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Bo H, Jiang H, Xiong J, Zhang W, Shi Y, Pan C, Wang H. T cell receptor repertoire deciphers anti-tuberculosis immunity. Int Immunopharmacol 2024; 138:112252. [PMID: 38976948 DOI: 10.1016/j.intimp.2024.112252] [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: 01/02/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 07/10/2024]
Abstract
T cell induced cellular immunity is considered to be extremely important for the control of tuberculosis (TB). T cell receptor (TCR), the key component responsible for the specificity and clustering of T cells, holds the potential to advance our understanding of T cell immunity against TB infection. This review systematically expounded the study progressions made in the field of TB-relevant TCRs based on single cell sequencing together with GLIPH2 technology and initiated a comparison of the T cell distribution between peripheral blood and infected organs. We divided clonal expanded T cell clones into recirculation subsets and local subsets to summarize their distinctions in clonal abundance, TCR sequences and antigenic specificity. Notably, local expansion appears to drive the primary variances in T cell subsets between these two contexts, indicating the necessity for further exploration into the functions and specificity of local subsets.
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Affiliation(s)
- Haohui Bo
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Haiqin Jiang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China.
| | - Jingshu Xiong
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Wenyue Zhang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Ying Shi
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Chun Pan
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China
| | - Hongsheng Wang
- Department of Mycobacterium, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology & Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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2
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Jin R, Du F, Han X, Guo J, Song W, Xia Y, Yue X, Yang D, Tong J, Zhang Q, Liu Y. Prognostic Value of Insulin Growth Factor-Like Receptor 1 (IGFLR1) in Stage II and III Colorectal Cancer and Its Association with Immune Cell Infiltration. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05006-1. [PMID: 39141178 DOI: 10.1007/s12010-024-05006-1] [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] [Accepted: 07/23/2024] [Indexed: 08/15/2024]
Abstract
IGFLR1 is a novel biomarker, and some evidences suggested that is involved in the immune microenvironment of CRC. Here, we explored the expression of IGFLR1 and its association with the prognosis as well as immune cell infiltration in CRC, with the aim to provide a basis for further studies on IGFLR1. Immunohistochemical staining for IGFLR1, TIM-3, FOXP3, CD4, CD8, and PD-1 was performed in eligible tissues to analyze the expression of IGFLR1 and its association with prognosis and immune cell infiltration. Then, we screened colon cancer samples from TCGA and grouped patients according to IGFLR1-related genes. We also evaluated the co-expression and immune-related pathways of IGFLR1 to identify the potential mechanism of it in CRC. When P < 0.05, the results were considered statistically significant. IGFLR1 and IGFLR1-related genes were associated with the prognosis and immune cell infiltration (P < 0.05). In stage II and III CRC tissue and normal tissue, we found (1) IGFLR1 was expressed in both the cell membrane and cytoplasm and which was differentially expressed between cancer tissue and normal tissue. IGFLR1 expression was associated with the expression of FOXP3, CD8, and gender but was not associated with microsatellite instability. (2) IGFLR1 was an independent prognostic factor and patients with high IGFLR1 had a better prognosis. (3) A model including IGFLR1, FOXP3, PD-1, and CD4 showed good prognostic stratification ability. (4) There was a significant interaction between IGFLR1 and GATA3, and IGFLR1 had a significant co-expression with related factors in the INFR pathway. IGFLR1 has emerged as a new molecule related to disease prognosis and immune cell infiltration in CRC patients and showed a good ability to predict the prognosis of patients.
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Affiliation(s)
- Ran Jin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fenqi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinhao Han
- Department of Biostatistics, Public Health School of Harbin Medical University, Harbin, China
| | - Junnan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wenjie Song
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yixiu Xia
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xinyu Yue
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Da Yang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinxue Tong
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Qiuju Zhang
- Health Management Centre, Harbin Medical University Cancer Hospital, Harbin, China.
- Department of Biostatistics, Public Health School of Harbin Medical University, Harbin, China.
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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3
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Stary V, Pandey RV, List J, Kleissl L, Deckert F, Kabiljo J, Laengle J, Gerakopoulos V, Oehler R, Watzke L, Farlik M, Lukowski SW, Vogt AB, Stary G, Stockinger H, Bergmann M, Pilat N. Dysfunctional tumor-infiltrating Vδ1 + T lymphocytes in microsatellite-stable colorectal cancer. Nat Commun 2024; 15:6949. [PMID: 39138181 PMCID: PMC11322529 DOI: 10.1038/s41467-024-51025-1] [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: 06/23/2023] [Accepted: 07/24/2024] [Indexed: 08/15/2024] Open
Abstract
Although γδ T cells are known to participate in immune dysregulation in solid tumors, their relevance to human microsatellite-stable (MSS) colorectal cancer (CRC) is still undefined. Here, using integrated gene expression analysis and T cell receptor sequencing, we characterized γδ T cells in MSS CRC, with a focus on Vδ1 + T cells. We identified Vδ1+ T cells with shared motifs in the third complementarity-determining region of the δ-chain, reflective of antigen recognition. Changes in gene and protein expression levels suggested a dysfunctional effector state of Vδ1+ T cells in MSS CRC, distinct from Vδ1+ T cells in microsatellite-instable (MSI). Interaction analysis highlighted an immunosuppressive role of fibroblasts in the dysregulation of Vδ1+ T cells in MSS CRC via the TIGIT-NECTIN2 axis. Blocking this pathway with a TIGIT antibody partially restored cytotoxicity of the dysfunctional Vδ1 phenotype. These results define an operative pathway in γδ T cells in MSS CRC.
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MESH Headings
- Humans
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/immunology
- Microsatellite Instability
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Microsatellite Repeats/genetics
- Gene Expression Regulation, Neoplastic
- Female
- Male
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
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Affiliation(s)
- Victoria Stary
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria.
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria.
| | - Ram V Pandey
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Julia List
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lisa Kleissl
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Florian Deckert
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julijan Kabiljo
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Johannes Laengle
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Vasileios Gerakopoulos
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Rudolf Oehler
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Lukas Watzke
- Medical University of Vienna, Department of Pathology, Vienna, Austria
| | - Matthias Farlik
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
| | - Samuel W Lukowski
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Anne B Vogt
- Department of Human Cancer Immunology, Boehringer Ingelheim RCV GmBH & Co KG., Dr. Boehringer Gasse 5-11, 1120, Vienna, Austria
| | - Georg Stary
- Medical University of Vienna, Department of Dermatology, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Hannes Stockinger
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Vienna, Austria
| | - Michael Bergmann
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
| | - Nina Pilat
- Medical University of Vienna, Department of General Surgery, Division of Visceral Surgery, Comprehensive Cancer Center, Vienna, Austria
- Medical University of Vienna, Department of Cardiac Surgery, Vienna, Austria
- Medical University of Vienna, Center for Biomedical Research and Translational Surgery, Vienna, Austria
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4
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Zhang Y, Liu G, Zeng Q, Wu W, Lei K, Zhang C, Tang M, Zhang Y, Xiang X, Tan L, Cui R, Qin S, Song X, Yin C, Chen Z, Kuang M. CCL19-producing fibroblasts promote tertiary lymphoid structure formation enhancing anti-tumor IgG response in colorectal cancer liver metastasis. Cancer Cell 2024; 42:1370-1385.e9. [PMID: 39137726 DOI: 10.1016/j.ccell.2024.07.006] [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: 08/12/2023] [Revised: 05/05/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Tertiary lymphoid structures (TLSs) are associated with enhanced immunity in tumors. However, their formation and functions in colorectal cancer liver metastasis (CRLM) remain unclear. Here, we reveal that intra- and peri-tumor mature TLSs (TLS+) are associated with improved clinical outcomes than TLS- tumors. Using single-cell-RNA-sequencing and spatial-enhanced-resolution-omics-sequencing (Stereo-seq), we reveal that TLS+ tumors are enriched with IgG+ plasma cells (PCs), while TLS- tumors are characterized with IgA+ PCs. By generating TLS-associated PC-derived monoclonal antibodies in vitro, we show that TLS-PCs secrete tumor-targeting antibodies. As the proof-of-concept, we demonstrate the anti-tumor activities of TLS-PC-mAb6 antibody in humanized mouse model of colorectal cancer. We identify a fibroblast lineage secreting CCL19 that facilitates lymphocyte trafficking to TLSs. CCL19 treatment promotes TLS neogenesis and prevents tumor growth in mice. Our data uncover the central role of CCL19+ fibroblasts in TLS formation, which in turn generates therapeutic antibodies to restrict CRLM.
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Affiliation(s)
- Yifan Zhang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Guangjian Liu
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Qianwen Zeng
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenrui Wu
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Kai Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Chuankai Zhang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Department of Oncology, Cancer Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoling Tang
- Department of Oncology, Cancer Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuting Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiao Xiang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Li Tan
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui Cui
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Si Qin
- Department of Medical Ultrasonics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xinming Song
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Changjun Yin
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University, 80336 Munich, Germany.
| | - Zhihang Chen
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Sun Yat-sen University Zhongshan School of Medicine, Guangzhou 510080, China.
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5
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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 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] [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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6
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Jiang Z, Kang Q, Qian H, Xu Z, Tong H, Yang J, Li L, Li R, Li G, Chen F, Lin N, Zhao Y, Shi H, Huang J, Ma X. Revealing the crucial roles of suppressive immune microenvironment in cardiac myxoma progression. Signal Transduct Target Ther 2024; 9:193. [PMID: 39090109 PMCID: PMC11294589 DOI: 10.1038/s41392-024-01912-2] [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: 11/09/2023] [Revised: 06/26/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024] Open
Abstract
Cardiac myxoma is a commonly encountered tumor within the heart that has the potential to be life-threatening. However, the cellular composition of this condition is still not well understood. To fill this gap, we analyzed 75,641 cells from cardiac myxoma tissues based on single-cell sequencing. We defined a population of myxoma cells, which exhibited a resemblance to fibroblasts, yet they were distinguished by an increased expression of phosphodiesterases and genes associated with cell proliferation, differentiation, and adhesion. The clinical relevance of the cell populations indicated a higher proportion of myxoma cells and M2-like macrophage infiltration, along with their enhanced spatial interaction, were found to significantly contribute to the occurrence of embolism. The immune cells surrounding the myxoma exhibit inhibitory characteristics, with impaired function of T cells characterized by the expression of GZMK and TOX, along with a substantial infiltration of tumor-promoting macrophages expressed growth factors such as PDGFC. Furthermore, in vitro co-culture experiments showed that macrophages promoted the growth of myxoma cells significantly. In summary, this study presents a comprehensive single-cell atlas of cardiac myxoma, highlighting the heterogeneity of myxoma cells and their collaborative impact on immune cells. These findings shed light on the complex pathobiology of cardiac myxoma and present potential targets for intervention.
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Affiliation(s)
- Zedong Jiang
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Qianlong Kang
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Qian
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Huan Tong
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiaqing Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Li
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Renwei Li
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guangqi Li
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Chen
- Institute of Clinical Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Nan Lin
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunuo Zhao
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huashan Shi
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Juan Huang
- Department of Hematology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
| | - Xuelei Ma
- Department of Biotherapy, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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7
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Tian Y, Liu C, Yang W, Li X, Zhang M, Xiong Y, Ren X, Ma Z, Jin X, Wu Y, Dong X, Hu N, Xie Z, Qin Y, Wu S. Highlighting immune features of the tumor ecosystem and prognostic value of Tfh and Th17 cell infiltration in head and neck squamous cell carcinoma by single-cell RNA-seq. Cancer Immunol Immunother 2024; 73:187. [PMID: 39093451 PMCID: PMC11297013 DOI: 10.1007/s00262-024-03767-6] [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: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) typically present with a complex anatomical distribution, often accompanied by insidious symptoms. This combination contributes to its high incidence and poor prognosis. It is now understood that the immune features of cellular components within the tumor ecosystem and their complex interactions are critical factors influencing both tumor progression and the effective immune response. METHODS We obtained single-cell RNA sequencing data of 26,496 cells from three tumor tissues and five normal tissues and performed subsequent analyses. Immunohistochemical staining on tumor sections was used to validate the presence of malignant cells. Additionally, we included bulk RNA sequencing data from 502 HNSCC patients. Kaplan-Meier analysis and the log-rank test were employed to assess predictors of patient outcomes. RESULTS We identified three epithelial subclusters exhibiting immune-related features. These subclusters promoted the infiltration of T cells, dendritic cells, and monocytes into the tumor microenvironment. Additionally, cancer-associated fibroblasts displayed tumor-promoting and angiogenesis characteristics, contrasting with the predominant antigen-presenting and inflammatory roles observed in fibroblasts from normal tissues. Furthermore, tumor endothelial subsets exhibited a double-sided effect, promoting tumor progression and enhancing the effectiveness of immune response. Finally, follicular helper T cells and T helper 17 cells were found to be significantly correlated with improved outcomes in HNSCC patients. These CD4+ T cell subpopulations could promote the anti-tumor immune response by recruiting and activating B and T cells. CONCLUSION Our findings provide deeper insights into the immune features of the tumor ecosystem and reveal the prognostic significance of follicular helper T cells and T helper 17 cells. These findings may pave the way for the development of therapeutic approaches.
