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Liang T, Tao T, Wu K, Liu L, Xu W, Zhou D, Fang H, Ding Q, Huang G, Wu S. Cancer-Associated Fibroblast-Induced Remodeling of Tumor Microenvironment in Recurrent Bladder Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303230. [PMID: 37743226 PMCID: PMC10625065 DOI: 10.1002/advs.202303230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/24/2023] [Indexed: 09/26/2023]
Abstract
Bladder carcinoma (BC) recurrence is a major clinical challenge, and targeting the tumor microenvironment (TME) is a promising therapy. However, the relationship between individual TME components, particularly cancer-associated fibroblasts (CAFs), and tumor recurrence is unclear. Here, TME heterogeneity in primary and recurrent BC is investigated using single-cell RNA sequence profiling of 62 460 cells. Two cancer stem cell (CSC) subtypes are identified in recurrent BC. An inflammatory CAF subtype, ICAM1+ iCAFs, specifically associated with BC recurrence is also identified. iCAFs are found to secrete FGF2, which acts on the CD44 receptor of rCSC-M, thereby maintaining tumor stemness and epithelial-mesenchymal transition. Additionally, THBS1+ monocytes, a group of myeloid-derived suppressor cells (MDSCs), are enriched in recurrent BC and interacted with CAFs. ICAM1+ iCAFs are found to secrete CCL2, which binds to CCR2 in MDSCs. Moreover, elevated STAT3, NFKB2, VEGFA, and CTGF levels in iCAFs reshape the TME in recurrent tumors. CCL2 inhibition in an in situ BC mouse model suppressed tumor growth, decreased MDSCs and Tregs, and fostered tumor immune suppression. The study results highlight the role of iCAFs in TME cell-cell crosstalk during recurrent BC. The identification of pivotal signaling factors driving BC relapse is promising for the development of novel therapies.
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Affiliation(s)
- Ting Liang
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Tao Tao
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Kai Wu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Lisha Liu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Wuwu Xu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Dewang Zhou
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Hu Fang
- Department of UrologySouth China Hospital of Shenzhen UniversityShenzhen518000China
| | - Qiuxia Ding
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
| | - Guixiao Huang
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
| | - Song Wu
- Institute of UrologyThe Third Affiliated Hospital of Shenzhen UniversityShenzhen518116China
- Shenzhen Following Precision Medical Research InstituteLuohu Hospital GroupShenzhen518000China
- Department of UrologySouth China Hospital of Shenzhen UniversityShenzhen518000China
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Shu DH, Ho WJ, Kagohara LT, Girgis A, Shin SM, Danilova L, Lee JW, Sidiropoulos DN, Mitchell S, Munjal K, Howe K, Bendinelli KJ, Qi H, Mo G, Montagne J, Leatherman JM, Lopez-Vidal TY, Zhu Q, Huff AL, Yuan X, Hernandez A, Coyne EM, Zaidi N, Zabransky DJ, Engle LL, Ogurtsova A, Baretti M, Laheru D, Durham JN, Wang H, Anders R, Jaffee EM, Fertig EJ, Yarchoan M. Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562104. [PMID: 37904980 PMCID: PMC10614819 DOI: 10.1101/2023.10.16.562104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Neoadjuvant immunotherapy is thought to produce long-term remissions through induction of antitumor immune responses before removal of the primary tumor. Tertiary lymphoid structures (TLS), germinal center-like structures that can arise within tumors, may contribute to the establishment of immunological memory in this setting, but understanding of their role remains limited. Here, we investigated the contribution of TLS to antitumor immunity in hepatocellular carcinoma (HCC) treated with neoadjuvant immunotherapy. We found that neoadjuvant immunotherapy induced the formation of TLS, which were associated with superior pathologic response, improved relapse free survival, and expansion of the intratumoral T and B cell repertoire. While TLS in viable tumor displayed a highly active mature morphology, in areas of tumor regression we identified an involuted TLS morphology, which was characterized by dispersion of the B cell follicle and persistence of a T cell zone enriched for ongoing antigen presentation and T cell-mature dendritic cell interactions. Involuted TLS showed increased expression of T cell memory markers and expansion of CD8+ cytotoxic and tissue resident memory clonotypes. Collectively, these data reveal the circumstances of TLS dissolution and suggest a functional role for late-stage TLS as sites of T cell memory formation after elimination of viable tumor.
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Affiliation(s)
- Daniel H. Shu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Won Jin Ho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Luciane T. Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Alexander Girgis
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah M. Shin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ludmila Danilova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jae W. Lee
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Dimitrios N. Sidiropoulos
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Sarah Mitchell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kabeer Munjal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathryn Howe
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kayla J. Bendinelli
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hanfei Qi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Guanglan Mo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Janelle Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - James M. Leatherman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tamara Y. Lopez-Vidal
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Qingfeng Zhu
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Amanda L. Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Xuan Yuan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexei Hernandez
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Erin M. Coyne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Daniel J. Zabransky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Logan L. Engle
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Aleksandra Ogurtsova
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Mark Foundation Center for Advanced Genomics and Imaging, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Marina Baretti
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel Laheru
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
| | - Jennifer N. Durham
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hao Wang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Anders
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Elana J. Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Convergence Institute, Johns Hopkins University, Baltimore, Maryland
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
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Norberg SM, Bai K, Sievers C, Robbins Y, Friedman J, Yang X, Kenyon M, Ward E, Schlom J, Gulley J, Lankford A, Semnani R, Sabzevari H, Brough DE, Allen CT. The tumor microenvironment state associates with response to HPV therapeutic vaccination in patients with respiratory papillomatosis. Sci Transl Med 2023; 15:eadj0740. [PMID: 37878675 PMCID: PMC11279704 DOI: 10.1126/scitranslmed.adj0740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023]
Abstract
Recurrent respiratory papillomatosis (RRP) is a rare, debilitating neoplastic disorder caused by chronic infection with human papillomavirus (HPV) type 6 or 11 and characterized by growth of papillomas in the upper aerodigestive tract. There is no approved medical therapy, and patients require repeated debulking procedures to maintain voice and airway function. PRGN-2012 is a gorilla adenovirus immune-therapeutic capable of enhancing HPV 6/11-specific T cell immunity. This first-in-human, phase 1 study (NCT04724980) of adjuvant PRGN-2012 treatment in adult patients with severe, aggressive RRP demonstrates the overall safety and clinically meaningful benefit observed with PRGN-2012, with a 50% complete response rate in patients treated at the highest dose. Responders demonstrate greater expansion of peripheral HPV-specific T cells compared with nonresponders. Additional correlative studies identify an association between reduced baseline papilloma HPV gene expression, greater interferon responses and expression of CXCL9 and CXCL10, and greater papilloma T cell infiltration in responders. Conversely, nonresponders were characterized by greater HPV and CXCL8 gene expression, increased neutrophilic cell infiltration, and reduced T cell papilloma infiltration. These results suggest that papilloma HPV gene expression may regulate interferon signaling and chemokine expression profiles within the tumor microenvironment that cooperate to govern clinical response to therapeutic HPV vaccination in patients with respiratory papillomatosis.
