple brain cell subclasses including two distinct microglial disease states that correlate, respectively, to beta-amyloid and tau pathology. We find that beta-amyloid-associated microglia are a major hub of multicellular cross-talk gained in disease, including interactions involving both vulnerable neuronal subtypes and CD8 T cells. We reproduce prior reports that amyloid-response microglia are depleted in APOE4 carriers. Overall, these human-based studies provide additional support for the potential relevance of effector memory CD8 T cells as a lymphocyte population of interest in AD dementia and provide new candidate interacting partners and drug targets for further functional study.
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Affiliation(s)
| | - Jessica E. Rexach
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA;
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119
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Lin X, Tang S, Guo Y, Tang R, Li Z, Pan X, Chen G, Qiu L, Dong X, Zhang L, Liu X, Cai Z, Xie B. Personalized neoantigen vaccine enhances the therapeutic efficacy of bevacizumab and anti-PD-1 antibody in advanced non-small cell lung cancer. Cancer Immunol Immunother 2024; 73:26. [PMID: 38280084 PMCID: PMC10821847 DOI: 10.1007/s00262-023-03598-x] [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: 10/20/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024]
Abstract
Clinically, a considerable number of non-small cell lung cancer (NSCLC) patients are unable to receive or resist chemotherapy, and the efficacy of non-chemotherapy treatment strategies based on anti-angiogenic agents combined with immune checkpoint blockade is still unsatisfactory. Neoantigen vaccine, based on personalized tumor DNA mutations, could elicit tumor specific T cell infiltration into the tumor site, exerting potent anti-tumor efficacy. Here, we evaluated the feasibility and safety of a new antitumor strategy by adding neoantigen vaccine to the regimen of bevacizumab and anti-PD-1 antibody. Firstly, 7 novel immunogenic neoantigen peptides were identified and developed for neoantigen vaccine (LLCvac), which can elicit strong antitumor immune response in vivo. Then, in orthotopic lung cancer model, LLCvac further combining with bevacizumab and anti-PD-1 antibody exerted a stronger antitumor effect, exhibiting significant decrease of tumor volume without obvious toxicity. Furthermore, tumor immune microenvironment assessment also showed that the proportion of neoantigen-specific T cells in blood could be induced dramatically by the combined therapy. And a large amount of neoantigen-specific Ki67-positive CD8+ T cells were found in tumor tissues, which infiltrated tumor tissues effectively to kill tumor cells expressing identified neoantigens. Overall, these results suggested that this combined therapy could safely induce robust antitumor efficacy, serving as an effective chemotherapy-free strategy for NSCLC treatment.
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Affiliation(s)
- Xiuhua Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Shichuan Tang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Yutong Guo
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Ruijing Tang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Xinting Pan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Liman Qiu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Ling Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Fujian Key Laboratory of Integrative Medicine On Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China.
| | - Baosong Xie
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China.
- Department of Pulmonary and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, China.
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Ahluwalia P, Ballur K, Leeman T, Vashisht A, Singh H, Omar N, Mondal AK, Vaibhav K, Baban B, Kolhe R. Incorporating Novel Technologies in Precision Oncology for Colorectal Cancer: Advancing Personalized Medicine. Cancers (Basel) 2024; 16:480. [PMID: 38339232 PMCID: PMC10854941 DOI: 10.3390/cancers16030480] [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: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most heterogeneous and deadly diseases, with a global incidence of 1.5 million cases per year. Genomics has revolutionized the clinical management of CRC by enabling comprehensive molecular profiling of cancer. However, a deeper understanding of the molecular factors is needed to identify new prognostic and predictive markers that can assist in designing more effective therapeutic regimens for the improved management of CRC. Recent breakthroughs in single-cell analysis have identified new cell subtypes that play a critical role in tumor progression and could serve as potential therapeutic targets. Spatial analysis of the transcriptome and proteome holds the key to unlocking pathogenic cellular interactions, while liquid biopsy profiling of molecular variables from serum holds great potential for monitoring therapy resistance. Furthermore, gene expression signatures from various pathways have emerged as promising prognostic indicators in colorectal cancer and have the potential to enhance the development of equitable medicine. The advancement of these technologies for identifying new markers, particularly in the domain of predictive and personalized medicine, has the potential to improve the management of patients with CRC. Further investigations utilizing similar methods could uncover molecular subtypes specific to emerging therapies, potentially strengthening the development of personalized medicine for CRC patients.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kalyani Ballur
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Tiffanie Leeman
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kumar Vaibhav
- Department of Neurosurgery, Augusta University, Augusta, GA 30912, USA;
| | - Babak Baban
- Departments of Neurology and Surgery, Augusta University, Augusta, GA 30912, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
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Nersesian S, Arseneau RJ, Mejia JP, Lee SN, Westhaver LP, Griffiths NW, Grantham SR, Meunier L, Communal L, Mukherjee A, Mes-Masson AM, Arnason T, Nelson BH, Boudreau JE. Improved overall survival in patients with high-grade serous ovarian cancer is associated with CD16a+ immunologic neighborhoods containing NK cells, T cells and macrophages. Front Immunol 2024; 14:1307873. [PMID: 38318505 PMCID: PMC10838965 DOI: 10.3389/fimmu.2023.1307873] [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: 10/05/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Background For patients with high grade serous carcinoma of the ovary (HGSC), survival rates have remained static for the last half century. Despite the presence of tumor mutations and infiltration of immune cells, existing immunotherapies have achieved little success against HGSC. These observations highlight a gap in the understanding of how the immune system functions and interacts within HGSC tumors. Methods We analyzed duplicate core samples from 939 patients with HGSC to understand patterns of immune cell infiltration, localization, and associations with clinical features. We used high-parameter immunohistochemical/Opal multiplex, digital pathology, computational biology, and multivariate analysis to identify immune cell subsets and their associations with HGSC tumors. Results We defined six patterns of cellular infiltration by spatially restricted unsupervised clustering of cell subsets. Each pattern was represented to some extent in most patient samples, but their specific distributions differed. Overall (OS) and progression-free survival (PFS) corresponded with higher infiltration of CD16a+ cells, and their co-localization with macrophages, T cells, NK cells, in one of six cellular neighborhoods that we defined with our spatial assessment. Conclusions Immune cell neighborhoods containing CD16a+ cells are associated with improved OS and PFS for patients with HGSC. Patterns of immunologic neighborhoods differentiate patient outcomes, and could inform future, more precise approaches to treatment.
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Affiliation(s)
- Sarah Nersesian
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Riley J. Arseneau
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Jorge P. Mejia
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Stacey N. Lee
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | | | | | | | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Laudine Communal
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
| | | | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l’Université de Montréal and Institut du cancer de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Thomas Arnason
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Pathology & Laboratory Medicine, QEII Health Sciences Centre, Nova Scotia Health (Central Zone), Halifax, NS, Canada
| | - Brad H. Nelson
- Deeley Research Centre, British Columbia Cancer Research Institute, Victoria, BC, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jeanette E. Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
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Li J, Hu H, Qin G, Bai F, Wu X, Ke H, Zhang J, Xie Y, Wu Z, Fu Y, Zheng H, Gong L, Xie Z, Deng Y. Biomarkers of Pathologic Complete Response to Neoadjuvant Immunotherapy in Mismatch Repair-Deficient Colorectal Cancer. Clin Cancer Res 2024; 30:368-378. [PMID: 37906636 DOI: 10.1158/1078-0432.ccr-23-2213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/13/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
PURPOSE Immune checkpoint inhibitors (ICI) have become the standard of care for patients with mismatch repair-deficient/microsatellite instability-high (dMMR/MSI-H) colorectal cancer. However, biomarkers of response to ICI are still lacking. EXPERIMENTAL DESIGN Forty-two patients with dMMR colorectal cancer treated with neoadjuvant PD-1 blockade were prospectively enrolled. To identify biomarkers of pathologic complete response (pCR) to neoadjuvant therapy, we analyzed genomic and transcriptomic profiles based on next-generation sequencing, and immune cell density based on multiplex immunofluorescence (mIF) staining. An integrated analysis of single-cell RNA sequencing from our previous study and GSE178341, as well as mIF was performed to further explore the significance of the tumor microenvironment (TME) on pCR response. RESULTS The tumor mutation burden of both tumor tissue and plasma blood samples was comparable between the pCR and non-pCR groups, while HLA-DQA1 and HLA-DQB1 were significantly overexpressed in the pCR group. Gene signature enrichment analysis showed that pathways including T-cell receptor pathway, antigen presentation pathway were significantly enriched in the pCR group. In addition, higher pre-existing CD8+ T-cell density was associated with pCR response (767.47 per.mm2 vs. 326.64 per.mm2, P = 0.013 Wilcoxon test). Further integrated analysis showed that CD8+ T cells with low PD-1 expression (PD-1lo CD8+ T cells) expressing high levels of TRGC2, CD160, and KLRB1 and low levels of proliferated and exhausted genes were significantly associated with pCR response. CONCLUSIONS Immune-associated transcriptomic features, particularly CD8+ T cells were associated with pCR response to ICI in dMMR colorectal cancer. Heterogeneity of TME within dMMR colorectal cancer may help to discriminate patients with complete response to neoadjuvant ICI.
