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Kippenberger M, Schönberg G, Kaczorowski A, Schneider F, Böning S, Sun A, Schwab C, Görtz M, Schütz V, Stenzinger A, Hohenfellner M, Duensing A, Duensing S. Immune landscape of renal cell carcinoma with metastasis to the pancreas. Urol Oncol 2024; 42:373.e9-373.e17. [PMID: 38981801 DOI: 10.1016/j.urolonc.2024.06.006] [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: 02/20/2024] [Revised: 05/17/2024] [Accepted: 06/02/2024] [Indexed: 07/11/2024]
Abstract
INTRODUCTION Clear cell Renal Cell Carcinoma (ccRCC) has a poor prognosis once metastatic. However, certain metastatic sites have been reported to have a different impact on the patient prognosis. For example, patients with pancreatic metastases have a much more favorable prognosis than those with metastases to other organs. The biological basis for this observation remains poorly understood. The aim of this study was to characterize the immune landscape of pancreatic metastases and the corresponding primary tumors in order to identify possible immunological features that correlate with disease biology. PATIENTS AND METHODS A detailed assessment of immune cell populations was performed using a total of 1,700 microscopic images from ccRCCs from 11 patients, their corresponding pancreatic metastases and ccRCCs from 10 patients without pancreatic metastases. Tumor specimens were stained for CD45, CD8, CD163 and FOXP3 and the densities of the respective immune cells were assessed semiquantitatively in the intratumoral and extratumoral compartment. Multispectral imaging was performed in selected tumors. RESULTS We found that pancreatic metastases show the lowest intratumoral infiltration with CD8+ cytotoxic T lymphocytes of all tumor specimens analyzed. The frequency of CD8+ lymphocytes was on 1.9 fold lower in pancreatic metastases (median density 8.3 cells per field of view [FOV] = 1.23 mm2) when compared to the corresponding primary tumor (15.6 cells per FOV, P = 0.0002) and more than 3-fold lower when compared to ccRCCs without pancreatic metastases (27.2 cells per FOV, P = 0.0012). There was also a significantly reduced intratumoral infiltration with immunosuppressive FOXP3+ lymphocytes in pancreatic metastases (2.6 cells per FOV, P = 0.009) and corresponding primary tumors (2 cells per FOV, P = 0.028) when compared to ccRCCs without pancreatic metastases (5.6 cells per FOV). CONCLUSIONS In this proof-of-concept study, we show that pancreatic metastases of ccRCC present with unique immunological features including a low intratumoral density of CD8+ and FOXP3+ lymphocytes. The low counts of CD8+ and FOXP3+ lymphocytes may reflect less aggressive features of ccRCC with pancreatic metastasis that may result in a more favorable patient prognosis.
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Affiliation(s)
- Maximilian Kippenberger
- Department of Urology, Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Gita Schönberg
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Adam Kaczorowski
- Department of Urology, Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Schneider
- Department of Urology, Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah Böning
- Department of Urology, Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Angela Sun
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Constantin Schwab
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Magdalena Görtz
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Viktoria Schütz
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | | | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Anette Duensing
- Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA; Department of Urology, Precision Oncology of Urological Malignancies, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany.
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Ge J, Meng Y, Guo J, Chen P, Wang J, Shi L, Wang D, Qu H, Wu P, Fan C, Zhang S, Liao Q, Zhou M, Xiang B, Wang F, Tan M, Gong Z, Xiong W, Zeng Z. Human papillomavirus-encoded circular RNA circE7 promotes immune evasion in head and neck squamous cell carcinoma. Nat Commun 2024; 15:8609. [PMID: 39366979 DOI: 10.1038/s41467-024-52981-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 09/27/2024] [Indexed: 10/06/2024] Open
Abstract
Immune evasion represents a crucial milestone in the progression of cancer and serves as the theoretical foundation for tumor immunotherapy. In this study, we reveal a negative association between Human Papillomavirus (HPV)-encoded circular RNA, circE7, and the infiltration of CD8+ T cells in head and neck squamous cell carcinoma (HNSCC). Both in vitro and in vivo experiments demonstrate that circE7 suppresses the function and activity of T cells by downregulating the transcription of LGALS9, which encodes the galectin-9 protein. The molecular mechanism involves circE7 binding to acetyl-CoA carboxylase 1 (ACC1), promoting its dephosphorylation and thereby activating ACC1. Activated ACC1 reduces H3K27 acetylation at the LGALS9 gene promoter, leading to decreased galectin-9 expression. Notably, galectin-9 interacts with immune checkpoint molecules TIM-3 and PD-1, inhibiting the secretion of cytotoxic cytokines by T cells and promoting T cell apoptosis. Here, we demonstrate a mechanism by which HPV promotes immune evasion in HNSCC through a circE7-driven epigenetic modification and propose a potential immunotherapy strategy for HNSCC that involves the combined use of anti-PD-1 and anti-TIM-3 inhibitors.
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Affiliation(s)
- Junshang Ge
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yi Meng
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiayue Guo
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Pan Chen
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jie Wang
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Hongke Qu
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Pan Wu
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Fuyan Wang
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Ming Tan
- Institute of Biochemistry & Molecular Biology and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- Furong Laboratory, Changsha, Hunan, China.
| | - Zhaoyang Zeng
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- NHC Key Laboratory of Carcinogenesis and Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
- Furong Laboratory, Changsha, Hunan, China.
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Liang Y, Bu Q, You W, Zhang R, Xu Z, Gan X, Zhou J, Qiao L, Huang T, Lu L. Single-cell analysis reveals hypoxia-induced immunosuppressive microenvironment in intrahepatic cholangiocarcinoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167276. [PMID: 38844114 DOI: 10.1016/j.bbadis.2024.167276] [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: 01/17/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
The role of hypoxia in the tumor microenvironment of intrahepatic cholangiocarcinoma (iCCA) remains unclear. Here, we generated a comprehensive atlas of the entire tumor microenvironment and delineated the multifaceted cell-cell interactions to decipher hypoxia-induced pro-tumor immune suppression. We discovered hypoxia is significantly associated with iCCA progression via the activation of HIF1A expression. Moreover, hypoxia-dependent PPARγ-mediated fatty acid oxidation in APOE+ TAMs promoted M2 macrophage polarization by activating the HIF1A-PPARG-CD36 axis. These polarized APOE+ TAMs recruited Treg cell infiltration via the CCL3-CCR5 pair to form an immunosuppressive microenvironment. APOE+ TAMs tended to co-localize spatially with Treg cells in the malignant tissue based on spatial transcriptome data and immunofluorescence analysis results. We identified tumor-reactive CXCL13+ CD8-PreTex with specific high expression of ENTPD1 and ITGAE, which acted as precursors of CD8-Tex and had higher cytotoxicity, lower exhaustion, and more vigorous proliferation. Consequently, CXCL13+ CD8-PreTex functioned as a positive regulator of antitumor immunity by expressing the pro-inflammatory cytokines IFNG and TNF, associated with a better survival outcome. Our study reveals the mechanisms involved in hypoxia-induced immunosuppression and suggests that targeting precursor-exhausted CXCL13+CD8+ T cells might provide a pratical immunotherapeutic approach.
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Affiliation(s)
- Yuan Liang
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Qingfa Bu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Wenhua You
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Rui Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Zibo Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaojie Gan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jinren Zhou
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Lei Qiao
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tianning Huang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Ling Lu
- School of Biological Science & Medical Engineering, Southeast University, Nanjing, China; Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, NHC Key Laboratory of Liver Transplantation, Research Unit of Liver Transplantation and Transplant Immunology, Chinese Academy of Medical Sciences, Nanjing, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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4
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Zhang Q, Ding L, Li J, Liu K, Xia C, Chen S, Huang X, Pu Y, Song Y, Hu Q, Wang Y. Single-cell RNA sequencing of OSCC primary tumors and lymph nodes reveals distinct origin and phenotype of fibroblasts. Cancer Lett 2024; 600:217180. [PMID: 39154702 DOI: 10.1016/j.canlet.2024.217180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/02/2024] [Accepted: 08/09/2024] [Indexed: 08/20/2024]
Abstract
Desmoplasia in fibroblasts within metastatic lymph nodes (MLNs) serves as an indicator of extranodal extension (ENE), which led mortality in oral squamous cell carcinoma (OSCC). However, systematic studies on fibroblasts in MLNs are lacking. Therefore, this study characterized the differences in phenotype, function, and origin of fibroblasts between primary tumors (PTs) and lymph nodes (LNs) in OSCC. We generated single-cell maps of PTs and paired MLNs and draining LNs from three OSCC patients. The transcriptomic atlas, pseudotime analysis, intercellular communication networks and enrichment analysis of the single cells were characterized. Phenotype and function heterogeneity of fibroblast cells between PTs and MLNs were further verified in vitro. Among 44,052 fibroblasts, we identified two distinct subpopulations of cancer-associated myofibroblastic cells (mCAFs): RGS4+ mCAF1 and COMP + mCAF2. Notably, they exhibited distinct distributions, with mCAF1 predominantly localized in the PTs and mCAF2 in the MLNs. Moreover, pseudotime analysis revealed their distinct origins: mCAF1 originated from inherent normal myofibroblastic cells in the PT, whereas mCAF2 originated from fibroblastic reticular cells in the LNs. Further functional experiments using primary fibroblasts revealed that, compared to mCAF1, mCAF2 in MLNs exhibited weaker crosstalk with immune cells but enhanced extracellular matrix activity, which is closely linked to ENE formation in OSCC. Additionally, we identified two fibroblast subgroups in a transforming state, indicating a potential epithelial-mesenchymal transition. Our research offers profound insights into the heterogeneity of fibroblasts between the PT and MLN in OSCC, serving as an essential resource for future drug discovery endeavors.
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Affiliation(s)
- Qian Zhang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Liang Ding
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Jingyi Li
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Kunyu Liu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Chengwan Xia
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Sheng Chen
- Pathology Department, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Xiaofeng Huang
- Pathology Department, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Yumei Pu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Yuxian Song
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, China
| | - Qingang Hu
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China.
| | - Yuxin Wang
- Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University, China.
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5
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Yao Z, Zeng Y, Liu C, Jin H, Wang H, Zhang Y, Ding C, Chen G, Wu D. Focusing on CD8 + T-cell phenotypes: improving solid tumor therapy. J Exp Clin Cancer Res 2024; 43:266. [PMID: 39342365 PMCID: PMC11437975 DOI: 10.1186/s13046-024-03195-5] [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: 07/31/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
Vigorous CD8+ T cells play a crucial role in recognizing tumor cells and combating solid tumors. How T cells efficiently recognize and target tumor antigens, and how they maintain the activity in the "rejection" of solid tumor microenvironment, are major concerns. Recent advances in understanding of the immunological trajectory and lifespan of CD8+ T cells have provided guidance for the design of more optimal anti-tumor immunotherapy regimens. Here, we review the newly discovered methods to enhance the function of CD8+ T cells against solid tumors, focusing on optimizing T cell receptor (TCR) expression, improving antigen recognition by engineered T cells, enhancing signal transduction of the TCR-CD3 complex, inducing the homing of polyclonal functional T cells to tumors, reversing T cell exhaustion under chronic antigen stimulation, and reprogramming the energy and metabolic pathways of T cells. We also discuss how to participate in the epigenetic changes of CD8+ T cells to regulate two key indicators of anti-tumor responses, namely effectiveness and persistence.
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Affiliation(s)
- Zhouchi Yao
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Yayun Zeng
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Cheng Liu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Huimin Jin
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Hong Wang
- Department of Scientific Research, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, 121001, China
| | - Yue Zhang
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Chengming Ding
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Guodong Chen
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
| | - Daichao Wu
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital, Laboratory of Structural Immunology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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6
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Duan X, Hu J, Zhang Y, Zhao X, Yang M, Sun T, Liu S, Chen X, Feng J, Li W, Yang Z, Zhang Y, Lin X, Liu D, Meng Y, Yang G, Lin Q, Zhang G, Lei H, Yi Z, Liu Y, Liang X, Wu Y, Diao W, Li Z, Liang H, Zhan M, Sun HW, Li XY, Lu L. RIG-I is an intracellular checkpoint that limits CD8 + T-cell antitumour immunity. EMBO Mol Med 2024:10.1038/s44321-024-00136-9. [PMID: 39322862 DOI: 10.1038/s44321-024-00136-9] [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: 11/22/2023] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/27/2024] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor involved in innate immunity, but its role in adaptive immunity, specifically in the context of CD8+ T-cell antitumour immunity, remains unclear. Here, we demonstrate that RIG-I is upregulated in tumour-infiltrating CD8+ T cells, where it functions as an intracellular checkpoint to negatively regulate CD8+ T-cell function and limit antitumour immunity. Mechanistically, the upregulation of RIG-I in CD8+ T cells is induced by activated T cells, and directly inhibits the AKT/glycolysis signalling pathway. In addition, knocking out RIG-I enhances the efficacy of adoptively transferred T cells against solid tumours, and inhibiting RIG-I enhances the response to PD-1 blockade. Overall, our study identifies RIG-I as an intracellular checkpoint and a potential target for alleviating inhibitory constraints on T cells in cancer immunotherapy, either alone or in combination with an immune checkpoint inhibitor.