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Affiliation(s)
- Scott M. Norberg
- Center for Immune-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ke Bai
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Cem Sievers
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yvette Robbins
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jay Friedman
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xinping Yang
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Meg Kenyon
- Center for Immune-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Jeffrey Schlom
- Center for Immune-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - James Gulley
- Center for Immune-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | | | - Clint T. Allen
- Center for Immune-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Zhang M, Huang Y, Pan J, Sang C, Lin Y, Dong L, Shen X, Wu Y, Song G, Ji S, Liu F, Wang M, Zheng Y, Zhang S, Wang Z, Ren J, Gao D, Zhou J, Fan J, Wei W, Lin J, Gao Q. An Inflammatory Checkpoint Generated by IL1RN Splicing Offers Therapeutic Opportunity for KRAS-Mutant Intrahepatic Cholangiocarcinoma. Cancer Discov 2023; 13:2248-2269. [PMID: 37486241 DOI: 10.1158/2159-8290.cd-23-0282] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/30/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
KRAS mutations are causally linked to protumor inflammation and are identified as driving factors in tumorigenesis. Here, using multiomics data gathered from a large set of patients, we showed that KRAS mutation was associated with a specific landscape of alternative mRNA splicing that connected to myeloid inflammation in intrahepatic cholangiocarcinoma (iCCA). Then, we identified a negative feedback mechanism in which the upregulation of interleukin 1 receptor antagonist (IL1RN)-201/203 due to alternative splicing confers vital anti-inflammatory effects in KRAS-mutant iCCA. In KRAS-mutant iCCA mice, both IL1RN-201/203 upregulation and anakinra treatment ignited a significant antitumor immune response by altering neutrophil recruitment and phenotypes. Furthermore, anakinra treatment synergistically enhanced anti-PD-1 therapy to activate intratumoral GZMB+ CD8+ T cells in KRAS-mutant iCCA mice. Clinically, we found that high IL1RN-201/203 levels in patients with KRAS-mutant iCCA were significantly associated with superior response to anti-PD-1 immunotherapy. SIGNIFICANCE This work describes a novel inflammatory checkpoint mediated by IL1RN alternative splicing variants that may serve as a promising basis to develop therapeutic options for KRAS-mutant iCCA and other cancers. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Mao Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Yingying Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiaomeng Pan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Chen Sang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Liangqing Dong
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Xia Shen
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
| | - Shuyi Ji
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Fen Liu
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Mengcheng Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuyan Zheng
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianke Ren
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Lingang Laboratory, Shanghai, China
- Translational Medicine Institute of Jiangxi, The First Affiliated Hospital of Nanchang University, Jiangxi, China
| | - Jian Lin
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai, China
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
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55
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Ren S, Lan T, Wu F, Chen S, Jiang X, Huo C, Li Z, Xie S, Wu D, Wang R, Li Y, Qiu L, Huang G, Li S, Wang X, Cen M, Cai T, Lin Z, Li J, Li B. Intratumoral CD103 + CD8 + T cells predict response to neoadjuvant chemoimmunotherapy in advanced head and neck squamous cell carcinoma. Cancer Commun (Lond) 2023; 43:1143-1163. [PMID: 37658605 PMCID: PMC10565384 DOI: 10.1002/cac2.12480] [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: 03/03/2023] [Revised: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Immune cell heterogenicity is known to determine the therapeutic response to cancer progression. Neoadjuvant chemoimmunotherapy (NACI) has shown clinical benefits in some patients with advanced head and neck squamous cell carcinoma (HNSCC), but the underlying mechanism behind this clinical response is unknown. The efficacy of NACI needs to be potentiated by identifying accurate biomarkers to predict clinical responses. Here, we attempted to identify molecules predicting NACI response in advanced HNSCC. METHODS We performed combined single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence (mIHC) staining with tumor samples derived from NACI-treated HNSCC patients to identify a new tumor-infiltrating cell (TIL) subtype, CD103+ CD8+ TILs, associated with clinical response, while both in vitro and in vivo assays were carried out to determine its antitumor efficiency. The regulatory mechanism of the CD103+ CD8+ TILs population was examined by performing cell-cell interaction analysis of the scRNA-seq data and spatial analysis of the mIHC images. RESULTS We established intratumoral CD103+ CD8+ TILs density as a determinant of NACI efficacy in cancers. Our scRNA-seq results indicated that the population of CD103+ CD8+ TILs was dramatically increased in the responders of NACI-treated HNSCC patients, while mIHC analysis confirmed the correlation between intratumoral CD103+ CD8+ TILs density and NACI efficacy in HNSCC patients. Further receiver operating characteristic curve analysis defined this TIL subset as a potent marker to predict patient response to NACI. Functional assays showed that CD103+ CD8+ TILs were tumor-reactive T cells, while programmed cell death protein-1 (PD-1) blockade enhanced CD103+ CD8+ TILs cytotoxicity against tumor growth in vivo. Mechanistically, targeting the triggering receptor expressed on myeloid cells 2-positive (TREM2+ ) macrophages might enhance the population of CD103+ CD8+ TILs and facilitate antitumor immunity during NACI treatment. CONCLUSIONS Our study highlights the impact of intratumoral CD103+ CD8+ TILs density on NACI efficacy in different cancers, while the efforts to elevate its population warrant further clinical investigation.
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Affiliation(s)
- Siqi Ren
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Tianjun Lan
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Fan Wu
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Suling Chen
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Xue Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Chuying Huo
- Department of Gynecological OncologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Zitian Li
- School of Stomatology, Jilin UniversityJilinP. R. China
| | - Shule Xie
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Donghui Wu
- Stomatology Hospital of Haizhu districtGuangdongP. R. China
| | - Ruixin Wang
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Yanyan Li
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Lin Qiu
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Guoxin Huang
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Shurui Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Xiaojuan Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Meifeng Cen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Tingting Cai
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
| | - Zhaoyu Lin
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Jinsong Li
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
| | - Bowen Li
- Department of Oral and Maxillofacial SurgerySun Yat‐sen Memorial Hospital of Sun Yat‐sen UniversityGuangdongP. R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong‐Hong Kong Joint Laboratory for RNA MedicineMedical Research Center, Sun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangdongP. R. China
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56
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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57
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Luo Y, Liang H. Single-cell dissection of tumor microenvironmental response and resistance to cancer therapy. Trends Genet 2023; 39:758-772. [PMID: 37658004 PMCID: PMC10529478 DOI: 10.1016/j.tig.2023.07.005] [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: 05/25/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 09/03/2023]
Abstract
Cancer treatment strategies have evolved significantly over the years, with chemotherapy, targeted therapy, and immunotherapy as major pillars. Each modality leads to unique treatment outcomes by interacting with the tumor microenvironment (TME), which imposes a fundamental selective pressure on cancer progression. The advent of single-cell profiling technologies has revolutionized our understanding of the intricate and heterogeneous nature of the TME at an unprecedented resolution. This review delves into the commonalities and differential manifestations of how cancer therapies reshape the microenvironment in diverse cancer types. We highlight how groundbreaking immune checkpoint blockade (ICB) strategies alone or in combination with tumor-targeting treatments are endowed with comprehensive mechanistic insights when decoded at the single-cell level, aiming to drive forward future research directions on personalized treatments.
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Affiliation(s)
- Yikai Luo
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
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58
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Baysoy A, Bai Z, Satija R, Fan R. The technological landscape and applications of single-cell multi-omics. Nat Rev Mol Cell Biol 2023; 24:695-713. [PMID: 37280296 PMCID: PMC10242609 DOI: 10.1038/s41580-023-00615-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
Abstract
Single-cell multi-omics technologies and methods characterize cell states and activities by simultaneously integrating various single-modality omics methods that profile the transcriptome, genome, epigenome, epitranscriptome, proteome, metabolome and other (emerging) omics. Collectively, these methods are revolutionizing molecular cell biology research. In this comprehensive Review, we discuss established multi-omics technologies as well as cutting-edge and state-of-the-art methods in the field. We discuss how multi-omics technologies have been adapted and improved over the past decade using a framework characterized by optimization of throughput and resolution, modality integration, uniqueness and accuracy, and we also discuss multi-omics limitations. We highlight the impact that single-cell multi-omics technologies have had in cell lineage tracing, tissue-specific and cell-specific atlas production, tumour immunology and cancer genetics, and in mapping of cellular spatial information in fundamental and translational research. Finally, we discuss bioinformatics tools that have been developed to link different omics modalities and elucidate functionality through the use of better mathematical modelling and computational methods.
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Affiliation(s)
- Alev Baysoy
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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59
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Hou P, Luo Y, Wu N. TCL1A+ B cells predict prognosis in triple-negative breast cancer through integrative analysis of single-cell and bulk transcriptomic data. Open Life Sci 2023; 18:20220707. [PMID: 37791059 PMCID: PMC10543705 DOI: 10.1515/biol-2022-0707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high mortality rates. It remains a prevailing clinical need to distinguish whether the patient can benefit from therapy, such as chemotherapy. By integrating single-cell and global transcriptome data, we have for the first time identified TCL1A+ B cell functions that are prognostically relevant in TNBC. This finding broadens the perspective of traditional tumor-infiltrating lymphocytes in predicting survival, especially the potential value of B cells in TNBC. Single-cell RNA-seq data from five TNBC patients were collected to identify the association between immune cell populations and clinical outcomes. Functional analysis was according to gene set enrichment analysis using pathways from MsigDB. Subsequently, the gene signature of TCL1A+ B cells based on differential expression genes of TCL1A+ B cells versus other immune cells was used to explore the correlation with tumor microenvironment (TME) and construct a prognostic signature using a non-parametric and unsupervised method. We identified TCL1A+ B cells as a cluster of B cells associated with clinical outcomes in TNBC. Functional analysis demonstrated its function in B cell activation and regulation of immune response. The highly enriched TCL1A+ B cell population was found to be associated with a thermal TME with anti-tumor effects. A high abundance of TCL1A+ B cell population is positively correlated with a favorable therapeutic outcome, as indicated by longer overall survival. The present study suggests that TCL1A+ B cells play a key role in the treatment and prognostic prediction of TNBC, although further studies are needed to validate our findings. Moreover, the integration of transcriptome data at various resolutions provides a viable approach for the discovery of novel prognostic markers.