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Affiliation(s)
- Jianxia Li
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huabin Hu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ge Qin
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fan Bai
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianrui Wu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haoxian Ke
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianwei Zhang
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuqian Xie
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zehua Wu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yang Fu
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Deng
- Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Katopodi T, Petanidis S, Anestakis D, Charalampidis C, Chatziprodromidou I, Floros G, Eskitzis P, Zarogoulidis P, Koulouris C, Sevva C, Papadopoulos K, Dagher M, Karakousis VA, Varsamis N, Theodorou V, Mystakidou CM, Vlassopoulos K, Kosmidis S, Katsios NI, Farmakis K, Kosmidis C. Tumor cell metabolic reprogramming and hypoxic immunosuppression: driving carcinogenesis to metastatic colonization. Front Immunol 2024; 14:1325360. [PMID: 38292487 PMCID: PMC10824957 DOI: 10.3389/fimmu.2023.1325360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
A significant factor in the antitumor immune response is the increased metabolic reprogramming of immunological and malignant cells. Increasing data points to the fact that cancer metabolism affects not just cancer signaling, which is essential for maintaining carcinogenesis and survival, but also the expression of immune cells and immune-related factors such as lactate, PGE2, arginine, IDO, which regulate the antitumor immune signaling mechanism. In reality, this energetic interaction between the immune system and the tumor results in metabolic competition in the tumor ecosystem, limiting the amount of nutrients available and causing microenvironmental acidosis, which impairs the ability of immune cells to operate. More intriguingly, different types of immune cells use metabolic reprogramming to keep the body and self in a state of homeostasis. The process of immune cell proliferation, differentiation, and performance of effector functions, which is crucial to the immune response, are currently being linked to metabolic reprogramming. Here, we cover the regulation of the antitumor immune response by metabolic reprogramming in cancer cells and immune cells as well as potential strategies for metabolic pathway targeting in the context of anticancer immunotherapy. We also discuss prospective immunotherapy-metabolic intervention combinations that might be utilized to maximize the effectiveness of current immunotherapy regimes.
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Affiliation(s)
- Theodora Katopodi
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Petanidis
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Doxakis Anestakis
- Department of Anatomy, Medical School, University of Cyprus, Nicosia, Cyprus
| | | | | | - George Floros
- Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
| | | | - Paul Zarogoulidis
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Charilaos Koulouris
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christina Sevva
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Papadopoulos
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Marios Dagher
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Nikolaos Varsamis
- Department of Surgery, Interbalkan Medical Center, Thessaloniki, Greece
| | - Vasiliki Theodorou
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysi Maria Mystakidou
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Vlassopoulos
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stylianos Kosmidis
- Department of Medicine, Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | - Konstantinos Farmakis
- Pediatric Surgery Clinic, General Hospital of Thessaloniki “G. Gennimatas”, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christoforos Kosmidis
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Mangelinck A, Dubuisson A, Becht E, Dromaint-Catesson S, Fasquel M, Provost N, Walas D, Darville H, Galizzi JP, Lefebvre C, Blanc V, Lombardi V. Characterization of CD4 + and CD8 + T cells responses in the mixed lymphocyte reaction by flow cytometry and single cell RNA sequencing. Front Immunol 2024; 14:1320481. [PMID: 38283342 PMCID: PMC10820991 DOI: 10.3389/fimmu.2023.1320481] [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: 10/12/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Background The Mixed Lymphocyte Reaction (MLR) consists in the allogeneic co-culture of monocytes derived dendritic cells (MoDCs) with T cells from another donor. This in vitro assay is largely used for the assessment of immunotherapy compounds. Nevertheless, the phenotypic changes associated with lymphocyte responsiveness under MLR have never been thoroughly evaluated. Methods Here, we used multiplex cytokine and chemokine assays, multiparametric flow cytometry and single cell RNA sequencing to deeply characterize T cells activation and function in the context of CD4+- and CD8+-specific MLR kinetics. Results We showed that CD4+ and CD8+ T cells in MLR share common classical markers of response such as polyfunctionality, increased proliferation and CD25 expression but differ in their kinetics and amplitude of activation as well as their patterns of cytokines secretion and immune checkpoints expression. The analysis of immunoreactive Ki-67+CD25+ T cells identified PBK, LRR1 and MYO1G as new potential markers of MLR response. Using cell-cell communication network inference and pathway analysis on single cell RNA sequencing data, we also highlighted key components of the immunological synapse occurring between T cells and the stimulatory MoDCs together with downstream signaling pathways involved in CD4+ and CD8+ T cells activation. Conclusion These results provide a deep understanding of the kinetics of the MLR assay for CD4+ or CD8+ T cells and may allow to better characterize compounds impacting MLR and eventually identify new strategies for immunotherapy in cancer.
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125
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Wang Y, He S, Calendo G, Bui T, Tian Y, Lee CY, Zhou Y, Zhao X, Abraham C, Mo W, Chen M, Sanders-Braggs R, Madzo J, Issa JP, Hexner EO, Wiest DL, Reshef R, Xue HH, Zhang Y. Tissue-infiltrating alloreactive T cells require Id3 to deflect PD-1-mediated immune suppression during GVHD. Blood 2024; 143:166-177. [PMID: 37871574 PMCID: PMC10797551 DOI: 10.1182/blood.2023021126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/25/2023] Open
Abstract
ABSTRACT Persisting alloreactive donor T cells in target tissues are a determinant of graft-versus-host disease (GVHD), but the transcriptional regulators that control the persistence and function of tissue-infiltrating T cells remain elusive. We demonstrate here that Id3, a DNA-binding inhibitor, is critical for sustaining T-cell responses in GVHD target tissues in mice, including the liver and intestine. Id3 loss results in aberrantly expressed PD-1 in polyfunctional T helper 1 (Th1) cells, decreased tissue-infiltrating PD-1+ polyfunctional Th1 cell numbers, impaired maintenance of liver TCF-1+ progenitor-like T cells, and inhibition of GVHD. PD-1 blockade restores the capacity of Id3-ablated donor T cells to mediate GVHD. Single-cell RNA-sequencing analysis revealed that Id3 loss leads to significantly decreased CD28- and PI3K/AKT-signaling activity in tissue-infiltrating polyfunctional Th1 cells, an indicator of active PD-1/PD-L1 effects. Id3 is also required for protecting CD8+ T cells from the PD-1 pathway-mediated suppression during GVHD. Genome-wide RNA-sequencing analysis reveals that Id3 represses transcription factors (e.g., Nfatc2, Fos, Jun, Ets1, and Prdm1) that are critical for PD-1 transcription, exuberant effector differentiation, and interferon responses and dysfunction of activated T cells. Id3 achieves these effects by restraining the chromatin accessibility for these transcription factors. Id3 ablation in donor T cells preserved their graft vs tumor effects in mice undergoing allogeneic hematopoietic stem cell transplantation. Furthermore, CRISPR/Cas9 knockout of ID3 in human CD19-directed chimeric antigen receptor T cells retained their antitumor activity in NOD/SCID/IL2Rg-/- mice early after administration. These findings identify that ID3 is an important target to reduce GVHD, and the gene-editing program of ID3 may have broad implications in T-cell-based immunotherapy.
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Affiliation(s)
- Ying Wang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Shan He
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | | | - Tien Bui
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yuanyuan Tian
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Che Young Lee
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yan Zhou
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Ciril Abraham
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Wenbin Mo
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Mimi Chen
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | | | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, NJ
| | | | - Elizabeth O. Hexner
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David L. Wiest
- Fox Chase Cancer Center, Temple University, Philadelphia, PA
| | - Ran Reshef
- Blood and Marrow Transplantation and Cell Therapy Program, Columbia University Irving Medical Center, New York, NY
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
| | - Yi Zhang
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ
- Fels Institute and Department of Cancer Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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Peng Y, Dong Y, Sun Q, Zhang Y, Zhou X, Li X, Ma Y, Liu X, Li R, Guo F, Guo L. Integrative analysis of single-cell and bulk RNA-sequencing data revealed T cell marker genes based molecular sub-types and a prognostic signature in lung adenocarcinoma. Sci Rep 2024; 14:964. [PMID: 38200058 PMCID: PMC10781781 DOI: 10.1038/s41598-023-50787-w] [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: 04/28/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Immunotherapy has emerged as a promising modality for addressing advanced or conventionally drug-resistant malignancies. When it comes to lung adenocarcinoma (LUAD), T cells have demonstrated significant influence on both antitumor activity and the tumor microenvironment. However, their specific contributions remain largely unexplored. This investigation aimed to delineate molecular subtypes and prognostic indicators founded on T cell marker genes, thereby shedding light on the significance of T cells in LUAD prognosis and precision treatment. The cellular phenotypes were identified by scrutinizing the single-cell data obtained from the GEO repository. Subsequently, T cell marker genes derived from single-cell sequencing analyses were integrated with differentially expressed genes from the TCGA repository to pinpoint T cell-associated genes. Utilizing Cox analysis, molecular subtypes and prognostic signatures were established and subsequently verified using the GEO dataset. The ensuing molecular and immunological distinctions, along with therapy sensitivity between the two sub-cohorts, were examined via the ESTIMATE, CIBERSORT, and ssGSEA methodologies. Compartmentalization, somatic mutation, nomogram development, chemotherapy sensitivity prediction, and potential drug prediction analyses were also conducted according to the risk signature. Additionally, real-time qPCR and the HPA database corroborated the mRNA and protein expression patterns of signature genes in LUAD tissues. In summary, this research yielded an innovative T cell marker gene-based signature with remarkable potential to prognosis and anticipate immunotherapeutic outcomes in LUAD patients.