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Affiliation(s)
- Xiaobing Duan
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China.
| | - Jiali Hu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Yuncong Zhang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Xiaoguang Zhao
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Mingqi Yang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Taoping Sun
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Siya Liu
- The Third People's Hospital of Zhuhai, Zhuhai, 519000, China
| | - Xin Chen
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Juan Feng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Wenting Li
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Ze Yang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Yitian Zhang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Xiaowen Lin
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Dingjie Liu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Ya Meng
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Guang Yang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Guihai Zhang
- Department of Oncology, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Haihong Lei
- Department of Radiation Oncology, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Zhengsheng Yi
- Department of Radiation Oncology, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Yanyan Liu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
| | - Xiaobing Liang
- Guangdong Huixin Life Science Co., Ltd., Zhuhai, 519000, China
| | - Yujuan Wu
- Zhuhai Central Blood Station, Zhuhai, 519000, China
| | - Wenqing Diao
- Zhuhai Central Blood Station, Zhuhai, 519000, China
| | - Zesong Li
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumours, Shenzhen Key Laboratory of Genitourinary Tumour, Department of Urology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
| | - Haihai Liang
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China
- Guangzhou First Pepople's Hospital, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Hong-Wei Sun
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
| | - Xian-Yang Li
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumour Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, 519000, China.
- Guangzhou First Pepople's Hospital, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
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7
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Giangreco G, Rullan A, Naito Y, Biswas D, Liu YH, Hooper S, Nenclares P, Bhide S, Chon U Cheang M, Chakravarty P, Hirata E, Swanton C, Melcher A, Harrington K, Sahai E. Cancer cell - Fibroblast crosstalk via HB-EGF, EGFR, and MAPK signaling promotes the expression of macrophage chemo-attractants in squamous cell carcinoma. iScience 2024; 27:110635. [PMID: 39262776 PMCID: PMC11387794 DOI: 10.1016/j.isci.2024.110635] [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: 07/07/2023] [Revised: 04/09/2024] [Accepted: 07/30/2024] [Indexed: 09/13/2024] Open
Abstract
Interactions between cells in the tumor microenvironment (TME) shape cancer progression and patient prognosis. To gain insights into how the TME influences cancer outcomes, we derive gene expression signatures indicative of signaling between stromal fibroblasts and cancer cells, and demonstrate their prognostic significance in multiple and independent squamous cell carcinoma cohorts. By leveraging information within the signatures, we discover that the HB-EGF/EGFR/MAPK axis represents a hub of tumor-stroma crosstalk, promoting the expression of CSF2 and LIF and favoring the recruitment of macrophages. Together, these analyses demonstrate the utility of our approach for interrogating the extent and consequences of TME crosstalk.
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Affiliation(s)
- Giovanni Giangreco
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Antonio Rullan
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Yutaka Naito
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Yun-Hsin Liu
- Bioinformatics Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steven Hooper
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pablo Nenclares
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Shreerang Bhide
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Maggie Chon U Cheang
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Probir Chakravarty
- Bioinformatics Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eishu Hirata
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Alan Melcher
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Kevin Harrington
- Department of Radiotherapy and Imaging, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
- Head and Neck Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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8
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Pan Y, Gao Z, Cui X, Li Z, Jiang R. collectNET: a web server for integrated inference of cell-cell communication network. Database (Oxford) 2024; 2024:baae098. [PMID: 39283594 PMCID: PMC11403813 DOI: 10.1093/database/baae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/03/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Cell-cell communication (CCC) through ligand-receptor (L-R) pairs forms the cornerstone for complex functionalities in multicellular organisms. Deciphering such intercellular signaling can contribute to unraveling disease mechanisms and enable targeted therapy. Nonetheless, notable biases and inconsistencies are evident among the inferential outcomes generated by current methods for inferring CCC network. To fill this gap, we developed collectNET (http://health.tsinghua.edu.cn/collectnet) as a comprehensive web platform for analyzing CCC network, with efficient calculation, hierarchical browsing, comprehensive statistics, advanced searching, and intuitive visualization. collectNET provides a reliable online inference service with prior knowledge of three public L-R databases and systematic integration of three mainstream inference methods. Additionally, collectNET has assembled a human CCC atlas, including 126 785 significant communication pairs based on 343 023 cells. We anticipate that collectNET will benefit researchers in gaining a more holistic understanding of cell development and differentiation mechanisms. Database URL: http://health.tsinghua.edu.cn/collectnet.
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Affiliation(s)
- Yan Pan
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, FIT 1-107, Beijing 100084, China
| | - Zijing Gao
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, FIT 1-107, Beijing 100084, China
| | - Xuejian Cui
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, FIT 1-107, Beijing 100084, China
| | - Zhen Li
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, FIT 1-107, Beijing 100084, China
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics, Bioinformatics Division at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, FIT 1-107, Beijing 100084, China
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9
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Grebinoski S, Pieklo G, Zhang Q, Visperas A, Cui J, Goulet J, Xiao H, Brunazzi EA, Cardello C, Herrada AA, Das J, Workman CJ, Vignali DAA. Regulatory T Cell Insufficiency in Autoimmune Diabetes Is Driven by Selective Loss of Neuropilin-1 on Intraislet Regulatory T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:779-794. [PMID: 39109924 PMCID: PMC11371503 DOI: 10.4049/jimmunol.2300216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/08/2024] [Indexed: 09/05/2024]
Abstract
Approaches to reverse or limit regulatory T cell (Treg) insufficiency are of great interest for development of immunotherapeutic treatments for autoimmune patients, including type 1 diabetes. Treg insufficiency is heavily implicated in the progression of autoimmune diabetes in the NOD mouse model and is characterized by defects in Treg numbers, development, and/or function. Utilizing a Treg-centric screen, we show that intraislet Tregs have a uniquely dysfunctional phenotype, hallmarked by an almost complete lack of neuropilin-1 (Nrp1), a cell surface receptor required to maintain Treg stability. Intraislet Nrp1- Tregs exhibit hallmark features of fragility, including reduced suppressive capacity, decreased CD73 and Helios, and increased Rorγt and Tbet. Intraislet Nrp1- Tregs also exhibit decreased Foxp3 expression on a per cell basis, suggesting that Nrp1 may also be required for long-term Treg stability. Mechanistically, Treg-restricted augmentation of Nrp1 expression limited the onset of autoimmune diabetes in NOD mice suggesting that Nrp1 critically impacts intraislet Treg function. Transcriptional analysis showed that Nrp1 restoration led to an increase in markers and pathways of TCR signaling, survival, and suppression, and when Nrp1 protein expression is examined by cellular indexing of transcriptomes and epitopes by sequencing, significant differences were observed between Nrp1+ and Nrp1- Tregs in all tissues, particularly in markers of Treg fragility. This translated into substantive differences between Nrp1+ and Nrp1- Tregs that afforded the former with a competitive advantage in the islets. Taken together, these data suggest that maintenance of Nrp1 expression and signaling on Tregs limits diabetes onset and may serve as a strategy to combat Treg insufficiency in autoimmune disease.
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Affiliation(s)
- Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Gwenyth Pieklo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Qianxia Zhang
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Anabelle Visperas
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Jordana Goulet
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Hanxi Xiao
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- CMU-Pitt Joint Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Erin A Brunazzi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Andrés A Herrada
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Jishnu Das
- CMU-Pitt Joint Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh PA
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10
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Ding Q, Yang W, Xue G, Liu H, Cai Y, Que J, Jin X, Luo M, Pang F, Yang Y, Lin Y, Liu Y, Sun H, Tan R, Wang P, Xu Z, Jiang Q. Dimension reduction, cell clustering, and cell-cell communication inference for single-cell transcriptomics with DcjComm. Genome Biol 2024; 25:241. [PMID: 39252099 PMCID: PMC11382422 DOI: 10.1186/s13059-024-03385-6] [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: 01/09/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
Advances in single-cell transcriptomics provide an unprecedented opportunity to explore complex biological processes. However, computational methods for analyzing single-cell transcriptomics still have room for improvement especially in dimension reduction, cell clustering, and cell-cell communication inference. Herein, we propose a versatile method, named DcjComm, for comprehensive analysis of single-cell transcriptomics. DcjComm detects functional modules to explore expression patterns and performs dimension reduction and clustering to discover cellular identities by the non-negative matrix factorization-based joint learning model. DcjComm then infers cell-cell communication by integrating ligand-receptor pairs, transcription factors, and target genes. DcjComm demonstrates superior performance compared to state-of-the-art methods.
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Affiliation(s)
- Qian Ding
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Wenyi Yang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Guangfu Xue
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Hongxin Liu
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yideng Cai
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Jinhao Que
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Xiyun Jin
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Meng Luo
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Fenglan Pang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yuexin Yang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Yi Lin
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Yusong Liu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Haoxiu Sun
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Renjie Tan
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China
| | - Pingping Wang
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
| | - Zhaochun Xu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
| | - Qinghua Jiang
- Center for Bioinformatics, School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150076, China.
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), Harbin Medical University, Harbin, 150076, China.
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11
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von der Grün J, Broglie M, Guckenberger M, Balermpas P. A comprehensive and longitudinal evaluation of the different populations of lymphoid and myeloid cells in the peripheral blood of patients treated with chemoradiotherapy for head and neck cancer. Cancer Immunol Immunother 2024; 73:222. [PMID: 39235625 PMCID: PMC11377404 DOI: 10.1007/s00262-024-03810-6] [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: 04/23/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Immunotherapy provided significant survival benefits for recurrent and metastatic patients with head and neck cancer. These improvements could not be reproduced in patients treated with curative-intent chemoradiotherapy (CRT) and the optimal radio-immunotherapy (RIT) concepts have yet to be designed. Exploration and analysis of the pre-therapeutic immune status of these patients and the changes occurring during the treatment course could be crucial in rationally designing future combined treatments. METHODS Blood samples were collected from a cohort of 25 head and neck cancer patients treated with curative-intended (C)-RT prior to therapy, after the first week of treatment, and three months after treatment completion. Peripheral blood mononuclear cells (PBMCs) or all nucleated blood cells were isolated and analyzed via flow cytometry. RESULTS At baseline, patients showed reduced monocyte and lymphocyte counts compared to healthy individuals. Although overall CD8+ T-cell frequencies were reduced, the proportion of memory subsets were increased in patients. Radiotherapy (RT) treatment led to a further increase in CD8+ effector memory T-cells. Among myeloid populations, tumor-promoting subsets became less abundant after RT, in favor of pro-inflammatory cells. CONCLUSION The present study prospectively demonstrated a complex interplay and distinct longitudinal changes in the composition of lymphocytic and myeloid populations during curative (C)-RT of head and neck cancer. Further validation of this method in a larger cohort could allow for better treatment guidance and tailored incorporation of immunotherapies (IT) in the future.
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Affiliation(s)
- Jens von der Grün
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Universitäts Spital Zürich (USZ), Rämistrasse 100, 8091, Zurich, Switzerland
| | - Martina Broglie
- Department of Otorhinolaryngology-Head and Neck Surgery, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Universitäts Spital Zürich (USZ), Rämistrasse 100, 8091, Zurich, Switzerland
| | - Panagiotis Balermpas
- Department of Radiation Oncology, University Hospital Zurich, University of Zurich, Universitäts Spital Zürich (USZ), Rämistrasse 100, 8091, Zurich, Switzerland.
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12
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Cao Y, Chang T, Schischlik F, Wang K, Sinha S, Hannenhalli S, Jiang P, Ruppin E. Inferring Characteristics of the Tumor Immune Microenvironment of Patients with HNSCC from Single-Cell Transcriptomics of Peripheral Blood. CANCER RESEARCH COMMUNICATIONS 2024; 4:2335-2348. [PMID: 39113621 PMCID: PMC11375407 DOI: 10.1158/2767-9764.crc-24-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/06/2024]
Abstract
In this study, we explore the possibility of inferring characteristics of the tumor immune microenvironment from the blood. Specifically, we investigate two datasets of patients with head and neck squamous cell carcinoma with matched single-cell RNA sequencing (scRNA-seq) from peripheral blood mononuclear cells (PBMCs) and tumor tissues. Our analysis shows that the immune cell fractions and gene expression profiles of various immune cells within the tumor microenvironment can be inferred from the matched PBMC scRNA-seq data. We find that the established exhausted T-cell signature can be predicted from the blood and serve as a valuable prognostic blood biomarker of immunotherapy response. Additionally, our study reveals that the inferred ratio between tumor memory B- and regulatory T-cell fractions is predictive of immunotherapy response and is superior to the well-established cytolytic and exhausted T-cell signatures. These results highlight the promising potential of PBMC scRNA-seq in cancer immunotherapy and warrant, and will hopefully facilitate, further investigations on a larger scale. The code for predicting tumor immune microenvironment from PBMC scRNA-seq, TIMEP, is provided, offering other researchers the opportunity to investigate its prospective applications in various other indications. SIGNIFICANCE Our work offers a new and promising paradigm in liquid biopsies to unlock the power of blood single-cell transcriptomics in cancer immunotherapy.
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Affiliation(s)
- Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Tiangen Chang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Fiorella Schischlik
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
- Boehringer Ingelheim RCV Gmbh & Co KG, Vienna, Austria
| | - Kun Wang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Sanju Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, San Diego, California
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland
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13
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Teillaud JL, Houel A, Panouillot M, Riffard C, Dieu-Nosjean MC. Tertiary lymphoid structures in anticancer immunity. Nat Rev Cancer 2024; 24:629-646. [PMID: 39117919 DOI: 10.1038/s41568-024-00728-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Tertiary lymphoid structures (TLS) are transient ectopic lymphoid aggregates where adaptive antitumour cellular and humoral responses can be elaborated. Initially described in non-small cell lung cancer as functional immune lymphoid structures associated with better clinical outcome, TLS have also been found in many other carcinomas, as well as melanomas and sarcomas, and associated with improved response to immunotherapy. The manipulation of TLS as a therapeutic strategy is now coming of age owing to the likely role of TLS in the improved survival of patients with cancer receiving immune checkpoint inhibitor treatment. TLS have also garnered considerable interest as a predictive biomarker of the response to antitumour therapies, including immune checkpoint blockade and, possibly, chemotherapy. However, several important questions still remain regarding the definition of TLS in terms of both their cellular composition and functions. Here, we summarize the current views on the composition of TLS at different stages of their development. We also discuss the role of B cells and T cells associated with TLS and their dialogue in mounting antibody and cellular antitumour responses, as well as some of the various mechanisms that negatively regulate antitumour activity of TLS. The prognostic value of TLS to the clinical outcome of patients with cancer and the relationship between TLS and the response to therapy are then addressed. Finally, we present some preclinical evidence that favours the idea that manipulating the formation and function of TLS could lead to a potent next-generation cancer immunotherapy.