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Affiliation(s)
- Peifeng Hou
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian, 350000, China
- Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian, 350000, China
| | - Yang Luo
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Ningzi Wu
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
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Garman B, Jiang C, Daouti S, Kumar S, Mehta P, Jacques MK, Menard L, Manjarrez-Orduno N, Dolfi S, Mukherjee P, Rai SC, Lako A, Koenitzer JD, David JM. Comprehensive immunophenotyping of solid tumor-infiltrating immune cells reveals the expression characteristics of LAG-3 and its ligands. Front Immunol 2023; 14:1151748. [PMID: 37795090 PMCID: PMC10546411 DOI: 10.3389/fimmu.2023.1151748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Background Immune cell expression profiling from patient samples is critical for the successful development of immuno-oncology agents and is useful to understand mechanism-of-action, to identify exploratory biomarkers predictive of response, and to guide treatment selection and combination therapy strategies. LAG-3 is an inhibitory immune checkpoint that can suppress antitumor T-cell responses and targeting LAG-3, in combination with PD-1, is a rational approach to enhance antitumor immunity that has recently demonstrated clinical success. Here, we sought to identify human immune cell subsets that express LAG-3 and its ligands, to characterize the marker expression profile of these subsets, and to investigate the potential relationship between LAG-3 expressing subsets and clinical outcomes to immuno-oncology therapies. Methods Comprehensive high-parameter immunophenotyping was performed using mass and flow cytometry of tumor-infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells (PBMCs) from two independent cohorts of samples from patients with various solid tumor types. Profiling of circulating immune cells by single cell RNA-seq was conducted on samples from a clinical trial cohort of melanoma patients treated with immunotherapy. Results LAG-3 was most highly expressed by subsets of tumor-infiltrating CD8 T central memory (TCM) and effector memory (TEM) cells and was frequently co-expressed with PD-1. We determined that these PD-1+ LAG-3+ CD8 memory T cells exhibited a unique marker profile, with greater expression of activation (CD69, HLA-DR), inhibitory (TIM-3, TIGIT, CTLA-4) and stimulatory (4-1BB, ICOS) markers compared to cells that expressed only PD-1 or LAG-3, or that were negative for both checkpoints. In contrast to tumors, LAG-3 expression was more limited in circulating immune cells from healthy donors and solid tumor patients. Additionally, we found abundant expression of the LAG-3 ligands MHC-II and galectin-3 in diverse immune cell types, whereas FGL1 and LSECtin were minimally expressed by immune cells in the tumor microenvironment (TME). Lastly, we found an inverse relationship between baseline and on-treatment levels of circulating LAG3 transcript-expressing CD8 memory T cells and response to combination PD-1 and CTLA-4 blockade in a clinical trial cohort of melanoma patients profiled by scRNAseq. Conclusions These results provide insights into the nature of LAG-3- and ligand-expressing immune cells within the TME, and suggest a biological basis for informing mechanistic hypotheses, treatment selection strategies, and combination immunotherapy approaches to support continued development of dual PD-1 and LAG-3 blockade.
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Affiliation(s)
- Bradley Garman
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Can Jiang
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Sherif Daouti
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Sanah Kumar
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Priyanka Mehta
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Miye K. Jacques
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Laurence Menard
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | | | - Sonia Dolfi
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | - Piali Mukherjee
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
- Epigenomics Core Facility, Weill Cornell Medicine, New York City, NY, United States
| | | | - Ana Lako
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
| | | | - Justin M. David
- Translational Medicine, Bristol Myers Squibb, Lawrenceville, NJ, United States
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61
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Zhao H, Wu L, Dai J, Sun K, Zi Z, Guan J, Zhang L. Ligand-based adoptive T cell targeting CA125 in ovarian cancer. J Transl Med 2023; 21:596. [PMID: 37670338 PMCID: PMC10481596 DOI: 10.1186/s12967-023-04271-8] [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: 02/27/2023] [Accepted: 06/13/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a highly aggressive gynecological malignancy prevalent worldwide. Most OC cases are typically diagnosed at advanced stages, which has led to a 5-year overall survival rate of less than 35% following conventional treatment. Furthermore, immune checkpoint inhibitor therapy has shown limited efficacy in the treatment of patients with OC, and CAR-T therapy has also demonstrated modest results owing to inadequate T cell infiltration. Therefore, novel strategies must be developed to enhance T cell persistence and trafficking within the OC tumor microenvironment. METHODS In this study, we developed a novel adoptive T-cell therapy for ovarian cancer based on a chimeric antigen receptor structure. We used a ligand-receptor binding motif to enhance the therapeutic effect of targeting CA125. Since mesothelin can naturally bind to CA125 with high affinity, we concatenated the core-binding fragment of mesothelin with the 4-1BB and CD3ζ signal fragments to assemble a novel CA125-targeting chimeric receptor (CR). The CAR structure targeting CA125 derived from the 4H11 antibody was also constructed. CR- and CAR-encoding RNA were electroporated into T cells to evaluate their antitumor activity both in vitro and in vivo. RESULTS While CR-T or CAR-T cells exhibited moderate activity against two ovarian cancer cell lines, T cells co-expressing CR and CAR exhibited a superior killing effect compared to T cells expressing either CR or CAR alone. Furthermore, upon interaction with ovarian tumors, the ability of CR and CAR T cells to release activation markers and functional cytokines increased significantly. Similarly, CR and CAR co-expressing T cells persistently controlled the growth of transplanted ovarian cancer tumors in NSG mice and significantly prolonged the overall survival of tumor-challenged mice. Transcriptome sequencing revealed that the survival and cytotoxicity of T cells co-expressing CR and CAR were significantly altered compared with those of T cells expressing either CR or CAR. CONCLUSION Our findings demonstrate that CA125 targeting CR and CAR can synergistically kill ovarian cancer cells, indicating that CA125 targeting by the two binding motifs simultaneously in tumors may improve the therapeutic outcomes of ovarian cancer treatment.
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Affiliation(s)
- Haihong Zhao
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Lina Wu
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Jiemin Dai
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Ke Sun
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China
| | - Zhenguo Zi
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Junhua Guan
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.
| | - Liwen Zhang
- Department of Obstetrics and Gynecology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, 200240, China.
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Lan X, Zebley CC, Youngblood B. Cellular and molecular waypoints along the path of T cell exhaustion. Sci Immunol 2023; 8:eadg3868. [PMID: 37656775 PMCID: PMC10618911 DOI: 10.1126/sciimmunol.adg3868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Thirty years of foundational research investigating molecular and cellular mechanisms promoting T cell exhaustion are now enabling rational design of T cell-based therapies for the treatment of chronic infections and cancer. Once described as a static cell fate, it is now well appreciated that the developmental path toward exhaustion is composed of a heterogeneous pool of cells with varying degrees of effector potential that ultimately converge on a terminally differentiated state. Recent description of the developmental stages along the differentiation trajectory of T cell exhaustion has provided insight into past immunotherapeutic success and future opportunities. Here, we discuss the hallmarks of distinct developmental stages occurring along the path to T cell dysfunction and the impact of these discrete CD8+ T cell fates on cancer immunotherapy.
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Caitlin C. Zebley
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Sun L, Kienzler JC, Reynoso JG, Lee A, Shiuan E, Li S, Kim J, Ding L, Monteleone AJ, Owens GC, Phillips JJ, Everson RG, Nathanson D, Cloughesy TF, Li G, Liau LM, Hugo W, Kim W, Prins RM. Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors. J Clin Invest 2023; 133:e169314. [PMID: 37655659 PMCID: PMC10471177 DOI: 10.1172/jci169314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
In comparison with responses in recurrent glioblastoma (rGBM), the intracranial response of brain metastases (BrM) to immune checkpoint blockade (ICB) is less well studied. Here, we present an integrated single-cell RNA-Seq (scRNA-Seq) study of 19 ICB-naive and 9 ICB-treated BrM samples from our own and published data sets. We compared them with our previously published scRNA-Seq data from rGBM and found that ICB led to more prominent T cell infiltration into BrM than rGBM. These BrM-infiltrating T cells exhibited a tumor-specific phenotype and displayed greater activated/exhausted features. We also used multiplex immunofluorescence and spatial transcriptomics to reveal that ICB reduced a distinct CD206+ macrophage population in the perivascular space, which may modulate T cell entry into BrM. Furthermore, we identified a subset of progenitor exhausted T cells that correlated with longer overall survival in BrM patients. Our study provides a comprehensive immune cellular landscape of ICB's effect on metastatic brain tumors and offers insights into potential strategies for improving ICB efficacy for brain tumor patients.