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Affiliation(s)
- Yan Tian
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Chao Liu
- Department of Radiation Oncology, Peking University First Hospital, Beijing, China
| | - Wenhui Yang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaohui Li
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Min Zhang
- Department of Radiation Oncology, Peking University People's Hospital, Beijing, China
| | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing, China
| | - Xueying Ren
- Department of Radiation Oncology, Peking University First Hospital, Beijing, China
| | - Zhiguo Ma
- Department of Neurology, Xi' an Aerospace General Hospital, Xian, China
| | - Xuan Jin
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Yanping Wu
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Xin Dong
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Nanlin Hu
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Zhijun Xie
- Department of Medical Oncology, Peking University First Hospital, Beijing, China
| | - Yong Qin
- Department of Otolaryngology Head and Neck Surgery, Peking University First Hospital, Beijing, China.
| | - Shikai Wu
- Department of Medical Oncology, Peking University First Hospital, Beijing, China.
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Li D, Zhang Z, Zhang C, Guo Q, Chen C, Peng X. Unraveling the connection between Hashimoto's Thyroiditis and non-alcoholic fatty liver disease: exploring the role of CD4 +central memory T cells through integrated genetic approaches. Endocrine 2024; 85:751-765. [PMID: 38400881 DOI: 10.1007/s12020-024-03745-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
PURPOSE Exploring the connection between Hashimoto's thyroiditis (HT) and non-alcoholic fatty liver disease (NAFLD) through integrated genetic approaches. METHODS We utilized integrated genetic approaches, such as single-cell RNA sequencing (scRNA-seq) data analysis, Mendelian Randomization (MR), colocalization analysis, cell communication, and metabolic analyses, to investigate potential correlations between HT and NAFLD. RESULTS Through the integrated analysis of scRNA-seq data from individuals with HT, NAFLD, and healthy controls, we observed an upregulation in the proportion of CD4+central memory (CD4+CM) T cells among T cells in both diseases. A total of 63 differentially expressed genes (DEGs) were identified in the CD4+CM cells after the differential analysis. By using MR, 8 DEGs (MAGI3, CSGALNACT1, CAMK4, GRIP1, TRAT1, IL7R, ERN1, and MB21D2) were identified to have a causal relationship with HT, and 4 DEGs (MAGI3, RCAN3, DOCK10, and SAMD12) had a causal relationship with NAFLD. MAGI3 was found to be causally linked to both HT and NAFLD. Therefore, MAGI3 was designated as the marker gene. Reverse MR and Steiger filtering showed no evidence of reverse causality. Colocalization analyses further indicated close links between MAGI3 and HT as well as NAFLD. Finally, based on the expression levels of MAGI3, we stratified CD4+CM cells into two subsets: MAGI3+CD4+CM cells and MAGI3-CD4+CM cells. Functional analyses revealed significant differences between the two subsets, potentially related to the progression of the two diseases. CONCLUSION This study delves into the potential connections between HT and NAFLD through integrated genetic methods. Our research reveals an elevated proportion of CD4+CM cells within T cells in both HT and NAFLD. Through MR and colocalization analysis, we identify specific genes causally linked to HT and NAFLD, such as MAGI3. Ultimately, based on MAGI3 expression levels, we categorize CD4+CM cells into MAGI3+CD4+CM cells and MAGI3-CD4+CM cells, uncovering significant differences between them through functional analyses.
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Affiliation(s)
- Dairui Li
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Zeji Zhang
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Cheng Zhang
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Qiannan Guo
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Chen Chen
- Department of Orthopedics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xinzhi Peng
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
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Pan X, Li X, Dong L, Liu T, Zhang M, Zhang L, Zhang X, Huang L, Shi W, Sun H, Fang Z, Sun J, Huang Y, Shao H, Wang Y, Yin M. Tumour vasculature at single-cell resolution. Nature 2024; 632:429-436. [PMID: 38987599 DOI: 10.1038/s41586-024-07698-1] [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: 07/13/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Tumours can obtain nutrients and oxygen required to progress and metastasize through the blood supply1. Inducing angiogenesis involves the sprouting of established vessel beds and their maturation into an organized network2,3. Here we generate a comprehensive atlas of tumour vasculature at single-cell resolution, encompassing approximately 200,000 cells from 372 donors representing 31 cancer types. Trajectory inference suggested that tumour angiogenesis was initiated from venous endothelial cells and extended towards arterial endothelial cells. As neovascularization elongates (through angiogenic stages SI, SII and SIII), APLN+ tip cells at the SI stage (APLN+ TipSI) advanced to TipSIII cells with increased Notch signalling. Meanwhile, stalk cells, following tip cells, transitioned from high chemokine expression to elevated TEK (also known as Tie2) expression. Moreover, APLN+ TipSI cells not only were associated with disease progression and poor prognosis but also hold promise for predicting response to anti-VEGF therapy. Lymphatic endothelial cells demonstrated two distinct differentiation lineages: one responsible for lymphangiogenesis and the other involved in antigen presentation. In pericytes, endoplasmic reticulum stress was associated with the proangiogenic BASP1+ matrix-producing pericytes. Furthermore, intercellular communication analysis showed that neovascular endothelial cells could shape an immunosuppressive microenvironment conducive to angiogenesis. This study depicts the complexity of tumour vasculature and has potential clinical significance for anti-angiogenic therapy.
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Affiliation(s)
- Xu Pan
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xin Li
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Liang Dong
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Teng Liu
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Min Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Lining Zhang
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Xiyuan Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Lingjuan Huang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China
| | - Wensheng Shi
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyin Sun
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Zhaoyu Fang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University, Changsha, China
| | - Jie Sun
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Yaoxuan Huang
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Hua Shao
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China
- School of Medicine, Chongqing University, Chongqing, China
| | - Yeqi Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
| | - Mingzhu Yin
- Clinical Research Center (CRC), Medical Pathology Center (MPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, China.
- Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs, Chongqing, China.
- School of Medicine, Chongqing University, Chongqing, China.
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, China.
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Chen Q, Shen M, Yan M, Han X, Mu S, Li Y, Li L, Wang Y, Li S, Li T, Wang Y, Wang W, Wei Z, Hu C, Jin A. Targeting tumor-infiltrating CCR8 + regulatory T cells induces antitumor immunity through functional restoration of CD4 + T convs and CD8 + T cells in colorectal cancer. J Transl Med 2024; 22:709. [PMID: 39080766 PMCID: PMC11290082 DOI: 10.1186/s12967-024-05518-8] [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: 05/12/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Chemokine (C-C motif) receptor 8 (CCR8) is a chemokine receptor selectively expressed on tumor-infiltrating regulatory T cells (Tregs). Strong immunosuppression mediated by CCR8+ Tregs observed in breast and lung malignancies suggest for their functional significance in cancer therapy. To date, detailed characterization of tumor-infiltrating CCR8+ Tregs cells in colorectal cancer (CRC) is limited. METHODS To study the presence and functional involvement of CCR8+ Tregs in CRC, we analyzed the proportions of CCR8-expressing T cells in different T cell subsets in tumor and adjacent normal tissues and peripheral blood mononuclear cells (PBMCs) from CRC patients by Flow cytometry. Also, we compared the distribution of CCR8+ T cells in malignant tissues and peripheral lymphoid organs from a subcutaneous CRC murine model. Bioinformatic analysis was performed to address the significance of CCR8 expression levels in CRC prognosis, immune regulatory gene expression profiles and potential molecular mechanisms associated with CCR8+ Tregs in CRC tumors. Further, we administrated an anti-CCR8 monoclonal antibody to CT26 tumor-bearing mice and examined the antitumor activity of CCR8-targeted therapy both in vivo and in an ex vivo confirmative model. RESULTS Here, we showed that Tregs was predominantly presented in the tumors of CRC patients (13.4 ± 5.8, p < 0.0001) and the CRC subcutaneous murine model (35.0 ± 2.6, p < 0.0001). CCR8 was found to be preferentially expressed on these tumor-infiltrating Tregs (CRC patients: 63.6 ± 16.0, p < 0.0001; CRC murine model: 65.3 ± 9.5, p < 0.0001), which correlated with poor survival. We found that majority of the CCR8+ Tregs expressed activation markers and exhibited strong suppressive functions. Treatment with anti-CCR8 antibody hampered the growth of subcutaneous CRC tumor through effectively restoring the anti-tumor immunity of CD4+ conventional T cells (CD4+ Tconvs) and CD8+ T cells, which was confirmed in the ex vivo examinations. CONCLUSIONS Collectively, these findings illustrate the importance of CCR8+ Tregs for an immunosuppressive microenvironment in CRC tumors by functional inhibition of CD4+ Tconvs and CD8+ T cells, and suggest for the applicable value of CCR8-targeted therapy for CRC.
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Affiliation(s)
- Qian Chen
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Meiying Shen
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Min Yan
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Xiaojian Han
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Song Mu
- Department of Colorectal Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Ya Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Luo Li
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Yingming Wang
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Shenglong Li
- School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
| | - Tingting Li
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Yingying Wang
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Wang Wang
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China
| | - Zhengqiang Wei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Chao Hu
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China.
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China.
| | - Aishun Jin
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400010, China.
- Chongqing Key Laboratory of Tumor Immune Regulation and Immune Intervention, Chongqing Medical University, Chongqing, 400010, China.
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Zhao L, Wang H, Zhang Y, Shi Y, Zhou C, Yu M, Wang Y, Zhang L, Xu Z, Zhang Z, Gao L, Zhang J, Yang B, Huang H, Wang FS. Characteristics and functions of an atypical inflammation-associated GZMK +GZMB +CD8 + T subset in people living with HIV-1. Mol Immunol 2024; 173:40-52. [PMID: 39053388 DOI: 10.1016/j.molimm.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/26/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
HIV-1 chronically infects host CD4+ T lymphocytes and further affects a variety of immune cells, including CD8+ T cells. In our previous study, by analyzing unbiased high-dimensional single-cell RNA-seq data (scRNA-seq), we found that the frequency of GZMK+CD8+ T cells expressing granzyme K (GZMK) was increased in people living with HIV-1 (PLWHs). However, the phenotypic and functional characteristics of these cells in chronic HIV-1 infection and their correlation with disease are not well understood. In this study, we conducted a comprehensive analysis of scRNA-seq and matched T-cell receptor repertoire (TCR) sequencing data to delve into the characterizations of GZMK+CD8+ T cells, which was further validated by flow cytometry. We observed heterogeneity within the GZMK+CD8+ T cells, which could be further subdivided into a GZMK+GZMB- subset and a GZMK+GZMB+ subset, with the latter being significantly enriched in PLWHs. The GZMK+GZMB+ cells are a unique subset within CD8+ T cells, characterized by high proliferation, activation, inflammatory response, clone transition, etc., and are one of the differentiation endpoints by pseudotemporal analysis of CD8+αβ T cells. Despite being predominantly composed of effector memory T cells (Tem), similar to the GZMK+GZMB- subset, the GZMK+GZMB+ subset exhibits differentiation at a later stage than the GZMK+GZMB- subset. We also observed that the frequency/count of GZMK+GZMB+CD8+ T cells was negatively correlated with CD4/CD8 ratio, and positively correlated with HIV DNA, IP-10, and MIG levels in PLWHs. In vitro experiments demonstrate that GZMK can potentiate the stimulatory effects of lipopolysaccharide (LPS) on THP-1 macrophages via the TLR-4 pathway, significantly enhancing the secretion of IP-10, MIG, and MCP-1, as well as increasing the proportion of TNF-α+ cells. In conclusion, in PLWHs, GZMK+GZMB+CD8+ T cells are a highly reactive and inflammatory-inducing subset that may be associated with systemic inflammation.
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Affiliation(s)
- Liang Zhao
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Huifang Wang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Senior Department of Infectious Diseases and Hepatology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanze Shi
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chunbao Zhou
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Minrui Yu
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanhu Wang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Liping Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zheng Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China; Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Ziying Zhang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lingyu Gao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jiyuan Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Baopeng Yang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Huihuang Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Fu-Sheng Wang
- Medical School of Chinese PLA, Beijing, China; Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Hirsch T, Neyens D, Duhamel C, Bayard A, Vanhaver C, Luyckx M, Sala de Oyanguren F, Wildmann C, Dauguet N, Squifflet JL, Montiel V, Deschamps M, van der Bruggen P. IRF4 impedes human CD8 T cell function and promotes cell proliferation and PD-1 expression. Cell Rep 2024; 43:114401. [PMID: 38943641 DOI: 10.1016/j.celrep.2024.114401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/03/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024] Open
Abstract
Human CD8 tumor-infiltrating lymphocytes (TILs) with impaired effector functions and PD-1 expression are categorized as exhausted. However, the exhaustion-like features reported in TILs might stem from their activation rather than the consequence of T cell exhaustion itself. Using CRISPR-Cas9 and lentiviral overexpression in CD8 T cells from non-cancerous donors, we show that the T cell receptor (TCR)-induced transcription factor interferon regulatory factor 4 (IRF4) promotes cell proliferation and PD-1 expression and hampers effector functions and expression of nuclear factor κB (NF-κB)-regulated genes. While CD8 TILs with impaired interferon γ (IFNγ) production exhibit activation markers IRF4 and CD137 and exhaustion markers thymocyte selection associated high mobility group box (TOX) and PD-1, activated T cells in patients with COVID-19 do not demonstrate elevated levels of TOX and PD-1. These results confirm that IRF4+ TILs are exhausted rather than solely activated. Our study indicates, however, that PD-1 expression, low IFNγ production, and active cycling in TILs are all influenced by IRF4 upregulation after T cell activation.