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Affiliation(s)
- Jean-Luc Teillaud
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
| | - Ana Houel
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
- Transgene, Illkirch-Graffenstaden, France
| | - Marylou Panouillot
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
- Sanofi, Vitry-sur-Seine, France
| | - Clémence Riffard
- Sorbonne University UMRS1135, Paris, France
- Inserm U1135, Paris, France
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France
| | - Marie-Caroline Dieu-Nosjean
- Sorbonne University UMRS1135, Paris, France.
- Inserm U1135, Paris, France.
- Center of Immunology and Microbial Infections (Cimi), Faculty of Health, Paris, France.
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14
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Niu L, Chen T, Yang A, Yan X, Jin F, Zheng A, Song X. Macrophages and tertiary lymphoid structures as indicators of prognosis and therapeutic response in cancer patients. Biochim Biophys Acta Rev Cancer 2024; 1879:189125. [PMID: 38851437 DOI: 10.1016/j.bbcan.2024.189125] [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: 02/20/2024] [Revised: 05/24/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Tertiary lymphoid structures (TLS) can reflect cancer prognosis and clinical outcomes in various tumour tissues. Tumour-associated macrophages (TAMs) are indispensable components of the tumour microenvironment and play crucial roles in tumour development and immunotherapy. TAMs are associated with TLS induction via the modulation of the T cell response, which is a major component of the TLS. Despite their important roles in cancer immunology, the subtypes of TAMs that influence TLS and their correlation with prognosis are not completely understood. Here, we provide novel insights into the role of TAMs in regulating TLS formation. Furthermore, we discuss the prognostic value of these TAM subtypes and TLS, as well as the current antitumour therapies for inducing TLS. This study highlights an entirely new field of TLS regulation that may lead to the development of an innovative perspective on immunotherapy for cancer treatment.
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Affiliation(s)
- Li Niu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China
| | - Ting Chen
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Aodan Yang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, China
| | - Xiwen Yan
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, China
| | - Feng Jin
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, China
| | - Ang Zheng
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang, China.
| | - Xinyue Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.
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15
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Chu X, Li X, Zhang Y, Dang G, Miao Y, Xu W, Wang J, Zhang Z, Cheng S. Integrative single-cell analysis of human colorectal cancer reveals patient stratification with distinct immune evasion mechanisms. NATURE CANCER 2024; 5:1409-1426. [PMID: 39147986 DOI: 10.1038/s43018-024-00807-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
The tumor microenvironment (TME) considerably influences colorectal cancer (CRC) progression, therapeutic response and clinical outcome, but studies of interindividual heterogeneities of the TME in CRC are lacking. Here, by integrating human colorectal single-cell transcriptomic data from approximately 200 donors, we comprehensively characterized transcriptional remodeling in the TME compared to noncancer tissues and identified a rare tumor-specific subset of endothelial cells with T cell recruitment potential. The large sample size enabled us to stratify patients based on their TME heterogeneity, revealing divergent TME subtypes in which cancer cells exploit different immune evasion mechanisms. Additionally, by associating single-cell transcriptional profiling with risk genes identified by genome-wide association studies, we determined that stromal cells are major effector cell types in CRC genetic susceptibility. In summary, our results provide valuable insights into CRC pathogenesis and might help with the development of personalized immune therapies.
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Affiliation(s)
| | | | - Yu Zhang
- Changping Laboratory, Beijing, China
| | - Guohui Dang
- Changping Laboratory, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | | | - Wenbin Xu
- Changping Laboratory, Beijing, China
| | | | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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16
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Liao YH, Chen L, Feng BH, Lv W, Huang XP, Li H, Li CP. Revelation of comprehensive cell profiling of primary and metastatic tumour ecosystems in oral squamous cell carcinoma by single-cell transcriptomic analysis. Int J Med Sci 2024; 21:2293-2304. [PMID: 39310253 PMCID: PMC11413902 DOI: 10.7150/ijms.97404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/31/2024] [Indexed: 09/25/2024] Open
Abstract
Background: The analysis of single-cell transcriptome profiling of tumour tissue isolates helps to identify heterogeneous tumour cells, neighbouring stromal cells and immune cells. Local metastasis of lymph nodes is the most dominant and influential biological behaviors of oral squamous cell carcinoma (OSCC) in terms of treatment prognosis. Understanding metastasis initiation and progression is important for the discovery of new treatments for OSCC and prediction of clinical responses to immunotherapy. However, the identity of metastasis-initiating cells in human OSCC remains elusive, and whether metastases are hierarchically organized is unknown. Therefore, this study was conducted to understand the cellular origins and gene expression signature of OSCC at the single-cell level. Methods: Single-cell RNA sequencing (scRNA-seq) was used to analyze cells from tissue of para-carcinoma (PCA: adjacent normal tissue not less than 2 cm from the tumour), carcinoma (CA), lymph node metastasis (LNM) from patients with OSCC and PCA and CA tissue from patients with second primary OSCC (SPOSCC) after radiotherapy of nasopharyngeal carcinoma (NPC). The cell types and their underlying functions were classified. The comparisons were then conducted between the homology and heterogeneity from cell types and both conservative and heterogeneous aspects of evolution were identified. Immunohistochemistry was performed to verify the makers of cell clusters and the expression level of novel genes. Results: A single-cell transcriptomic map of OSCC was created, including 16 clusters of PCA cells, 17 clusters of CA cells, 14 clusters of left LNM cells, and 14 clusters of right LNM cells. We also discovered two novel types of cells including CD1C-CD141-dendritic cells and CD1C+_B dendritic cells. Most of the non-cancer cells are immune cells, with two distinct clusters of T lymphocytes, B lymphocytes, CD1C-CD141-dendritic cells+ and CD1C+_B dendritic cells. We also classified cells into 15 clusters for SPOSCC after radiotherapy of NPC. Determining the upregulated expression levels of IL1RN and C15orf48 as novel markers using immunohistochemistry facilitated the correct classification of OSCC including SPOSCC after radiotherapy of NPC and the prediction of their prognosis. Conclusions: The findings provided an unprecedented and valuable view of the functional states and heterogeneity of cell populations in LNM of OSCC and SPOSCC after radiotherapy of NPC at single-cell genomic resolution. Moreover, this transcriptomic map discovered new cell types in mouth, and novel tumour cell-specific markers/oncogene.
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Affiliation(s)
- Yin-han Liao
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
| | - Li Chen
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
| | - Bing-hua Feng
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
| | - Wei Lv
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
| | - Xuan-ping Huang
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning 530021, P. R. China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning 530021, P. R. China
| | - Hao Li
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning 530021, P. R. China
| | - Cui-ping Li
- College & Hospital of Stomatology, Guangxi Medical University, Nanning 530021, P. R. China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning 530021, P. R. China
- Guangxi Health Commission Key laboratory of prevention and treatment for oral infectious diseases, Nanning 530021, P. R. China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning 530021, P. R. China
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17
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Restaino AC, Ahmadi M, Nikpoor AR, Walz A, Balood M, Eichwald T, Talbot S, Vermeer PD. TUMOR-INFILTRATING NOCICEPTOR NEURONS PROMOTE IMMUNOSUPPRESSION. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609450. [PMID: 39253487 PMCID: PMC11382997 DOI: 10.1101/2024.08.23.609450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Nociceptor neurons impact tumor immunity. Removing nociceptor neurons reduced myeloid-derived suppressor cell (MDSCs) tumor infiltration in mouse models of head and neck carcinoma and melanoma. Carcinoma-released small extracellular vesicles (sEVs) attract nociceptive nerves to tumors. sEV-deficient tumors fail to develop in mice lacking nociceptor neurons. Exposure of dorsal root ganglia (DRG) neurons to cancer sEVs elevated expression of Substance P, IL-6 and injury-related neuronal markers while treatment with cancer sEVs and cytotoxic CD8 T-cells induced an immunosuppressive state (increased exhaustion ligands and cytokines). Cancer patient sEVs enhanced DRG responses to capsaicin, indicating increased nociceptor sensitivity. Conditioned media from DRG and cancer cell co-cultures promoted expression of MDSC markers in primary bone marrow cells while DRG conditioned media together with cancer sEVs induced checkpoint expression on T-cells. Our findings indicate that nociceptor neurons facilitate CD8+ T cell exhaustion and enhance MDSC infiltration. Targeting nociceptor-released IL-6 emerges as a novel strategy to disrupt harmful neuro-immune interactions in cancer and enhance anti-tumor immunity.
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Affiliation(s)
- Anthony C. Restaino
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, USA
| | - Maryam Ahmadi
- Department of Biomedical and Molecular Sciences, Queen’s University. Kingston. Canada
| | - Amin Reza Nikpoor
- Department of Biomedical and Molecular Sciences, Queen’s University. Kingston. Canada
| | - Austin Walz
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, USA
| | - Mohammad Balood
- Department of Biomedical and Molecular Sciences, Queen’s University. Kingston. Canada
| | - Tuany Eichwald
- Department of Biomedical and Molecular Sciences, Queen’s University. Kingston. Canada
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Sebastien Talbot
- Department of Biomedical and Molecular Sciences, Queen’s University. Kingston. Canada
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden
| | - Paola D. Vermeer
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, USA
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18
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Zhang C, Li K, Zhu H, Cheng M, Chen S, Ling R, Wang C, Chen D. ITGB6 modulates resistance to anti-CD276 therapy in head and neck cancer by promoting PF4 + macrophage infiltration. Nat Commun 2024; 15:7077. [PMID: 39152118 PMCID: PMC11329676 DOI: 10.1038/s41467-024-51096-0] [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: 11/03/2023] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Enoblituzumab, an immunotherapeutic agent targeting CD276, shows both safety and efficacy in activating T cells and oligodendrocyte-like cells against various cancers. Preclinical studies and mouse models suggest that therapies targeting CD276 may outperform PD1/PD-L1 blockade. However, data from mouse models indicate a significant non-responsive population to anti-CD276 treatment, with the mechanisms of resistance still unclear. In this study, we evaluate the activity of anti-CD276 antibodies in a chemically-induced murine model of head and neck squamous cell carcinoma. Using models of induced and orthotopic carcinogenesis, we identify ITGB6 as a key gene mediating differential responses to anti-CD276 treatment. Through single-cell RNA sequencing and gene-knockout mouse models, we find that ITGB6 regulates the expression of the tumor-associated chemokine CX3CL1, which recruits and activates PF4+ macrophages that express high levels of CX3CR1. Inhibition of the CX3CL1-CX3CR1 axis suppresses the infiltration and secretion of CXCL16 by PF4+ macrophages, thereby reinvigorating cytotoxic CXCR6+ CD8+ T cells and enhancing sensitivity to anti-CD276 treatment. Further investigations demonstrate that inhibiting ITGB6 restores sensitivity to PD1 antibodies in mice resistant to anti-PD1 treatment. In summary, our research reveals a resistance mechanism associated with immune checkpoint inhibitor therapy and identifies potential targets to overcome resistance in cancer treatment.
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MESH Headings
- Animals
- Mice
- B7 Antigens/metabolism
- B7 Antigens/genetics
- B7 Antigens/antagonists & inhibitors
- Humans
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/immunology
- Head and Neck Neoplasms/drug therapy
- Head and Neck Neoplasms/pathology
- Mice, Knockout
- CX3C Chemokine Receptor 1/metabolism
- CX3C Chemokine Receptor 1/genetics
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/immunology
- Macrophages/immunology
- Macrophages/metabolism
- Cell Line, Tumor
- Mice, Inbred C57BL
- Squamous Cell Carcinoma of Head and Neck/drug therapy
- Squamous Cell Carcinoma of Head and Neck/immunology
- Squamous Cell Carcinoma of Head and Neck/genetics
- Squamous Cell Carcinoma of Head and Neck/pathology
- Squamous Cell Carcinoma of Head and Neck/metabolism
- Disease Models, Animal
- Female
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
- Gene Expression Regulation, Neoplastic/drug effects
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Affiliation(s)
- Caihua Zhang
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Kang Li
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongzhang Zhu
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Maosheng Cheng
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuang Chen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Rongsong Ling
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Cheng Wang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Demeng Chen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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19
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Patin EC, Nenclares P, Chan Wah Hak C, Dillon MT, Patrikeev A, McLaughlin M, Grove L, Foo S, Soliman H, Barata JP, Marsden J, Baldock H, Gkantalis J, Roulstone V, Kyula J, Burley A, Hubbard L, Pedersen M, Smith SA, Clancy-Thompson E, Melcher AA, Ono M, Rullan A, Harrington KJ. Sculpting the tumour microenvironment by combining radiotherapy and ATR inhibition for curative-intent adjuvant immunotherapy. Nat Commun 2024; 15:6923. [PMID: 39134540 PMCID: PMC11319479 DOI: 10.1038/s41467-024-51236-6] [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: 01/05/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
The combination of radiotherapy/chemoradiotherapy and immune checkpoint blockade can result in poor outcomes in patients with locally advanced head and neck squamous cell carcinoma (HNSCC). Here, we show that combining ATR inhibition (ATRi) with radiotherapy (RT) increases the frequency of activated NKG2A+PD-1+ T cells in animal models of HNSCC. Compared with the ATRi/RT treatment regimen alone, the addition of simultaneous NKG2A and PD-L1 blockade to ATRi/RT, in the adjuvant, post-radiotherapy setting induces a robust antitumour response driven by higher infiltration and activation of cytotoxic T cells in the tumour microenvironment. The efficacy of this combination relies on CD40/CD40L costimulation and infiltration of activated, proliferating memory CD8+ and CD4+ T cells with persistent or new T cell receptor (TCR) signalling, respectively. We also observe increased richness in the TCR repertoire and emergence of numerous and large TCR clonotypes that cluster based on antigen specificity in response to NKG2A/PD-L1/ATRi/RT. Collectively, our data point towards potential combination approaches for the treatment of HNSCC.