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Affiliation(s)
- Yueling Peng
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Yafang Dong
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, 030001, China
| | - Qihui Sun
- South China University of Technology, Guangzhou, 510006, China
| | - Yue Zhang
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Xiangyang Zhou
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Cell Biology, School of Basic Medicine, Shanxi Medical University, Taiyuan, 030001, China
| | - Xiaoyang Li
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Yuehong Ma
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Xingwei Liu
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Rongshan Li
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China
| | - Fengjie Guo
- South China University of Technology, Guangzhou, 510006, China.
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| | - Lili Guo
- Shanxi Provincial Key Laboratory of Kidney Disease, Shanxi Provincial People's Hospital of Shanxi Medical University, Taiyuan, 030012, Shanxi, China.
- Department of Nephrology, Shanxi Provincial People's Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, 030012, China.
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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Lacouture C, Chaves B, Guipouy D, Houmadi R, Duplan-Eche V, Allart S, Destainville N, Dupré L. LFA-1 nanoclusters integrate TCR stimulation strength to tune T-cell cytotoxic activity. Nat Commun 2024; 15:407. [PMID: 38195629 PMCID: PMC10776856 DOI: 10.1038/s41467-024-44688-3] [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: 02/05/2023] [Accepted: 12/29/2023] [Indexed: 01/11/2024] Open
Abstract
T-cell cytotoxic function relies on the cooperation between the highly specific but poorly adhesive T-cell receptor (TCR) and the integrin LFA-1. How LFA-1-mediated adhesion may scale with TCR stimulation strength is ill-defined. Here, we show that LFA-1 conformation activation scales with TCR stimulation to calibrate human T-cell cytotoxicity. Super-resolution microscopy analysis reveals that >1000 LFA-1 nanoclusters provide a discretized platform at the immunological synapse to translate TCR engagement and density of the LFA-1 ligand ICAM-1 into graded adhesion. Indeed, the number of high-affinity conformation LFA-1 nanoclusters increases as a function of TCR triggering strength. Blockade of LFA-1 conformational activation impairs adhesion to target cells and killing. However, it occurs at a lower TCR stimulation threshold than lytic granule exocytosis implying that it licenses, rather than directly controls, the killing decision. We conclude that the organization of LFA-1 into nanoclusters provides a calibrated system to adjust T-cell killing to the antigen stimulation strength.
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Affiliation(s)
- Claire Lacouture
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Beatriz Chaves
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
- National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- Computational Modeling Group, Oswaldo Cruz Foundation (Fiocruz), Eusébio, Brazil
| | - Delphine Guipouy
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Raïssa Houmadi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Valérie Duplan-Eche
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Sophie Allart
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Loïc Dupré
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France.
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.
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Hosseinalizadeh H, Hussain QM, Poshtchaman Z, Ahsan M, Amin AH, Naghavi S, Mahabady MK. Emerging insights into keratin 7 roles in tumor progression and metastasis of cancers. Front Oncol 2024; 13:1243871. [PMID: 38260844 PMCID: PMC10800941 DOI: 10.3389/fonc.2023.1243871] [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: 06/21/2023] [Accepted: 10/26/2023] [Indexed: 01/24/2024] Open
Abstract
Keratin 7 (KRT7), also known as cytokeratin-7 (CK-7) or K7, constitutes the principal constituent of the intermediate filament cytoskeleton and is primarily expressed in the simple epithelia lining the cavities of the internal organs, glandular ducts, and blood vessels. Various pathological conditions, including cancer, have been linked to the abnormal expression of KRT7. KRT7 overexpression promotes tumor progression and metastasis in different human cancers, although the mechanisms of these processes caused by KRT7 have yet to be established. Studies have indicated that the suppression of KRT7 leads to rapid regression of tumors, highlighting the potential of KRT7 as a novel candidate for therapeutic interventions. This review aims to delineate the various roles played by KRT7 in the progression and metastasis of different human malignancies and to investigate its prognostic significance in cancer treatment. Finally, the differential diagnosis of cancers based on the KRT7 is emphasized.
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Affiliation(s)
- Hamed Hosseinalizadeh
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | - Zahra Poshtchaman
- Department of Nursing, Esfarayen Faculty of Medical Sciences, Esfarayen, Iran
| | | | - Ali H. Amin
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Soroush Naghavi
- Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmood Khaksary Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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129
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Yang G, Cai S, Hu M, Li C, Yang L, Zhang W, Sun J, Sun F, Xing L, Sun X. Spatial features of specific CD103 +CD8 + tissue-resident memory T cell subsets define the prognosis in patients with non-small cell lung cancer. J Transl Med 2024; 22:27. [PMID: 38183111 PMCID: PMC10770937 DOI: 10.1186/s12967-023-04839-4] [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: 08/09/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Tissue-resident memory T (TRM) cells can reside in the tumor microenvironment and are considered the primary response cells to immunotherapy. Heterogeneity in functional status and spatial distribution may contribute to the controversial role of TRM cells but we know little about it. METHODS Through multiplex immunofluorescence (mIF) (CD8, CD103, PD-1, Tim-3, GZMB, CK), the quantity and spatial location of TRM cell subsets were recognized in the tissue from 274 patients with NSCLC after radical surgery. By integrating multiple machine learning methods, we constructed a TRM-based spatial immune signature (TRM-SIS) to predict the prognosis. Furthermore, we conducted a CD103-related gene set enrichment analysis (GSEA) and verified its finding by another mIF panel (CD8, CD103, CK, CD31, Hif-1α). RESULTS The density of TRM cells was significantly correlated with the expression of PD-1, Tim-3 and GZMB. Four types of TRM cell subsets was defined, including TRM1 (PD-1-Tim-3-TRM), TRM2 (PD-1+Tim-3-TRM), TRM3 (PD-1-Tim-3+TRM) and TRM4 (PD-1+Tim-3+TRM). The cytotoxicity of TRM2 was the strongest while that of TRM4 was the weakest. Compare with TRM1 and TRM2, TRM3 and TRM4 had better infiltration and stronger interaction with cancer cells. The TRM-SIS was an independent prognostic factor for disease-free survival [HR = 2.43, 95%CI (1.63-3.60), P < 0.001] and showed a better performance than the TNM staging system for recurrence prediction. Furthermore, by CD103-related GSEA and mIF validation, we found a negative association between tumor angiogenesis and infiltration of TRM cells. CONCLUSIONS These findings reveal a significant heterogeneity in the functional status and spatial distribution of TRM cells, and support it as a biomarker for the prognosis of NSCLC patients. Regulating TRM cells by targeting tumor angiogenesis may be a potential strategy to improve current immunotherapy.
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Affiliation(s)
- Guanqun Yang
- Shandong University Cancer Center, Shandong University, Jinan, Shandong, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Siqi Cai
- Shandong University Cancer Center, Shandong University, Jinan, Shandong, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Mengyu Hu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Chaozhuo Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- School of Clinical Medicine, Weifang Medical University, Weifang, Shandong, China
| | - Liying Yang
- Shandong University Cancer Center, Shandong University, Jinan, Shandong, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Wei Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jujie Sun
- Department of Pathology, Shandong Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, Shandong, China
| | - Fenghao Sun
- Department of Nuclear Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ligang Xing
- Shandong University Cancer Center, Shandong University, Jinan, Shandong, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaorong Sun
- Shandong University Cancer Center, Shandong University, Jinan, Shandong, China.
- Department of Nuclear Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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Meyer L, Eling N, Bodenmiller B. cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinformatics 2024; 25:9. [PMID: 38172724 PMCID: PMC10765786 DOI: 10.1186/s12859-023-05546-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: 08/07/2023] [Accepted: 10/27/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive visualization of multiplexed imaging data is crucial at any step of data analysis to facilitate quality control and the spatial exploration of single cell features. However, tools for interactive visualization of multiplexed imaging data are not available in the statistical programming language R. RESULTS Here, we describe cytoviewer, an R/Bioconductor package for interactive visualization and exploration of multi-channel images and segmentation masks. The cytoviewer package supports flexible generation of image composites, allows side-by-side visualization of single channels, and facilitates the spatial visualization of single-cell data in the form of segmentation masks. As such, cytoviewer improves image and segmentation quality control, the visualization of cell phenotyping results and qualitative validation of hypothesis at any step of data analysis. The package operates on standard data classes of the Bioconductor project and therefore integrates with an extensive framework for single-cell and image analysis. The graphical user interface allows intuitive navigation and little coding experience is required to use the package. We showcase the functionality and biological application of cytoviewer by analysis of an imaging mass cytometry dataset acquired from cancer samples. CONCLUSIONS The cytoviewer package offers a rich set of features for highly multiplexed imaging data visualization in R that seamlessly integrates with the workflow for image and single-cell data analysis. It can be installed from Bioconductor via https://www.bioconductor.org/packages/release/bioc/html/cytoviewer.html . The development version and further instructions can be found on GitHub at https://github.com/BodenmillerGroup/cytoviewer .