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Affiliation(s)
- Thibault Hirsch
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium.
| | - Damien Neyens
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Céline Duhamel
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Alexandre Bayard
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | | | - Mathieu Luyckx
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium; Département de Gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | | | - Claude Wildmann
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Nicolas Dauguet
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Jean-Luc Squifflet
- Département de Gynécologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Virginie Montiel
- Unité de Soins Intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Mélanie Deschamps
- Unité de Soins Intensifs, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Pierre van der Bruggen
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium; WELBIO Department, WEL Research Institute, Wavre, Belgium
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Zheng X, Wu W, Zhao Z, Zhang X, Yu S. Single-cell transcriptomic insights into chemotherapy-induced remodeling of the osteosarcoma tumor microenvironment. J Cancer Res Clin Oncol 2024; 150:356. [PMID: 39033089 PMCID: PMC11271355 DOI: 10.1007/s00432-024-05787-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/07/2024] [Indexed: 07/23/2024]
Abstract
PURPOSE Neoadjuvant chemotherapy serves as an effective strategy for treating osteosarcoma (OS) not only by targeting cancerous cells but also by influencing the tumor's immune and stromal elements. Gaining insights into how chemotherapy reshapes the tumor's local environment is crucial for advancing OS treatment protocols. METHODS Using single-cell RNA sequencing, this study analyzed tumor samples from patients with advanced osteosarcoma collected both before and after chemotherapy. RESULTS The results revealed that chemotherapy caused the remaining OS cells to express higher levels of genes associated with stemness. Additionally, this process enhances the presence of cancer-associated fibroblasts, increasing their ability to modify the extracellular matrix (ECM). Chemotherapy also increases the number of endothelial cells, albeit with compromised differentiation capabilities. Importantly, the treatment reduced the immune cell population, including myeloid and T/NK cells, particularly impacting the subpopulations with tumor-fighting capabilities. CONCLUSION These findings highlight the complex reaction of the tumor environment to chemotherapy, providing valuable insights into how chemotherapy influences OS cells and the tumor microenvironment (TME). This knowledge is essential for understanding OS resistance mechanisms to treatments, potentially guiding the development of novel therapies for managing advanced OS.
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Affiliation(s)
- Xuejing Zheng
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Wence Wu
- Department of Orthopedics, Peking University First Hospital, Beijing, 100021, China
| | - Zhenguo Zhao
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Xinxin Zhang
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China
| | - Shengji Yu
- Departments of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, China.
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Ran R, Trapecar M, Brubaker DK. Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604156. [PMID: 39071278 PMCID: PMC11275756 DOI: 10.1101/2024.07.18.604156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Gamma delta (γδ) T cells play a crucial role in anti-tumor immunity due to their cytotoxic properties. However, the role and extent of γδ T cells in production of pro-tumorigenic interleukin- 17 (IL-17) within the tumor microenvironment (TME) of colorectal cancer (CRC) remains controversial. In this study, we re-analyzed nine published human CRC whole-tissue single-cell RNA sequencing (scRNA-seq) datasets, identifying 18,483 γδ T cells out of 951,785 total cells, in the neoplastic or adjacent normal tissue of 165 human CRC patients. Our results confirm that tumor-infiltrating γδ T cells exhibit high cytotoxicity-related transcription in both tumor and adjacent normal tissues, but critically, none of the γδ T cell clusters showed IL-17 production potential. We also identified various γδ T cell subsets, including Teff, TRM, Tpex, and Tex, and noted an increased expression of cytotoxic molecules in tumor-infiltrating γδ T cells compared to their normal area counterparts. Our work demonstrates that γδ T cells in CRC primarily function as cytotoxic effector cells rather than IL-17 producers, mitigating the concerns about their potential pro-tumorigenic roles in CRC, highlighting the importance of accurately characterizing these cells for cancer immunotherapy research and the unneglectable cross-species discrepancy between the mouse and human immune system in the study of cancer immunology.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Martin Trapecar
- Department of Medicine, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH
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15
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Majumder B, Nataraj NB, Maitreyi L, Datta S. Mismatch repair-proficient tumor footprints in the sands of immune desert: mechanistic constraints and precision platforms. Front Immunol 2024; 15:1414376. [PMID: 39100682 PMCID: PMC11294168 DOI: 10.3389/fimmu.2024.1414376] [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: 04/08/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Mismatch repair proficient (MMRp) tumors of colorectal origin are one of the prevalent yet unpredictable clinical challenges. Despite earnest efforts, optimal treatment modalities have yet to emerge for this class. The poor prognosis and limited actionability of MMRp are ascribed to a low neoantigen burden and a desert-like microenvironment. This review focuses on the critical roadblocks orchestrated by an immune evasive mechanistic milieu in the context of MMRp. The low density of effector immune cells, their weak spatiotemporal underpinnings, and the high-handedness of the IL-17-TGF-β signaling are intertwined and present formidable challenges for the existing therapies. Microbiome niche decorated by Fusobacterium nucleatum alters the metabolic program to maintain an immunosuppressive state. We also highlight the evolving strategies to repolarize and reinvigorate this microenvironment. Reconstruction of anti-tumor chemokine signaling, rational drug combinations eliciting T cell activation, and reprograming the maladapted microbiome are exciting developments in this direction. Alternative vulnerability of other DNA damage repair pathways is gaining momentum. Integration of liquid biopsy and ex vivo functional platforms provide precision oncology insights. We illustrated the perspectives and changing landscape of MMRp-CRC. The emerging opportunities discussed in this review can turn the tide in favor of fighting the treatment dilemma for this elusive cancer.
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16
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Rigopoulos C, Georgakopoulos-Soares I, Zaravinos A. A Multi-Omics Analysis of an Exhausted T Cells' Molecular Signature in Pan-Cancer. J Pers Med 2024; 14:765. [PMID: 39064019 PMCID: PMC11278172 DOI: 10.3390/jpm14070765] [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: 06/03/2024] [Revised: 07/06/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
T cells are essential tumor suppressors in cancer immunology, but their dysfunction induced by cancer cells can result in T cell exhaustion. Exhausted T cells (Tex) significantly influence the tumor immune environment, and thus, there is a need for their thorough investigation across different types of cancer. Here, we address the role of Tex cells in pan-cancer, focusing on the expression, mutations, methylation, immune infiltration, and drug sensitivity of a molecular signature comprising of the genes HAVCR2, CXCL13, LAG3, LAYN, TIGIT, and PDCD1across multiple cancer types, using bioinformatics analysis of TCGA data. Our analysis revealed that the Tex signature genes are differentially expressed across 14 cancer types, being correlated with patient survival outcomes, with distinct survival trends. Pathway analysis indicated that the Tex genes influence key cancer-related pathways, such as apoptosis, EMT, and DNA damage pathways. Immune infiltration analysis highlighted a positive correlation between Tex gene expression and immune cell infiltration in bladder cancer, while mutations in these genes were associated with specific immune cell enrichments in UCEC and SKCM. CNVs in Tex genes were widespread across cancers. We also highlight high LAYN methylation in most tumors and a negative correlation between methylation levels and immune cell infiltration in various cancers. Drug sensitivity analysis identified numerous correlations, with CXCL13 and HAVCR2 expressions influencing sensitivity to several drugs, including Apitolisib, Belinostat, and Docetaxel. Overall, these findings highlight the importance of reviving exhausted T cells to enhance the treatment efficacy to significantly boost anti-tumor immunity and achieve better clinical outcomes.
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Affiliation(s)
- Christos Rigopoulos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus;
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1678, Cyprus
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus;
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1678, Cyprus
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17
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Chen C, Zou P, Wu X. Development and Validation of an Immune Prognostic Index Related to Infiltration of CD4+ and CD8+ T Cells in Colorectal Cancer. Mol Biotechnol 2024:10.1007/s12033-024-01237-z. [PMID: 39026041 DOI: 10.1007/s12033-024-01237-z] [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: 04/05/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
Colorectal cancer (CRC) is a highly prevalent cancer worldwide, but treatment outcomes can vary significantly among patients with similar clinical or historical stages. This study aimed to investigate the differences in immune cell abundance associated with malignant progression in CRC patients. We utilized data from patients with CRC obtained from The Cancer Genome Atlas as our training set. To assess immune cell infiltration levels, an immune cell risk score (ICRS) was calculated. Furthermore, we performed network analysis to identify effective T cell-related genes (ETRGs) and subsequently constructed an effective T cell prognostic index (ETPI). The performance of the ETPI was evaluated through external validation using four Gene Expression Omnibus datasets. Additionally, a nomogram analysis and drug sensitivity analysis were conducted to explore the clinical utility of the ETRGs. We also examined the expression of ETRGs in clinical samples. Based on the ICRS, we identified activated CD4+ and CD8+ T cells as protective factors in terms of prognosis. Six ETRGs were identified to develop the ETPI, which exhibited remarkable prognostic performance. In the external validation of immunotherapy, the low ETPI group demonstrated a significantly lower recurrence rate. To optimize therapeutic strategies, we developed a nomogram. Notably, patients with different ETPI values exhibited varying responses to tumor pathway inhibitors. Finally, we observed higher protein expression of certain ETRGs in normal tissues compared to tumors. Our findings suggest that the ETPI may contribute to the precise selection of patients based on tumor microenvironment and key genomic landscape interactions, thereby optimizing drug benefits and informing clinical strategies in future.
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Affiliation(s)
- Chengru Chen
- Department of Gastrointestinal Surgery, The Eighth Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518033, Guangdong Province, China
| | - Peng Zou
- Department of Gastrointestinal Surgery, The Eighth Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518033, Guangdong Province, China
| | - Xiaobin Wu
- Department of Gastrointestinal Surgery, The Eighth Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, 518033, Guangdong Province, China.
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18
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Tooley K, Jerby L, Escobar G, Krovi SH, Mangani D, Dandekar G, Cheng H, Madi A, Goldschmidt E, Lambden C, Krishnan RK, Rozenblatt-Rosen O, Regev A, Anderson AC. Pan-cancer mapping of single CD8 + T cell profiles reveals a TCF1:CXCR6 axis regulating CD28 co-stimulation and anti-tumor immunity. Cell Rep Med 2024; 5:101640. [PMID: 38959885 PMCID: PMC11293343 DOI: 10.1016/j.xcrm.2024.101640] [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: 05/31/2023] [Revised: 01/05/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024]
Abstract
CD8+ T cells must persist and function in diverse tumor microenvironments to exert their effects. Thus, understanding common underlying expression programs could better inform the next generation of immunotherapies. We apply a generalizable matrix factorization algorithm that recovers both shared and context-specific expression programs from diverse datasets to a single-cell RNA sequencing (scRNA-seq) compendium of 33,161 CD8+ T cells from 132 patients with seven human cancers. Our meta-single-cell analyses uncover a pan-cancer T cell dysfunction program that predicts clinical non-response to checkpoint blockade in melanoma and highlights CXCR6 as a pan-cancer marker of chronically activated T cells. Cxcr6 is trans-activated by AP-1 and repressed by TCF1. Using mouse models, we show that Cxcr6 deletion in CD8+ T cells increases apoptosis of PD1+TIM3+ cells, dampens CD28 signaling, and compromises tumor growth control. Our study uncovers a TCF1:CXCR6 axis that counterbalances PD1-mediated suppression of CD8+ cell responses and is essential for effective anti-tumor immunity.
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Affiliation(s)
- Katherine Tooley
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Division of Medical Sciences, Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulia Escobar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - S Harsha Krovi
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Davide Mangani
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gitanjali Dandekar
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hanning Cheng
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella Goldschmidt
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Conner Lambden
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rajesh K Krishnan
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Ana C Anderson
- The Gene Lay Institute of Immunology and Inflammation of Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, USA; Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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19
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Aala WJF, Hou PC, Hong YK, Lin YC, Lee YR, Tu WT, Papanikolaou M, Benzian-Olsson N, Onoufriadis A, I Chen Harn H, Hwang DY, Cheng SM, Lu K, Chen PC, McGrath JA, Hsu CK. Dominant dystrophic epidermolysis bullosa is associated with glycolytically active GATA3+ T helper 2 cells which may contribute to pruritus in lesional skin. Br J Dermatol 2024; 191:252-260. [PMID: 38477474 DOI: 10.1093/bjd/ljae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Dominant dystrophic epidermolysis bullosa (DDEB) is characterized by trauma-induced blisters and, in some individuals, intense pruritus. Precisely what causes itch in DDEB and optimal ways to reduce it have not been fully determined. OBJECTIVES To characterize DDEB skin transcriptomes to identify therapeutic targets to reduce pruritus in patients. METHODS Using bulk RNA sequencing, we evaluated affected and unaffected skin biopsy samples from six patients with DDEB (all with the very itchy pruriginosa subtype) and four healthy individuals. Single-cell transcriptomes of affected (n = 2) and unaffected (n = 1) DDEB skin and healthy skin (n = 2) were obtained. Dupilumab treatment was provided for three patients. RESULTS The skin bulk transcriptome showed significant enrichment of T helper (Th)1/2 and Th17 pathways in affected DDEB skin compared with nonlesional DDEB skin and healthy skin. Single-cell transcriptomics showed an association of glycolytically active GATA3+ Th2 cells in affected DDEB skin. Treatment with dupilumab in three people with DDEB led to significantly reduced visual analogue scale (VAS) itch scores after 12 weeks (mean VAS 3.83) compared with pretreatment (mean VAS 7.83). Bulk RNAseq and quantitative polymerase chain reaction showed that healthy skin and dupilumab-treated epidermolysis bullosa (EB) pruriginosa skin have similar transcriptomic profiles and reduced Th1/Th2 and Th17 pathway enrichment. CONCLUSIONS Single-cell RNAseq helps define an enhanced DDEB-associated Th2 profile and rationalizes drug repurposing of anti-Th2 drugs in treating DDEB pruritus.