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Affiliation(s)
- Lu Sun
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
| | - Jenny C. Kienzler
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Inflammation Research Group, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Alexander Lee
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
| | | | | | | | - Lizhong Ding
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | | | | | - Joanna J. Phillips
- Helen Diller Family Comprehensive Cancer Center and
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Richard G. Everson
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - David Nathanson
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Timothy F. Cloughesy
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Neurology/Neuro-Oncology, UCLA, Los Angeles, California, USA
| | | | - Linda M. Liau
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Willy Hugo
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Won Kim
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Robert M. Prins
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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Zhang H, Lu X, Lu B, Chen L. scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data. Cancers (Basel) 2023; 15:4277. [PMID: 37686554 PMCID: PMC10486867 DOI: 10.3390/cancers15174277] [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: 07/20/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Single-cell transcriptome analysis has fundamentally changed biological research by allowing higher-resolution computational analysis of individual cells and subsets of cell types. However, few methods have met the need to recognize and quantify the underlying cellular programs that determine the specialization and differentiation of the cell types. METHODS In this study, we present scGEM, a nested tree-structured nonparametric Bayesian model, to reveal the gene co-expression modules (GEMs) reflecting transcriptome processes in single cells. RESULTS We show that scGEM can discover shared and specialized transcriptome signals across different cell types using peripheral blood mononuclear single cells and early brain development single cells. scGEM outperformed other methods in perplexity and topic coherence (p < 0.001) on our simulation data. Larger datasets, deeper trees and pre-trained models are shown to be positively associated with better scGEM performance. The GEMs obtained from triple-negative breast cancer single cells exhibited better correlations with lymphocyte infiltration (p = 0.009) and the cell cycle (p < 0.001) than other methods in additional validation on the bulk RNAseq dataset. CONCLUSIONS Altogether, we demonstrate that scGEM can be used to model the hidden cellular functions of single cells, thereby unveiling the specialization and generalization of transcriptomic programs across different types of cells.
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Affiliation(s)
- Han Zhang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
- UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Binfeng Lu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Lujia Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA; (H.Z.)
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66
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Shen J, Wang R, Chen Y, Fang Z, Tang J, Yao J, Gao J, Chen X, Shi X. Prognostic significance and mechanisms of CXCL genes in clear cell renal cell carcinoma. Aging (Albany NY) 2023; 15:7974-7996. [PMID: 37540227 PMCID: PMC10497021 DOI: 10.18632/aging.204922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
This study aimed to investigate the clinical significance, biological functions, and underlying mechanisms of CXCL genes in clear cell renal cell carcinoma (ccRcc) based on patient datasets and pan-cancer analysis. The interaction between CXCL genes in ccRcc and immune components, particularly in relation to neutrophil recruitment and polarization mechanisms, was also evaluated. Furthermore, a risk score was developed using a signature for neutrophil polarization. The role of CXCL2 was assessed through in vitro experiments. Results showed that five CXCL genes (CXCL 2, 5, 9, 10, and 11) were upregulated in renal cancer tissue, while seven genes (CXCL 1, 2, 3, 5, 8, 13, and 14) significantly impacted patient survival. Moreover, CXCL 1, 5, and 13 affected progression-free survival. Besides, differences in mRNA expression and immune components affected renal cancer outcomes. Furthermore, three pairs of CXCL gene-immune cell interactions (CXCL13-CD8+ T cells, CXCL9/10-M1 cells, CXCL1/2/3/8-neutrophils) were identified through single-cell and pan-cancer analysis. A TAN risk score with prognostic value for KIRC patients was constructed using 11 genes and a TAN signature. Neutrophil polarization significantly impacted survival. Notably, CXCL2 was involved in neutrophil recruitment and polarization, thus promoting ccRcc progression. In conclusion, seven prognostic CXCL genes (CXCL 1/2/3/5/8/13/14) for ccRcc patients and three pairs of CXCL gene-immune cell interactions were identified. Furthermore, results showed that CXCL 2 promotes ccRcc progression through neutrophil recruitment and polarization.
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Affiliation(s)
- Junwen Shen
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
- Huzhou Key Laboratory of Precise Diagnosis and Treatment of Urinary Tumors, Huzhou, Zhejiang 31300, China
| | - Rongjiang Wang
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
- Huzhou Key Laboratory of Precise Diagnosis and Treatment of Urinary Tumors, Huzhou, Zhejiang 31300, China
| | - Yu Chen
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Zhihai Fang
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Jianer Tang
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Jianxiang Yao
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Jianguo Gao
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Xiaonong Chen
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
| | - Xinli Shi
- The Department of Urology, The First Affiliated Hospital of Huzhou Normal College, Huzhou, Zhejiang 31300, China
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Zeng X, Huang X, Yin L, Yu H, Wang S, Li L. Molecular subtyping and immune score system by a novel pyroptosis-based gene signature precisely predict immune infiltrating, survival and response to immune-checkpoint blockade in breast cancer. Cancer Genet 2023; 276-277:60-69. [PMID: 37506530 DOI: 10.1016/j.cancergen.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Breast cancer is one of the most prevalent and lethal types of cancer affecting women globally. Pyroptosis is a recently elucidated form of inflammatory cell death mediated by the gasdermin family and is considered to be associated with the tumor immune microenvironment. However, the impact of pyroptosis on breast cancer patients remains unclear. In this study, we identified 31 Pyroptosis-Related-Genes (PRGs) and investigated their association with patient survival using data from the TCGA database. We then established a gene signature comprising 6 PRGs that were significantly correlated with prognosis, and used these genes to classify breast cancer into 2 molecular subtypes. We investigated the characteristics of these two subtypes and found that our molecular subtyping accurately separated the samples into two groups with distinct immune infiltration and prognosis. Patients with higher expression of these genes had significantly greater immune infiltrating, T cell signaling, and better prognosis. Moreover, we developed an immune score system based on these 6 genes that accurately predicted the immune infiltrating of patients and their response to immune-checkpoint blockade, which was difficult to achieve with previous models. Additionally, through single-cell analyses, we found that patients with higher immune scores had stronger cytotoxic immune cells. In summary, our study identified a novel gene set and developed an immune scoring system based on this gene set that can precisely predict the immune microenvironment and responses to immunotherapy of breast cancer (BRCA) patients, which could be useful in clinical trials.
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Affiliation(s)
- Xiaomei Zeng
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, PR China; Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, PR China
| | - Xun Huang
- Oncology department, The First People's Hospital of Yibin City, Sichuan Province, PR China
| | - Lingxi Yin
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, PR China; Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, PR China
| | - Hui Yu
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, PR China; Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, PR China
| | - Shiyu Wang
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, PR China; Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, PR China
| | - Lijuan Li
- Rehabilitation Medicine Center and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, PR China; Key Laboratory of Rehabilitation Medicine in Sichuan Province, Sichuan University, Chengdu, PR China.
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Wu S, Huang H, Sun R, Gao DS, Ye F, Huang J, Li E, Ni A, Lu KG, Chen K, Jiang J, Morel PA, Zhong Z, Lu B. Synergism Between IL21 and Anti-PD-1 Combination Therapy is Underpinned by the Coordinated Reprogramming of the Immune Cellular Network in the Tumor Microenvironment. CANCER RESEARCH COMMUNICATIONS 2023; 3:1460-1472. [PMID: 37546701 PMCID: PMC10402650 DOI: 10.1158/2767-9764.crc-23-0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023]
Abstract
T cell-stimulating cytokines and immune checkpoint inhibitors (ICI) are an ideal combination for increasing response rates of cancer immunotherapy. However, the results of clinical trials have not been satisfying. It is important to understand the mechanism of synergy between these two therapeutic modalities. Here, through integrated analysis of multiple single-cell RNA sequencing (scRNA-seq) datasets of human tumor-infiltrating immune cells, we demonstrate that IL21 is produced by tumor-associated T follicular helper cells and hyperactivated/exhausted CXCL13+CD4+ T cells in the human tumor microenvironment (TME). In the mouse model, the hyperactivated/exhausted CD4+ T cell-derived IL21 enhances the helper function of CD4+ T cells that boost CD8+ T cell-mediated immune responses during PD-1 blockade immunotherapy. In addition, we demonstrated that IL21's antitumor activity did not require T-cell trafficking. Using scRNA-seq analysis of the whole tumor-infiltrating immune cells, we demonstrated that IL21 treatment in combination with anti-PD-1 blockade synergistically drives tumor antigen-specific CD8+ T cells to undergo clonal expansion and differentiate toward the hyperactive/exhausted functional state in the TME. In addition, IL21 treatment and anti-PD-1 blockade synergistically promote dendritic cell (DC) activation and maturation to mature DC as well as monocyte to type 1 macrophage (M1) differentiation in the TME. Furthermore, the combined treatment reprograms the immune cellular network by reshaping cell-cell communication in the TME. Our study establishes unique mechanisms of synergy between IL21 and PD-1-based ICI in the TME through the coordinated promotion of type 1 immune responses. Significance This study reveals how cytokine and checkpoint inhibitor therapy can be combined to increase the efficacy of cancer immunotherapy.