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Affiliation(s)
- Emmanuel C Patin
- Targeted Therapy Team, The Institute of Cancer Research, London, UK.
| | - Pablo Nenclares
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Charleen Chan Wah Hak
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Magnus T Dillon
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Anton Patrikeev
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | | | - Lorna Grove
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Shane Foo
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | | | | | | | - Holly Baldock
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Jim Gkantalis
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | | | - Joan Kyula
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Amy Burley
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Lisa Hubbard
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | - Malin Pedersen
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
| | | | | | - Alan A Melcher
- Translational Immunotherapy Team, The Institute of Cancer Research, London, UK
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London, UK
| | - Antonio Rullan
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - Kevin J Harrington
- Targeted Therapy Team, The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
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20
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Zhang Y, Zhang J, Zhao S, Xu Y, Huang Y, Liu S, Su P, Wang C, Li Y, Li H, Yang P, Yang C. Single-cell RNA sequencing highlights the immunosuppression of IDO1 + macrophages in the malignant transformation of oral leukoplakia. Theranostics 2024; 14:4787-4805. [PMID: 39239507 PMCID: PMC11373622 DOI: 10.7150/thno.99112] [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: 05/31/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024] Open
Abstract
Rationale: Immunosuppressive tumor microenvironment (iTME) plays an important role in carcinogenesis, and some macrophage subsets are associated with iTME generation. However, the sub-population characterization of macrophages in oral carcinogenesis remains largely unclear. Here, we investigated the immunosuppressive status with focus on function of a macrophage subset that expressed indoleamine 2,3 dioxygenase 1 (Macro-IDO1) in oral carcinogenesis. Methods: We built a single cell transcriptome atlas from 3 patients simultaneously containing oral squamous cell carcinoma (OSCC), precancerous oral leukoplakia (preca-OLK) and paracancerous tissue (PCA). Through single-cell RNA sequencing and further validation using multicolor immunofluorescence staining and the in vitro/in vivo experiments, the immunosuppressive cell profiles were built and the role of a macrophage subset that expressed indoleamine 2,3 dioxygenase 1 (Macro-IDO1) in the malignant transformation of oral leukoplakia was evaluated. Results: The iTME formed at preca-OLK stage, as evidenced by increased exhausted T cells, Tregs and some special subsets of macrophages and fibroblasts. Macro-IDO1 was predominantly enriched in preca-OLK and OSCC, distributed near exhausted T cells and possessed tumor associated macrophage transformation potentials. Functional analysis revealed the established immunosuppressive role of Macro-IDO1 in preca-OLK and OSCC: enriching the immunosuppression related genes; having an established level of immune checkpoint score; exerting strong immunosuppressive interaction with T cells; positively correlating with the CD8-exhausted. The immunosuppression related gene expression of macrophages also increased in preca-OLK/OSCC compared to PCA. The use of the IDO1 inhibitor reduced 4NQO induced oral carcinogenesis in mice. Mechanistically, IFN-γ-JAK-STAT pathway was associated with IDO1 upregulation in OLK and OSCC. Conclusions: These results highlight that Macro-IDO1-enriched in preca-OLK possesses a strong immunosuppressive role and contributes to oral carcinogenesis, providing a potential target for preventing precancerous legions from transformation into OSCC.
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Affiliation(s)
- Yu Zhang
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Jie Zhang
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
| | - Simin Zhao
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yan Xu
- Jinan Stomatological Hospital, Jinan, Shandong, China
| | - Yingying Huang
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Shaopeng Liu
- Department of Stomatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Department of Stomatology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Caijiao Wang
- Department of Pathology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Yahui Li
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Hao Li
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Pishan Yang
- Department of Periodontology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, China
| | - Chengzhe Yang
- Department of Oral and Maxillofacial Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, China
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21
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Lin X, Zhao R, Bin Y, Huo R, Xue G, Wu J. TIMP1 promotes thyroid cancer cell progression through macrophage phenotypic polarization via the PI3K/AKT signaling pathway. Genomics 2024; 116:110914. [PMID: 39128817 DOI: 10.1016/j.ygeno.2024.110914] [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: 05/01/2024] [Revised: 07/21/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024]
Abstract
Increasing evidence suggests that tissue inhibitor of metalloproteinase 1 (TIMP1) played a pivotal role in immune regulation. Our study focused on examining the expression and function of TIMP1 in humans, particularly in its regulation of tumor-associated macrophages (TAMs) in papillary thyroid carcinoma (PTC). We observed an upregulation of TIMP1 in 16 different types of malignancies, including thyroid cancer. TIMP1 shaped the inflammatory TME in PTC. Inhibiting the expression of TIMP1 has been demonstrated to reduce the malignant biological traits of PTC cells. Furthermore, reducing TIMP1 expression impeded M2 macrophage polarization as well as facilitated M1 macrophage polarization in PTC. ELISA results demonstrated that downregulated TIMP1 expression correlated with decreased levels of IL10 and TGF-β in cell supernatants. Furthermore, the supernatant from polarized macrophages in the TIMP1-silenced group inhibited the motility of wild-type PTC cells. Therefore, TIMP1 may enhance the progression of PTC by stimulating the PI3K/AKT pathway via the secretion of IL10 and TGF-β, consequently influencing M2-type polarization in TAMs.
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Affiliation(s)
- Xu Lin
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Ruhua Zhao
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Yu Bin
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Ronghua Huo
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China
| | - Gang Xue
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China; Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou 075000, China.
| | - Jingfang Wu
- Department of Morphology Laboratory, Hebei North University, Zhangjiakou 075000, China.
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22
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Cillo AR, Cardello C, Shan F, Karapetyan L, Kunning S, Sander C, Rush E, Karunamurthy A, Massa RC, Rohatgi A, Workman CJ, Kirkwood JM, Bruno TC, Vignali DAA. Blockade of LAG-3 and PD-1 leads to co-expression of cytotoxic and exhaustion gene modules in CD8 + T cells to promote antitumor immunity. Cell 2024; 187:4373-4388.e15. [PMID: 39121849 PMCID: PMC11346583 DOI: 10.1016/j.cell.2024.06.036] [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: 02/09/2023] [Revised: 05/09/2024] [Accepted: 06/26/2024] [Indexed: 08/12/2024]
Abstract
Relatlimab (rela; anti-LAG-3) plus nivolumab (nivo; anti-PD-1) is safe and effective for treatment of advanced melanoma. We designed a trial (NCT03743766) where advanced melanoma patients received rela, nivo, or rela+nivo to interrogate the immunologic mechanisms of rela+nivo. Analysis of biospecimens from this ongoing trial demonstrated that rela+nivo led to enhanced capacity for CD8+ T cell receptor signaling and altered CD8+ T cell differentiation, leading to heightened cytotoxicity despite the retention of an exhaustion profile. Co-expression of cytotoxic and exhaustion signatures was driven by PRDM1, BATF, ETV7, and TOX. Effector function was upregulated in clonally expanded CD8+ T cells that emerged after rela+nivo. A rela+nivo intratumoral CD8+ T cell signature was associated with a favorable prognosis. This intratumoral rela+nivo signature was validated in peripheral blood as an elevated frequency of CD38+TIM3+CD8+ T cells. Overall, we demonstrated that cytotoxicity can be enhanced despite the retention of exhaustion signatures, which will inform future therapeutic strategies.
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Affiliation(s)
- Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Integrative Systems Biology (ISB) Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lilit Karapetyan
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sheryl Kunning
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Cindy Sander
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Elizabeth Rush
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Ryan C Massa
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anjali Rohatgi
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John M Kirkwood
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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Su J, Song Y, Zhu Z, Huang X, Fan J, Qiao J, Mao F. Cell-cell communication: new insights and clinical implications. Signal Transduct Target Ther 2024; 9:196. [PMID: 39107318 PMCID: PMC11382761 DOI: 10.1038/s41392-024-01888-z] [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: 12/29/2023] [Revised: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 09/11/2024] Open
Abstract
Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication. Cell-cell communication (CCC) is essential for growth, development, differentiation, tissue and organ formation, maintenance, and physiological regulation. Cells communicate through direct contact or at a distance using ligand-receptor interactions. So cellular communication encompasses two essential processes: cell signal conduction for generation and intercellular transmission of signals, and cell signal transduction for reception and procession of signals. Deciphering intercellular communication networks is critical for understanding cell differentiation, development, and metabolism. First, we comprehensively review the historical milestones in CCC studies, followed by a detailed description of the mechanisms of signal molecule transmission and the importance of the main signaling pathways they mediate in maintaining biological functions. Then we systematically introduce a series of human diseases caused by abnormalities in cell communication and their progress in clinical applications. Finally, we summarize various methods for monitoring cell interactions, including cell imaging, proximity-based chemical labeling, mechanical force analysis, downstream analysis strategies, and single-cell technologies. These methods aim to illustrate how biological functions depend on these interactions and the complexity of their regulatory signaling pathways to regulate crucial physiological processes, including tissue homeostasis, cell development, and immune responses in diseases. In addition, this review enhances our understanding of the biological processes that occur after cell-cell binding, highlighting its application in discovering new therapeutic targets and biomarkers related to precision medicine. This collective understanding provides a foundation for developing new targeted drugs and personalized treatments.
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Affiliation(s)
- Jimeng Su
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ying Song
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Cancer Center, Peking University Third Hospital, Beijing, China
| | - Xinyue Huang
- Biomedical Research Institute, Shenzhen Peking University-the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
- Cancer Center, Peking University Third Hospital, Beijing, China.
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24
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Yan S, Zhang X, Lin Q, Du M, Li Y, He S, Chen J, Li X, Bei J, Chen S, Song M. Deciphering the interplay of HPV infection, MHC-II expression, and CXCL13 + CD4 + T cell activation in oropharyngeal cancer: implications for immunotherapy. Cancer Immunol Immunother 2024; 73:206. [PMID: 39105803 PMCID: PMC11303625 DOI: 10.1007/s00262-024-03789-0] [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: 03/30/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Human papillomavirus (HPV) infection has become an important etiological driver of oropharyngeal squamous cell carcinoma (OPSCC), leading to unique tumor characteristics. However, the interplay between HPV-associated tumor cells and tumor microenvironment (TME) remains an enigma. METHODS We performed a single-cell RNA-sequencing (scRNA-seq) on HPV-positive (HPV+) and HPV-negative (HPV‒) OPSCC tumors, each for three samples, and one normal tonsil tissue. Ex vivo validation assays including immunofluorescence staining, cell line co-culture, and flow cytometry analysis were used to test specific subtypes of HPV+ tumor cells and their communications with T cells. RESULTS Through a comprehensive single-cell transcriptome analysis, we uncover the distinct transcriptional signatures between HPV+ and HPV‒ OPSCC. Specifically, HPV+ OPSCC tumor cells manifest an enhanced interferon response and elevated expression of the major histocompatibility complex II (MHC-II), potentially bolstering tumor recognition and immune response. Furthermore, we identify a CXCL13+CD4+ T cell subset that exhibits dual features of both follicular and pro-inflammatory helper T cells. Noteworthily, HPV+ OPSCC tumor cells embrace extensive intercellular communications with CXCL13+CD4+ T cells. Interaction with HPV+ OPSCC tumor cells amplifies CXCL13 and IFNγ release in CD4+T cells, fostering a pro-inflammatory TME. Additionally, HPV+ tumor cells expressing high MHC-II and CXCL13+CD4+ T cell prevalence are indicative of favorable overall survival rates in OPSCC patients. CONCLUSIONS Together, our study underscores a synergistic inflammatory immune response orchestrated by highly immunogenic tumor cells and CXCL13+CD4+ T cells in HPV+ OPSCC, offering useful insights into strategy development for patient stratification and effective immunotherapy in OPSCC.
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Affiliation(s)
- Shida Yan
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xing Zhang
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Qiaohong Lin
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Mingyuan Du
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yiqi Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Shuai He
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jingtao Chen
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiyuan Li
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jinxin Bei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Shuwei Chen
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Ming Song
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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25
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Yan M, Xiao LY, Gosau M, Smeets R, Feng HC, Burg S, Fu LL, Friedrich RE. The role of herpes simplex virus infection in the etiology of head and neck cancer-a Mendelian randomization study. Front Immunol 2024; 15:1278327. [PMID: 39161761 PMCID: PMC11331341 DOI: 10.3389/fimmu.2024.1278327] [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: 08/16/2023] [Accepted: 04/29/2024] [Indexed: 08/21/2024] Open
Abstract
Introduction Head and neck cancer (HNC) is a complex disease, and multiple risk factors can lead to its progression. Observational studies indicated that herpes simplex virus (HSV) may be correlated with the risk of HNC. However, the causal effects and direction between them were still unclear. Methods This study utilized a Mendelian randomization (MR) approach for causality assessment between HSV infection and Head and neck cancer based on the latest public health data and Genome-Wide Association Study (GWAS) data. The causal effects were estimated using IVW, weighted median, and MR-Egger. A reverse MR analysis was subsequently performed. Cochrans Q test, MR-Egger intercept test, leave one out analysis, and the funnel plot were all used in sensitivity analyses. Results Genetically predicted higher level of HSV-1 IgG was causally related to HNC (OR=1.0019, 95%CI=1.0003-1.0036, p=0.0186, IVW) and oral and oropharyngeal cancer (OR=1.0018, 95%CI=1.0004-1.0033, p=0.0105, IVW). The reverse MR analysis did not demonstrate a reverse causal relationship between HSV and HNC. However, HSV-2 infection was not causally related to HNC data and oropharyngeal cancer data. Sensitivity analysis was performed and revealed no heterogeneity and horizontal pleiotropy. Conclusion Collectively, a significant association was noted between HSV infection and increased risk of HNC, providing valuable insights into the etiology of this malignancy. Further in-depth study is needed to validate these findings and elucidate the underpinning mechanisms.