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Affiliation(s)
- Wilson Jr F Aala
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Chen Hou
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Kai Hong
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chen Lin
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Rong Lee
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Ting Tu
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Marieta Papanikolaou
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Natashia Benzian-Olsson
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
- Laboratory of Medical Biology and Genetics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Hans I Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Siao Muk Cheng
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Kurt Lu
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - John A McGrath
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Chao-Kai Hsu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Dermatology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan
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20
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Yang Y, Chen X, Pan J, Ning H, Zhang Y, Bo Y, Ren X, Li J, Qin S, Wang D, Chen MM, Zhang Z. Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. Cell 2024:S0092-8674(24)00712-8. [PMID: 39047727 DOI: 10.1016/j.cell.2024.06.038] [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: 06/09/2023] [Revised: 04/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells (TIBs) is important for advancing our understanding of their role in cancer development. Here, we establish a comprehensive resource of human B cells by integrating single-cell RNA sequencing data of B cells from 649 patients across 19 major cancer types. We demonstrate substantial heterogeneity in their total abundance and subtype composition and observe immunoglobulin G (IgG)-skewness of antibody-secreting cell isotypes. Moreover, we identify stress-response memory B cells and tumor-associated atypical B cells (TAABs), two tumor-enriched subpopulations with prognostic potential, shared in a pan-cancer manner. In particular, TAABs, characterized by a high clonal expansion level and proliferative capacity as well as by close interactions with activated CD4 T cells in tumors, are predictive of immunotherapy response. Our integrative resource depicts distinct clinically relevant TIB subsets, laying a foundation for further exploration of functional commonality and diversity of B cells in cancer.
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Affiliation(s)
- Yu Yang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jieying Pan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Huiheng Ning
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yaojun Zhang
- State Key Laboratory of Oncology in South China, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yufei Bo
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jiesheng Li
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Min-Min Chen
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, and School of Life Sciences, Peking University, Beijing 100871, China.
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21
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Kong W, He J, Zhou Q, Zhou X, Wei X, Yang Y, Mei Y, Wang S, Zhang X, Yao B, Yue Y, Xu J, Jiang M, Xu C. Histone lactylation-related genes correlate with the molecular patterns and functions of cancer-associated fibroblasts and have significant clinical implications in clear cell renal cell carcinoma. Heliyon 2024; 10:e33554. [PMID: 39035489 PMCID: PMC11259888 DOI: 10.1016/j.heliyon.2024.e33554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Recent research emphasised the indispensable role of histone lactylation in the activation of hepatic stellate cells. The VHL mutation is extremely common in clear cell renal cell carcinoma, which normally causes a metabolic shift in cancer cells and increases lactate production, eventually creating a lactate-enriched tumour microenvironment. Cancer-associated fibroblasts (CAFs) promote tumour progression, which is also vital in clear cell renal cell carcinoma. Therefore, this study investigated histone lactylation in CAFs and its impact on patient survival. Multiomics technology was employed to determine the role of histone lactylation-related genes in the evolution of CAFs which correlated with the function and molecular signatures of CAFs. The results suggested that TIMP1 was the hub gene of histone lactylation-related genes in clear cell renal cell carcinoma.
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Affiliation(s)
- Weiyu Kong
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiaxin He
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Qinyao Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhou
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xiyi Wei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yonglin Yang
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China
| | - Yiwen Mei
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Shuai Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Bing Yao
- National Experimental Teaching Center of Basic Medical Science, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yulin Yue
- Department of Clinical Laboratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiali Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Minjun Jiang
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
| | - Chen Xu
- Department of Urology, Suzhou Ninth People's Hospital, Soochow University, Suzhou, 215000, China
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22
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Ren L, Liu Y, Wang Y, Wu C, Guo L, Chen L, Wang X, Xiao Y, Huang L, Zhong J, Yao J, Liu L, Li H, Wang Y, Ma Y, Zhang Y, Di L, Dong T, Knight J, Wang J, Huang Y, Cao B, Ren X, Wang J. Longitudinal landscape of immune reconstitution after acute SARS-CoV-2 infection at single-cell resolution. Sci Bull (Beijing) 2024:S2095-9273(24)00488-2. [PMID: 39107149 DOI: 10.1016/j.scib.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/16/2024] [Accepted: 07/04/2024] [Indexed: 08/09/2024]
Affiliation(s)
- Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China.
| | - Yiwei Liu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yeming Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Chao Wu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Lixue Huang
- Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingchuan Zhong
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Jiacheng Yao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lu Liu
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Li
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yongchao Ma
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Yichunzi Zhang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
| | - Lin Di
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford OX3 9DS, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 9DS, UK
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 9DS, UK
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology (ICSB), Tsinghua University, Beijing 100084, China; Chinese Institute for Brain Research (CIBR), Beijing 102206, China.
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518107, China.
| | - Bin Cao
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Institute of Respiratory Medicine of Chinese Academy of Medical Science, National Center for Respiratory Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing 100029, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
| | - Xianwen Ren
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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23
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Yu Y, Yu M, Luo L, Zhang Z, Zeng H, Chen Y, Lin Z, Chen M, Wang W. Molecular characteristics and immune microenvironment of gastrointestinal stromal tumours: targets for therapeutic strategies. Front Oncol 2024; 14:1405727. [PMID: 39070147 PMCID: PMC11272528 DOI: 10.3389/fonc.2024.1405727] [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: 03/23/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours, arising mainly from the interstitial cells of Cajal (ICCs) of the gastrointestinal tract. As radiotherapy and chemotherapy are generally ineffective for GISTs, the current primary treatment is surgical resection. However, surgical resection is not choice for most patients. Therefore, new therapeutic strategies are urgently needed. Targeted therapy, represented by tyrosine kinase inhibitors (TKIs), and immunotherapy, represented by immune checkpoint inhibitor therapies and chimeric antigen receptor T-cell immunotherapy (CAR-T), offer new therapeutic options in GISTs and have shown promising treatment responses. In this review, we summarize the molecular classification and immune microenvironment of GISTs and discuss the corresponding targeted therapy and immunotherapy options. This updated knowledge may provide more options for future therapeutic strategies and applications in GISTs.
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Affiliation(s)
- Yang Yu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Mengdie Yu
- Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou, Guangdong, China
| | - Lijie Luo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Zijing Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Haiping Zeng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Yan Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Zeyu Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Mengnan Chen
- Department of Thyroid and Breast Surgery, Baiyun Hospital, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong, China
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24
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Acosta-Iborra B, Gil-Acero AI, Sanz-Gómez M, Berrouayel Y, Puente-Santamaría L, Alieva M, del Peso L, Jiménez B. Bhlhe40 Regulates Proliferation and Angiogenesis in Mouse Embryoid Bodies under Hypoxia. Int J Mol Sci 2024; 25:7669. [PMID: 39062912 PMCID: PMC11277088 DOI: 10.3390/ijms25147669] [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: 06/04/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Knowledge of the molecular mechanisms that underlie the regulation of major adaptive responses to an unbalanced oxygen tension is central to understanding tissue homeostasis and disease. Hypoxia-inducible transcription factors (HIFs) coordinate changes in the transcriptome that control these adaptive responses. Here, we focused on the functional role of the transcriptional repressor basic-helix-loop-helix family member e40 (Bhlhe40), which we previously identified in a meta-analysis as one of the most consistently upregulated genes in response to hypoxia across various cell types. We investigated the role of Bhlhe40 in controlling proliferation and angiogenesis using a gene editing strategy in mouse embryonic stem cells (mESCs) that we differentiated in embryoid bodies (EBs). We observed that hypoxia-induced Bhlhe40 expression was compatible with the rapid proliferation of pluripotent mESCs under low oxygen tension. However, in EBs, hypoxia triggered a Bhlhe40-dependent cell cycle arrest in most progenitor cells and endothelial cells within vascular structures. Furthermore, Bhlhe40 knockout increased the basal vascularization of the EBs in normoxia and exacerbated the hypoxia-induced vascularization, supporting a novel role for Bhlhe40 as a negative regulator of blood vessel formation. Our findings implicate Bhlhe40 in mediating key functional adaptive responses to hypoxia, such as proliferation arrest and angiogenesis.
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Affiliation(s)
- Bárbara Acosta-Iborra
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Ana Isabel Gil-Acero
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Marta Sanz-Gómez
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Yosra Berrouayel
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Laura Puente-Santamaría
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
- Biocomputing Unit, Instituto Aragonés de Ciencias de la Salud, San Juan Bosco, 50009 Zaragoza, Spain
| | - Maria Alieva
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
| | - Luis del Peso
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Unidad Asociada de Biomedicina CSIC-UCLM, 02006 Albacete, Spain
| | - Benilde Jiménez
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain
- IdiPaz, Instituto de Investigación Sanitaria del Hospital Universitario La Paz, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Unidad Asociada de Biomedicina CSIC-UCLM, 02006 Albacete, Spain
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25
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Ji H, Fan Y, Long Y, Dai K, Zheng G, Jia X, Liu A, Yu J. Structural analysis of Salvia miltiorrhiza polysaccharide and its regulatory functions on T cells subsets in tumor-bearing mice combined with thymopentin. Int J Biol Macromol 2024:133832. [PMID: 39002910 DOI: 10.1016/j.ijbiomac.2024.133832] [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: 03/10/2024] [Revised: 05/18/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Salvia miltiorrhiza ethanol-extracted polysaccharide (SMEP) and thymopentin (TP5) have been proved with strong immunomodulatory activity, and T cells subsets play pivotal roles in the inhibition of solid tumors growth. In the present study, the structure of SMEP was further identified via methylation and nuclear magnetic resonance spectra, and the immunomodulatory activity in combination with TP5 was investigated via evaluating T cell subsets spatial distributions in tumor-bearing mice, finally the cellular status of solid tumor cells was analyzed. The results revealed that SMEP was a neutral heteropolysaccharide using (1 → 4)-α-D-Glcp and (2 → 1)-β-D-Fruf as the main chain, along with branched chains of (1 → 6)-α-D-Galp. The SMEP+TP5 treatments could effectively promote the differentiation and improve the specific recognition capacity of CD4+ T cells in tumor-bearing mice, thereby activate tumor-infiltrating CD8+ T cells to exert cytotoxic effects, finally promoting the tumor cells apoptosis via blocking cell cycle at G0/G1 phase, which might be relevant with suppression of Wnt/β-catenin signaling pathway. These findings highlighted the potential of SMEP as an immunoadjuvant for patients bearing immune-deficiency related diseases, and provided data support for the functional researches of T cell subsets in tumor immunity.
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Affiliation(s)
- Haiyu Ji
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Yuting Fan
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Yan Long
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Keyao Dai
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guoqiang Zheng
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaoyu Jia
- Xinjiang Yuanxiang Agricultural Technology Co., Ltd., Hetian, Xinjiang 848000, China
| | - Anjun Liu
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Juan Yu
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China.
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26
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Chen Y, Wang D, Li Y, Qi L, Si W, Bo Y, Chen X, Ye Z, Fan H, Liu B, Liu C, Zhang L, Zhang X, Li Z, Zhu L, Wu A, Zhang Z. Spatiotemporal single-cell analysis decodes cellular dynamics underlying different responses to immunotherapy in colorectal cancer. Cancer Cell 2024; 42:1268-1285.e7. [PMID: 38981439 DOI: 10.1016/j.ccell.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 04/10/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Expanding the efficacy of immune checkpoint blockade (ICB) in colorectal cancer (CRC) presses for a comprehensive understanding of treatment responsiveness. Here, we analyze multiple sequential single-cell samples from 22 patients undergoing PD-1 blockade to map the evolution of local and systemic immunity of CRC patients. In tumors, we identify coordinated cellular programs exhibiting distinct response associations. Specifically, exhausted T (Tex) or tumor-reactive-like CD8+ T (Ttr-like) cells are closely related to treatment efficacy, and Tex cells show correlated proportion changes with multiple other tumor-enriched cell types following PD-1 blockade. In addition, we reveal the less-exhausted phenotype of blood-associated Ttr-like cells in tumors and find that their higher abundance suggests better treatment outcomes. Finally, a higher major histocompatibility complex (MHC) II-related signature in circulating CD8+ T cells at baseline is linked to superior responses. Our study provides insights into the spatiotemporal cellular dynamics following neoadjuvant PD-1 blockade in CRC.
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Affiliation(s)
- Yuqing Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dongfang Wang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Yingjie Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Lu Qi
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Wen Si
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yufei Bo
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhaochen Ye
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hongtao Fan
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Baolin Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chang Liu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Li Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Xiaoyan Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Radiology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zhongwu Li
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Linna Zhu
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China
| | - Aiwen Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Gastrointestinal Cancer Center, Unit III, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| | - Zemin Zhang
- Biomedical Pioneering Innovative Center (BIOPIC) and School of Life Sciences, Peking University, Beijing 100871, China.