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Affiliation(s)
- Shaoxian Wu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Hao Huang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Runzi Sun
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - David Shihong Gao
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Fan Ye
- Anwita Biosciences Inc, San Carlos, California
| | | | - Ella Li
- Anwita Biosciences Inc, San Carlos, California
| | - Andrew Ni
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kevin GuoKai Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kong Chen
- Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, P.R. China
| | - Penelope A. Morel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Binfeng Lu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey
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Li X, Gao Z, Chen J, Feng S, Luo X, Shi Y, Tang Z, Liu W, Zhang X, Huang A, Gao Q, Ke A, Zhou J, Fan J, Fu X, Ding Z. Integrated single cell and bulk sequencing analysis identifies tumor reactive CXCR6 + CD8 T cells as a predictor of immune infiltration and immunotherapy outcomes in hepatocellular carcinoma. Front Oncol 2023; 13:1099385. [PMID: 37593098 PMCID: PMC10430781 DOI: 10.3389/fonc.2023.1099385] [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: 11/15/2022] [Accepted: 06/30/2023] [Indexed: 08/19/2023] Open
Abstract
Background Various immune cell types in the tumor microenvironment (TME) of hepatocellular carcinoma (HCC) have been identified as important parameters associated with prognosis and responsiveness to immunotherapy. However, how various factors influence immune cell infiltration remains incompletely understood. Hence, we investigated the single cell multi-omics landscape of immune infiltration in HCC, particularly key gene and cell subsets that influence immune infiltration, thus potentially linking the immunotherapy response and immune cell infiltration. Methods We grouped patients with HCC according to immune cell infiltration scores calculated by single sample gene set enrichment analysis (ssGSEA). Differential expression analysis, functional enrichment, clinical trait association, gene mutation analysis, tumor immune dysfunction and exclusion (TIDE) and prognostic model construction were used to investigate the immune infiltration landscape through multi-omics. Stepwise regression was further used to identify key genes regulating immune infiltration. Single cell analysis was performed to explore expression patterns of candidate genes and investigate associated cellular populations. Correlation analysis, ROC analysis, Immunotherapy cohorts were used to explore and confirm the role of key gene and cellular population in predicting immune infiltration state and immunotherapy response. Immunohistochemistry and multiplexed fluorescence staining were used to further validated our results. Results Patients with HCC were clustered into high and low immune infiltration groups. Mutations of CTNNB1 and TTN were significantly associated with immune infiltration and altered enrichment of cell populations in the TME. TIDE analysis demonstrated that T cell dysfunction and the T cell exclusion score were elevated in the high and low infiltration groups, respectively. Six risk genes and five risk immune cell types were identified and used to construct risk scores and a nomogram model. CXCR6 and LTA, identified by stepwise regression, were highly associated with immune infiltration. Single cell analysis revealed that LTA was expressed primarily in tumor infiltrating T lymphocytes and partial B lymphocytes, whereas CXCR6 was enriched predominantly in T and NK cells. Notably, CXCR6+ CD8 T cells were characterized as tumor enriched cells that may be potential predictors of high immune infiltration and the immune-checkpoint blockade response, and may serve as therapeutic targets. Conclusion We constructed a comprehensive single cell and multi-omics landscape of immune infiltration in HCC, and delineated key genes and cellular populations regulating immune infiltration and immunotherapy response, thus providing insights into the mechanisms of immune infiltration and future therapeutic control.
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Affiliation(s)
- Xiaogang Li
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Zheng Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Jiafeng Chen
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Shanru Feng
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Xuanming Luo
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Yinghong Shi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Zheng Tang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Weiren Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Xin Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Ao Huang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Aiwu Ke
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Xiutao Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
| | - Zhenbin Ding
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai, China
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
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Koppensteiner L, Mathieson L, Pattle S, Dorward DA, O'Connor R, Akram AR. Location of CD39 + T cell subpopulations within tumors predict differential outcomes in non-small cell lung cancer. J Immunother Cancer 2023; 11:e006770. [PMID: 37648263 PMCID: PMC10471883 DOI: 10.1136/jitc-2023-006770] [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: 06/25/2023] [Indexed: 09/01/2023] Open
Abstract
PURPOSE An improved mechanistic understanding of immunosuppressive pathways in non-small cell lung cancer (NSCLC) is important to develop novel diagnostic and therapeutic approaches. Here, we investigate the prognostic significance of the ectonucleotidases CD39 and CD73 in NSCLC. EXPERIMENTAL DESIGN The expression and localization of CD39, CD73 and CD103 was digitally quantified in a cohort of 162 early treatment naïve NSCLC patients using multiplex-immunofluorescence and related to patient outcome. Expression among different cell-populations was assessed via flow cytometry. Targeted RNA-Seq was performed on CD4+ and CD8+ T cells from digested NSCLC tumor tissue and single-cell RNA-Seq data was analyzed to investigate the functional significance of CD39+ T cell populations. RESULTS We demonstrate that flow cytometry of early untreated NSCLC patients shows an upregulation of CD39 expression in the tumor tissue among natural killer (NK) cells, fibroblasts and T cells. CD73 expression is mainly found among fibroblasts and Epcam+cells in the tumor tissue. Multiplex Immunofluorescence in a cohort of 162 early untreated NSCLC patients demonstrates that CD39 expression is mainly localized in the tumor stroma while CD73 expression is equally distributed between tumor nest and stroma, and high expression of CD39 and CD73 in the tumor stroma is associated with poor recurrence-free survival (RFS) at 5 years. Additionally, we find that CD8+T cells located in the tumor nest express CD103 and the density of CD39+CD103+CD8+ T cells in the tumor nest predicts improved RFS at 5 years. Targeted RNA-Seq shows that the tumor microenvironment of NSCLC upregulates regulatory pathways in CD4+ T cells and exhaustion in CD8+ T cells, and analysis of a single cell RNA sequencing dataset shows that CD39+CD4+ cells are enriched in Treg signature gene-sets, and CD39+CD103+ cytotoxic T lymphocyte show gene signatures indicative of an exhausted cytotoxic phenotype with upregulated expression of CXCL13. CONCLUSIONS Knowledge of patterns of distribution and location are required to understand the prognostic impact of CD39+ T cell populations in NSCLC. This study provides an improved understanding of spatial and functional characteristics of CD39+ T cells and their significance to patient outcome.
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Affiliation(s)
| | - Layla Mathieson
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
| | - Samuel Pattle
- Department of Pathology, Royal Infirmary, Edinburgh, UK
| | | | - Richard O'Connor
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
| | - Ahsan R Akram
- Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Molecular Medicine, The University of Edinburgh, Edinburgh, UK
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O’Connor RA, Martinez BR, Koppensteiner L, Mathieson L, Akram AR. Cancer-associated fibroblasts drive CXCL13 production in activated T cells via TGF-beta. Front Immunol 2023; 14:1221532. [PMID: 37520560 PMCID: PMC10373066 DOI: 10.3389/fimmu.2023.1221532] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Tumour-reactive T cells producing the B-cell attractant chemokine CXCL13, in solid tumours, promote development of tertiary lymphoid structures (TLS) and are associated with improved prognosis and responsiveness to checkpoint immunotherapy. Cancer associated fibroblasts are the dominant stromal cell type in non-small cell lung cancer (NSCLC) where they co-localise with T cells and can influence T cell activation and exhaustion. We questioned whether CAF directly promote CXCL13-production during T cell activation. Methods We characterised surface markers, cytokine production and transcription factor expression in CXCL13-producing T cells in NSCLC tumours and paired non-cancerous lung samples using flow cytometry. We then assessed the influence of human NSCLC-derived primary CAF lines on T cells from healthy donors and NSCLC patients during activation in vitro measuring CXCL13 production and expression of cell-surface markers and transcription factors by flow cytometry. Results CAFs significantly increased the production of CXCL13 by both CD4+ and CD8+ T cells. CAF-induced CXCL13-producing cells lacked expression of CXCR5 and BCL6 and displayed a T peripheral helper cell phenotype. Furthermore, we demonstrate CXCL13 production by T cells is induced by TGF-β and limited by IL-2. CAF provide TGF-β during T cell activation and reduce availability of IL-2 both directly (by reducing the capacity for IL-2 production) and indirectly, by expanding a population of activated Treg. Inhibition of TGF-β signalling prevented both CAF-driven upregulation of CXCL13 and Treg expansion. Discussion Promoting CXCL13 production represents a newly described immune-regulatory function of CAF with the potential to shape the immune infiltrate of the tumour microenvironment both by altering the effector-function of tumour infiltrating T-cells and their capacity to attract B cells and promote TLS formation.