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Affiliation(s)
- Lasse Meyer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Nils Eling
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
- Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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Liang S, Dang B, Chen S, Mi H. Prognostic value and immunological role of cathepsin S gene in pan‑cancer. Oncol Lett 2024; 27:41. [PMID: 38108072 PMCID: PMC10722551 DOI: 10.3892/ol.2023.14175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
The cathepsin S (CTSS) gene encodes a lysine cysteine protease and serves an important role in the development of autoimmune diseases, inflammation and nervous system diseases. Furthermore, CTSS is implicated in tumor invasion and metastasis by the induction of tumor angiogenesis and the degradation of the tumor extracellular matrix. Nevertheless, the precise impact of CTSS on predicting pan-cancer prognosis and its influence on the tumor microenvironment and immune infiltration in human cancers remains unknown. This present study employed a comprehensive array of bioinformatic methods to evaluate the expression of CTSS and its associations with prognosis, clinicopathological characteristics, tumor microenvironment, tumor immune infiltration, tumor mutational burden and microsatellite instability across numerous cancer types. The current study demonstrated abnormal expression and distinct genomic alteration profiles of CTSS in many of the cancers tested. Furthermore, CTSS expression exhibited close associations with the prognosis of numerous cancers. High CTSS expression was significantly associated with better overall survival and disease-specific survival in bladder urothelial carcinoma (BLCA) and skin cutaneous melanoma (SKCM) but worse outcomes in brain lower grade glioma (LGG) and uveal melanoma (UVM). Moreover, CTSS demonstrated significant correlations with tumor mutational burden and microsatellite instability in 8 and 12 cancer types respectively, as well as different responses in immunotherapy sub-cohorts, especially in melanoma and bladder cancers. CTSS expression showed a positive correlation with stromal and immune cell scores in the four aforementioned cancers. Moreover, CTSS expression was correlated with the number of infiltrating CD8+ T cells, CD4+ T cells and macrophages. Conversely, CTSS was negatively associated with resting Mast cells, resting NK cells and resting memory CD4+ T cell infiltration in BLCA, SKCM and kidney renal clear cell carcinoma (KIRC). Furthermore, CTSS expression was correlated with immune-related gene expression, notably PDCD1, LAG3, PDCD1 and TIGIT in BLCA, KIRC, SKCM, LGG and UVM. Functional enrichment analysis suggested that CTSS could drive a dynamic adjustment of biological functions and pathways in BLCA, SKCM, LGG and UVM, including immune response regulating signaling pathways, regulation of lymphocyte activation and T cell receptor singling pathways. The current study suggested that CTSS could be an essential biomarker for prognosis and immune infiltration features in multiple cancers.
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Affiliation(s)
- Shengsheng Liang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Bowen Dang
- Department of Urology, The First People's Hospital of Yulin, Yulin, Guangxi Zhuang Autonomous Region 537000, P.R. China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hua Mi
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Wu Z, You C, Zhu Z, Wu W, Cao J, Xie Q, Deng C, Huang X, Hu S. SLA2 is a prognostic marker in HNSCC and correlates with immune cell infiltration in the tumor microenvironment. Eur Arch Otorhinolaryngol 2024; 281:427-440. [PMID: 37688682 PMCID: PMC10764518 DOI: 10.1007/s00405-023-08213-4] [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: 11/27/2022] [Accepted: 08/25/2023] [Indexed: 09/11/2023]
Abstract
PURPOSE To investigate Src-like adaptor 2 gene (SLA2) expression in head and neck squamous cell carcinoma (HNSCC), its potential prognostic value, and its effect on immune cell infiltration. METHODS Through a variety of bioinformatics analyses, we extracted and analyzed data sets from the Cancer Genome Atlas (TCGA), Tumor Immune Estimation Resource (TIMER), and Gene Expression Profile Interaction Analysis (GEPIA) to analyze the correlation between SLA2 and the prognosis, immune checkpoint, tumor microenvironment (TME) and immune cell infiltration of HNSCC, and to explore its potential oncogenic mechanism. To further explore the potential role of SLA2 in HNSCC by Gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. RESULTS SLA2 messenger ribonucleic acid (mRNA) levels were increased in HNSCC tumor tissues compared with normal tissues. In addition, we found that SLA2 may be an independent prognostic factor for HNSCC, and high SLA2 expression is associated with favorable prognosis in HNSCC. SLA2 expression was positively correlated with B cells, cluster of differentiation 8-positive T cells (CD8 + T cells), cluster of differentiation 4-positive T cells (CD4 + T cells), macrophages, neutrophil and dendritic cells infiltration. SLA2 has also been shown to co-express immune-related genes and immune checkpoints. Significant GO term analysis by Gene Set Enrichment Analysis (GSEA) indicated that genes correlated with SLA2 were located mainly in the side of membrane, receptor complex, secretory granule membrane, endocytic vesicle, membrane region, and endosome membrane, where they were involved in leukocyte cell-cell adhesion, response to interferon-gamma, and regulation of immune effector process. These related genes also served as antigen binding, cytokine receptor activity, phosphatidylinositol 3-kinase activity, peptide receptor activity, Src homology domain 3 (SH3) domain binding, and cytokine receptor binding. KEGG pathway analysis demonstrated that these genes related to SLA2 were mainly enriched in signal pathways, such as hematopoietic cell lineage, cell adhesion molecules (CAMs), natural killer cell mediated cytotoxicity, measles, and chemokine signaling pathway. CONCLUSIONS SLA2 is increased in HNSCC, and high SLA2 expression is associated with favorable prognosis. SLA2 may affect tumor development by regulating tumor infiltrating cells in TME. SLA2 may be a potential target for immunotherapy.
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Affiliation(s)
- Zhongbiao Wu
- Department of Otolaryngology, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, 90 Bayi Avenue, Xihu District, Nanchang, 330003, Jiangxi, China
| | - Chengkun You
- Department of Neurology, Pinghu Hospital of Traditional Chinese Medicine, Jiaxing, 314200, China
| | - Zhongyan Zhu
- Department of Rehabilitation, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, Nanchang, 330003, China
| | - Weikun Wu
- Department of Otolaryngology, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, 90 Bayi Avenue, Xihu District, Nanchang, 330003, Jiangxi, China
| | - Jian Cao
- Department of Otolaryngology, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, 90 Bayi Avenue, Xihu District, Nanchang, 330003, Jiangxi, China
| | - Qiang Xie
- Department of Otolaryngology, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, 330019, China
| | - Chengcheng Deng
- Department of Otolaryngology, Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang, 330019, China
| | - Xinmei Huang
- Department of Otolaryngology, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, Jiangxi, China
| | - Shiping Hu
- Department of Otolaryngology, Jiangxi Hospital of Integrated Traditional Chinese and Western Medicine, 90 Bayi Avenue, Xihu District, Nanchang, 330003, Jiangxi, China.
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Kreiniz N, Eiza N, Tadmor T, Levy Yurkovski I, Matarasso Greenfeld S, Sabag A, Mubariki R, Suriu C, Votinov E, Toubi E, Vadasz Z. The Involvement of LAG-3 positive Plasma Cells in the Development of Multiple Myeloma. Int J Mol Sci 2023; 25:549. [PMID: 38203720 PMCID: PMC10778841 DOI: 10.3390/ijms25010549] [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: 11/22/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
The Lymphocyte-Activation Protein 3 (LAG-3) inhibitory receptor is expressed on regulatory plasma cells (PCs). Micro-environmental cells that express LAG-3 were found to be increased during the progression of smoldering multiple myeloma (SMM). To assess the possible role of LAG-3 expression on regulatory PCs in patients with plasma cell dyscrasia. Purified Cluster of Differentiation 138 (CD138+) PCs from patients with premalignant conditions, active multiple myeloma (MM), and controls were analyzed for the expression of LAG-3 by flow cytometry. Autologous CD8+T cells were incubated with sorted LAG-3pos or LAG-3neg PCs for 24 h. The expression of granzyme (Grz) in CD8+T cells was assessed by flow cytometry. LAG-3 expression on PCs in active MM (newly diagnosed and relapse refractory MM) was significantly increased compared to monoclonal gammopathy of undetermined significance (MGUS)/ SMM. Grz expression was significantly decreased in CD8+T cells incubated with CD138+LAG-3pos PCs, compared to CD138+LAG-3neg PCs in patients with plasma cell dyscrasia, n = 31, p = 0.0041. LAG-3 expression on malignant PCs can be involved in the development of MM from MGUS by decreasing the expression of Grz in CD8+T cells.
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Affiliation(s)
- Natalia Kreiniz
- The Division of Hematology, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3339419, Israel; (N.K.); (T.T.); (I.L.Y.); (S.M.G.)