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27
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Wei C, Wang W, Hu Z, Huang Z, Lu Y, Zhou W, Liu X, Jin X, Yin J, Li G. Predicting prognosis and immunotherapy response in colorectal cancer by pericytes insights from single-cell RNA sequencing. Hum Mol Genet 2024; 33:1215-1228. [PMID: 38652261 DOI: 10.1093/hmg/ddae064] [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: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Immunotherapy has revolutionized the treatment of tumors, but there are still a large number of patients who do not benefit from immunotherapy. Pericytes play an important role in remodeling the immune microenvironment. However, how pericytes affect the prognosis and treatment resistance of tumors is still unknown. This study jointly analyzed single-cell RNA sequencing (scRNA-seq) data and bulk RNA sequencing data of multiple cancers to reveal pericyte function in the colorectal cancer microenvironment. Analyzing over 800 000 cells, it was found that colorectal cancer had more pericyte enrichment in tumor tissues than other cancers. We then combined the TCGA database with multiple public datasets and enrolled more than 1000 samples, finding that pericyte may be closely related to poor prognosis due to the higher epithelial-mesenchymal transition (EMT) and hypoxic characteristics. At the same time, patients with more pericytes have higher immune checkpoint molecule expressions and lower immune cell infiltration. Finally, the contributions of pericyte in poor treatment response have been demonstrated in multiple immunotherapy datasets (n = 453). All of these observations suggest that pericyte can be used as a potential biomarker to predict patient disease progression and immunotherapy response.
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Affiliation(s)
- Chen Wei
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Weikai Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhihao Hu
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhuoli Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Ye Lu
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Wenwen Zhou
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaoying Liu
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xin Jin
- College of Life Sciences, University of Chinese Academy of Sciences, Yuquan Road, Shijingshan District, Beijing 100049, China
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Jianhua Yin
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Guibo Li
- BGI Research, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
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28
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Huang TX, Huang HS, Dong SW, Chen JY, Zhang B, Li HH, Zhang TT, Xie Q, Long QY, Yang Y, Huang LY, Zhao P, Bi J, Lu XF, Pan F, Zou C, Fu L. ATP6V0A1-dependent cholesterol absorption in colorectal cancer cells triggers immunosuppressive signaling to inactivate memory CD8 + T cells. Nat Commun 2024; 15:5680. [PMID: 38971819 PMCID: PMC11227557 DOI: 10.1038/s41467-024-50077-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 06/27/2024] [Indexed: 07/08/2024] Open
Abstract
Obesity shapes anti-tumor immunity through lipid metabolism; however, the mechanisms underlying how colorectal cancer (CRC) cells utilize lipids to suppress anti-tumor immunity remain unclear. Here, we show that tumor cell-intrinsic ATP6V0A1 drives exogenous cholesterol-induced immunosuppression in CRC. ATP6V0A1 facilitates cholesterol absorption in CRC cells through RAB guanine nucleotide exchange factor 1 (RABGEF1)-dependent endosome maturation, leading to cholesterol accumulation within the endoplasmic reticulum and elevated production of 24-hydroxycholesterol (24-OHC). ATP6V0A1-induced 24-OHC upregulates TGF-β1 by activating the liver X receptor (LXR) signaling. Subsequently, the release of TGF-β1 into the tumor microenvironment by CRC cells activates the SMAD3 pathway in memory CD8+ T cells, ultimately suppressing their anti-tumor activities. Moreover, we identify daclatasvir, a clinically used anti-hepatitis C virus (HCV) drug, as an ATP6V0A1 inhibitor that can effectively enhance the memory CD8+ T cell activity and suppress tumor growth in CRC. These findings shed light on the potential for ATP6V0A1-targeted immunotherapy in CRC.
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Affiliation(s)
- Tu-Xiong Huang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Hui-Si Huang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Shao-Wei Dong
- Department of Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, 518000, Guangdong, China
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen, 518038, Guangdong, China
| | - Jia-Yan Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Bin Zhang
- Department of Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, 518000, Guangdong, China
| | - Hua-Hui Li
- Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, 518055, Guangdong, China
| | - Tian-Tian Zhang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Qiang Xie
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Qiao-Yun Long
- Department of Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, 518000, Guangdong, China
| | - Yang Yang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Lin-Yuan Huang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China
| | - Pan Zhao
- Department of Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, 518000, Guangdong, China
| | - Jiong Bi
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | - Xi-Feng Lu
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Fan Pan
- Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences (CAS), Shenzhen, 518055, Guangdong, China
| | - Chang Zou
- Department of Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, 518000, Guangdong, China.
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 518000, Guangdong, China.
| | - Li Fu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pharmacology and International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, Guangdong, China.
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29
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Wang Y, Zhang W, Li T, Liu M, Gao M, Li X, Chen Y, Song Y, Li W, Du C, Wang F, Liu L. Identification of potential immune-related mechanisms related to the development of multiple myeloma. Chin Med J (Engl) 2024; 137:1603-1613. [PMID: 38844445 PMCID: PMC11230759 DOI: 10.1097/cm9.0000000000003116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Although significant advances have been made in the treatment of multiple myeloma (MM), leading to unprecedented response and survival rates among patients, the majority eventually relapse, and a cure remains elusive. This situation is closely related to an incomplete understanding of the immune microenvironment, especially monocytes/macrophages in patients with treatment-naïve MM. The aim of this study was to provide insight into the immune microenvironment, especially monocytes/macrophages, in patients with treatment-naïve MM. METHODS This study used the single-cell RNA sequencing (scRNA-seq) data of both patients with MM and heathy donors to identify immune cells, including natural killer (NK) cells, T cells, dendritic cells (DCs), and monocytes/macrophages. Transcriptomic data and flow cytometry analysis of monocytes/macrophages were used to further examine the effect of monocytes/macrophages in treatment-naïve MM patients. RESULTS A significant difference was observed between the bone marrow (BM) immune cells of the healthy controls and treatment-naïve MM patients through scRNA-seq. It is noteworthy that, through an scRNA-seq data analysis, this study found that interferon (IFN)-induced NK/T cells, terminally differentiated effector memory (TEMRA) cells, T-helper cells characterized by expression of IFN-stimulated genes (ISG + Th cells), IFN-responding exhausted T cells, mannose receptor C-type 1 (MRC1) + DCs, IFN-responding DCs, MHCII + DCs, and immunosuppressive monocytes/macrophages were enriched in patients with treatment-naïve MM. Significantly, transcriptomic data of monocytes/macrophages demonstrated that "don't eat me"-related genes and IFN-induced genes increase in treatment-naïve MM patients. Furthermore, scRNA-seq, transcriptomic data, and flow cytometry also showed an increased proportion of CD16 + monocytes/macrophages and expression level of CD16. Cell-cell communication analysis indicated that monocytes/macrophages, whose related important signaling pathways include migration inhibitory factor (MIF) and interleukin 16 (IL-16) signaling pathway, are key players in treatment-naïve MM patients. CONCLUSIONS Our findings provide a comprehensive and in-depth molecular characterization of BM immune cell census in MM patients, especially for monocytes/macrophages. Targeting macrophages may be a novel treatment strategy for patients with MM.
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Affiliation(s)
- Yaomei Wang
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Wenli Zhang
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan 450008, China
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Tiandong Li
- College of Public Health, Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Mengmeng Liu
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Research and Foreign Affairs, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Mengya Gao
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Research and Foreign Affairs, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Xinqing Li
- Department of Clinical Medicine, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yufei Chen
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yongping Song
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Wei Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Chunyan Du
- Laboratory Animal Center, School of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Fang Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Lina Liu
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan 450008, China
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Wu C, Yu H, Liang F, Huang X, Jiang B, Lou Z, Liu Y, Wu Z, Wang Q, Shen H, Chen M, Wu P, Wu M. Hypoxia inhibits the iMo/cDC2/CD8+ TRMs immune axis in the tumor microenvironment of human esophageal cancer. J Immunother Cancer 2024; 12:e008889. [PMID: 38964786 PMCID: PMC11227851 DOI: 10.1136/jitc-2024-008889] [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: 05/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Esophageal cancer (ESCA) is a form of malignant tumor associated with chronic inflammation and immune dysregulation. However, the specific immune status and key mechanisms of immune regulation in this disease require further exploration. METHODS To investigate the features of the human ESCA tumor immune microenvironment and its possible regulation, we performed mass cytometry by time of flight, single-cell RNA sequencing, multicolor fluorescence staining of tissue, and flow cytometry analyses on tumor and paracancerous tissue from treatment-naïve patients. RESULTS We depicted the immune landscape of the ESCA and revealed that CD8+ (tissue-resident memory CD8+ T cells (CD8+ TRMs) were closely related to disease progression. We also revealed the heterogeneity of CD8+ TRMs in the ESCA tumor microenvironment (TME), which was associated with their differentiation and function. Moreover, the subset of CD8+ TRMs in tumor (called tTRMs) that expressed high levels of granzyme B and immune checkpoints was markedly decreased in the TME of advanced ESCA. We showed that tTRMs are tumor effector cells preactivated in the TME. We then demonstrated that conventional dendritic cells (cDC2s) derived from intermediate monocytes (iMos) are essential for maintaining the proliferation of CD8+ TRMs in the TME. Our preliminary study showed that hypoxia can promote the apoptosis of iMos and impede the maturation of cDC2s, which in turn reduces the proliferative capacity of CD8+ TRMs, thereby contributing to the progression of cancer. CONCLUSIONS Our study revealed the essential antitumor roles of CD8+ TRMs and preliminarily explored the regulation of the iMo/cDC2/CD8+ TRM immune axis in the human ESCA TME.
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Affiliation(s)
- Chuanqiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Huan Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Fuxiang Liang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xiancong Huang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang Province, People's Republic of China
| | - Bin Jiang
- Department of Thoracic Surgery, Shandong Provincial Hospital, Jinan, Shandong Province, People's Republic of China
| | - Zhiling Lou
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yafei Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Hong Shen
- Department of Medical Oncology, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Pin Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ming Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine,Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
- Laboratory of Clinical Research Center of Zhejiang Province, The Second Affiliated Hospital Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of China
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Wu X, Hao L, Lin J, Guo X, Luo Y, Li C. Unraveling the role of Major Vault Protein as a novel immune-related biomarker that promotes the proliferation and migration in pancreatic adenocarcinoma. Front Immunol 2024; 15:1399222. [PMID: 39026679 PMCID: PMC11254802 DOI: 10.3389/fimmu.2024.1399222] [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: 03/11/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is a formidable challenge in oncology research, with a complex pathogenesis that requires to be explored. Major Vault Protein (MVP) is the principal structural component of the vault complex, and its expression level is remarkably upregulated in various cancers. Extensive investigations have been conducted to explore the role of MVP in specific cancer contexts, yet the potential molecular mechanisms and biological functions of MVP in PAAD still remain considerably elusive. This study aims to explore the role of MVP as a novel immune-related biomarker in the pathogenesis and clinical treatment of PAAD. Methods Gene expression data and clinical information were collected from TCGA, GTEx and GEO databases. Survival, prognostic and functional enrichment analysis were employed with R software. Immunological correlation analysis was performed using TIMER2.0, TIDE scores, TISIDB and TISCH. Epigenetic analysis was implemented by MethSurv, CPTAC, UALCAN, and cBioPortal. Drug analysis was conducted using Enrichr and CellMiner. Moreover, cellular experiments, like RNA interference, qRT-PCR, Western blot, cell cycle analysis, cell apoptosis analysis, colony formation assay, transwell assay, and wound healing assay, were performed for verifying the functional properties of MVP in the PAAD progression. Results We demonstrated an abnormally upregulated expression of MVP in PAAD tissues, which notably correlated with an adverse prognosis in PAAD patients. Functional analysis suggested the conceivable involvement of MVP in immune modulation, and immunotherapy. Additionally, we identified genetic alterations, reduced promoter methylation, and heightened phosphorylation in MVP. We also clarified Suloctidil and Tetradioxin as the most notable potential drugs targeting MVP in PAAD. Moreover, our experimental observations consistently highlighted the significant impact of MVP deficiency on impeding PAAD cell proliferation, inhibiting cell migration, and accelerating cell apoptosis. Interestingly, a potential link between MVP and ERK or AKT pathways was displayed, which opens new avenues for further exploration of the molecular mechanisms of MVP-targeted therapies in PAAD. Conclusions This study systematically describes MVP as an immune-related biomarker with remarkable potential for predicting the prognosis, tumor progression and immunotherapeutic efficacy in PAAD.
