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Liu B, Hu S, Wang X. Applications of single-cell technologies in drug discovery for tumor treatment. iScience 2024; 27:110486. [PMID: 39171294 PMCID: PMC11338156 DOI: 10.1016/j.isci.2024.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
Single-cell technologies have been known as advanced and powerful tools to study tumor biological systems at the single-cell resolution and are playing increasingly critical roles in multiple stages of drug discovery and development. Specifically, single-cell technologies can promote the discovery of drug targets, help high-throughput screening at single-cell level, and contribute to pharmacokinetic studies of anti-tumor drugs. Emerging single-cell analysis technologies have been developed to further integrating multidimensional single-cell molecular features, expanding the scale of single-cell data, profiling phenotypic impact of genes in single cell, and providing full-length coverage single-cell sequencing. In this review, we systematically summarized the applications of single-cell technologies in various sections of drug discovery for tumor treatment, including target identification, high-throughput drug screening, and pharmacokinetic evaluation and highlighted emerging single-cell technologies in providing in-depth understanding of tumor biology. Single-cell-technology-based drug discovery is expected to further optimize therapeutic strategies and improve clinical outcomes of tumor patients.
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Affiliation(s)
- Bingyu Liu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
| | - Shunfeng Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, China
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
- Taishan Scholars Program of Shandong Province, Jinan, Shandong 250021, China
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2
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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3
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Oh K, Yoo YJ, Torre-Healy LA, Rao M, Fassler D, Wang P, Caponegro M, Gao M, Kim J, Sasson A, Georgakis G, Powers S, Moffitt RA. Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype. Nat Commun 2023; 14:5226. [PMID: 37633924 PMCID: PMC10460409 DOI: 10.1038/s41467-023-40895-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Bulk analyses of pancreatic ductal adenocarcinoma (PDAC) samples are complicated by the tumor microenvironment (TME), i.e. signals from fibroblasts, endocrine, exocrine, and immune cells. Despite this, we and others have established tumor and stroma subtypes with prognostic significance. However, understanding of underlying signals driving distinct immune and stromal landscapes is still incomplete. Here we integrate 92 single cell RNA-seq samples from seven independent studies to build a reproducible PDAC atlas with a focus on tumor-TME interdependence. Patients with activated stroma are synonymous with higher myofibroblastic and immunogenic fibroblasts, and furthermore show increased M2-like macrophages and regulatory T-cells. Contrastingly, patients with 'normal' stroma show M1-like recruitment, elevated effector and exhausted T-cells. To aid interoperability of future studies, we provide a pretrained cell type classifier and an atlas of subtype-based signaling factors that we also validate in mouse data. Ultimately, this work leverages the heterogeneity among single-cell studies to create a comprehensive view of the orchestra of signaling interactions governing PDAC.
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Affiliation(s)
- Ki Oh
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Yun Jae Yoo
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Luke A Torre-Healy
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Manisha Rao
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
| | - Danielle Fassler
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
| | - Pei Wang
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michael Caponegro
- Department of Pharmacology, Stony Brook University, Stony Brook, NY, USA
| | - Mei Gao
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Joseph Kim
- Department of Surgery, University of Kentucky and Markey Cancer Center, Lexington, KY, USA
| | - Aaron Sasson
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Georgios Georgakis
- Department of Surgery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Scott Powers
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA
| | - Richard A Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA.
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA.
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA.