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Affiliation(s)
- Ming Yan
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Li-yuan Xiao
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
| | - Martin Gosau
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Smeets
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Oral and Maxillofacial Surgery, Division of Regenerative Orofacial Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hong-chao Feng
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
| | - Simon Burg
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ling-ling Fu
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reinhard E. Friedrich
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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26
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Talks BJ, Mather MW, Chahal M, Coates M, Clatworthy MR, Haniffa M. Mapping Human Immunity and the Education of Waldeyer's Ring. Annu Rev Genomics Hum Genet 2024; 25:161-182. [PMID: 38594932 DOI: 10.1146/annurev-genom-120522-012938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The development and deployment of single-cell genomic technologies have driven a resolution revolution in our understanding of the immune system, providing unprecedented insight into the diversity of immune cells present throughout the body and their function in health and disease. Waldeyer's ring is the collective name for the lymphoid tissue aggregations of the upper aerodigestive tract, comprising the palatine, pharyngeal (adenoids), lingual, and tubal tonsils. These tonsils are the first immune sentinels encountered by ingested and inhaled antigens and are responsible for mounting the first wave of adaptive immune response. An effective mucosal immune response is critical to neutralizing infection in the upper airway and preventing systemic spread, and dysfunctional immune responses can result in ear, nose, and throat pathologies. This review uses Waldeyer's ring to demonstrate how single-cell technologies are being applied to advance our understanding of the immune system and highlight directions for future research.
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Affiliation(s)
- Benjamin J Talks
- Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Michael W Mather
- Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Manisha Chahal
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Matthew Coates
- Department of Medicine, University of Cambridge, Cambridge, UK; ,
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Hinxton, UK;
- Department of Medicine, University of Cambridge, Cambridge, UK; ,
| | - Muzlifah Haniffa
- Department of Dermatology and National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Sanger Institute, Hinxton, UK;
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
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27
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Meng X, Zheng Y, Zhang L, Liu P, Liu Z, He Y. Single-Cell Analyses Reveal the Metabolic Heterogeneity and Plasticity of the Tumor Microenvironment during Head and Neck Squamous Cell Carcinoma Progression. Cancer Res 2024; 84:2468-2483. [PMID: 38718319 DOI: 10.1158/0008-5472.can-23-1344] [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: 05/04/2023] [Revised: 10/31/2023] [Accepted: 04/29/2024] [Indexed: 08/02/2024]
Abstract
Metabolic reprogramming is a hallmark of cancer. In addition to metabolic alterations in the tumor cells, multiple other metabolically active cell types in the tumor microenvironment (TME) contribute to the emergence of a tumor-specific metabolic milieu. Here, we defined the metabolic landscape of the TME during the progression of head and neck squamous cell carcinoma (HNSCC) by performing single-cell RNA sequencing on 26 human patient specimens, including normal tissue, precancerous lesions, early stage cancer, advanced-stage cancer, lymph node metastases, and recurrent tumors. The analysis revealed substantial heterogeneity at the transcriptional, developmental, metabolic, and functional levels in different cell types. SPP1+ macrophages were identified as a protumor and prometastatic macrophage subtype with high fructose and mannose metabolism, which was further substantiated by integrative analysis and validation experiments. An inhibitor of fructose metabolism reduced the proportion of SPP1+ macrophages, reshaped the immunosuppressive TME, and suppressed tumor growth. In conclusion, this work delineated the metabolic landscape of HNSCC at a single-cell resolution and identified fructose metabolism as a key metabolic feature of a protumor macrophage subpopulation. Significance: Fructose and mannose metabolism is a metabolic feature of a protumor and prometastasis macrophage subtype and can be targeted to reprogram macrophages and the microenvironment of head and neck squamous cell carcinoma.
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Affiliation(s)
- Xiaoyan Meng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yang Zheng
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Lingfang Zhang
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Peipei Liu
- Suzhou Lingdian Biotechnology Co., Ltd., Suzhou, P.R. China
| | - Zhonglong Liu
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
| | - Yue He
- Department of Oral Maxillofacial & Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, P.R. China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology Shanghai, Shanghai, P.R. China
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28
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Li W, Wang H, Zhao J, Xia J, Sun X. scHyper: reconstructing cell-cell communication through hypergraph neural networks. Brief Bioinform 2024; 25:bbae436. [PMID: 39276328 PMCID: PMC11401449 DOI: 10.1093/bib/bbae436] [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: 05/26/2024] [Revised: 07/14/2024] [Accepted: 08/07/2024] [Indexed: 09/16/2024] Open
Abstract
Cell-cell communications is crucial for the regulation of cellular life and the establishment of cellular relationships. Most approaches of inferring intercellular communications from single-cell RNA sequencing (scRNA-seq) data lack a comprehensive global network view of multilayered communications. In this context, we propose scHyper, a new method that can infer intercellular communications from a global network perspective and identify the potential impact of all cells, ligand, and receptor expression on the communication score. scHyper designed a new way to represent tripartite relationships, by extracting a heterogeneous hypergraph that includes the source (ligand expression), the target (receptor expression), and the relevant ligand-receptor (L-R) pairs. scHyper is based on hypergraph representation learning, which measures the degree of match between the intrinsic attributes (static embeddings) of nodes and their observed behaviors (dynamic embeddings) in the context (hyperedges), quantifies the probability of forming hyperedges, and thus reconstructs the cell-cell communication score. Additionally, to effectively mine the key mechanisms of signal transmission, we collect a rich dataset of multisubunit complex L-R pairs and propose a nonparametric test to determine significant intercellular communications. Comparing with other tools indicates that scHyper exhibits superior performance and functionality. Experimental results on the human tumor microenvironment and immune cells demonstrate that scHyper offers reliable and unique capabilities for analyzing intercellular communication networks. Therefore, we introduced an effective strategy that can build high-order interaction patterns, surpassing the limitations of most methods that can only handle low-order interactions, thus more accurately interpreting the complexity of intercellular communications.
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Affiliation(s)
- Wenying Li
- School of Mathematics and System Science, Xinjiang University, No. 777 Huarui Street, Shuimogou District, Urumqi, Xinjiang 830017, China
| | - Haiyun Wang
- School of Mathematics and System Science, Xinjiang University, No. 777 Huarui Street, Shuimogou District, Urumqi, Xinjiang 830017, China
| | - Jianping Zhao
- School of Mathematics and System Science, Xinjiang University, No. 777 Huarui Street, Shuimogou District, Urumqi, Xinjiang 830017, China
| | - Junfeng Xia
- School of Mathematics and System Science, Xinjiang University, No. 777 Huarui Street, Shuimogou District, Urumqi, Xinjiang 830017, China
- Institute of Physical Science and Information Technology, Anhui University, No. 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Xiaoqiang Sun
- School of Mathematics, Sun Yat-sen University, No. 135 Xingang Xi Road, Haizhu District, Guangzhou, Guangdong 510275, China
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29
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Muijlwijk T, Nijenhuis DNLM, Ganzevles SH, Ekhlas F, Ballesteros-Merino C, Peferoen LAN, Bloemena E, Fox BA, Poell JB, Leemans CR, Brakenhoff RH, van de Ven R. Immune cell topography of head and neck cancer. J Immunother Cancer 2024; 12:e009550. [PMID: 39053947 DOI: 10.1136/jitc-2024-009550] [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] [Accepted: 07/13/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Approximately 50% of head and neck squamous cell carcinomas (HNSCC) recur after treatment with curative intent. Immune checkpoint inhibitors are treatment options for recurrent/metastatic HNSCC; however, less than 20% of patients respond. To increase this response rate, it is fundamental to increase our understanding of the spatial tumor immune microenvironment (TIME). METHODS In total, 53 HNSCC specimens were included. Using a seven-color multiplex immunohistochemistry panel we identified tumor cells, CD163+macrophages, B cells, CD8+T cells, CD4+T helper cells and regulatory T cells (Tregs) in treatment-naive surgical resection specimens (n=29) and biopsies (n=18). To further characterize tumor-infiltrating CD8+T cells, we stained surgical resection specimens (n=12) with a five-color tumor-resident panel including CD103, Ki67, CD8 and pan-cytokeratin. Secretome analysis was performed on matched tumor suspensions (n=11) to measure protein levels. RESULTS Based on CD8+T cell infiltrates, we identified four different immunotypes: fully infiltrated, stroma-restricted, immune-excluded, and immune-desert. We found higher cytokine levels in fully infiltrated tumors compared with other immunotypes. While the highest immune infiltrates were observed in the invasive margin for all immune cells, CD163+macrophages and Tregs had the highest tendency to infiltrate the tumor center. Within the tumor center, especially B cells stayed at the tumor stroma, whereas CD163+macrophages, followed by T cells, were more often localized within tumor fields. Also, B cells were found further away from other cells and often formed aggregates while T cells and CD163+macrophages tended to be more closely located to each other. Across resection specimens from various anatomical sites within the head and neck, oral cavity tumors exhibited the highest densities of Tregs. Moreover, the distance from B cells and T cells to tumor cells was shortest in oral cavity squamous cell carcinoma (OCSCC), suggesting more interaction between lymphocytes and tumor cells. Also, the fraction of T cells within 10 µm of CD163+macrophages was lowest in OCSCC, indicating fewer myeloid/T-cell suppressive interactions in OCSCC. CONCLUSIONS We comprehensively described the TIME of HNSCC using a unique data set of resection specimens. We discovered that the composition, as well as the relative localization of immune cells in the TIME, differed in distinct anatomical sites of the head and neck.
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Affiliation(s)
- Tara Muijlwijk
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Dennis N L M Nijenhuis
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Sonja H Ganzevles
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Fatima Ekhlas
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Carmen Ballesteros-Merino
- Molecular and Tumor Immunology Laboratory, Providence Cancer Institute, Robert W. Franz Research Center at the Earle A. Chiles Research Institute, Portland, Oregon, USA
| | - Laura A N Peferoen
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Pathology, Amsterdam UMC - Locatie VUMC, Amsterdam, The Netherlands
- Maxillofacial Surgery/ Oral Pathology, Academic Center for Dentistry, Amsterdam, The Netherlands
| | - Elisabeth Bloemena
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Pathology, Amsterdam UMC - Locatie VUMC, Amsterdam, The Netherlands
- Maxillofacial Surgery/ Oral Pathology, Academic Center for Dentistry, Amsterdam, The Netherlands
| | - Bernard A Fox
- Molecular and Tumor Immunology Laboratory, Providence Cancer Institute, Robert W. Franz Research Center at the Earle A. Chiles Research Institute, Portland, Oregon, USA
| | - Jos B Poell
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
| | - C René Leemans
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
| | - Rieneke van de Ven
- Otolaryngology / Head and Neck Surgery, Amsterdam UMC Locatie VUmc, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Centre Amsterdam, Amsterdam, The Netherlands
- Cancer Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
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30
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Li Z, Zhang Y, Huang X, Gopinath D. MRE11 as a plausible biomarker and prognostic bioindicator for head and neck squamous cell carcinoma. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101970. [PMID: 39032645 DOI: 10.1016/j.jormas.2024.101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
OBJECTIVE Head and Neck Squamous Cell Carcinoma (HNSCC) ranks as the sixth most prevalent form of cancer worldwide. MRE11 protein contains multiple domains that play a role in the initiation of DNA repair. This study aimed to elucidate the expression and prognostic significance of MRE11 in HNSCC. MATERIAL AND METHODS The Cancer Genome Atlas (TCGA-HNSCC) dataset comprising 520 HNSCC tissues and 44 normal tissues was initially used to evaluate the association between MRE11 expression and clinicopathologic characteristics. Kaplan-Meier plot was utilized for survival analysis. MRE11-immune cell interaction was analyzed using Tumor Immune Estimation Resource (TIMER) database. Further, Insilco methods were used to explore the protein network and its association with other pathways. Quantitative reverse transcription PCR (RT-qPCR) was used to validate the MRE11 mRNA expression in oral squamous cell carcinoma (OSCC) tissues in patient samples. RESULTS MRE11 expression was upregulated in HNSCC, and the expression significantly varied across different clinical stages, pathological grades, and initial treatment outcomes. Further, high MRE11 expression is associated with poorer survival outcomes. MRE11 overexpression is also linked to the activation of the HIPPO signaling pathway, the mTOR signaling pathway, and the MYC/MYCN signaling pathway. CONCLUSION MRE 11 can be considered a novel prognostic biomarker for HNSCC, which can be leveraged for promising treatment outcomes. This research highlights MRE11 as a novel molecular biomarker for HNSCC and offers a new direction for its treatment, explicitly targeting MRE11 and its network for therapeutic intervention.