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Affiliation(s)
- Xinyi Wu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Leiyu Hao
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Jianghua Lin
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Xinyu Guo
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chun Li
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, Tongji University School of Medicine, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Zhao W, Chen J, Xia Y, Wei Z, Wan S, Guo H, Hao Y, Jiang W, Zhang H, Ren F, An P, Luo Y, Luo J. Temporal-specific single-cell atlas of human type A aortic dissection reveals immune cell dynamics and therapeutic targets. Sci Bull (Beijing) 2024:S2095-9273(24)00462-6. [PMID: 38987092 DOI: 10.1016/j.scib.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Affiliation(s)
- Wenting Zhao
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Juan Chen
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yi Xia
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Zhixi Wei
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Sitong Wan
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Huiyuan Guo
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yanling Hao
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Wenjian Jiang
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Hongjia Zhang
- Department of Cardiovascular Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Fazheng Ren
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
| | - Peng An
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
| | - Yongting Luo
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
| | - Junjie Luo
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
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Wang H, Yao Z, Kang K, Zhou L, Xiu W, Sun J, Xie C, Yu M, Li Y, Zhang Y, Zheng Y, Lin G, Pan X, Wu Y, Luo R, Wang L, Tang M, Liao S, Zhu J, Zhou X, Zhang X, Xu Y, Liu Y, Peng F, Wang J, Xiang L, Yin L, Deng L, Huang M, Gong Y, Zou B, Wang H, Wu L, Yuan Z, Bi N, Fan M, Xu Y, Tong R, Yi L, Gan L, Xue J, Mo X, Chen C, Na F, Lu Y. Preclinical study and phase II trial of adapting low-dose radiotherapy to immunotherapy in small cell lung cancer. MED 2024:S2666-6340(24)00248-4. [PMID: 38964333 DOI: 10.1016/j.medj.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/11/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) provide modest but unsatisfactory benefits for extensive-stage small cell lung cancer (ES-SCLC). Developing strategies for treating ES-SCLC is critical. METHODS We preliminarily explored the outcomes of salvage low-dose radiotherapy (LDRT) plus ICI on refractory SCLC patients. Next, we evaluated the combinational efficacy in murine SCLC. The tumor immune microenvironment (TIME) was analyzed for mechanistic study. Subsequently, we conducted a multicenter, prospective phase II trial that administered concurrent thoracic LDRT plus chemoimmunotherapy to treatment-naive ES-SCLC patients (MATCH trial, NCT04622228). The primary endpoint was confirmed objective response rate (ORR), and the key secondary endpoints included progression-free survival (PFS) and safety. FINDINGS Fifteen refractory SCLC patients treated with LDRT plus ICI were retrospectively reviewed. The ORR was 73.3% (95% confidence interval [CI], 44.9-92.2). We identified a specific dose of LDRT (15 Gy/5 fractions) that exhibited growth retardation and improved survival in murine SCLC when combined with ICIs. This combination recruited a special T cell population, TCF1+ PD-1+ CD8+ stem-like T cells, from tumor-draining lymph nodes into the TIME. The MATCH trial showed a confirmed ORR of 87.5% (95% CI, 75.9-94.8). The median PFS was 6.9 months (95% CI, 5.4-9.3). CONCLUSIONS These findings verified that LDRT plus chemoimmunotherapy was safe, feasible, and effective for ES-SCLC, warranting further investigation. FUNDING This research was funded by West China Hospital (no. ZYJC21003), the National Natural Science Foundation of China (no. 82073336), and the MATCH trial was fully funded by Roche (China) Holding Ltd. (RCHL) and Shanghai Roche Pharmaceuticals Ltd. (SRPL).
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Affiliation(s)
- Hui Wang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhuoran Yao
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kai Kang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Zhou
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Weigang Xiu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianguo Sun
- Cancer Institute, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Min Yu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanying Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Zhang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Center of Lung Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Zheng
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Guo Lin
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiangyu Pan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yijun Wu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ren Luo
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Laduona Wang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Tang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shuangsi Liao
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiang Zhu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaojuan Zhou
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xuanwei Zhang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Xu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yongmei Liu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Feng Peng
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Wang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lisha Xiang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Limei Yin
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Health Management & Institute of Health Management, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Deng
- University of Washington School of Medicine/Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Meijuan Huang
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Youling Gong
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bingwen Zou
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Wang
- Department of Radiation Oncology, Hunan Cancer Hospital, Changsha, China
| | - Lin Wu
- Department of Thoracic Medicine, Hunan Cancer Hospital, Changsha, China
| | - Zhiyong Yuan
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Nan Bi
- Department of Radiation Oncology, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Min Fan
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yaping Xu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruizhan Tong
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Linglu Yi
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lu Gan
- Research Laboratory of Emergency Medicine, Department of Emergency Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jianxin Xue
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, Chengdu, China
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Feifei Na
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - You Lu
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, China; Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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Rezvan A, Romain G, Fathi M, Heeke D, Martinez-Paniagua M, An X, Bandey IN, Montalvo MJ, Adolacion JRT, Saeedi A, Sadeghi F, Fousek K, Puebla-Osorio N, Cooper LJN, Bernatchez C, Singh H, Ahmed N, Mattie M, Bot A, Neelapu S, Varadarajan N. Identification of a clinically efficacious CAR T cell subset in diffuse large B cell lymphoma by dynamic multidimensional single-cell profiling. NATURE CANCER 2024; 5:1010-1023. [PMID: 38750245 DOI: 10.1038/s43018-024-00768-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 04/10/2024] [Indexed: 05/24/2024]
Abstract
Chimeric antigen receptor (CAR) T cells used for the treatment of B cell malignancies can identify T cell subsets with superior clinical activity. Here, using infusion products of individuals with large B cell lymphoma, we integrated functional profiling using timelapse imaging microscopy in nanowell grids with subcellular profiling and single-cell RNA sequencing to identify a signature of multifunctional CD8+ T cells (CD8-fit T cells). CD8-fit T cells are capable of migration and serial killing and harbor balanced mitochondrial and lysosomal volumes. Using independent datasets, we validate that CD8-fit T cells (1) are present premanufacture and are associated with clinical responses in individuals treated with axicabtagene ciloleucel, (2) longitudinally persist in individuals after treatment with CAR T cells and (3) are tumor migrating cytolytic cells capable of intratumoral expansion in solid tumors. Our results demonstrate the power of multimodal integration of single-cell functional assessments for the discovery and application of CD8-fit T cells as a T cell subset with optimal fitness in cell therapy.
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Affiliation(s)
- Ali Rezvan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Gabrielle Romain
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | | | | | | | - Xingyue An
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Irfan N Bandey
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Melisa J Montalvo
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay R T Adolacion
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Arash Saeedi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Fatemeh Sadeghi
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Kristen Fousek
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Nahum Puebla-Osorio
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Chantale Bernatchez
- Department of Biologics Development, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harjeet Singh
- Divsion of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nabil Ahmed
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Mike Mattie
- Kite, a Gilead Company, Santa Monica, CA, USA
| | - Adrian Bot
- Kite, a Gilead Company, Santa Monica, CA, USA
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
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Wang Z, Zhao Y, Wo Y, Peng Y, Hu W, Wu Z, Liu P, Shang Y, Liu C, Chen X, Huang K, Chen Y, Hong H, Li F, Sun Y. The single cell immunogenomic landscape after neoadjuvant immunotherapy combined chemotherapy in esophageal squamous cell carcinoma. Cancer Lett 2024; 593:216951. [PMID: 38734159 DOI: 10.1016/j.canlet.2024.216951] [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: 11/18/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/13/2024]
Abstract
Neoadjuvant immunotherapy represents promising strategy in the treatment of esophageal squamous cell carcinoma (ESCC). However, the mechanisms underlying its impact on treatment sensitivity or resistance remain a subject of controversy. In this study, we conducted single-cell RNA and T/B cell receptor (scTCR/scBCR) sequencing of CD45+ immune cells on samples from 10 patients who received neoadjuvant immunotherapy and chemotherapy. We also validated our findings using multiplexed immunofluorescence and analyzed bulk RNA-seq from other cohorts in public database. By integrating analysis of 87357 CD45+ cells, we found GZMK + effector memory T cells (Tem) were relatively enriched and CXCL13+ exhausted T cells (Tex) and regulator T cells (Treg) decreased among responders, indicating a persistent anti-tumor memory process. Additionally, the enhanced presence of BCR expansion and somatic hypermutation process within TNFRSF13B + memory B cells (Bmem) suggested their roles in antigen presentation. This was further corroborated by the evidence of the T-B co-stimulation pattern and CXCL13-CXCR5 axis. The complexity of myeloid cell heterogeneity was also particularly pronounced. The elevated expression of S100A7 in ESCC, as detected by bulk RNA-seq, was associated with an exhausted and immunosuppressive tumor microenvironment. In summary, this study has unveiled a potential regulatory network among immune cells and the clonal dynamics of their functions, and the mechanisms of exhaustion and memory conversion between GZMK + Tem and TNFRSF13B + Bmem from antigen presentation and co-stimulation perspectives during neoadjuvant PD-1 blockade treatment in ESCC.
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MESH Headings
- Humans
- Neoadjuvant Therapy/methods
- Esophageal Squamous Cell Carcinoma/immunology
- Esophageal Squamous Cell Carcinoma/genetics
- Esophageal Squamous Cell Carcinoma/therapy
- Esophageal Squamous Cell Carcinoma/drug therapy
- Esophageal Squamous Cell Carcinoma/pathology
- Esophageal Neoplasms/immunology
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/therapy
- Esophageal Neoplasms/drug therapy
- Esophageal Neoplasms/pathology
- Immunotherapy/methods
- Single-Cell Analysis/methods
- Female
- Male
- Tumor Microenvironment/immunology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Chemokine CXCL13/genetics
- Chemokine CXCL13/metabolism
- Middle Aged
- Aged
- Memory T Cells/immunology
- Memory T Cells/metabolism
- Leukocyte Common Antigens/metabolism
- Leukocyte Common Antigens/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/drug effects
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, B-Cell/immunology
- Receptors, CXCR5/metabolism
- Receptors, CXCR5/genetics
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Affiliation(s)
- Zheyi Wang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wo
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizhou Peng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weilei Hu
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China; State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Zhigang Wu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Shang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunnan Liu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kan Huang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuting Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Hong
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Shen R, Huang Y, Kong D, Ma W, Liu J, Zhang H, Cheng S, Feng L. Spatial distribution pattern of immune cells is associated with patient prognosis in colorectal cancer. J Transl Med 2024; 22:606. [PMID: 38951801 PMCID: PMC11218284 DOI: 10.1186/s12967-024-05418-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND The spatial context of tumor-infiltrating immune cells (TIICs) is important in predicting colorectal cancer (CRC) patients' clinical outcomes. However, the prognostic value of the TIIC spatial distribution is unknown. Thus, we aimed to investigate the association between TIICs in situ and patient prognosis in a large CRC sample. METHODS We implemented multiplex immunohistochemistry staining technology in 190 CRC samples to quantify 14 TIIC subgroups in situ. To delineate the spatial relationship of TIICs to tumor cells, tissue slides were segmented into tumor cell and microenvironment compartments based on image recognition technology, and the distance between immune and tumor cells was calculated by implementing the computational pipeline phenoptr. RESULTS MPO+ neutrophils and CD68+IDO1+ tumor-associated macrophages (TAMs) were enriched in the epithelial compartment, and myeloid lineage cells were located nearest to tumor cells. Except for CD68+CD163+ TAMs, other cells were all positively associated with favorable prognosis. The prognostic predictive power of TIICs was highly related to their distance to tumor cells. Unsupervised clustering analysis divided colorectal cancer into three subtypes with distinct prognostic outcomes, and correlation analysis revealed the synergy among B cells, CD68+IDO1+TAMs, and T lineage cells in producing an effective immune response. CONCLUSIONS Our study suggests that the integration of spatial localization with TIIC abundance is important for comprehensive prognostic assessment.
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Affiliation(s)
- Rongfang Shen
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China
| | - Ying Huang
- Department of Head and Neck Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Deyang Kong
- Department of Colorectal Surgery, State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China
| | - Wenhui Ma
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Liu
- Department of Head and Neck Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haizeng Zhang
- Department of Colorectal Surgery, State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China.
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China.
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuannanli, Chaoyang District, Beijing, 100021, China.
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Mathew D, Marmarelis ME, Foley C, Bauml JM, Ye D, Ghinnagow R, Ngiow SF, Klapholz M, Jun S, Zhang Z, Zorc R, Davis CW, Diehn M, Giles JR, Huang AC, Hwang WT, Zhang NR, Schoenfeld AJ, Carpenter EL, Langer CJ, Wherry EJ, Minn AJ. Combined JAK inhibition and PD-1 immunotherapy for non-small cell lung cancer patients. Science 2024; 384:eadf1329. [PMID: 38900877 DOI: 10.1126/science.adf1329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/05/2024] [Indexed: 06/22/2024]
Abstract
Persistent inflammation driven by cytokines such as type-one interferon (IFN-I) can cause immunosuppression. We show that administration of the Janus kinase 1 (JAK1) inhibitor itacitinib after anti-PD-1 (programmed cell death protein 1) immunotherapy improves immune function and antitumor responses in mice and results in high response rates (67%) in a phase 2 clinical trial for metastatic non-small cell lung cancer. Patients who failed to respond to initial anti-PD-1 immunotherapy but responded after addition of itacitinib had multiple features of poor immune function to anti-PD-1 alone that improved after JAK inhibition. Itacitinib promoted CD8 T cell plasticity and therapeutic responses of exhausted and effector memory-like T cell clonotypes. Patients with persistent inflammation refractory to itacitinib showed progressive CD8 T cell terminal differentiation and progressive disease. Thus, JAK inhibition may improve the efficacy of anti-PD-1 immunotherapy by pivoting T cell differentiation dynamics.