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4
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Madaci L, Gard C, Nin S, Venton G, Rihet P, Puthier D, Loriod B, Costello R. The Contribution of Multiplexing Single Cell RNA Sequencing in Acute Myeloid Leukemia. Diseases 2023; 11:96. [PMID: 37489448 PMCID: PMC10366847 DOI: 10.3390/diseases11030096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
Decades ago, the treatment for acute myeloid leukemia relied on cytarabine and anthracycline. However, advancements in medical research have introduced targeted therapies, initially employing monoclonal antibodies such as ant-CD52 and anti-CD123, and subsequently utilizing specific inhibitors that target molecular mutations like anti-IDH1, IDH2, or FLT3. The challenge lies in determining the role of these therapeutic options, considering the inherent tumor heterogeneity associated with leukemia diagnosis and the clonal drift that this type of tumor can undergo. Targeted drugs necessitate an examination of various therapeutic targets at the individual cell level rather than assessing the entire population. It is crucial to differentiate between the prognostic value and therapeutic potential of a specific molecular target, depending on whether it is found in a terminally differentiated cell with limited proliferative potential or a stem cell with robust capabilities for both proliferation and self-renewal. However, this cell-by-cell analysis is accompanied by several challenges. Firstly, the scientific aspect poses difficulties in comparing different single cell analysis experiments despite efforts to standardize the results through various techniques. Secondly, there are practical obstacles as each individual cell experiment incurs significant financial costs and consumes a substantial amount of time. A viable solution lies in the ability to process multiple samples simultaneously, which is a distinctive feature of the cell hashing technique. In this study, we demonstrate the applicability of the cell hashing technique for analyzing acute myeloid leukemia cells. By comparing it to standard single cell analysis, we establish a strong correlation in various parameters such as quality control, gene expression, and the analysis of leukemic blast markers in patients. Consequently, this technique holds the potential to become an integral part of the biological assessment of acute myeloid leukemia, contributing to the personalized and optimized management of the disease, particularly in the context of employing targeted therapies.
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Affiliation(s)
- Lamia Madaci
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Charlyne Gard
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Sébastien Nin
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Geoffroy Venton
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
- Hematology and Cellular Therapy Department, Conception Hospital, 13005 Marseille, France
| | - Pascal Rihet
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Denis Puthier
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Béatrice Loriod
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Régis Costello
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
- Hematology and Cellular Therapy Department, Conception Hospital, 13005 Marseille, France
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5
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Phillips JD, Fay KA, Bergeron AJ, Zhang P, Mielcarz DW, Calkins AM, Searles TG, Christensen BC, Finley DJ, Turk MJ, Channon JY. The Effect of Lung Resection for NSCLC on Circulating Immune Cells: A Pilot Study. Curr Oncol 2023; 30:5116-5134. [PMID: 37232845 PMCID: PMC10217048 DOI: 10.3390/curroncol30050387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
This pilot study sought to evaluate the circulating levels of immune cells, particularly regulatory T-cell (Treg) subsets, before and after lung resection for non-small cell lung cancer. Twenty-five patients consented and had specimens collected. Initially, peripheral blood of 21 patients was collected for circulating immune cell studies. Two of these patients were excluded due to technical issues, leaving 19 patients for the analyses of circulating immune cells. Standard gating and high-dimensional unsupervised clustering flow cytometry analyses were performed. The blood, tumors and lymph nodes were analyzed via single-cell RNA and TCR sequencing for Treg analyses in a total of five patients (including four additional patients from the initial 21 patients). Standard gating flow cytometry revealed a transient increase in neutrophils immediately following surgery, with a variable neutrophil-lymphocyte ratio and a stable CD4-CD8 ratio. Unexpectedly, the total Treg and Treg subsets did not change with surgery with standard gating in short- or long-term follow-up. Similarly, unsupervised clustering of Tregs revealed a dominant cluster that was stable perioperatively and long-term. Two small FoxP3hi clusters slightly increased following surgery. In the longer-term follow-up, these small FoxP3hi Treg clusters were not identified, indicating that they were likely a response to surgery. Single-cell sequencing demonstrated six CD4+FoxP3+ clusters among the blood, tumors and lymph nodes. These clusters had a variable expression of FoxP3, and several were mainly, or only, present in tumor and lymph node tissue. As such, serial monitoring of circulating Tregs may be informative, but not completely reflective of the Tregs present in the tumor microenvironment.