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Efron St 1, Haifa 3525433, Israel
| | - Nasren Eiza
- The Proteomic Unit, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3104802, Israel; (N.E.); (A.S.); (R.M.); (E.T.)
| | - Tamar Tadmor
- The Division of Hematology, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3339419, Israel; (N.K.); (T.T.); (I.L.Y.); (S.M.G.)
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Efron St 1, Haifa 3525433, Israel
| | - Ilana Levy Yurkovski
- The Division of Hematology, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3339419, Israel; (N.K.); (T.T.); (I.L.Y.); (S.M.G.)
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Efron St 1, Haifa 3525433, Israel
| | - Sarah Matarasso Greenfeld
- The Division of Hematology, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3339419, Israel; (N.K.); (T.T.); (I.L.Y.); (S.M.G.)
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Efron St 1, Haifa 3525433, Israel
| | - Adi Sabag
- The Proteomic Unit, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3104802, Israel; (N.E.); (A.S.); (R.M.); (E.T.)
| | - Raeda Mubariki
- The Proteomic Unit, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3104802, Israel; (N.E.); (A.S.); (R.M.); (E.T.)
| | - Celia Suriu
- The Division of Hematology, Galilee Medical Center, Nahariya-Cabri 89, Nahariyya 221001, Israel;
- Azrieli Faculty of Medicine, Bar-Ilan University, Henrietta Szold St 8, Safed 1311502, Israel
| | - Ekaterina Votinov
- The Division of Hematology, Kaplan Medical Center, Derech Pasternak 1, Rehovot 7610001, Israel;
| | - Elias Toubi
- The Proteomic Unit, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3104802, Israel; (N.E.); (A.S.); (R.M.); (E.T.)
| | - Zahava Vadasz
- The Proteomic Unit, Bnai Zion Medical Center, Sderot Eliyahu Golomb 47, Haifa 3104802, Israel; (N.E.); (A.S.); (R.M.); (E.T.)
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Su F, Zhang Y, Maimaiti S, Chen S, Shen Y, Feng M, Guo Z, Tan L, He J. Mechanisms and characteristics of subcapsular sinus macrophages in tumor immunity: a narrative review. Transl Cancer Res 2023; 12:3779-3791. [PMID: 38192994 PMCID: PMC10774050 DOI: 10.21037/tcr-23-2032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Background and Objective Lymph nodes constitute an integral component of the secondary lymphoid organs, housing a diverse population of macrophages. Macrophages exhibit heterogeneity in terms of localization, phenotype and ontogeny. Recent evidence has established that subcapsular sinus macrophages (SCSMs) are the initial cells exposed to antigens from afferent lymph vessels, playing a crucial role in the host immune response against invading pathogens and tumor cells. In order to summarize the role and mechanisms of SCSM in tumor immunity, this study systematically reviews research on SCSMs in tumor immunity. Methods A systematic search was conducted in PubMed and Web of Science to identify articles investigating clinical significance and mechanisms of SCSMs. Study eligibility was independently evaluated by two authors based on the assessment of titles, abstracts and full-texts. Key Content and Findings The narrative review included a total of 17 studies. Previous research consistently showed that a high level of SCSM in patients with various carcinomas is associated with a favorable long-term prognosis. SCSM acts as the front-line defender in antitumor activity, engaging in intricate communication with other immune cells. Moreover, SCSM could directly and indirectly modulate tumor immunity, and the integrity of SCSM layer is interrupted in disease status. Several studies explored the feasibility of targeting SCSM to activate immunity against tumors. However, the direct molecular interactions and alternation in signal pathway in the tumor immunity of SCSM are less well established in previous researches. Conclusions This narrative review underscores the critical role of SCSM in tumor immunity. Future studies should focus on the deeper mechanism underlying SCSMs and explore their clinical applications.
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Affiliation(s)
- Feng Su
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yutao Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology, Shanghai, China
| | | | - Shanglin Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yaxing Shen
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mingxiang Feng
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiqiang Guo
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology, Shanghai, China
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Su Y, Wang F, Lei Z, Li J, Ma M, Yan Y, Zhang W, Chen X, Xu B, Hu T. An Integrated Multi-Omics Analysis Identifying Immune Subtypes of Pancreatic Cancer. Int J Mol Sci 2023; 25:142. [PMID: 38203311 PMCID: PMC10779306 DOI: 10.3390/ijms25010142] [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: 10/17/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Limited studies have explored novel pancreatic cancer (PC) subtypes or prognostic biomarkers based on the altered activity of relevant signaling pathway gene sets. Here, we employed non-negative matrix factorization (NMF) to identify three immune subtypes of PC based on C7 immunologic signature gene set activity in PC and normal samples. Cluster 1, the immune-inflamed subtype, showed a higher response rate to immune checkpoint blockade (ICB) and had the lowest tumor immune dysfunction and exclusion (TIDE) scores. Cluster 2, the immune-excluded subtype, exhibited strong associations with stromal activation, characterized by elevated expression levels of transforming growth factor (TGF)-β, cell adhesion, extracellular matrix remodeling, and epithelial-to-mesenchymal transition (EMT) related genes. Cluster 3, the immune-desert subtype, displayed limited immune activity. For prognostic prediction, we developed an immune-related prognostic risk model (IRPM) based on four immune-related prognostic genes in pancreatic cancer, RHOF, CEP250, TSC1, and KIF20B. The IRPM demonstrated excellent prognostic efficacy and successful validation in an external cohort. Notably, the key gene in the prognostic model, RHOF, exerted significant influence on the proliferation, migration, and invasion of pancreatic cancer cells through in vitro experiments. Furthermore, we conducted a comprehensive analysis of somatic mutational landscapes and immune landscapes in PC patients with different IRPM risk scores. Our findings accurately stratified patients based on their immune microenvironment and predicted immunotherapy responses, offering valuable insights for clinicians in developing more targeted clinical strategies.
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Affiliation(s)
- Yongcheng Su
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Fen Wang
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Ziyu Lei
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Jiangquan Li
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Miaomiao Ma
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Ying Yan
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Wenqing Zhang
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Xiaolei Chen
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Beibei Xu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianhui Hu
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
- Shenzhen Research Institute of Xiamen University, Shenzhen 518057, China
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Lu X, Luo Y, Nie X, Zhang B, Wang X, Li R, Liu G, Zhou Q, Liu Z, Fan L, Hotaling JM, Zhang Z, Bo H, Guo J. Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment. Nat Commun 2023; 14:8462. [PMID: 38123589 PMCID: PMC10733385 DOI: 10.1038/s41467-023-44305-9] [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: 04/06/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.
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Affiliation(s)
- Xiaojian Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanwei Luo
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xichen Nie
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bailing Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ran Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guangmin Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Qianyin Zhou
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhizhong Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Liqing Fan
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Zhe Zhang
- Department of Urology, Peking University Third Hospital, Beijing, China.
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.
| | - Jingtao Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Hioki KA, Ryan DJ, Thesmar I, Lynch AC, Pobezinsky LA, Pobezinskaya EL. The mosquito effect: regulatory and effector T cells acquire cytoplasmic material from tumor cells through intercellular transfer. Front Immunol 2023; 14:1272918. [PMID: 38179041 PMCID: PMC10765531 DOI: 10.3389/fimmu.2023.1272918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
The phenomenon of intercellular transfer of cellular material, including membranes, cytoplasm, and even organelles, has been observed for decades. The functional impact and molecular mechanisms of such transfer in the immune system remain largely elusive due to the absence of a robust in vivo model. Here, we introduce a new tumor mouse model, where tumor cells express the soluble ultra-bright fluorescent protein ZsGreen, which allows detection and measurement of intercellular transfer of cytoplasm from tumor cells to infiltrating immune cells. We found that in addition to various types of myeloid lineage cells, a large fraction of T regulatory cells and effector CD8 T cells acquire tumor material. Based on the distribution of tumor-derived ZsGreen, the majority of T cells integrate captured cytoplasm into their own, while most myeloid cells store tumor material in granules. Furthermore, scRNA-seq analysis revealed significant alterations in transcriptomes of T cells that acquired tumor cell cytoplasm, suggesting potential impact on T cell function. We identified that the participation of T cells in intercellular transfer requires cell-cell contact and is strictly dependent on the activation status of T lymphocytes. Finally, we propose to name the described phenomenon of intercellular transfer for tumor infiltrating T cells the "mosquito effect".