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Affiliation(s)
- Divij Mathew
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Melina E Marmarelis
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caitlin Foley
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua M Bauml
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Darwin Ye
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reem Ghinnagow
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Klapholz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Soyeong Jun
- Department of Radiation Oncology and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhaojun Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Zorc
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christiana W Davis
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maximillian Diehn
- Department of Radiation Oncology and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy R Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam J Schoenfeld
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erica L Carpenter
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Corey J Langer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andy J Minn
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Huang A, Sun Z, Hong H, Yang Y, Chen J, Gao Z, Gu J. Novel hypoxia- and lactate metabolism-related molecular subtyping and prognostic signature for colorectal cancer. J Transl Med 2024; 22:587. [PMID: 38902737 PMCID: PMC11191174 DOI: 10.1186/s12967-024-05391-5] [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: 04/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a serious global health burden because of its high morbidity and mortality rates. Hypoxia and massive lactate production are hallmarks of the CRC microenvironment. However, the effects of hypoxia and lactate metabolism on CRC have not been fully elucidated. This study aimed to develop a novel molecular subtyping based on hypoxia-related genes (HRGs) and lactate metabolism-related genes (LMRGs) and construct a signature to predict the prognosis of patients with CRC and treatment efficacy. METHODS Bulk and single-cell RNA-sequencing and clinical data of CRC were downloaded from the TCGA and GEO databases. HRGs and LMRGs were obtained from the Molecular Signatures Database. The R software package DESeq2 was used to perform differential expression analysis. Molecular subtyping was performed using unsupervised clustering. A predictive signature was developed using univariate Cox regression, random forest model, LASSO, and multivariate Cox regression analyses. Finally, the sensitivity of tumor cells to chemotherapeutic agents before and after hypoxia was verified using in vitro experiments. RESULTS We classified 575 patients with CRC into three molecular subtypes and were able to distinguish their prognoses clearly. The C1 subtype, which exhibits high levels of hypoxia, has a low proportion of CD8 + T cells and a high proportion of macrophages. The expression of immune checkpoint genes is generally elevated in C1 patients with severe immune dysfunction. Subsequently, we constructed a predictive model, the HLM score, which effectively predicts the prognosis of patients with CRC and the efficacy of immunotherapy. The HLM score was validated in GSE39582, GSE106584, GSE17536, and IMvigor210 datasets. Patients with high HLM scores exhibit high infiltration of CD8 + exhausted T cells (Tex), especially terminal Tex, and oxidative phosphorylation (OXPHOS)-Tex in the immune microenvironment. Finally, in vitro experiments confirmed that CRC cell lines were less sensitive to 5-fluorouracil, oxaliplatin, and irinotecan under hypoxic conditions. CONCLUSION We constructed novel hypoxia- and lactate metabolism-related molecular subtypes and revealed their immunological and genetic characteristics. We also developed an HLM scoring system that could be used to predict the prognosis and efficacy of immunotherapy in patients with CRC.
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Affiliation(s)
- An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Haidian District, Beijing, 100142, China
| | - Zhuang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Haidian District, Beijing, 100142, China
| | - Haopeng Hong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Haidian District, Beijing, 100142, China
| | - Yong Yang
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100144, China
| | - Jiajia Chen
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100144, China
| | - Zhaoya Gao
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100144, China
- Department of General Surgery, Peking University First Hospital, Beijing, 100034, China
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery III, Peking University Cancer Hospital & Institute, Haidian District, Beijing, 100142, China.
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100144, China.
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Li Y, Zhang J, Gao X, Zhang QC. Tissue module discovery in single-cell-resolution spatial transcriptomics data via cell-cell interaction-aware cell embedding. Cell Syst 2024; 15:578-592.e7. [PMID: 38823396 DOI: 10.1016/j.cels.2024.05.001] [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: 05/25/2023] [Revised: 01/08/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Computational methods are desired for single-cell-resolution spatial transcriptomics (ST) data analysis to uncover spatial organization principles for how individual cells exert tissue-specific functions. Here, we present ST data analysis via interaction-aware cell embedding (SPACE), a deep-learning method for cell-type identification and tissue module discovery from single-cell-resolution ST data by learning a cell representation that captures its gene expression profile and interactions with its spatial neighbors. SPACE identified spatially informed cell subtypes defined by their special spatial distribution patterns and distinct proximal-interacting cell types. SPACE also automatically discovered "cell communities"-tissue modules with discernible boundaries and a uniform spatial distribution of constituent cell types. For each cell community, SPACE outputs a characteristic proximal cell-cell interaction network associated with physiological processes, which can be used to refine ligand-receptor-based intercellular signaling analyses. We envision that SPACE can be used in large-scale ST projects to understand how proximal cell-cell interactions contribute to emergent biological functions within cell communities. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Yuzhe Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia; BioMap, Beijing 100086, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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Cheng X, Yang F, Li Y, Cao Y, Zhang M, JI J, Bai Y, Li Q, Yu Q, Gao D. The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer. Aging (Albany NY) 2024; 16:10512-10538. [PMID: 38888512 PMCID: PMC11236303 DOI: 10.18632/aging.205945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/15/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND Cuproptosis is a type of cell death characterized by excessive copper-lipid reactions in the tricarboxylic acid cycle, resulting in protein toxicity stress and cell death. Although known as a cuproptosis inhibitor through CRISPR-Cas9 screening, the role of cyclin-dependent kinase inhibitor 2A (CDKN2A) in cuproptosis resistance and its connection to tumor development remains unclear. METHODS In this study, we combined single-cell sequencing, spatial transcriptomics, pathological image analysis, TCGA multi-omics analysis and in vitro experimental validation to comprehensively investigate CDKN2A distribution, expression, epigenetic modification, regulation and genomic features in colorectal cancer cells. We further explored the associations between CDKN2A and cellular pathway, immune infiltration and spatial signal communication. RESULTS Our findings showed an increasing trend in cuproptosis in the trajectory of tumor progression, accompanied by an upward trend of CDKN2A. CDKN2A underwent transcriptional activation by MEF2D and via the SNHG7/miR-133b axis, upregulating glycolysis, copper metabolism and copper ion efflux. CDKN2A likely drives epithelial-mesenchymal transition (EMT) and progression by activating Wnt signaling. CDKN2A is associated with high genomic instability and sensitivity to radiation and chemotherapy. Tumor regions expressing CDKN2A exhibit distinctive SPP1+ tumor-associated macrophage (TAM) infiltration and MMP7 enrichment, along with unique signaling crosstalk with adjacent areas. CONCLUSIONS CDKN2A mediates cuproptosis resistance through regulating glycolysis and copper homeostasis, accompanied by a malignant phenotype and pro-tumor niche. Radiation and chemotherapy are expected to potentially serve as therapeutic approaches for cuproptosis-resistant colorectal cancer with high CDKN2A expression.
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Affiliation(s)
- Xifu Cheng
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Famin Yang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuanheng Li
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- Department of Gastroenterology and Hepatology, Shenzhen Hospital of Southern Medical University, Shenzhen 518000, China
| | - Yuke Cao
- School of Ophthalmology and Optometry, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Meng Zhang
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Jiameng JI
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yuxiao Bai
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qing Li
- Department of Oncology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Qiongfang Yu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Dian Gao
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
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Dong Q, Wu X, Mok T, Cai G, Zha Z, She G, Chen J. Identification of therapeutic targets and medicines for comorbid Crohn's disease and rheumatoid arthritis: A comprehensive analysis. Heliyon 2024; 10:e32406. [PMID: 38933947 PMCID: PMC11200351 DOI: 10.1016/j.heliyon.2024.e32406] [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: 01/18/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Objective The incidence of Crohn's disease (CD) and rheumatoid arthritis (RA) co-morbidity, as well as the number of individuals affected, is on the rise due to their shared molecular and cellular factors. This study aimed to identify potential therapeutic targets and medicines for comorbid CD and RA. Methods We integrated single-cell RNA sequencing, Mendelian randomization, and colocalization analysis results from public databases to analyse immune cell subgroups in CD and RA patients and identify candidate therapeutic targets. We further screened potential medicines for the identified candidate targets using the Comparative Toxicogenomics Database (CTD) and molecular docking and molecular dynamics simulations. Results The proportion of CD8 effector memory T cells (Tem) was consistently elevated in the peripheral blood mononuclear cells (PBMCs) of both CD and RA patients. MYBL1 had a causal effect on the onset of both CD (OR = 1.23; 95 % CI, 1.05-1.45; P = 0.046) and RA (OR = 1.45; 95 % CI, 1.14-1.85; P = 0.04). Four potential therapeutic molecules were retrieved from the CTD database, among which tretinoin (docking score: -6.3 kcal/mol) showed the best potential. Conclusion Our comprehensive analysis suggests that CD8 Tem cells are a key cell group in comorbid RA and CD and that MYBL1 has a causal effect. Tretinoin was identified as a potential targeted therapeutic drug, which is of great clinical research value.
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Affiliation(s)
- Qiu Dong
- Center for Bone, Joint and Sports Medicine, The First Affiliated Hospital of Jinan University, Guang Zhou, 510665, China
| | - Xiaoting Wu
- Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guang Zhou, 510665, China
| | - Tsz Mok
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, 999077, China
| | - Gaohan Cai
- Center for Bone, Joint and Sports Medicine, The First Affiliated Hospital of Jinan University, Guang Zhou, 510665, China
| | - Zhengang Zha
- Center for Bone, Joint and Sports Medicine, The First Affiliated Hospital of Jinan University, Guang Zhou, 510665, China
| | - Guorong She
- Center for Bone, Joint and Sports Medicine, The First Affiliated Hospital of Jinan University, Guang Zhou, 510665, China
| | - Junyuan Chen
- Center for Bone, Joint and Sports Medicine, The First Affiliated Hospital of Jinan University, Guang Zhou, 510665, China
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Hu H, Tang L, Zhao Y, Cheng J, Huang M, You Y, Zou P, Lei Q, Zhu X, Guo AY. Single-cell analysis of the survival mechanisms of fratricidal CAR-T targeting of T cell malignancies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102225. [PMID: 38948332 PMCID: PMC11214519 DOI: 10.1016/j.omtn.2024.102225] [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: 11/17/2023] [Accepted: 05/16/2024] [Indexed: 07/02/2024]
Abstract
Chimeric antigen receptor T (CAR-T) cell therapy targeting T cell tumors still faces many challenges, one of which is its fratricide due to the target gene expressed on CAR-T cells. Despite this, these CAR-T cells can be expanded in vitro by extending the culture time and effectively eliminating malignant T cells. However, the mechanisms underlying CAR-T cell survival in cell subpopulations, the molecules involved, and their regulation are still unknown. We performed single-cell transcriptome profiling to investigate the fratricidal CAR-T products (CD26 CAR-Ts and CD44v6 CAR-Ts) targeting T cells, taking CD19 CAR-Ts targeting B cells from the same donor as a control. Compared with CD19 CAR-Ts, fratricidal CAR-T cells exhibit no unique cell subpopulation, but have more exhausted T cells, fewer cytotoxic T cells, and more T cell receptor (TCR) clonal amplification. Furthermore, we observed that fratricidal CAR-T cell survival was accompanied by target gene expression. Gene expression results suggest that fratricidal CAR-T cells may downregulate their human leukocyte antigen (HLA) molecules to evade T cell recognition. Single-cell regulatory network analysis and suppression experiments revealed that exhaustion mediated by critical regulatory factors may contribute to fratricidal CAR-T cell survival. Together, these data provide valuable and first-time insights into the survival of fratricidal CAR-T cells.
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Affiliation(s)
- Hui Hu
- Department of Hematology, West China Biomedical Big Data Center, West China Hospital, Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Ling Tang
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yuyan Zhao
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jiali Cheng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yong You
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ping Zou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qian Lei
- Department of Hematology, West China Biomedical Big Data Center, West China Hospital, Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Xiaojian Zhu
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - An-Yuan Guo
- Department of Hematology, West China Biomedical Big Data Center, West China Hospital, Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
- Hubei Bioinformatics & Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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43
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Wang W, Dong G, Yang Z, Li S, Li J, Wang L, Zhu Q, Wang Y. Single-cell analysis of tumor microenvironment and cell adhesion reveals that interleukin-1 beta promotes cancer cell proliferation in breast cancer. Animal Model Exp Med 2024. [PMID: 38860503 DOI: 10.1002/ame2.12445] [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: 01/29/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC), which is so called because of the lack of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptor 2 (HER2) receptors on the cancer cells, accounts for 10%-15% of all breast cancers. The heterogeneity of the tumor microenvironment is high. However, the role of plasma cells controlling the tumor migration progression in TNBC is still not fully understood. METHODS We analyzed single-cell RNA sequencing data from five HER2 positive, 12 ER positive/PR positive, and nine TNBC samples. The potential targets were validated by immunohistochemistry. RESULTS Plasma cells were enriched in TNBC samples, which was consistent with validation using data from The Cancer Genome Atlas. Cell communication analysis revealed that plasma cells interact with T cells through the intercellular adhesion molecule 2-integrin-aLb2 complex, and then release interleukin 1 beta (IL1B), as verified by immunohistochemistry, ultimately promoting tumor growth. CONCLUSION Our results revealed the role of plasma cells in TNBC and identified IL1B as a new prognostic marker for TNBC.