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Affiliation(s)
- Joseph D. Phillips
- Department of Surgery, Dartmouth-Hitchcock Medical Center, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Kayla A. Fay
- Department of Surgery, Dartmouth-Hitchcock Medical Center, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Peisheng Zhang
- DartLab, Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | | | | | - Tyler G. Searles
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C. Christensen
- Departments of Epidemiology and Molecular & Systems Biology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J. Finley
- Department of Surgery, Dartmouth-Hitchcock Medical Center, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Mary Jo Turk
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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6
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Chi X, Luo S, Ye P, Hwang WL, Cha JH, Yan X, Yang WH. T-cell exhaustion and stemness in antitumor immunity: Characteristics, mechanisms, and implications. Front Immunol 2023; 14:1104771. [PMID: 36891319 PMCID: PMC9986432 DOI: 10.3389/fimmu.2023.1104771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
T cells play a crucial role in the regulation of immune response and are integral to the efficacy of cancer immunotherapy. Because immunotherapy has emerged as a promising treatment for cancer, increasing attention has been focused on the differentiation and function of T cells in immune response. In this review, we describe the research progress on T-cell exhaustion and stemness in the field of cancer immunotherapy and summarize advances in potential strategies to intervene and treat chronic infection and cancer by reversing T-cell exhaustion and maintaining and increasing T-cell stemness. Moreover, we discuss therapeutic strategies to overcome T-cell immunodeficiency in the tumor microenvironment and promote continuous breakthroughs in the anticancer activity of T cells.
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Affiliation(s)
- Xiaoxia Chi
- Affiliated Cancer Hospital & Institute and Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shahang Luo
- Affiliated Cancer Hospital & Institute and Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Peng Ye
- Department of Infectious Diseases, Guangzhou Panyu Central Hospital, Guangzhou, Guangdong, China
| | - Wei-Lun Hwang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jong-Ho Cha
- Department of Biomedical Science, College of Medicine, and Program in Biomedical Sciences and Engineering, Inha University, Incheon, Republic of Korea
| | - Xiuwen Yan
- Affiliated Cancer Hospital & Institute and Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wen-Hao Yang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
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7
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John J, Woolaver RA, Popolizio V, Chen SMY, Ge H, Krinsky AL, Vashisht M, Kramer Y, Chen Z, Wang JH. Divergent outcomes of anti-PD-L1 treatment coupled with host-intrinsic differences in TCR repertoire and distinct T cell activation states in responding versus non-responding tumors. Front Immunol 2022; 13:992630. [PMID: 36330507 PMCID: PMC9624473 DOI: 10.3389/fimmu.2022.992630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
Differential responses to immune checkpoint inhibitors (ICI) may be attributed to tumor-intrinsic factors or environmental cues; however, these mechanisms cannot fully explain the variable ICI responses in different individuals. Here, we investigate the potential contribution of immunological heterogeneity with a focus on differences in T-cell receptor (TCR) repertoire to ICI responses, which has not been defined previously. To reveal additional factors underlying heterogeneous responses to ICI, we employed a squamous cell carcinoma (SCC) mouse model in which tumor-bearing recipients unambiguously diverged into responders (R) or non-responders (NR) upon anti-PD-L1 treatment. Treatment efficacy absolutely required CD8 T-cells and correlated positively with effector functions of CD8 tumor-infiltrating lymphocytes (TILs). We showed that TCR repertoires exhibited a similar magnitude of clonal expansion in R vs. NR CD8 TILs. However, the top expanded TCR clonotypes appeared to be mutually exclusive between R and NR CD8 TILs, which also occurred in a recipient-specific manner, demonstrating preferential expansion of distinct TCR clonotypes against the same SCC tumor. Unexpectedly, R vs. NR CD8 TILs reached all activation clusters and did not exhibit substantial global differences in transcriptomes. By linking single-cell transcriptomic data with unique TCR clonotypes, CD8 TILs harboring top TCR clonotypes were found to occupy distinct activation clusters and upregulate genes favoring anti-tumor immunity to different extents in R vs. NR. We conclude that stochastic differences in CD8 TIL TCR repertoire and distinct activation states of top TCR clonotypes may contribute to differential anti-PD-L1 responses. Our study suggests that host-intrinsic immunological heterogeneity may offer a new explanation for differential ICI responses in different individuals, which could impact on strategies for personalized cancer immunotherapy.