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Affiliation(s)
- Kaito A. Hioki
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
- UMass Biotech Training Program (BTP), University of Massachusetts, Amherst, MA, United States
| | - Daniel J. Ryan
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
| | - Iris Thesmar
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
| | - Adam C. Lynch
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
| | - Leonid A. Pobezinsky
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
| | - Elena L. Pobezinskaya
- Department of Veterinary and Animal Science, University of Massachusetts, Amherst, MA, United States
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138
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Lima BM, de Azevedo ALK, Giner IS, Gomig THB, Ribeiro EMDSF, Cavalli IJ. Biomarker potential of the LEF1/TCF family members in breast cancer: Bioinformatic investigation on expression and clinical significance. Genet Mol Biol 2023; 46:e20220346. [PMID: 38100720 PMCID: PMC10723634 DOI: 10.1590/1678-4685-gmb-2022-0346] [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: 11/11/2022] [Accepted: 10/18/2023] [Indexed: 12/17/2023] Open
Abstract
The LEF1/TCF transcription factor family is related to the development of diverse tissue types, including the mammary tissue, and dysregulation of its expression and function has been described to favor breast tumorigenesis. However, the clinical and biological relevance of this gene family in breast cancer is still poorly understood. Here, we used bioinformatics approaches aiming to reduce this gap. We investigated its expression patterns in molecular and immune breast cancer subtypes; its correlation with immune cell infiltration, and its prognostic values in predicting outcomes. Also, through regulons construction, we determined the genes whose expression is influenced by these transcription factors, and the pathways in which they are involved. We found that LEF1 and TCF3 are over-expressed in breast tumors regarding non-tumor samples, while TCF4 and TCF7 are down-expressed, with the gene's methylation status being associated with its expression dysregulation. All four transcription factors presented significance at the diagnostic and prognostic levels. LEF1, TCF4, and TCF7 presented a significant correlation with immune cell infiltration, being associated with the immune subtypes of less favorable outcomes. Altogether, this research contributes to a more accurate understanding of the expression and clinical and biomarker significance of the LEF1/TCF transcription factors in breast cancer.
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Affiliation(s)
- Beatriz Miotto Lima
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
| | | | - Igor Samesima Giner
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
| | | | | | - Iglenir João Cavalli
- Universidade Federal do Paraná, Departamento de Genética,
Curitiba, Paraná, Brasil
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139
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Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8 + T cells in patients with metastatic cancers. Cancer Cell 2023; 41:2154-2165.e5. [PMID: 38039963 PMCID: PMC10843665 DOI: 10.1016/j.ccell.2023.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 08/07/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Circulating T cells from peripheral blood (PBL) can provide a rich and noninvasive source for antitumor T cells. By single-cell transcriptomic profiling of 36 neoantigen-specific T cell clones from 6 metastatic cancer patients, we report the transcriptional and cell surface signatures of antitumor PBL-derived CD8+ T cells (NeoTCRPBL). Comparison of tumor-infiltrating lymphocyte (TIL)- and PBL-neoantigen-specific T cells revealed that NeoTCRPBL T cells are low in frequency and display less-dysfunctional memory phenotypes relative to their TIL counterparts. Analysis of 100 antitumor TCR clonotypes indicates that most NeoTCRPBL populations target the same neoantigens as TILs. However, NeoTCRPBL TCR repertoire is only partially shared with TIL. Prediction and testing of NeoTCRPBL signature-derived TCRs from PBL of 6 prospective patients demonstrate high enrichment of clonotypes targeting tumor mutations, a viral oncogene, and patient-derived tumor. Thus, the NeoTCRPBL signature provides an alternative source for identifying antitumor T cells from PBL of cancer patients, enabling immune monitoring and immunotherapies.
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Affiliation(s)
- Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Dinerman
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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140
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Gu X, Wei H, Suo C, Shen S, Zhu C, Chen L, Yan K, Li Z, Bian Z, Zhang P, Yuan M, Yu Y, Du J, Zhang H, Sun L, Gao P. Itaconate promotes hepatocellular carcinoma progression by epigenetic induction of CD8 + T-cell exhaustion. Nat Commun 2023; 14:8154. [PMID: 38071226 PMCID: PMC10710408 DOI: 10.1038/s41467-023-43988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Itaconate is a well-known immunomodulatory metabolite; however, its role in hepatocellular carcinoma (HCC) remains unclear. Here, we find that macrophage-derived itaconate promotes HCC by epigenetic induction of Eomesodermin (EOMES)-mediated CD8+ T-cell exhaustion. Our results show that the knockout of immune-responsive gene 1 (IRG1), responsible for itaconate production, suppresses HCC progression. Irg1 knockout leads to a decreased proportion of PD-1+ and TIM-3+ CD8+ T cells. Deletion or adoptive transfer of CD8+ T cells shows that IRG1-promoted tumorigenesis depends on CD8+ T-cell exhaustion. Mechanistically, itaconate upregulates PD-1 and TIM-3 expression levels by promoting succinate-dependent H3K4me3 of the Eomes promoter. Finally, ibuprofen is found to inhibit HCC progression by targeting IRG1/itaconate-dependent tumor immunoevasion, and high IRG1 expression in macrophages predicts poor prognosis in HCC patients. Taken together, our results uncover an epigenetic link between itaconate and HCC and suggest that targeting IRG1 or itaconate might be a promising strategy for HCC treatment.
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Affiliation(s)
- Xuemei Gu
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Haoran Wei
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Caixia Suo
- Department of Colorectal Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Shengqi Shen
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chuxu Zhu
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Liang Chen
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Kai Yan
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhikun Li
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhenhua Bian
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Pinggen Zhang
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Mengqiu Yuan
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yingxuan Yu
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Jinzhi Du
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Huafeng Zhang
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China.
| | - Linchong Sun
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Ping Gao
- School of Medicine, South China University of Technology, Guangzhou, China.
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
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141
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Hickey JW, Agmon E, Horowitz N, Lamore M, Sunwoo J, Covert M, Nolan GP. Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570168. [PMID: 38106218 PMCID: PMC10723382 DOI: 10.1101/2023.12.06.570168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cancer progression is a complex process involving interactions that unfold across molecular, cellular, and tissue scales. These multiscale interactions have been difficult to measure and to simulate. Here we integrated CODEX multiplexed tissue imaging with multiscale modeling software, to model key action points that influence the outcome of T cell therapies with cancer. The initial phenotype of therapeutic T cells influences the ability of T cells to convert tumor cells to an inflammatory, anti-proliferative phenotype. This T cell phenotype could be preserved by structural reprogramming to facilitate continual tumor phenotype conversion and killing. One takeaway is that controlling the rate of cancer phenotype conversion is critical for control of tumor growth. The results suggest new design criteria and patient selection metrics for T cell therapies, call for a rethinking of T cell therapeutic implementation, and provide a foundation for synergistically integrating multiplexed imaging data with multiscale modeling of the cancer-immune interface.
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Affiliation(s)
- John W Hickey
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eran Agmon
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nina Horowitz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew Lamore
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - John Sunwoo
- Department of Otolaryngology, Head and Neck Surgery, Stanford Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Markus Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
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142
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Lee H, Neri P, Bahlis NJ. Current use of bispecific antibodies to treat multiple myeloma. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2023; 2023:332-339. [PMID: 38066842 PMCID: PMC10727080 DOI: 10.1182/hematology.2023000433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Targeted immunotherapy has significantly improved the outcome of patients with hematological malignancies by leveraging the power of the immune system to eliminate tumor cells. In multiple myeloma (MM), bispecific T-cell engagers (BsAb) targeting B-cell maturation antigen (BCMA), G protein-coupled receptor, class C, group 5, member D (GPRC5D), and Fc receptor-like 5 (FcRL5) have already demonstrated remarkable clinical activity in triple-class refractory patients. However, responses to BsAb are not universal, and resistance often emerges while on therapy. Mechanisms mediating resistance are tumor intrinsic or immune dependent. Reported tumor intrinsic factors include antigenic loss (biallelic or functional) through deletions or mutations of target genes, increased soluble BCMA (for BCMA targeting BsAb), high tumor burden, and extramedullary disease. Immune-mediated resistance are largely dependent on T-cell fitness and tolerant immune environment. Understanding these mechanisms will allow the design of optimized BsAb therapy and an informed approach to sequencing and combining these molecules with other anti-MM agents and immune therapies.
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Affiliation(s)
- Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
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143
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Chen Q, Shan T, Liang Y, Xu Y, Shi E, Wang Y, Li C, Wang Y, Cao M. A biomimetic phototherapeutic nanoagent based on bacterial double-layered membrane vesicles for comprehensive treatment of oral squamous cell carcinoma. J Mater Chem B 2023; 11:11265-11279. [PMID: 37974456 DOI: 10.1039/d3tb02046k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
As one of the most common malignancies, oral squamous cell carcinoma (OSCC) with high rates of invasiveness and metastasis threatens people's health worldwide, while traditional therapeutic approaches have not met the requirement of its cure. Phototherapies including photothermal therapy (PTT) and photodynamic therapy (PDT) have shown great potential for OSCC treatment due to their noninvasiveness or minimal invasiveness, high selectivity and little tolerance. However, PTT or PDT alone makes it difficult to eradicate OSCC and prevent its metastasis and recurrence. Here, double-layered membrane vesicles (DMVs) were extracted from attenuated Porphyromonas gingivalis, one of the most common pathogens inside the oral region, and served as an immune adjuvant to develop a biomimetic phototherapeutic nanoagent named PBAE/IR780@DMV for OSCC treatment via combining dual PTT/PDT and robust antitumor immunity. To obtain PBAE/IR780@DMV, poly(β-amino) ester (PBAE) was used as a carrier material to prepare the nanoparticles for loading IR780, a widely known photosensitizer possessing both PTT and PDT capabilities, followed by surface wrapping with DMVs. Upon 808 nm laser irradiation, PBAE/IR780@DMV exerted strong antitumor effects against OSCC both in vitro and in vivo, via combining PTT/PDT and specific immune responses triggered by tumor-associated antigens and DMVs. Altogether, this study provides a promising biomimetic phototherapeutic nanoagent for comprehensive treatment of OSCC.