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Affiliation(s)
- Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Shanghai Research Institute of Stomatology, Shanghai, China; Shanghai Center of Head and Neck Oncology Clinical and Translational Science, Shanghai, China; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yuhan Zhang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China; Shanghai Research Institute of Stomatology, Shanghai, China; Shanghai Center of Head and Neck Oncology Clinical and Translational Science, Shanghai, China; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Divya Gopinath
- Basic Medical and Dental Sciences Dept, College of Dentistry, Ajman University, PO Box 346, United Arab Emirates; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, UAE.
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Veliz K, Shen F, Shestova O, Shestov M, Shestov A, Sleiman S, Hansen T, O’Connor RS, Gill S. Deletion of CD38 enhances CD19 chimeric antigen receptor T cell function. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200819. [PMID: 38912091 PMCID: PMC11193011 DOI: 10.1016/j.omton.2024.200819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024]
Abstract
Cell surface molecules transiently upregulated on activated T cells can play a counter-regulatory role by inhibiting T cell function. Deletion or blockade of such immune checkpoint receptors has been investigated to improve the function of engineered immune effector cells. CD38 is upregulated on activated T cells, and although there have been studies showing that CD38 can play an inhibitory role in T cells, how it does so has not fully been elucidated. In comparison with molecules such as PD1, CTLA4, LAG3, and TIM3, we found that CD38 displays more sustained and intense expression following acute activation. After deleting CD38 from human chimeric antigen receptor (CAR) T cells, we showed relative resistance to exhaustion in vitro and improved anti-tumor function in vivo. CD38 is a multifunctional ectoenzyme with hydrolase and cyclase activities. Reintroduction of CD38 mutants into T cells lacking CD38 provided further evidence supporting the understanding that CD38 plays a crucial role in producing the immunosuppressive metabolite adenosine and utilizing nicotinamide adenine dinucleotide (NAD) in human T cells. Taken together, these results highlight a role for CD38 as an immunometabolic checkpoint in T cells and lead us to propose CD38 deletion as an additional avenue for boosting CAR T cell function.
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Affiliation(s)
- Kimberly Veliz
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Feng Shen
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Olga Shestova
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maksim Shestov
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexander Shestov
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sara Sleiman
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tyler Hansen
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roddy S. O’Connor
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Saar Gill
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cell Therapy and Transplant Program, Division of Hematology-Oncology and Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
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32
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Shirai R, Biebighauser T, Walker D, Oviedo J, Nelson-Taylor S, Bodlak A, Porfilio T, Oike N, Goodspeed A, Hayashi M. Cadherin-11 contributes to the heterogenous and dynamic Wnt-Wnt-β-catenin pathway activation in Ewing sarcoma. PLoS One 2024; 19:e0305490. [PMID: 38875295 PMCID: PMC11178195 DOI: 10.1371/journal.pone.0305490] [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: 07/01/2023] [Accepted: 05/30/2024] [Indexed: 06/16/2024] Open
Abstract
Ewing sarcoma is the second most common bone cancer in children, and while patients who present with metastatic disease at the time of diagnosis have a dismal prognosis. Ewing sarcoma tumors are driven by the fusion gene EWS/Fli1, and while these tumors are genetically homogenous, the transcriptional heterogeneity can lead to a variety of cellular processes including metastasis. In this study, we demonstrate that in Ewing sarcoma cells, the canonical Wnt/β-Catenin signaling pathway is heterogeneously activated in vitro and in vivo, correlating with hypoxia and EWS/Fli1 activity. Ewing sarcoma cells predominantly express β-Catenin on the cell membrane bound to CDH11, which can respond to exogenous Wnt ligands leading to the immediate activation of Wnt/β-Catenin signaling within a tumor. Knockdown of CDH11 leads to delayed and decreased response to exogenous Wnt ligand stimulation, and ultimately decreased metastatic propensity. Our findings strongly indicate that CDH11 is a key component of regulating Wnt//β-Catenin signaling heterogeneity within Ewing sarcoma tumors, and is a promising molecular target to alter Wnt//β-Catenin signaling in Ewing sarcoma patients.
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Affiliation(s)
- Ryota Shirai
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Tyler Biebighauser
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Deandra Walker
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jillian Oviedo
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Sarah Nelson-Taylor
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Avery Bodlak
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Timothy Porfilio
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Naoki Oike
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Division of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Andrew Goodspeed
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Masanori Hayashi
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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33
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Cha J, Kim DH, Kim G, Cho JW, Sung E, Baek S, Hong MH, Kim CG, Sim NS, Hong HJ, Lee JE, Hemberg M, Park S, Yoon SO, Ha SJ, Koh YW, Kim HR, Lee I. Single-cell analysis reveals cellular and molecular factors counteracting HPV-positive oropharyngeal cancer immunotherapy outcomes. J Immunother Cancer 2024; 12:e008667. [PMID: 38857913 PMCID: PMC11168198 DOI: 10.1136/jitc-2023-008667] [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] [Accepted: 05/19/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Oropharyngeal squamous cell carcinoma (OPSCC) induced by human papillomavirus (HPV-positive) is associated with better clinical outcomes than HPV-negative OPSCC. However, the clinical benefits of immunotherapy in patients with HPV-positive OPSCC remain unclear. METHODS To identify the cellular and molecular factors that limited the benefits associated with HPV in OPSCC immunotherapy, we performed single-cell RNA (n=20) and T-cell receptor sequencing (n=10) analyses of tonsil or base of tongue tumor biopsies prior to immunotherapy. Primary findings from our single-cell analysis were confirmed through immunofluorescence experiments, and secondary validation analysis were performed via publicly available transcriptomics data sets. RESULTS We found significantly higher transcriptional diversity of malignant cells among non-responders to immunotherapy, regardless of HPV infection status. We also observed a significantly larger proportion of CD4+ follicular helper T cells (Tfh) in HPV-positive tumors, potentially due to enhanced Tfh differentiation. Most importantly, CD8+ resident memory T cells (Trm) with elevated KLRB1 (encoding CD161) expression showed an association with dampened antitumor activity in patients with HPV-positive OPSCC, which may explain their heterogeneous clinical outcomes. Notably, all HPV-positive patients, whose Trm presented elevated KLRB1 levels, showed low expression of CLEC2D (encoding the CD161 ligand) in B cells, which may reduce tertiary lymphoid structure activity. Immunofluorescence of HPV-positive tumors treated with immune checkpoint blockade showed an inverse correlation between the density of CD161+ Trm and changes in tumor size. CONCLUSIONS We found that CD161+ Trm counteracts clinical benefits associated with HPV in OPSCC immunotherapy. This suggests that targeted inhibition of CD161 in Trm could enhance the efficacy of immunotherapy in HPV-positive oropharyngeal cancers. TRIAL REGISTRATION NUMBER NCT03737968.
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Affiliation(s)
- Junha Cha
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Da Hee Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Gamin Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae-Won Cho
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
| | - Euijeong Sung
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Seungbyn Baek
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang Gon Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Nam Suk Sim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jun Hong
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Eun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Martin Hemberg
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA
| | - Seyeon Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sun Ock Yoon
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yoon Woo Koh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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34
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Zhao Y, Yu J, Zheng C, Zhou B. Establishment of a prognostic model for hypoxia-associated genes in OPSCC and revelation of intercellular crosstalk. Front Immunol 2024; 15:1371365. [PMID: 38887298 PMCID: PMC11181350 DOI: 10.3389/fimmu.2024.1371365] [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: 01/16/2024] [Accepted: 05/16/2024] [Indexed: 06/20/2024] Open
Abstract
Hypoxia exerts a profound influence on the tumor microenvironment and immune response, shaping treatment outcomes and prognosis. Utilizing consistency clustering, we discerned two hypoxia subtypes in OPSCC bulk sequencing data from GEO. Key modules within OPSCC were identified through weighted gene correlation network analysis (WGCNA). Core modules underwent CIBERSORT immune infiltration analysis and GSEA functional enrichment. Univariate Cox and LASSO analyses were employed to construct prognostic models for seven hypoxia-related genes. Further investigation into clinical characteristics, the immune microenvironment, and TIDE algorithm prediction for immunotherapy response was conducted in high- and low-risk groups. scRNA-seq data were visually represented through TSNE clustering, employing the scissors algorithm to map hypoxia phenotypes. Interactions among cellular subpopulations were explored using the Cellchat package, with additional assessments of metabolic and transcriptional activities. Integration with clinical data unveiled a prevalence of HPV-positive patients in the low hypoxia and low-risk groups. Immunohistochemical validation demonstrated low TDO2 expression in HPV-positive (P16-positive) patients. Our prediction suggested that HPV16 E7 promotes HIF-1α inhibition, leading to reduced glycolytic activity, ultimately contributing to better prognosis and treatment sensitivity. The scissors algorithm effectively segregated epithelial cells and fibroblasts into distinct clusters based on hypoxia characteristics. Cellular communication analysis illuminated significant crosstalk among hypoxia-associated epithelial, fibroblast, and endothelial cells, potentially fostering tumor proliferation and metastasis.
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Affiliation(s)
| | | | | | - Baosen Zhou
- Department of Clinical Epidemiology and Center of Evidence-Based Medicine, The First Hospital of China Medical University, Shenyang, China
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35
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Cheng D, Qiu K, Li D, Mao M, Rao Y, Song Y, Feng L, Shao X, Jiang C, Wang Y, Li L, Chen X, Wu S, Wang H, Liu J, Yu H, Zhang W, Chen F, Zhao Y, Ren J. Molecular and transcriptional basis of bidirectional CD4 + T cell exhaustion in oropharyngeal squamous cell carcinoma. MedComm (Beijing) 2024; 5:e572. [PMID: 38868329 PMCID: PMC11167179 DOI: 10.1002/mco2.572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 03/05/2024] [Accepted: 03/24/2024] [Indexed: 06/14/2024] Open
Abstract
Tumor-infiltrating CD4+ T cells orchestrate the adaptive immune response through remarkable plasticity, and the expression patterns of exhaustion-related inhibitory receptors in these cells differ significantly from those of CD8+ T cells. Thus, a better understanding of the molecular basis of CD4+ T cell exhaustion and their responses to immune checkpoint blockade (ICB) is required. Here, we integrated multiomics approaches to define the phenotypic and molecular profiles of exhausted CD4+ T cells in oropharyngeal squamous cell carcinoma (OPSCC). Two distinct immune-promoting (Module 1) and immunosuppressive (Module 2) functional modules in tumor-infiltrating CD4+ T cells were identified, and both the immune-promoting function of Module 1 cells and immunosuppressive function of Module 2 cells were positively associated with their corresponding exhaustion states. Furthermore, the application of ICBs targeting effector CD4+ T cells in Module 1 (αPD-1) and Treg cells in Module 2 (αCTLA-4) in mouse models could help reinvigorate the effector function of Module 1-exhausted CD4+ T cells and reduce the immunosuppressive function of Module 2-exhausted CD4+ T cells, ultimately promoting OPSCC tumor regression. Taken together, our study provides a crucial cellular basis for the selection of optimal ICB in treating OPSCC.
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Affiliation(s)
- Danni Cheng
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Ke Qiu
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Daibo Li
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Minzi Mao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yufang Rao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yao Song
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lan Feng
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Xiuli Shao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Chuanhuan Jiang
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yan Wang
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Li Li
- Institute of Clinical PathologyWest China HospitalSichuan UniversityChengduSichuanChina
| | - Xuemei Chen
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Sisi Wu
- Research Core FacilityWest China HospitalSichuan UniversityChengduChina
| | - Haiyang Wang
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Jun Liu
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Haopeng Yu
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Wei Zhang
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Fei Chen
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
| | - Yu Zhao
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
| | - Jianjun Ren
- Department of Oto‐Rhino‐LaryngologyWest China Hospital, Sichuan UniversityChengduSichuanChina
- West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengduSichuanChina
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36
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Paparoditis P, Shulman Z. The tumor-driven antibody-mediated immune response in cancer. Curr Opin Immunol 2024; 88:102431. [PMID: 38866666 DOI: 10.1016/j.coi.2024.102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024]
Abstract
Immune cells in the tumor microenvironment play a crucial role in cancer prognosis and response to immunotherapy. Recent studies highlight the significance of tumor-infiltrating B cells and tertiary lymphoid structures as markers of favorable prognosis and patient-positive response to immune checkpoint blockers in some types of cancer. Although the presence of germinal center B cells and plasma cells in the tumor microenvironment has been established, determining their tumor reactivity remains challenging. The few known tumor targets range from viral proteins to self and altered self-proteins. The emergence of self-reactive antibodies in patients with cancer, involves the opposing forces of antigen-driven affinity increase and peripheral tolerance mechanisms. Here, B cell tumor antigen specificity and affinity maturation in tumor-directed immune responses in cancer are discussed.
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Affiliation(s)
- Philipp Paparoditis
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Department of Systems Immunology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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37
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Armingol E, Baghdassarian HM, Lewis NE. The diversification of methods for studying cell-cell interactions and communication. Nat Rev Genet 2024; 25:381-400. [PMID: 38238518 PMCID: PMC11139546 DOI: 10.1038/s41576-023-00685-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 05/20/2024]
Abstract
No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell-cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell-cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries.