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Affiliation(s)
- Richard A. O’Connor
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Begoña Roman Martinez
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Lilian Koppensteiner
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Layla Mathieson
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Ahsan R. Akram
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom
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Combes AJ, Samad B, Krummel MF. Defining and using immune archetypes to classify and treat cancer. Nat Rev Cancer 2023:10.1038/s41568-023-00578-2. [PMID: 37277485 DOI: 10.1038/s41568-023-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Tumours are surrounded by a host immune system that can suppress or promote tumour growth. The tumour microenvironment (TME) has often been framed as a singular entity, suggesting a single type of immune state that is defective and in need of therapeutic intervention. By contrast, the past few years have highlighted a plurality of immune states that can surround tumours. In this Perspective, we suggest that different TMEs have 'archetypal' qualities across all cancers - characteristic and repeating collections of cells and gene-expression profiles at the level of the bulk tumour. We discuss many studies that together support a view that tumours typically draw from a finite number (around 12) of 'dominant' immune archetypes. In considering the likely evolutionary origin and roles of these archetypes, their associated TMEs can be predicted to have specific vulnerabilities that can be leveraged as targets for cancer treatment with expected and addressable adverse effects for patients.
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Affiliation(s)
- Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
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Chu Y, Dai E, Li Y, Han G, Pei G, Ingram DR, Thakkar K, Qin JJ, Dang M, Le X, Hu C, Deng Q, Sinjab A, Gupta P, Wang R, Hao D, Peng F, Yan X, Liu Y, Song S, Zhang S, Heymach JV, Reuben A, Elamin YY, Pizzi MP, Lu Y, Lazcano R, Hu J, Li M, Curran M, Futreal A, Maitra A, Jazaeri AA, Ajani JA, Swanton C, Cheng XD, Abbas HA, Gillison M, Bhat K, Lazar AJ, Green M, Litchfield K, Kadara H, Yee C, Wang L. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Nat Med 2023; 29:1550-1562. [PMID: 37248301 DOI: 10.1038/s41591-023-02371-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Tumor-infiltrating T cells offer a promising avenue for cancer treatment, yet their states remain to be fully characterized. Here we present a single-cell atlas of T cells from 308,048 transcriptomes across 16 cancer types, uncovering previously undescribed T cell states and heterogeneous subpopulations of follicular helper, regulatory and proliferative T cells. We identified a unique stress response state, TSTR, characterized by heat shock gene expression. TSTR cells are detectable in situ in the tumor microenvironment across various cancer types, mostly within lymphocyte aggregates or potential tertiary lymphoid structures in tumor beds or surrounding tumor edges. T cell states/compositions correlated with genomic, pathological and clinical features in 375 patients from 23 cohorts, including 171 patients who received immune checkpoint blockade therapy. We also found significantly upregulated heat shock gene expression in intratumoral CD4/CD8+ cells following immune checkpoint blockade treatment, particularly in nonresponsive tumors, suggesting a potential role of TSTR cells in immunotherapy resistance. Our well-annotated T cell reference maps, web portal and automatic alignment/annotation tool could provide valuable resources for T cell therapy optimization and biomarker discovery.
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Affiliation(s)
- Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yating Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krupa Thakkar
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Jiang-Jiang Qin
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Can Hu
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pravesh Gupta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa P Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Hu
- Department of Human Genetics, Emory School of Medicine, Atlanta, GA, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Curran
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Xiang-Dong Cheng
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maura Gillison
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Michael Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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74
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Magen A, Hamon P, Fiaschi N, Soong BY, Park MD, Mattiuz R, Humblin E, Troncoso L, D'souza D, Dawson T, Kim J, Hamel S, Buckup M, Chang C, Tabachnikova A, Schwartz H, Malissen N, Lavin Y, Soares-Schanoski A, Giotti B, Hegde S, Ioannou G, Gonzalez-Kozlova E, Hennequin C, Le Berichel J, Zhao Z, Ward SC, Fiel I, Kou B, Dobosz M, Li L, Adler C, Ni M, Wei Y, Wang W, Atwal GS, Kundu K, Cygan KJ, Tsankov AM, Rahman A, Price C, Fernandez N, He J, Gupta NT, Kim-Schulze S, Gnjatic S, Kenigsberg E, Deering RP, Schwartz M, Marron TU, Thurston G, Kamphorst AO, Merad M. Intratumoral dendritic cell-CD4 + T helper cell niches enable CD8 + T cell differentiation following PD-1 blockade in hepatocellular carcinoma. Nat Med 2023; 29:1389-1399. [PMID: 37322116 PMCID: PMC11027932 DOI: 10.1038/s41591-023-02345-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Despite no apparent defects in T cell priming and recruitment to tumors, a large subset of T cell rich tumors fail to respond to immune checkpoint blockade (ICB). We leveraged a neoadjuvant anti-PD-1 trial in patients with hepatocellular carcinoma (HCC), as well as additional samples collected from patients treated off-label, to explore correlates of response to ICB within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+CH25H+IL-21+PD-1+CD4+ T helper cells ("CXCL13+ TH") and Granzyme K+ PD-1+ effector-like CD8+ T cells, whereas terminally exhausted CD39hiTOXhiPD-1hiCD8+ T cells dominated in nonresponders. CD4+ and CD8+ T cell clones that expanded post-treatment were found in pretreatment biopsies. Notably, PD-1+TCF-1+ (Progenitor-exhausted) CD8+ T cells shared clones mainly with effector-like cells in responders or terminally exhausted cells in nonresponders, suggesting that local CD8+ T cell differentiation occurs upon ICB. We found that these Progenitor CD8+ T cells interact with CXCL13+ TH within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ TH control the differentiation of tumor-specific Progenitor exhasuted CD8+ T cells following ICB.
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Affiliation(s)
- Assaf Magen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Hamon
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Fiaschi
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Brian Y Soong
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphaël Mattiuz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Etienne Humblin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanna Troncoso
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Darwin D'souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Kim
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Hamel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hara Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nausicaa Malissen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yonit Lavin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandra Soares-Schanoski
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samarth Hegde
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giorgio Ioannou
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Gonzalez-Kozlova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clotilde Hennequin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen C Ward
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Isabel Fiel
- The Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Baijun Kou
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Michael Dobosz
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Lianjie Li
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Christina Adler
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Min Ni
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Yi Wei
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Wei Wang
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Gurinder S Atwal
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kunal Kundu
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Kamil J Cygan
- VI NEXT, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Namita T Gupta
- Molecular Profiling & Data Science, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raquel P Deering
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Myron Schwartz
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Thomas U Marron
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gavin Thurston
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA.
| | - Alice O Kamphorst
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Institute for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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75
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Li C, Zhang L, Jin Q, Jiang H, Wu C. CD39 (ENTPD1) in tumors: a potential therapeutic target and prognostic biomarker. Biomark Med 2023; 17:563-576. [PMID: 37713234 DOI: 10.2217/bmm-2023-0202] [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] [Indexed: 09/16/2023] Open
Abstract
As a regulator of the dynamic balance between immune-activated extracellular ATP and immunosuppressive adenosine, CD39 ectonucleotidase impairs the ability of immune cells to exert anticancer immunity and plays an important role in the immune escape of tumor cells within the tumor microenvironment. In addition, CD39 has been studied in cancer patients to evaluate the prognosis, the efficacy of immunotherapy (e.g., PD-1 blockade) and the prediction of recurrence. This article reviews the importance of CD39 in tumor immunology, summarizes the preclinical evidence on targeting CD39 to treat tumors and focuses on the potential of CD39 as a biomarker to evaluate the prognosis and the response to immune checkpoint inhibitors in tumors.
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Affiliation(s)
- Cuicui Li
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, China
| | - Litian Zhang
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, China
| | - Qiqi Jin
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, China
| | - Haoyun Jiang
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, China
| | - Chongyang Wu
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou, 730000, China
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76
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Wischnewski V, Maas RR, Aruffo PG, Soukup K, Galletti G, Kornete M, Galland S, Fournier N, Lilja J, Wirapati P, Lourenco J, Scarpa A, Daniel RT, Hottinger AF, Brouland JP, Losurdo A, Voulaz E, Alloisio M, Hegi ME, Lugli E, Joyce JA. Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation. NATURE CANCER 2023; 4:908-924. [PMID: 37217652 PMCID: PMC10293012 DOI: 10.1038/s43018-023-00566-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
The immune-specialized environment of the healthy brain is tightly regulated to prevent excessive neuroinflammation. However, after cancer development, a tissue-specific conflict between brain-preserving immune suppression and tumor-directed immune activation may ensue. To interrogate potential roles of T cells in this process, we profiled these cells from individuals with primary or metastatic brain cancers via integrated analyses on the single-cell and bulk population levels. Our analysis revealed similarities and differences in T cell biology between individuals, with the most pronounced differences observed in a subgroup of individuals with brain metastasis, characterized by accumulation of CXCL13-expressing CD39+ potentially tumor-reactive T (pTRT) cells. In this subgroup, high pTRT cell abundance was comparable to that in primary lung cancer, whereas all other brain tumors had low levels, similar to primary breast cancer. These findings indicate that T cell-mediated tumor reactivity can occur in certain brain metastases and may inform stratification for treatment with immunotherapy.