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Affiliation(s)
- Qian Chen
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Tianhe Shan
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Yanjie Liang
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Yujing Xu
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
| | - Enyu Shi
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Yue Wang
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Changyi Li
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Yinsong Wang
- The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China.
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
| | - Mingxin Cao
- School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, China.
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144
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Zhu W, Wu C, Hu S, Liu S, Zhao S, Zhang D, Qiu G, Cheng X, Huang J. Chemokine- and chemokine receptor-based signature predicts immunotherapy response in female colorectal adenocarcinoma patients. Sci Rep 2023; 13:21358. [PMID: 38049474 PMCID: PMC10695967 DOI: 10.1038/s41598-023-48623-2] [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: 03/17/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The clinical significance and comprehensive characteristics of chemokines and chemokine receptors in female patients with advanced colorectal adenocarcinoma have not ever been reported. Our study explored the expression profiles of chemokines and chemokine receptors and constructed a chemokine- and chemokine receptor-based signature in female patients with advanced colorectal adenocarcinoma. Four independent cohorts containing 1335 patients were enrolled in our study. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were performed to construct the signature. CIBERSORT was used to evaluate the landscape of immune cell infiltration. Thirty-two pairs of tissue specimens of female advanced colorectal cancer (CRC) patients and two CRC cell lines were used to validate the signature in vitro. Quantitative real-time PCR and western blotting were performed to validate the mRNA and protein expression levels of signature genes. EdU and colony formation assays were performed to examine proliferative ability. Transwell and wound healing assays were used to evaluate cell invasion and migration capacity. During the signature construction and validation process, we found that the signature was more applicable to female patients with advanced colorectal adenocarcinoma. Hence, the subsequent study mainly focused on the particular subgroup. Enrichment analyses revealed that the signature was closely related to immunity. The landscape of immune cell infiltration presented that the signature was significantly associated with T cells CD8 and neutrophils. Gene set enrichment analysis (GSEA) confirmed that the high-risk group was chiefly enriched in the tumor-promoting related pathways and biological processes, whereas the low-risk group was mainly enriched in anti-tumor immune response pathways and biological processes. The signature was closely correlated with CTLA4, PDL1, PDL2, TMB, MSI, and TIDE, indicating that our signature could serve as a robust biomarker for immunotherapy and chemotherapy response. ROC curves verified that our signature had more robust prognostic power than all immune checkpoints and immunotherapy-related biomarkers. Finally, we used 32 pairs of tissue specimens and 2 CRC cell lines to validate our signature in vitro. We first provided a robust prognostic chemokine- and chemokine receptor-based signature, which could serve as a novel biomarker for immunotherapy and chemotherapy response to guide individualized treatment for female patients with advanced colorectal adenocarcinoma.
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Affiliation(s)
- Wenjie Zhu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Changlei Wu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shiqi Hu
- Queen Mary College, Medical Department, Nanchang University, Nanchang, Jiangxi, China
| | - Sicheng Liu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shimin Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Dongdong Zhang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Molecular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Guisheng Qiu
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiufeng Cheng
- Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jun Huang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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145
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Luo M, Gong W, Zhang Y, Li H, Ma D, Wu K, Gao Q, Fang Y. New insights into the stemness of adoptively transferred T cells by γc family cytokines. Cell Commun Signal 2023; 21:347. [PMID: 38049832 PMCID: PMC10694921 DOI: 10.1186/s12964-023-01354-3] [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: 08/30/2023] [Accepted: 10/11/2023] [Indexed: 12/06/2023] Open
Abstract
T cell-based adoptive cell therapy (ACT) has exhibited excellent antitumoral efficacy exemplified by the clinical breakthrough of chimeric antigen receptor therapy (CAR-T) in hematologic malignancies. It relies on the pool of functional T cells to retain the developmental potential to serially kill targeted cells. However, failure in the continuous supply and persistence of functional T cells has been recognized as a critical barrier to sustainable responses. Conferring stemness on infused T cells, yielding stem cell-like memory T cells (TSCM) characterized by constant self-renewal and multilineage differentiation similar to pluripotent stem cells, is indeed necessary and promising for enhancing T cell function and sustaining antitumor immunity. Therefore, it is crucial to identify TSCM cell induction regulators and acquire more TSCM cells as resource cells during production and after infusion to improve antitumoral efficacy. Recently, four common cytokine receptor γ chain (γc) family cytokines, encompassing interleukin-2 (IL-2), IL-7, IL-15, and IL-21, have been widely used in the development of long-lived adoptively transferred TSCM in vitro. However, challenges, including their non-specific toxicities and off-target effects, have led to substantial efforts for the development of engineered versions to unleash their full potential in the induction and maintenance of T cell stemness in ACT. In this review, we summarize the roles of the four γc family cytokines in the orchestration of adoptively transferred T cell stemness, introduce their engineered versions that modulate TSCM cell formation and demonstrate the potential of their various combinations. Video Abstract.
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Affiliation(s)
- Mengshi Luo
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjian Gong
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuewen Zhang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huayi Li
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinglei Gao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yong Fang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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146
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Li H, Lin WP, Zhang ZN, Sun ZJ. Tailoring biomaterials for monitoring and evoking tertiary lymphoid structures. Acta Biomater 2023; 172:1-15. [PMID: 37739247 DOI: 10.1016/j.actbio.2023.09.028] [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: 07/11/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Despite the remarkable clinical success of immune checkpoint blockade (ICB) in the treatment of cancer, the response rate to ICB therapy remains suboptimal. Recent studies have strongly demonstrated that intratumoral tertiary lymphoid structures (TLSs) are associated with a good prognosis and a successful clinical response to immunotherapy. However, there is still a shortage of efficient and wieldy approaches to image and induce intratumoral TLSs in vivo. Biomaterials have made great strides in overcoming the deficiencies of conventional diagnosis and therapies for cancer, and antitumor therapy has also benefited from biomaterial-based drug delivery models. In this review, we summarize the reported methods for TLS imaging and induction based on biomaterials and provide potential strategies that can further enhance the effectiveness of imaging and stimulating intratumoral TLSs to predict and promote the response rates of ICB therapies for patients. STATEMENT OF SIGNIFICANCE: In this review, we focused on the promising of biomaterials for imaging and induction of TLSs. We reviewed the applications of biomaterials in molecular imaging and immunotherapy, identified the biomaterials that may be suitable for TLS imaging and induction, and provided outlooks for further research. Accurate imaging and effective induction of TLSs are of great significance for understanding the mechanism and clinical application. We highlighted the need for multidisciplinary coordination and cooperation in this field, and proposed the possible future direction of noninvasive imaging and artificial induction of TLSs based on biomaterials. We believe that it can facilitate collaboration and galvanize a broader effort.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China
| | - Wen-Ping Lin
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China
| | - Zhong-Ni Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China.
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147
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Liang HQ, Liao NK, Yang SB, Wei QJ, Tan ST, Zhai GQ, Lu JT, Huang YC, Deng XB, Mo LJ, Cheng JW. Identification of tumor immunophenotypes associated with immunotherapy response in bladder cancer. Int J Urol 2023; 30:1122-1132. [PMID: 37602677 DOI: 10.1111/iju.15276] [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: 11/08/2022] [Accepted: 08/03/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVES This study aims to reveal immunophenotypes associated with immunotherapy response in bladder cancer, identify the signature genes of immune subtypes, and provide new molecular targets for improving immunotherapy response. METHODS Bladder cancer immunophenotypes were characterized in the bulk RNA sequencing dataset GSE32894 and Imvigor210, and gene expression signatures were established to identify the immunophenotypes. Expression of gene signatures were validated in single-cell RNA sequencing dataset GSE145140 and human proteins expression data source. Investigation of Immunotherapy Response was performed in IMvigor210 dataset. Prognosis of tumor immunophenotypes was further analyzed. RESULTS Inflamed and immune-excluded immunophenotypes were characterized based on the tumor immune cell scores. Risk score models that were established rely on RNA sequencing profiles and overall survival of bladder cancer cohorts. The inflamed tumors had lower risk scores, and the low-risk tumors were more likely to respond to atezolizumab, receiving complete response/partial response (CR/PR). Patients who responded to atezolizumab had higher SRRM4 and lower NPHS1 and TMEM72 expression than the non-responders. SRRM4 expression was a protective factor for bladder cancer prognosis, while the NPHS1 and TMEM72 showed the opposite pattern. CONCLUSION This study provided a novel classification method for tumor immunophenotypes. Bladder cancer immunophenotypes can predict the response to immune checkpoint blockade. The immunophenotypes can be identified by the expression of signature genes.