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Affiliation(s)
- Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Paediatrics, University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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38
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Majumder M, Janakiraman H, Chakraborty P, Vijayakumar A, Mayhue S, Yu H, Dincman T, Martin R, O’Quinn E, Mehrotra S, Palanisamy V. RNA-binding protein HuR reprograms immune T cells and promotes oral squamous cell carcinoma. ORAL ONCOLOGY REPORTS 2024; 10:100296. [PMID: 38681116 PMCID: PMC11044901 DOI: 10.1016/j.oor.2024.100296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Hu Antigen R, also known as ELAVL1 (HuR), is a key posttranscriptional regulator in eukaryotic cells. HuR overexpression promotes several malignancies, including head and neck squamous cell carcinoma (HNSCC). However, its immune dysfunction-associated tumorigenesis pathways remain unknown. We examined HuR's effects on oral malignancies and immune cell function in vitro and in vivo using oral carcinoma cells and transgenic HuR knockout (KO) mice. CRISPR/Cas9-mediated HuR deletion in mice syngeneic oral cancer cells eliminated colony formation and tumor development. HuR-KO tumors had a lower tumor volume, fewer CD4+CD25+FoxP3+ regulatory T cells, and more CD8+ T cells, suggesting that HuR may suppress the immune response during oral cancer progression. In contrast, HuR KO oral epithelial tissues are resistant to 4NQO-induced oral malignancies compared to control tumor-bearing mice. HuR KO mice showed fewer Tregs and greater IFN levels than WT tumor-bearing mice, suggesting anticancer activity. Finally, the HuR inhibitor pyrvinium pamoate lowers tumor burden by enhancing CD8+ infiltration at the expense of CD4+, suggesting anticancer benefits. Thus, HuR-dependent oral neoplasia relies on immunological dysfunction, suggesting that decreasing HuR may boost antitumor potential and offer a novel HNSCC therapy.
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Affiliation(s)
| | | | | | | | - Sari Mayhue
- Department of Biochemistry and Molecular Biology, USA
| | - Hong Yu
- Oral Health Sciences, College of Dental Medicine, USA
| | - Toros Dincman
- Department of Haematology and Oncology, College of Medicine, USA
| | - Romeo Martin
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Elizabeth O’Quinn
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, USA
- Division of Molecular Medicine, Department of Internal Medicine, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
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39
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Bell B, Flores-Lovon K, Cueva-Chicaña LA, Macedo R. Role of chemokine receptors in gastrointestinal mucosa. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 388:20-52. [PMID: 39260937 DOI: 10.1016/bs.ircmb.2024.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Chemokine receptors are essential for the immune response in the oral and gut mucosa. The gastrointestinal mucosa is characterized by the presence of immune populations because it is susceptible to inflammatory and infectious diseases, necessitating immune surveillance. Chemokine receptors are expressed on immune cells and play a role in gastrointestinal tissue-homing, although other non-immune cells also express them for various biological functions. CCR9, CXCR3 and CXCR6 play an important role in the T cell response in inflammatory and neoplastic conditions of the gastrointestinal mucosa. However, CXCR6 could also be found in gastric cancer cells, highlighting the different roles of chemokine receptors in different pathologies. On the other hand, CCR4 and CCR8 are critical for Treg migration in gastrointestinal tissues, correlating with poor prognosis in mucosal cancers. Other chemokine receptors are also important in promoting myeloid infiltration with context-dependent roles. Further, CXCR4 and CXCR7 are also present in gastrointestinal tumor cells and are known to stimulate proliferation, migration, and invasion into other tissues, among other pro-tumorigenic functions. Determining the processes underlying mucosal immunity and creating tailored therapeutic approaches for gastrointestinal diseases requires an understanding of the complex interactions that occur between chemokine receptors and their ligands in these mucosal tissues.
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Affiliation(s)
- Brett Bell
- Albert Einstein College of Medicine, New York, NY, United States
| | - Kevin Flores-Lovon
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología (GII), Arequipa, Peru
| | - Luis A Cueva-Chicaña
- Universidad Nacional de San Agustín de Arequipa, Arequipa, Peru; Grupo de Investigación en Inmunología (GII), Arequipa, Peru
| | - Rodney Macedo
- Albert Einstein College of Medicine, New York, NY, United States; Grupo de Investigación en Inmunología (GII), Arequipa, Peru; Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, United States.
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40
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Dankó B, Hess J, Unger K, Samaga D, Walz C, Walch A, Sun N, Baumeister P, Zeng PYF, Walter F, Marschner S, Späth R, Gires O, Herkommer T, Dazeh R, Matos T, Kreutzer L, Matschke J, Eul K, Klauschen F, Pflugradt U, Canis M, Ganswindt U, Mymryk JS, Wollenberg B, Nichols AC, Belka C, Zitzelsberger H, Lauber K, Selmansberger M. Metabolic pathway-based subtypes associate glycan biosynthesis and treatment response in head and neck cancer. NPJ Precis Oncol 2024; 8:116. [PMID: 38783045 PMCID: PMC11116554 DOI: 10.1038/s41698-024-00602-0] [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: 08/10/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is a heterogeneous malignancy that remains a significant challenge in clinical management due to frequent treatment failures and pronounced therapy resistance. While metabolic dysregulation appears to be a critical factor in this scenario, comprehensive analyses of the metabolic HNSCC landscape and its impact on clinical outcomes are lacking. This study utilized transcriptomic data from four independent clinical cohorts to investigate metabolic heterogeneity in HNSCC and define metabolic pathway-based subtypes (MPS). In HPV-negative HNSCCs, MPS1 and MPS2 were identified, while MPS3 was enriched in HPV-positive cases. MPS classification was associated with clinical outcome post adjuvant radio(chemo)therapy, with MPS1 consistently exhibiting the highest risk of therapeutic failure. MPS1 was uniquely characterized by upregulation of glycan (particularly chondroitin/dermatan sulfate) metabolism genes. Immunohistochemistry and pilot mass spectrometry imaging analyses confirmed this at metabolite level. The histological context and single-cell RNA sequencing data identified the malignant cells as key contributors. Globally, MPS1 was distinguished by a unique transcriptomic landscape associated with increased disease aggressiveness, featuring motifs related to epithelial-mesenchymal transition, immune signaling, cancer stemness, tumor microenvironment assembly, and oncogenic signaling. This translated into a distinct histological appearance marked by extensive extracellular matrix remodeling, abundant spindle-shaped cancer-associated fibroblasts, and intimately intertwined populations of malignant and stromal cells. Proof-of-concept data from orthotopic xenotransplants replicated the MPS phenotypes on the histological and transcriptome levels. In summary, this study introduces a metabolic pathway-based classification of HNSCC, pinpointing glycan metabolism-enriched MPS1 as the most challenging subgroup that necessitates alternative therapeutic strategies.
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Affiliation(s)
- Benedek Dankó
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Julia Hess
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Kristian Unger
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Samaga
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Philipp Baumeister
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, LMU University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Peter Y F Zeng
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON, Canada
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, ON, Canada
| | - Franziska Walter
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Sebastian Marschner
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Richard Späth
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Olivier Gires
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Timm Herkommer
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Ramin Dazeh
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thaina Matos
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa Kreutzer
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- German Cancer Consortium (DKTK) partner site Essen a partnership between DKFZ and University Hospital, Essen, Germany
| | - Katharina Eul
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frederick Klauschen
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Ulrike Pflugradt
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Head and Neck Surgery, LMU University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Ute Ganswindt
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Department of Radiation Oncology, Innsbruck Medical University, Innsbruck, Austria
- Comprehensive Cancer Center Innsbruck, Innsbruck, Austria
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, ON, Canada
- Department of Microbiology & Immunology, University of Western Ontario, London, ON, Canada
- Department of Oncology, University of Western Ontario, London, ON, Canada
| | - Barbara Wollenberg
- Comprehensive Cancer Center, Munich, Germany
- Clinic of Otorhinolaryngology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Department of Otorhinolaryngology, University of Luebeck, Luebeck, Germany
| | - Anthony C Nichols
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, ON, Canada
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, ON, Canada
- Department of Oncology, University of Western Ontario, London, ON, Canada
| | - Claus Belka
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Horst Zitzelsberger
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Kirsten Lauber
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center, Munich, Germany
| | - Martin Selmansberger
- Research Unit Translational Metabolic Oncology, Institute for Diabetes and Cancer, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer, " Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
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41
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Wang W, Li C, Dai Y, Wu Q, Yu W. Unraveling metabolic characteristics and clinical implications in gastric cancer through single-cell resolution analysis. Front Mol Biosci 2024; 11:1399679. [PMID: 38831933 PMCID: PMC11145399 DOI: 10.3389/fmolb.2024.1399679] [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: 03/19/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
Background: Gastric cancer is a highly prevalent malignant neoplasm. Metabolic reprogramming is intricately linked to both tumorigenesis and cancer immune evasion. The advent of single-cell RNA sequencing technology provides a novel perspective for evaluating cellular metabolism. This study aims to comprehensively investigate the metabolic pathways of various cell types in tumor and normal samples at high resolution and delve into the intricate regulatory mechanisms governing the metabolic activity of malignant cells in gastric cancer. Methods: Utilizing single-cell RNA sequencing data from gastric cancer, we constructed metabolic landscape maps for different cell types in tumor and normal samples. Employing unsupervised clustering, we categorized malignant cells in tumor samples into high and low metabolic subclusters and further explored the characteristics of these subclusters. Results: Our research findings indicate that epithelial cells in tumor samples exhibit significantly higher activity in most KEGG metabolic pathways compared to other cell types. Unsupervised clustering, based on the scores of metabolic pathways, classified malignant cells into high and low metabolic subclusters. In the high metabolic subcluster, it demonstrated the potential to induce a stronger immune response, correlating with a relatively favorable prognosis. In the low metabolic subcluster, a subset of cells resembling cancer stem cells (CSCs) was identified, and its prognosis was less favorable. Furthermore, a set of risk genes associated with this subcluster was discovered. Conclusion: This study reveals the intricate regulatory mechanisms governing the metabolic activity of malignant cells in gastric cancer, offering new perspectives for improving prognosis and treatment strategies.
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Affiliation(s)
- Wenyue Wang
- School of Life Sciences, Tianjin University, Tianjin, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Conghui Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuting Dai
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingfa Wu
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Weiqiang Yu
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
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42
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Rao Y, Qiu K, Song Y, Mao M, Feng L, Cheng D, Li J, Zhang Z, Zhang Y, Shao X, Pang W, Wang Y, Chen X, Jiang C, Wu S, Yu S, Liu J, Wang H, Peng X, Yang L, Chen L, Mu X, Zheng Y, Xu W, Liu G, Chen F, Yu H, Zhao Y, Ren J. The diversity of inhibitory receptor co-expression patterns of exhausted CD8 + T cells in oropharyngeal carcinoma. iScience 2024; 27:109668. [PMID: 38655196 PMCID: PMC11035373 DOI: 10.1016/j.isci.2024.109668] [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: 09/11/2023] [Revised: 01/05/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
Exhausted CD8+ T cells (Texs) are characterized by the expression of various inhibitory receptors (IRs), whereas the functional attributes of these co-expressed IRs remain limited. Here, we systematically characterized the diversity of IR co-expression patterns in Texs from both human oropharyngeal squamous cell carcinoma (OPSCC) tissues and syngeneic OPSCC model. Nearly 60% of the Texs population co-expressed two or more IRs, and the number of co-expressed IRs was positively associated with superior exhaustion and cytotoxicity phenotypes. In OPSCC patients, programmed cell death-1 (PD-1) blockade significantly enhanced PDCD1-based co-expression with other IR genes, whereas dual blockades of PD-1 and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) significantly upregulated CTLA4-based co-expression with other IR genes. Collectively, our findings demonstrate that highly diverse IR co-expression is a leading feature of Texs and represents their functional states, which might provide essential clues for the rational selection of immune checkpoint inhibitors in treating OPSCC.
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Affiliation(s)
- Yufang Rao
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ke Qiu
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yao Song
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Minzi Mao
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lan Feng
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Danni Cheng
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Junhong Li
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ziyan Zhang
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuyang Zhang
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiuli Shao
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wendu Pang
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yan Wang
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, China
| | - Xuemei Chen
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, China
| | - Chuanhuan Jiang
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, China
| | - Sisi Wu
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, China
| | - Shuaishuai Yu
- Research Core Facility of West China Hospital, Sichuan University, Chengdu, China
| | - Jun Liu
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haiyang Wang
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Yang
- MinSheng Ear-Nose-Throat Hospital, Chengdu, Sichuan, China
| | - Li Chen
- MinSheng Ear-Nose-Throat Hospital, Chengdu, Sichuan, China
| | - Xiaosong Mu
- Langzhong People’s Hospital, Nanchong, Sichuan, China
| | - Yongbo Zheng
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre and Dalla Lana School of Public Health, Toronto, ON, Canada
| | - Geoffrey Liu
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, and Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Medicine, Division of Medical Oncology and Hematology, Princess Margaret Cancer Center, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Fei Chen
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Zhao
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jianjun Ren
- Department of Otolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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43
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Zhao Y, Zhang B, Ma Y, Guo M, Zhao F, Chen J, Wang B, Jin H, Zhou F, Guan J, Zhao Q, Liu Q, Wang H, Zhao F, Wang X. Distinct molecular profiles drive multifaceted characteristics of colorectal cancer metastatic seeds. J Exp Med 2024; 221:e20231359. [PMID: 38502057 PMCID: PMC10949939 DOI: 10.1084/jem.20231359] [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: 08/02/2023] [Revised: 10/10/2023] [Accepted: 02/08/2024] [Indexed: 03/20/2024] Open
Abstract
Metastasis of primary tumors remains a challenge for early diagnosis and prevention. The cellular properties and molecular drivers of metastatically competent clones within primary tumors remain unclear. Here, we generated 10-16 single cell-derived lines from each of three colorectal cancer (CRC) tumors to identify and characterize metastatic seeds. We found that intrinsic factors conferred clones with distinct metastatic potential and cellular communication capabilities, determining organ-specific metastasis. Poorly differentiated or highly metastatic clones, rather than drug-resistant clones, exhibited poor clinical prognostic impact. Personalized genetic alterations, instead of mutation burden, determined the occurrence of metastatic potential during clonal evolution. Additionally, we developed a gene signature for capturing metastatic potential of primary CRC tumors and demonstrated a strategy for identifying metastatic drivers using isogenic clones with distinct metastatic potential in primary tumors. This study provides insight into the origin and mechanisms of metastasis and will help develop potential anti-metastatic therapeutic targets for CRC patients.