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Grants
- Breast Cancer Research Foundation, Carigest Foundation, Fondation ISREC, Ludwig Institute for Cancer Research, and the University of Lausanne
- Erwin-Schrödinger Fellowship from the Austrian Science Fund (FWF, J4343-B28)
- Fondazione Italiana per la Ricerca sul Cancro-Associazione Italiana per la Ricerca sul Cancro (FIRC-AIRC)
- Fondation ISREC, CHUV Lausanne
- Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, and the University of Lausanne
- Associazione Italiana per la Ricerca sul Cancro (AIRC IG 20676 and AIRC 5x1000 UniCanVax 22757)
- Humanitas Clinical and Research Center
- CRI Lloyd J. Old STAR (CRI Award 3914), Associazione Italiana per la Ricerca sul Cancro (AIRC IG 20676 and AIRC 5x1000 UniCanVax 22757), Italian Ministry of Health (Agreement 82/2015).
- CHUV Lausanne
- Ludwig Institute for Cancer Research, and the University of Lausanne
- Fondation ISREC
- Breast Cancer Research Foundation
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Affiliation(s)
- Vladimir Wischnewski
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roeltje R Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Paola Guerrero Aruffo
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Mara Kornete
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Pratyaksha Wirapati
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joao Lourenco
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alice Scarpa
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Agnese Losurdo
- Oncology Department, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Emanuele Voulaz
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Marco Alloisio
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland.
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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77
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Lim J, Chin V, Fairfax K, Moutinho C, Suan D, Ji H, Powell JE. Transitioning single-cell genomics into the clinic. Nat Rev Genet 2023:10.1038/s41576-023-00613-w. [PMID: 37258725 DOI: 10.1038/s41576-023-00613-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
The use of genomics is firmly established in clinical practice, resulting in innovations across a wide range of disciplines such as genetic screening, rare disease diagnosis and molecularly guided therapy choice. This new field of genomic medicine has led to improvements in patient outcomes. However, most clinical applications of genomics rely on information generated from bulk approaches, which do not directly capture the genomic variation that underlies cellular heterogeneity. With the advent of single-cell technologies, research is rapidly uncovering how genomic data at cellular resolution can be used to understand disease pathology and mechanisms. Both DNA-based and RNA-based single-cell technologies have the potential to improve existing clinical applications and open new application spaces for genomics in clinical practice, with oncology, immunology and haematology poised for initial adoption. However, challenges in translating cellular genomics from research to a clinical setting must first be overcome.
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Affiliation(s)
- Jennifer Lim
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Oncology, St George Hospital, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Venessa Chin
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kirsten Fairfax
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Catia Moutinho
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dan Suan
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Westmead Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Hanlee Ji
- School of Medicine, Stanford University, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Joseph E Powell
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
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78
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Hui Z, Ren Y, Zhang D, Chen Y, Yu W, Cao J, Liu L, Wang T, Xiao S, Zheng L, Pu Y, Wei F, You J, Ren X. PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127 + and KLRG1 + CD8 T cells. NPJ Precis Oncol 2023; 7:48. [PMID: 37231145 DOI: 10.1038/s41698-023-00384-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
The combination of PD-1 blockade with neoadjuvant chemotherapy (NAC) has achieved unprecedented clinical success in non-small cell lung cancer (NSCLC) compared to NAC alone, but the underlying mechanisms by which PD-1 blockade augments the effects of chemotherapy remain incompletely elucidated. Single-cell RNA sequencing was performed on CD45+ immune cells isolated from surgically resected fresh tumors of seven NSCLC patients receiving NAC or neoadjuvant pembrolizumab and chemotherapy (NAPC). Multiplex fluorescent immunohistochemistry was performed on FFPE tissues before and after NAC or NAPC from 65 resectable NSCLC patients, and results were validated with GEO dataset. NAC resulted in an increase only of CD20+ B cells, whereas NAPC increased the infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells. Synergistic increase in B and T cells promotes favorable therapeutic response after NAPC. Spatial distribution analysis discovered that CD8+ T cells and their CD127+ and KLRG1+ subsets were in closer proximity to CD4+ T/CD20+ B cells in NAPC versus NAC. GEO dataset validated that B-cell, CD4, memory, and effector CD8 signatures correlated with therapeutic responses and clinical outcomes. The addition of PD-1 blockade to NAC promoted anti-tumor immunity through T and B cells recruitment in the tumor microenvironment and induced tumor-infiltrating CD8+ T cells skewed toward CD127+ and KLRG1+ phenotypes, which may be assisted by CD4+ T cells and B cells. Our comprehensive study identified key immune cell subsets exerting anti-tumor responses during PD-1 blockade therapy and that may be therapeutically targeted to improve upon existing immunotherapies for NSCLC.
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Affiliation(s)
- Zhenzhen Hui
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Yulin Ren
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Dong Zhang
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Yulong Chen
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Lung Cancer, Tianjin Lung Cancer Center, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Wenwen Yu
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Jie Cao
- Wake Forest University, Winston-Salem, NC, USA
| | - Liang Liu
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China
- Department of Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China
| | - Tao Wang
- Department of R&D, Hangzhou Repugene Technology Co., Ltd., Hangzhou, 311100, China
| | - Shanshan Xiao
- Department of R&D, Hangzhou Repugene Technology Co., Ltd., Hangzhou, 311100, China
| | - Liuqing Zheng
- Department of R&D, Hangzhou Repugene Technology Co., Ltd., Hangzhou, 311100, China
| | - Yue Pu
- Department of R&D, Hangzhou Repugene Technology Co., Ltd., Hangzhou, 311100, China
| | - Feng Wei
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China.
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China.
| | - Jian You
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China.
- Department of Lung Cancer, Tianjin Lung Cancer Center, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China.
| | - Xiubao Ren
- Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
- Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, 300060, China.
- Department of Biotherapy, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China.
- Department of Immunology, Tianjin Medical University Cancer Institute & Hospital, Tianjin, 300060, China.
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79
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Wen R, Zhou L, Peng Z, Fan H, Zhang T, Jia H, Gao X, Hao L, Lou Z, Cao F, Yu G, Zhang W. Single-cell sequencing technology in colorectal cancer: a new technology to disclose the tumor heterogeneity and target precise treatment. Front Immunol 2023; 14:1175343. [PMID: 37256123 PMCID: PMC10225552 DOI: 10.3389/fimmu.2023.1175343] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 06/01/2023] Open
Abstract
Colorectal Cancer (CRC) is one of the most common gastrointestinal tumors, and its high tumor heterogeneity makes traditional sequencing methods incapable of obtaining information about the heterogeneity of individual cancer cells in CRC. Therefore, single-cell sequencing technology can be applied to better analyze the differences in genetic and protein information between cells, to obtain genomic sequence information of single cells, and to more thoroughly analyze the cellular characteristics and interactions in the CRC microenvironment. This will provide a more comprehensive understanding of colorectal cancer development and metastasis and indicate the treatment plan and prognosis. In this study, we review the application of single-cell sequencing to analyze the tumor microenvironment of CRC, explore the mechanisms involved in CRC metastasis and progression, and provide a reference for potential treatment options.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fuao Cao
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
| | - Guanyu Yu
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
| | - Wei Zhang
- *Correspondence: Wei Zhang, ; Guanyu Yu, ; Fuao Cao,
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80
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Sievers C, Craveiro M, Friedman J, Robbins Y, Yang X, Bai K, Nguyen A, Redman JM, Chari R, Soon-Shiong P, Schlom J, Gulley J, Allen CT. Phenotypic plasticity and reduced tissue retention of exhausted tumor-infiltrating T cells following neoadjuvant immunotherapy in head and neck cancer. Cancer Cell 2023; 41:887-902.e5. [PMID: 37059104 PMCID: PMC10175181 DOI: 10.1016/j.ccell.2023.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 04/16/2023]
Abstract
Neoadjuvant immunotherapies (NITs) have led to clinical benefits in several cancers. Characterization of the molecular mechanisms underlying responses to NIT may lead to improved treatment strategies. Here we show that exhausted, tumor-infiltrating CD8+ T (Tex) cells display local and systemic responses to concurrent neoadjuvant TGF-β and PD-L1 blockade. NIT induces a significant and selective increase in circulating Tex cells associated with reduced intratumoral expression of the tissue-retention marker CD103. TGF-β-driven CD103 expression on CD8+ T cells is reversed following TGF-β neutralization in vitro, implicating TGF-β in T cell tissue retention and impaired systemic immunity. Transcriptional changes implicate T cell receptor signaling and glutamine metabolism as important determinants of enhanced or reduced Tex treatment response, respectively. Our analysis illustrates physiological and metabolic changes underlying T cell responses to NIT, highlighting the interplay between immunosuppression, tissue retention, and systemic anti-tumor immunity and suggest antagonism of T cell tissue retention as a promising neoadjuvant treatment strategy.