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Affiliation(s)
- Hai-Qi Liang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Nai-Kai Liao
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shu-Bo Yang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiu-Ju Wei
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shu-Ting Tan
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Gao-Qiang Zhai
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiang-Ting Lu
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi-Cheng Huang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiao-Bin Deng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lin-Jian Mo
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ji-Wen Cheng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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148
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Elizaldi SR, Verma A, Ma ZM, Ott S, Rajasundaram D, Hawes CE, Lakshmanappa YS, Cottrell ML, Kashuba ADM, Ambrose Z, Lifson JD, Morrison JH, Iyer SS. Deep analysis of CD4 T cells in the rhesus CNS during SIV infection. PLoS Pathog 2023; 19:e1011844. [PMID: 38060615 PMCID: PMC10729971 DOI: 10.1371/journal.ppat.1011844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/19/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Virologic suppression with antiretroviral therapy (ART) has significantly improved health outcomes for people living with HIV, yet challenges related to chronic inflammation in the central nervous system (CNS)-known as Neuro-HIV- persist. As primary targets for HIV-1 with the ability to survey and populate the CNS and interact with myeloid cells to co-ordinate neuroinflammation, CD4 T cells are pivotal in Neuro-HIV. Despite their importance, our understanding of CD4 T cell distribution in virus-targeted CNS tissues, their response to infection, and potential recovery following initiation of ART remain limited. To address these gaps, we studied ten SIVmac251-infected rhesus macaques using an ART regimen simulating suboptimal adherence. We evaluated four macaques during the acute phase pre-ART and six during the chronic phase. Our data revealed that HIV target CCR5+ CD4 T cells inhabit both the brain parenchyma and adjacent CNS tissues, encompassing choroid plexus stroma, dura mater, and the skull bone marrow. Aligning with the known susceptibility of CCR5+ CD4 T cells to viral infection and their presence within the CNS, high levels of viral RNA were detected in the brain parenchyma and its border tissues during acute SIV infection. Single-cell RNA sequencing of CD45+ cells from the brain revealed colocalization of viral transcripts within CD4 clusters and significant activation of antiviral molecules and specific effector programs within T cells, indicating CNS CD4 T cell engagement during infection. Acute infection led to marked imbalance in the CNS CD4/CD8 ratio which persisted into the chronic phase. These observations underscore the functional involvement of CD4 T cells within the CNS during SIV infection, enhancing our understanding of their role in establishing CNS viral presence. Our findings offer insights for potential T cell-focused interventions while underscoring the challenges in eradicating HIV from the CNS, particularly in the context of sub-optimal ART.
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Affiliation(s)
- Sonny R. Elizaldi
- Graduate Group in Immunology, UC Davis, California, United States of America
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, United States of America
| | - Zhong-Min Ma
- California National Primate Research Center, UC Davis, California, United States of America
| | - Sean Ott
- California National Primate Research Center, UC Davis, California, United States of America
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pennsylvania, United States of America
| | - Chase E. Hawes
- Graduate Group in Immunology, UC Davis, California, United States of America
| | | | - Mackenzie L. Cottrell
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Angela D. M. Kashuba
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory, Frederick, Maryland, United States of America
| | - John H. Morrison
- California National Primate Research Center, UC Davis, California, United States of America
- Department of Neurology, School of Medicine, UC Davis, California, United States of America
| | - Smita S. Iyer
- Department of Pathology, School of Medicine, University of Pittsburgh, Pennsylvania, United States of America
- California National Primate Research Center, UC Davis, California, United States of America
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, UC Davis, California, United States of America
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149
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Roetman JJ, Erwin MM, Rudloff MW, Favret NR, Detrés Román CR, Apostolova MKI, Murray KA, Lee TF, Lee YA, Philip M. Tumor-Reactive CD8+ T Cells Enter a TCF1+PD-1- Dysfunctional State. Cancer Immunol Res 2023; 11:1630-1641. [PMID: 37844197 PMCID: PMC10841346 DOI: 10.1158/2326-6066.cir-22-0939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/25/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
T cells recognize several types of antigens in tumors, including aberrantly expressed, nonmutated proteins, which are therefore shared with normal tissue and referred to as self/shared-antigens (SSA), and mutated proteins or oncogenic viral proteins, which are referred to as tumor-specific antigens (TSA). Immunotherapies such as immune checkpoint blockade (ICB) can activate T-cell responses against TSA, leading to tumor control, and also against SSA, causing immune-related adverse events (irAE). To improve anti-TSA immunity while limiting anti-SSA autoreactivity, we need to understand how tumor-specific CD8+ T cells (TST) and SSA-specific CD8+ T (SST) cells differentiate in response to cognate antigens during tumorigenesis. Therefore, we developed a genetic cancer mouse model in which we can track TST and SST differentiation longitudinally as liver cancers develop. We found that both TST and SST lost effector function over time, but while TST persisted long term and had a dysfunctional/exhausted phenotype (including expression of PD1, CD39, and TOX), SST exited cell cycle prematurely and disappeared from liver lesions. However, SST persisted in spleens in a dysfunctional TCF1+PD-1- state: unable to produce effector cytokines or proliferate in response to ICB targeting PD-1 or PD-L1. Thus, our studies identify a dysfunctional T-cell state occupied by T cells reactive to SSA: a TCF1+PD-1- state lacking in effector function, demonstrating that the type/specificity of tumor antigen may determine tumor-reactive T-cell differentiation.
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Affiliation(s)
- Jessica J. Roetman
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Megan M. Erwin
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael W. Rudloff
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Natalie R. Favret
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Carlos R. Detrés Román
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Minna K. I. Apostolova
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kristen A. Murray
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ting-Fang Lee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Digestive Diseases Research Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Youngmin A. Lee
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Digestive Diseases Research Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary Philip
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Digestive Diseases Research Center, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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150
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Yilmaz I, Tavukcuoglu E, Horzum U, Yilmaz KB, Akinci M, Gulcelik MA, Oral HB, Esendagli G. Immune checkpoint status and exhaustion-related phenotypes of CD8 + T cells from the tumor-draining regional lymph nodes in breast cancer. Cancer Med 2023; 12:22196-22205. [PMID: 38069525 PMCID: PMC10757146 DOI: 10.1002/cam4.6802] [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: 07/05/2023] [Revised: 10/31/2023] [Accepted: 11/27/2023] [Indexed: 12/31/2023] Open
Abstract
BACKGROUND Functional status of T cells determines the responsiveness of cancer patients to immunotherapeutic interventions. Even though T cell-mediated immunity is inaugurated in the tumor-adjacent lymph nodes, peripheral blood has been routinely sampled for testing the immunological assays. The purpose of this study is to determine the immune checkpoint molecule expression and the exhaustion-related phenotype of cytotoxic T cells in the regional lymph nodes from breast cancer patients. PATIENTS AND METHODS Multicolor immunophenotyping was used to determine the expression of PD-1, TIM-3, LAG3, CTLA-4, CCR7, CD45RO, CD127, CD25, CXCR5, and ICOS molecules on CD3+ CD4- CD56- CD8+ cytotoxic T cells freshly obtained from the lymph nodes and the peripheral blood samples of the breast cancer patients. The results were assessed together with the clinical data. RESULTS A population of cytotoxic T cells was noted with high PD-1 and CXCR5 expression in the lymph nodes of the breast cancer patients. Co-expression of PD-1, CXCR5, TIM-3, and ICOS indicated a follicular helper T cell (Tfh)-like, exhaustion-related immunophenotype in these cytotoxic T cells. Only a minor population with CTLA-4 and LAG3 expression was noted. The PD-1+ CXCR5+ cytotoxic T cells largely displayed CD45RO+ CCR7+ central memory markers. The amount of CXCR5-expressing PD-1- cytotoxic T cells was elevated in the lymph nodes of the patients. CONCLUSION The regional lymph nodes of breast cancer patients harbor Tfh-like exhausted cytotoxic T lymphocytes with high PD-1 and TIM-3 checkpoint molecule expression. The immunological conditions in the regional lymph nodes should be implicated for immune checkpoint immunotherapy (ICI) of cancer.
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Affiliation(s)
- Izel Yilmaz
- Department of Medical Immunology, Institute of Health SciencesBursa Uludag UniversityBursaTurkey
- Department of Basic OncologyHacettepe University Cancer InstituteAnkaraTurkey
| | - Ece Tavukcuoglu
- Department of Basic OncologyHacettepe University Cancer InstituteAnkaraTurkey
| | - Utku Horzum
- Department of Basic OncologyHacettepe University Cancer InstituteAnkaraTurkey
| | - Kerim Bora Yilmaz
- Department of General Surgery, Gulhane Training and Research HospitalUniversity of Health SciencesAnkaraTurkey
- Department of Medical and Surgical ResearchHacettepe University Institute of Health SciencesAnkaraTurkey
| | - Melih Akinci
- Department of General Surgery, Gulhane Training and Research HospitalUniversity of Health SciencesAnkaraTurkey
| | - Mehmet Ali Gulcelik
- Department of General Surgery, Gulhane Training and Research HospitalUniversity of Health SciencesAnkaraTurkey
| | - Haluk Barbaros Oral
- Department of Immunology, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Gunes Esendagli
- Department of Basic OncologyHacettepe University Cancer InstituteAnkaraTurkey
- Department of Medical and Surgical ResearchHacettepe University Institute of Health SciencesAnkaraTurkey
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