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Affiliation(s)
- Yuanyuan Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
| | - Bing Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fuqiang Zhao
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianan Chen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingzhi Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Jin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fulai Zhou
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiawei Guan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Zhao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
- Institute for Intelligent Healthcare, Tsinghua University, Beijing, China
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Guo J, Si G, Si F. Association of immune cells and the risk of esophageal cancer: A Mendelian randomization study in a East Asian population. Medicine (Baltimore) 2024; 103:e38064. [PMID: 38701252 PMCID: PMC11062746 DOI: 10.1097/md.0000000000038064] [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: 11/16/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Immunotherapy has been used in esophageal cancer (EC), but the causal relationship between EC and immune cells is not clear. Although the cellular phenotype has been reported as a biomarker for immunotherapy, the biomarker studies for immunotherapy in EC still face great challenges. Comprehensive 2-sample Mendelian randomization (MR) analysis was performed to determine the causal association between immune cell signatures and EC in this study. Based on publicly available genetic data, we explored causal associations between 731 immune cell signatures and EC risk. EC had no statistically significant effect on immunophenotypes. Nine immunophenotype types were positively associated with the risk of EC: CD20-%B cell, CD20% lymphocytes, CD25 on IgD- CD27-, CD25 on IgD+ CD24+, CD27 on IgD+ CD24+, CD28+ CD45RA- CD8br AC, CD3 on TD CD8br, IgD-CD38dim%B cells, and Mo MDSC AC. In addition, a total of 15 immunophenotypes were identified as causally associated with EC. IgD+ CD38- %B cell, IgD- CD24- %lymphocyte, CD19 on IgD- CD38dim, CD20 on IgD+ CD24+, CD62L-myeloid DC AC, CD4+ AC, Lymphocyte %leukocyte, CD3 on HLA-DR+ T cell, CD3 on CD45RA- CD4+, HVEM on naive CD4+ AC, HVEM on CD45RA- CD4+, CD4 on TD CD4+, CD4 on CD4 Treg, and CD4 on CD39+ resting Treg, and CD4 on activated & secreting Treg. Our study has demonstrated the close connection between immune cells and EC by genetic means, thus providing guidance for future clinical research.
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Affiliation(s)
- Jinzhou Guo
- Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Laboratory of TCM Syndrome and Prescription Signaling, Academy of Zhongjing, Zhengzhou, Henan, China
- Henan Key Laboratory of TCM Syndrome and Prescription Signaling, Henan International Joint, Zhengzhou, Henan, China
| | - Gao Si
- Department of Orthopedic, Peking University Third Hospital, Beijing, China
| | - Fuchun Si
- Henan University of Chinese Medicine, Zhengzhou, Henan, China
- Laboratory of TCM Syndrome and Prescription Signaling, Academy of Zhongjing, Zhengzhou, Henan, China
- Henan Key Laboratory of TCM Syndrome and Prescription Signaling, Henan International Joint, Zhengzhou, Henan, China
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45
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Kürten CHL, Ferris RL. Neoadjuvant immunotherapy for head and neck squamous cell carcinoma. Laryngorhinootologie 2024; 103:S167-S187. [PMID: 38697147 DOI: 10.1055/a-2183-5802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
The neoadjuvant immunotherapy approach marks a significant shift in the treatment paradigm of potentially curable HNSCC. Here, current therapies, despite being highly individualized and advanced, often fall short in achieving satisfactory long-term survival rates and are frequently associated with substantial morbidity.The primary advantage of this approach lies in its potential to intensify and enhance treatment regimens, offering a distinct modality that complements the existing triad of surgery, radiotherapy, and chemotherapy. Checkpoint inhibitors have been at the forefront of this evolution. Demonstrating moderate yet significant survival benefits in the recurrent-metastatic setting with a relatively better safety profile compared to conventional treatments, these agents hold promise when considered for earlier stages of HNSCC.On the other hand, a significant potential benefit of introducing immunotherapy in the neoadjuvant phase is the possibility of treatment de-escalation. By reducing the tumor burden before surgery, this strategy could lead to less invasive surgical interventions. The prospect of organ-sparing protocols becomes a realistic and highly valued goal in this context. Further, the early application of immunotherapy might catalyze a more effective and durable immune response. The induction of an immune memory may potentially lead to a more effective surveillance of residual disease, decreasing the rates of local, regional, and distant recurrences, thereby enhancing overall and recurrence-free survival.However, neoadjuvant immunotherapy is not without its challenges. One of the primary concerns is the safety and adverse events profile. While data suggest that adverse events are relatively rare and manageable, the long-term safety profile in the neoadjuvant setting, especially in the context of curative intent, remains a subject for ongoing research. Another unsolved issue lies in the accurate assessment of treatment response. The discrepancy between radiographic assessment using RECIST criteria and histological findings has been noted, indicating a gap in current imaging techniques' ability to accurately reflect the true efficacy of immunotherapy. This gap underscores the necessity for improved imaging methodologies and the development of new radiologic and pathologic criteria tailored to evaluate the response to immunotherapy accurately.Treatment combinations and timing represent another layer of complexity. There is a vast array of possibilities in combining immunotherapy agents with conventional chemotherapy, targeted therapy, radiation, and other experimental treatments. Determining the optimal treatment regimen for individual patients becomes an intricate task, especially when comparing small, single-arm, non-randomized trials with varying regimens and outcome measures.Moreover, one needs to consider the importance of pre- and intraoperative decision-making in the context of neoadjuvant immunotherapy. As experience with this treatment paradigm grows, there is potential for more tailored surgical approaches based on the patient's remaining disease post-neoadjuvant treatment. This consideration is particularly relevant in extensive surgeries, where organ-sparing protocols could be evaluated.In practical terms, the multi-modal nature of this treatment strategy introduces complexities, especially outside clinical trial settings. Patients face challenges in navigating the treatment landscape, which involves coordination across multiple medical disciplines, highlighting the necessity for streamlined care pathways at specialized centers to facilitate effective treatment management if the neoadjuvant approach is introduced to the real-world.These potential harms and open questions underscore the critical need for meticulously designed clinical trials and correlational studies to ensure patient safety and efficacy. Only these can ensure that this new treatment approach is introduced in a safe way and fulfils the promise it theoretically holds.
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Affiliation(s)
- Cornelius H L Kürten
- Klinik für Hals-, Nasen- und Ohrenheilkunde, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen
| | - Robert L Ferris
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
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Sun W, Xie S, Liu SF, Hu X, Xing D. Evolving Tumor Characteristics and Smart Nanodrugs for Tumor Immunotherapy. Int J Nanomedicine 2024; 19:3919-3942. [PMID: 38708176 PMCID: PMC11070166 DOI: 10.2147/ijn.s453265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
Typical physiological characteristics of tumors, such as weak acidity, low oxygen content, and upregulation of certain enzymes in the tumor microenvironment (TME), provide survival advantages when exposed to targeted attacks by drugs and responsive nanomedicines. Consequently, cancer treatment has significantly progressed in recent years. However, the evolution and adaptation of tumor characteristics still pose many challenges for current treatment methods. Therefore, efficient and precise cancer treatments require an understanding of the heterogeneity degree of various factors in cancer cells during tumor evolution to exploit the typical TME characteristics and manage the mutation process. The highly heterogeneous tumor and infiltrating stromal cells, immune cells, and extracellular components collectively form a unique TME, which plays a crucial role in tumor malignancy, including proliferation, invasion, metastasis, and immune escape. Therefore, the development of new treatment methods that can adapt to the evolutionary characteristics of tumors has become an intense focus in current cancer treatment research. This paper explores the latest understanding of cancer evolution, focusing on how tumors use new antigens to shape their "new faces"; how immune system cells, such as cytotoxic T cells, regulatory T cells, macrophages, and natural killer cells, help tumors become "invisible", that is, immune escape; whether the diverse cancer-associated fibroblasts provide support and coordination for tumors; and whether it is possible to attack tumors in reverse. This paper discusses the limitations of targeted therapy driven by tumor evolution factors and explores future strategies and the potential of intelligent nanomedicines, including the systematic coordination of tumor evolution factors and adaptive methods, to meet this therapeutic challenge.
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Affiliation(s)
- Wenshe Sun
- The Affiliated Hospital of Qingdao University, Qingdao, 266071, People’s Republic of China
- Qingdao Cancer Institute, Qingdao University, Qingdao, 266071, People’s Republic of China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, People’s Republic of China
| | - Shaowei Xie
- Department of Ultrasound, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People’s Republic of China
| | - Shi Feng Liu
- The Affiliated Hospital of Qingdao University, Qingdao, 266071, People’s Republic of China
| | - Xiaokun Hu
- The Affiliated Hospital of Qingdao University, Qingdao, 266071, People’s Republic of China
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao, 266071, People’s Republic of China
- Qingdao Cancer Institute, Qingdao University, Qingdao, 266071, People’s Republic of China
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Pan L, Parini P, Tremmel R, Loscalzo J, Lauschke VM, Maron BA, Paci P, Ernberg I, Tan NS, Liao Z, Yin W, Rengarajan S, Li X. Single Cell Atlas: a single-cell multi-omics human cell encyclopedia. Genome Biol 2024; 25:104. [PMID: 38641842 PMCID: PMC11027364 DOI: 10.1186/s13059-024-03246-2] [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: 11/16/2022] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of human tissues through in-depth characterizations of datasets from five single-cell omics, spatial transcriptomics, and two bulk omics across 125 healthy adult and fetal tissues. We construct its complement web-based platform, the Single Cell Atlas (SCA, www.singlecellatlas.org ), to enable vast interactive data exploration of deep multi-omics signatures across human fetal and adult tissues. The atlas resources and database queries aspire to serve as a one-stop, comprehensive, and time-effective resource for various omics studies.
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Affiliation(s)
- Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Paolo Parini
- Cardio Metabolic Unit, Department of Medicine, and, Department of Laboratory Medicine , Karolinska Institutet, 141 86, Stockholm, Sweden
- Theme Inflammation and Ageing, Medicine Unit, Karolinska University Hospital, 141 86, Stockholm, Sweden
| | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Volker M Lauschke
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tuebingen, 72076, Tuebingen, Germany
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Bradley A Maron
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185, Rome, Italy
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, 308232, Singapore
| | - Zehuan Liao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Solna, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Weiyao Yin
- Institute of Environmental Medicine, Karolinska Institutet, 171 65, Solna, Sweden
| | - Sundararaman Rengarajan
- Department of Physical Therapy, Movement & Rehabilitation Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Solna, Sweden.
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48
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Tian J, Bai X, Quek C. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy. Int J Mol Sci 2024; 25:4485. [PMID: 38674070 PMCID: PMC11050520 DOI: 10.3390/ijms25084485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.
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Affiliation(s)
| | | | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.T.); (X.B.)
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Fay M, Clavijo PE, Allen CT. Heterogeneous characterization of neutrophilic cells in head and neck cancers. Head Neck 2024. [PMID: 38622975 DOI: 10.1002/hed.27774] [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: 12/08/2023] [Revised: 03/14/2024] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Neutrophilic cells are among the most abundant immune populations within the head and neck tumor microenvironment (TME) and harbor multiple mechanisms of immunosuppression. Despite these important features, neutrophilic cells may be underrepresented in contemporary studies that aim to comprehensively characterize the immune landscape of the TME due to discrepancies in tissue processing and analysis techniques. Here, we review the role of pathologically activated neutrophilic cells within the TME and pitfalls of various approaches used to study their frequency and function in clinical samples. METHODS The literature was identified by searching PubMed for "immune landscape" and "tumor immune microenvironment" in combination with keywords describing solid tumor malignancies. Key publications that assessed the immune composition of solid tumors derived from human specimens were included. The tumor and blood processing methodologies in each study were reviewed in depth and correlated with the reported abundance of neutrophilic cells. RESULTS Neutrophilic cells do not survive cryopreservation, and many studies fail to identify and study neutrophilic cell populations due to cryopreservation of clinical samples for practical reasons. Additional single-cell transcriptomic studies filter out neutrophilic cells due to low transcriptional counts. CONCLUSIONS This report can help readers critically interpret studies aiming to comprehensively study the immune TME that fail to identify and characterize neutrophilic cells.
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Affiliation(s)
- Magdalena Fay
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul E Clavijo
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Clint T Allen
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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50
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Badillo O, Helfridsson L, Niemi J, Hellström M. Exploring dendritic cell subtypes in cancer immunotherapy: unraveling the role of mature regulatory dendritic cells. Ups J Med Sci 2024; 129:10627. [PMID: 38716077 PMCID: PMC11075441 DOI: 10.48101/ujms.v129.10627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 05/24/2024] Open
Abstract
Dendritic cells (DCs) possess a specialized function in presenting antigens and play pivotal roles in both innate and adaptive immune responses. Their ability to cross-present antigens from tumor cells to naïve T cells is instrumental in generating specific T-cell-mediated antitumor responses, crucial for controlling tumor growth and preventing tumor cell dissemination. However, within a tumor immune microenvironment (TIME), the functions of DCs can be significantly compromised. This review focuses on the profile, function, and activation of DCs, leveraging recent studies that reveal insights into their phenotype acquisition, transcriptional state, and functional programs through single-cell RNA sequence (scRNA-seq) analysis. Additionally, the therapeutic potential of DC-mediated tumor antigen sensing in priming antitumor immunity is discussed.
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Affiliation(s)
- Oscar Badillo
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Liam Helfridsson
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jenni Niemi
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mats Hellström
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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