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Affiliation(s)
- Cem Sievers
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Marco Craveiro
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Friedman
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yvette Robbins
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xinping Yang
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ke Bai
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jason M Redman
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | | | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Gulley
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clint T Allen
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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81
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Abstract
Recent advances in cancer immunotherapy - ranging from immune-checkpoint blockade therapy to adoptive cellular therapy and vaccines - have revolutionized cancer treatment paradigms, yet the variability in clinical responses to these agents has motivated intense interest in understanding how the T cell landscape evolves with respect to response to immune intervention. Over the past decade, the advent of multidimensional single-cell technologies has provided the unprecedented ability to dissect the constellation of cell states of lymphocytes within a tumour microenvironment. In particular, the rapidly expanding capacity to definitively link intratumoural phenotypes with the antigen specificity of T cells provided by T cell receptors (TCRs) has now made it possible to focus on investigating the properties of T cells with tumour-specific reactivity. Moreover, the assessment of TCR clonality has enabled a molecular approach to track the trajectories, clonal dynamics and phenotypic changes of antitumour T cells over the course of immunotherapeutic intervention. Here, we review the current knowledge on the cellular states and antigen specificities of antitumour T cells and examine how fine characterization of T cell dynamics in patients has provided meaningful insights into the mechanisms underlying effective cancer immunotherapy. We highlight those T cell subsets associated with productive T cell responses and discuss how diverse immunotherapies might leverage the pre-existing tumour-reactive T cell pool or instruct de novo generation of antitumour specificities. Future studies aimed at elucidating the factors associated with the elicitation of productive antitumour T cell immunity are anticipated to instruct the design of more efficacious treatment strategies.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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82
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Wang D, Liu B, Zhang Z. Accelerating the understanding of cancer biology through the lens of genomics. Cell 2023; 186:1755-1771. [PMID: 37059071 DOI: 10.1016/j.cell.2023.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/11/2023] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
A core mission of cancer genomics is to comprehensively chart molecular underpinnings of cancer-driving events and to provide personalized therapeutic strategies. Primarily focused on cancer cells, cancer genomics studies have successfully uncovered many drivers for major cancer types. Since the emergence of cancer immune evasion as a critical cancer hallmark, the paradigm has been elevated to the holistic tumor ecosystem, with distinct cellular components and their functional states elucidated. We highlight the milestones of cancer genomics, depict the evolving path of the field, and discuss future directions in completing the understanding of the tumor ecosystem and in advancing therapeutic strategies.
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Affiliation(s)
- Dongfang Wang
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China
| | - Baolin Liu
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovative Center and School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing, China.
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83
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Chen JH, Nieman LT, Spurrell M, Jorgji V, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Raay KV, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee M, Korsunsky I, Mino-Kenudson M, Gainor JF, Hacohen N. Spatial analysis of human lung cancer reveals organized immune hubs enriched for stem-like CD8 T cells and associated with immunotherapy response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.04.535379. [PMID: 37066412 PMCID: PMC10104028 DOI: 10.1101/2023.04.04.535379] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially-localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens, and found that they were associated with beneficial responses to PD-1-blockade. Immunity hubs were enriched for many interferon-stimulated genes, T cells in multiple differentiation states, and CXCL9/10/11 + macrophages that preferentially interact with CD8 T cells. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcomes, distinct from mature tertiary lymphoid structures, and enriched for stem-like TCF7+PD-1+ CD8 T cells and activated CCR7 + LAMP3 + dendritic cells, as well as chemokines that organize these cells. These results elucidate the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
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84
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Sathe A, Ayala C, Bai X, Grimes SM, Lee B, Kin C, Shelton A, Poultsides G, Ji HP. GITR and TIGIT immunotherapy provokes divergent multi-cellular responses in the tumor microenvironment of gastrointestinal cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532299. [PMID: 36993756 PMCID: PMC10054933 DOI: 10.1101/2023.03.13.532299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Understanding the cellular mechanisms of novel immunotherapy agents in the human tumor microenvironment (TME) is critical to their clinical success. We examined GITR and TIGIT immunotherapy in gastric and colon cancer patients using ex vivo slice tumor slice cultures derived from cancer surgical resections. This primary culture system maintains the original TME in a near-native state. We applied paired single-cell RNA and TCR sequencing to identify cell type specific transcriptional reprogramming. The GITR agonist was limited to increasing effector gene expression only in cytotoxic CD8 T cells. The TIGIT antagonist increased TCR signaling and activated both cytotoxic and dysfunctional CD8 T cells, including clonotypes indicative of potential tumor antigen reactivity. The TIGIT antagonist also activated T follicular helper-like cells and dendritic cells, and reduced markers of immunosuppression in regulatory T cells. Overall, we identified cellular mechanisms of action of these two immunotherapy targets in the patients' TME.
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Affiliation(s)
- Anuja Sathe
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Carlos Ayala
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA, United States
| | - Xiangqi Bai
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Susan M. Grimes
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Byrne Lee
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA, United States
| | - Cindy Kin
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA, United States
| | - Andrew Shelton
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA, United States
| | - George Poultsides
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA, United States
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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85
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Wu Z, Yoshikawa T, Inoue S, Ito Y, Kasuya H, Nakashima T, Zhang H, Kotaka S, Hosoda W, Suzuki S, Kagoya Y. CD83 expression characterizes precursor exhausted T cell population. Commun Biol 2023; 6:258. [PMID: 36906640 PMCID: PMC10008643 DOI: 10.1038/s42003-023-04631-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023] Open
Abstract
T cell exhaustion is a main obstacle against effective cancer immunotherapy. Exhausted T cells include a subpopulation that maintains proliferative capacity, referred to as precursor exhausted T cells (TPEX). While functionally distinct and important for antitumor immunity, TPEX possess some overlapping phenotypic features with the other T-cell subsets within the heterogeneous tumor-infiltrating T-lymphocytes (TIL). Here we explore surface marker profiles unique to TPEX using the tumor models treated by chimeric antigen receptor (CAR)-engineered T cells. We find that CD83 is predominantly expressed in the CCR7+PD1+ intratumoral CAR-T cells compared with the CCR7-PD1+ (terminally differentiated) and CAR-negative (bystander) T cells. The CD83+CCR7+ CAR-T cells exhibit superior antigen-induced proliferation and IL-2 production compared with the CD83- T cells. Moreover, we confirm selective expression of CD83 in the CCR7+PD1+ T-cell population in primary TIL samples. Our findings identify CD83 as a marker to discriminate TPEX from terminally exhausted and bystander TIL.
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Affiliation(s)
- Zhiwen Wu
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Toshiaki Yoshikawa
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Inoue
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yusuke Ito
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Hitomi Kasuya
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takahiro Nakashima
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Haosong Zhang
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Saki Kotaka
- Department of Gynecologic Oncology, Aichi Cancer Center, Nagoya, Japan
| | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Shiro Suzuki
- Department of Gynecologic Oncology, Aichi Cancer Center, Nagoya, Japan
| | - Yuki Kagoya
- Division of Immune Response, Aichi Cancer Center Research Institute, Nagoya, Japan.
- Division of Cellular Oncology, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan.
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86
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van der Heide V, Humblin E, Vaidya A, Kamphorst AO. Advancing beyond the twists and turns of T cell exhaustion in cancer. Sci Transl Med 2022; 14:eabo4997. [PMID: 36350991 PMCID: PMC10000016 DOI: 10.1126/scitranslmed.abo4997] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Chronic antigen stimulation leads to T cell exhaustion. Nutrient restrictions and other suppressive factors in the tumor microenvironment further exacerbate T cell dysfunction. Better understanding of heterogeneity and dynamics of exhausted CD8 T cells will guide novel therapies that modulate T cell differentiation to achieve more effective antitumor responses.
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Affiliation(s)
- Verena van der Heide
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Etienne Humblin
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abishek Vaidya
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alice Oliffson Kamphorst
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, ISMMS, New York, NY 10029, USA.,Tisch Cancer Institute, ISMMS, New York, NY 10029, USA
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87
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Kaptein P, Thommen DS. Keeping track of the T cells that matter. NATURE CANCER 2022; 3:1015-1017. [PMID: 36138133 DOI: 10.1038/s43018-022-00432-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Paulien Kaptein
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniela S Thommen
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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