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Affiliation(s)
- Wenyan Wang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ziguo Yang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shaoxiang Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jia Li
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Wang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhu
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuchen Wang
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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44
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Seyedsadr M, Bang MF, McCarthy EC, Zhang S, Chen HC, Mohebbi M, Hugo W, Whitmire JK, Lechner MG, Su MA. A pathologically expanded, clonal lineage of IL-21-producing CD4+ T cells drives inflammatory neuropathy. J Clin Invest 2024; 134:e178602. [PMID: 39087473 PMCID: PMC11290969 DOI: 10.1172/jci178602] [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: 01/10/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024] Open
Abstract
Inflammatory neuropathies, which include chronic inflammatory demyelinating polyneuropathy (CIDP) and Guillain Barré syndrome (GBS), result from autoimmune destruction of the PNS and are characterized by progressive weakness and sensory loss. CD4+ T cells play a key role in the autoimmune destruction of the PNS. Yet, key properties of pathogenic CD4+ T cells remain incompletely understood. Here, we used paired single-cell RNA-Seq (scRNA-Seq) and single-cell T cell receptor-sequencing (scTCR-Seq) of peripheral nerves from an inflammatory neuropathy mouse model to identify IL-21-expressing CD4+ T cells that were clonally expanded and multifunctional. These IL-21-expressing CD4+ T cells consisted of 2 transcriptionally distinct expanded cell populations, which expressed genes associated with T follicular helper (Tfh) and T peripheral helper (Tph) cell subsets. Remarkably, TCR clonotypes were shared between these 2 IL-21-expressing cell populations, suggesting a common lineage differentiation pathway. Finally, we demonstrated that IL-21 receptor-KO (IL-21R-KO) mice were protected from neuropathy development and had decreased immune infiltration into peripheral nerves. IL-21 signaling upregulated CXCR6, a chemokine receptor that promotes CD4+ T cell localization in peripheral nerves. Together, these findings point to IL-21 signaling, Tfh/Tph differentiation, and CXCR6-mediated cellular localization as potential therapeutic targets in inflammatory neuropathies.
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Affiliation(s)
| | - Madison F. Bang
- Department of Microbiology, Immunology, and Molecular Genetics and
| | | | - Shirley Zhang
- Department of Microbiology, Immunology, and Molecular Genetics and
| | - Ho-Chung Chen
- Department of Microbiology, Immunology, and Molecular Genetics and
| | - Mahnia Mohebbi
- Department of Microbiology, Immunology, and Molecular Genetics and
| | - Willy Hugo
- Department of Medicine, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Jason K. Whitmire
- Department of Genetics, UNC Chapel Hill, Chapel Hill, North Carolina, USA
| | - Melissa G. Lechner
- Department of Medicine, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Maureen A. Su
- Department of Microbiology, Immunology, and Molecular Genetics and
- Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
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45
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Shi H, Tian H, Zhu T, Liao Q, Liu C, Yuan P, Li Y, Yang J, Zong C, Jia S, Ruan J, Ge S, Jia R, Chai P, Xu S, Fan X. Single-cell sequencing depicts tumor architecture and empowers clinical decision in metastatic conjunctival melanoma. Cell Discov 2024; 10:63. [PMID: 38862482 PMCID: PMC11166926 DOI: 10.1038/s41421-024-00683-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/25/2024] [Indexed: 06/13/2024] Open
Abstract
Conjunctival melanoma (CoM) is a potentially devastating tumor that can lead to distant metastasis. Despite various therapeutic strategies for distant metastatic CoM, the clinical outcomes remain unfavorable. Herein, we performed single-cell RNA sequencing (scRNA-seq) of 47,017 cells obtained from normal conjunctival samples (n = 3) and conjunctival melanomas (n = 7). Notably, we noticed a higher abundance of cancer-associated fibroblasts (CAFs) in tumor microenvironment (TME), correlated with enhanced angiogenic capacity and increased VEGFR expression in distal metastatic CoM. Additionally, we observed a significant decrease in the proportion of total CD8+ T cells and an increase in the proportion of naive CD8+ T cells, contributing to a relatively quiescent immunological environment in distal metastatic CoM. These findings were confirmed through the analyses of 70,303 single-cell transcriptomes of 7 individual CoM samples, as well as spatially resolved proteomes of an additional 10 samples of CoMs. Due to the increase of VEGFR-mediated angiogenesis and a less active T cell environment in distal metastatic CoMs, a clinical trial (ChiCTR2100045061) has been initiated to evaluate the efficacy of VEGFR blockade in combination with anti-PD1 therapy for patients with distant metastatic CoM, showing promising tumor-inhibitory effects. In conclusion, our study uncovered the landscape and heterogeneity of the TME during CoM tumorigenesis and progression, empowering clinical decisions in the management of distal metastatic CoM. To our knowledge, this is the initial exploration to translate scRNA-seq analysis to a clinical trial dealing with cancer, providing a novel concept by accommodating scRNA-seq data in cancer therapy.
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Affiliation(s)
- Hanhan Shi
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Tian
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyu Zhu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qili Liao
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Liu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Yuan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai, China
| | - Yongyun Li
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Yang
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunyan Zong
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shichong Jia
- Tianjin Eye Hospital, Tianjin Key Lab of Ophthalmology and Visual Science, Nankai University Affiliated Eye Hospital, Tianjin Eye Institute, Tianjin, China
| | - Jing Ruan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengfang Ge
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renbing Jia
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peiwei Chai
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Shiqiong Xu
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xianqun Fan
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
- Center for Basic Medical Research and Innovation in Visual System Diseases of Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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46
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Lee CY, Clatworthy MR, Withers DR. Decoding changes in tumor-infiltrating leukocytes through dynamic experimental models and single-cell technologies. Immunol Cell Biol 2024. [PMID: 38853634 DOI: 10.1111/imcb.12787] [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: 03/25/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024]
Abstract
The ability to characterize immune cells and explore the molecular interactions that govern their functions has never been greater, fueled in recent years by the revolutionary advance of single-cell analysis platforms. However, precisely how immune cells respond to different stimuli and where differentiation processes and effector functions operate remain incompletely understood. Inferring cellular fate within single-cell transcriptomic analyses is now omnipresent, despite the assumptions typically required in such analyses. Recently developed experimental models support dynamic analyses of the immune response, providing insights into the temporal changes that occur within cells and the tissues in which such transitions occur. Here we will review these approaches and discuss how these can be combined with single-cell technologies to develop a deeper understanding of the immune responses that should support the development of better therapeutic options for patients.
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Affiliation(s)
- Colin Yc Lee
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infection Disease, University of Cambridge, Cambridge, UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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47
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Zhang Y, Qian L, Chen K, Gu S, Meng Z, Wang J, Li Y, Wang P. Oncolytic adenovirus in treating malignant ascites: A phase II trial and longitudinal single-cell study. Mol Ther 2024; 32:2000-2020. [PMID: 38659226 PMCID: PMC11184408 DOI: 10.1016/j.ymthe.2024.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/24/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024] Open
Abstract
Malignant ascites is a common complication resulting from the peritoneal spread of malignancies, and currently lacks effective treatments. We conducted a phase II trial (NCT04771676) to investigate the efficacy and safety of oncolytic adenovirus H101 and virotherapy-induced immune response in 25 patients with malignant ascites. Oncolytic virotherapy achieved an increased median time to repeat paracentesis of 45 days (95% confidence interval 16.5-73.5 days), compared with the preset control value of 13 days. Therapy was well-tolerated, with pyrexia, fatigue, nausea, and abdominal pain as the most common toxicities. Longitudinal single-cell profiling identified marked oncolysis, early virus replication, and enhanced CD8+ T cells-macrophages immune checkpoint crosstalk, especially in responsive patients. H101 also triggered a proliferative burst of CXCR6+ and GZMK+CD8+ T cells with promoted tumor-specific cytotoxicity. Further establishment of oncolytic virus-induced T cell expansion signature (OiTE) implicated the potential benefits for H101-responsive patients from subsequent anti-PD(L)1 therapy. Patients with upregulated immune-signaling pathways in tumor cells and a higher proportion of CLEC10A+ dendritic cells and GZMK+CD8+ T cells at baseline showed a superior response to H101 treatment. Our study demonstrates promising clinical responses and tolerability of oncolytic adenovirus in treating malignant ascites and provides insights into the relevant cellular processes following oncolytic virotherapy.
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Affiliation(s)
- Yalei Zhang
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Qian
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kun Chen
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sijia Gu
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jia Wang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 300032, China.
| | - Ye Li
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Peng Wang
- Department of Hepatic Oncology, Zhongshan Hospital, Fudan University; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
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48
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Shasha C, Glass DR, Moelhman E, Islas L, Tian Y, Szeto GL, Peng T, Song X, Wurscher M, Bumol TF, Torgerson TR, Greenberg PD, Green DJ, Newell EW. Hallmarks of tumor-experienced T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597178. [PMID: 38895348 PMCID: PMC11185627 DOI: 10.1101/2024.06.03.597178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dysregulation of the bone marrow (BM) niche in multiple myeloma (MM) alters the composition and state of resident immune cells, potentially impeding anti-tumor immunity. One common mechanism of immune inhibition in solid tumors is the induction of exhaustion in tumor-specific T cells. However, the extent of T cell tumor recognition and exhaustion is not well-characterized in MM. As the specific mechanisms of immune evasion are critical for devising effective therapeutic strategies, we deeply profiled the CD8+ T cell compartment of newly-diagnosed MM (NDMM) patients for evidence of tumor reactivity and T cell exhaustion. We applied single-cell multi-omic sequencing and antigen-specific mass cytometry to longitudinal BM and peripheral blood (PB) samples taken from timepoints spanning from diagnosis through induction therapy, autologous stem cell transplant (ASCT), and maintenance therapy. We identified an exhausted-like population that lacked several canonical exhaustion markers, was not significantly enriched in NDMM patients, and consisted of small, nonpersistent clones. We also observed an activated population with increased frequency in the PB of NDMM patients exhibiting phenotypic and clonal features consistent with homeostatic, antigen-nonspecific activation. However, there was no evidence of "tumor-experienced" T cells displaying hallmarks of terminal exhaustion and/or tumor-specific activation/expansion in NDMM patients at any timepoint.
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Affiliation(s)
- Carolyn Shasha
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David R. Glass
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ernest Moelhman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Laura Islas
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yuan Tian
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tao Peng
- Allen Institute for Immunology, Seattle, WA, USA
| | - Xiaoling Song
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michelle Wurscher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | - Philip D. Greenberg
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Immunology, University of Washington, Seattle, WA, USA
| | - Damian J. Green
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Evan W. Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
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49
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Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, Khan SM, Li M, Anzaldua-Campos MI, Bradley JD, Leuthardt EC, Kim AH, Dowling JL, Chicoine MR, Jones PS, Choi BD, Cahill DP, Carter BS, Petti AA, Johanns TM, Dunn GP. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov 2024; 14:1106-1131. [PMID: 38416133 DOI: 10.1158/2159-8290.cd-23-0913] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing and single-cell RNA sequencing with paired V(D)J sequencing, respectively, on TILs from two cohorts of patients totaling 15 patients with high-grade glioma, including GBM or astrocytoma, IDH-mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared with matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T-cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T-cell subset within the GBM microenvironment and may harbor potential therapeutic implications. SIGNIFICANCE To understand the limited efficacy of immune-checkpoint blockade in GBM, we applied a multiomics approach to understand the TIL landscape. By highlighting the enrichment of GZMK+ effector T cells and the lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Anthony Z Wang
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryce L Mashimo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maximilian O Schaettler
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ngima D Sherpa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences Graduate Program, Harvard University, Cambridge, Massachusetts
| | - Lydia A Leavitt
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurosurgery, University of Louisville, Louisville, Kentucky
| | - Alexandra J Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Saad M Khan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mao Li
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Markus I Anzaldua-Campos
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Neuroscience Undergraduate Program, Harvard University, Cambridge, Massachusetts
| | - Joseph D Bradley
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Michael R Chicoine
- Department of Neurological Surgery, University of Missouri-Columbia, Columbia, Missouri
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allegra A Petti
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tanner M Johanns
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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50
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Kim SH, Lee BR, Kim SM, Kim S, Kim MS, Kim J, Lee I, Kim HS, Nam GH, Kim IS, Song K, Choi Y, Lee DS, Park WY. The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex. Exp Mol Med 2024; 56:1461-1471. [PMID: 38866910 PMCID: PMC11263684 DOI: 10.1038/s12276-024-01259-2] [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: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Neoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUSpMHC and VACINUSTCR: VACINUSpMHC incorporates physical binding between peptides and MHCs (pMHCs), and VACINUSTCR integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs). We then validated our neoantigen prediction workflows both in vitro and in vivo in patients with hepatocellular carcinoma (HCC) and in a B16F10 mouse melanoma model. The predictive abilities of VACINUSpMHC and VACINUSTCR were confirmed in a validation cohort of 8 patients with HCC. Of a total of 118 neoantigen candidates predicted by VACINUSpMHC, 48 peptides were ultimately selected using VACINUSTCR. In vitro validation revealed that among the 48 predicted neoantigen candidates, 13 peptides were immunogenic. Assessment of the antitumor efficacy of the candidate neoepitopes using a VACINUSTCR in vivo mouse model suggested that vaccination with the predicted neoepitopes induced neoantigen-specific T cell responses and enabled the trafficking of neoantigen-specific CD8 + T cell clones into the tumor tissue, leading to tumor suppression. This study showed that the prediction of immunogenic neoantigens can be improved by integrating a tumor-reactive TIL TCR-pMHC ternary complex.
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MESH Headings
- Antigens, Neoplasm/immunology
- Animals
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Cell Line, Tumor
- Melanoma, Experimental/immunology
- Melanoma, Experimental/therapy
- Major Histocompatibility Complex/immunology
- Liver Neoplasms/immunology
- Liver Neoplasms/therapy
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/therapy
- CD8-Positive T-Lymphocytes/immunology
- Female
- Immunotherapy/methods
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Affiliation(s)
| | | | | | | | | | - Jaehyun Kim
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
| | - Inkyu Lee
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
| | | | - Gi-Hoon Nam
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, 02841, Korea
| | - In-San Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
- Chemical & Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | | | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, Korea.
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Geninus Inc., Seoul, 05836, Korea.
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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