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Affiliation(s)
- Jessy John
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rachel A. Woolaver
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, United States
| | - Vince Popolizio
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, United States
| | - Samantha M. Y. Chen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, United States
| | - Huaibin Ge
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Alexandra L. Krinsky
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, United States
| | - Monika Vashisht
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yonatan Kramer
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO, United States
| | - Zhangguo Chen
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jing H. Wang
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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8
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Li XY, Shen Y, Zhang L, Guo X, Wu J. Understanding initiation and progression of hepatocellular carcinoma through single cell sequencing. Biochim Biophys Acta Rev Cancer 2022; 1877:188720. [PMID: 35304295 DOI: 10.1016/j.bbcan.2022.188720] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Unsatisfied clinical outcome drives to better understand hepatic carcinogenesis, microenvironment and escape of immune surveillance in hepatocellular carcinoma (HCC). Single cell RNA sequencing (scRNA-Seq) has generated enormous data to pinpoint pathophysiologic alterations in tumor microenvironment (TME) or trace lineage development in cancer stem cells (CSCs), circulating tumor cells (CTCs), and subsets of immune cells, such as exhausting T cells, tumor-associated macrophages (TAMs), dendritic cells or other lineages. New insights have significantly advanced current understanding in progression, poor responses to molecular-targeted therapeutics or immune checkpoint inhibitors, metastasis in both basic research and clinical practice. The present review intends to cover a basic workflow of the scRNA-seq technology, existing limitations and improvement areas. Moreover, in-depth understanding in TME, exhausting T cells, CSCs, CTCs, tumor-associated macrophages, dendritic cells in HCC facilitates implementation of personalized and precise therapy in an era of availability with an array of systemic regimens.
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Affiliation(s)
- Xin-Yue Li
- Dept. of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Yue Shen
- Dept. of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, China
| | - Li Zhang
- Dept. of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China
| | - Xiao Guo
- Dept. of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China; Pathogenic Research Core Facility, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jian Wu
- Dept. of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China; Dept. of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, China; Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai 200032, China.
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9
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Hirschhorn D, Betof Warner A, Maniyar R, Chow A, Mangarin LM, Cohen AD, Hamadene L, Rizzuto GA, Budhu S, Suek N, Liu C, Houghton AN, Merghoub T, Wolchok JD. Cyclophosphamide enhances the antitumor potency of GITR engagement by increasing oligoclonal cytotoxic T cell fitness. JCI Insight 2021; 6:151035. [PMID: 34676831 PMCID: PMC8564916 DOI: 10.1172/jci.insight.151035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023] Open
Abstract
Only a subset of cancer patients responds to checkpoint blockade inhibition in the clinic. Strategies to overcome resistance are promising areas of investigation. Targeting glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) has shown efficacy in preclinical models, but GITR engagement is ineffective in controlling advanced, poorly immunogenic tumors, such as B16 melanoma, and has not yielded benefit in clinical trials. The alkylating agent cyclophosphamide (CTX) depletes regulatory T cells (Tregs), expands tumor-specific effector T cells (Teffs) via homeostatic proliferation, and induces immunogenic cell death. GITR agonism has an inhibitory effect on Tregs and activates Teffs. We therefore hypothesized that CTX and GITR agonism would promote effective antitumor immunity. Here we show that the combination of CTX and GITR agonism controlled tumor growth in clinically relevant mouse models. Mechanistically, we show that the combination therapy caused tumor cell death, clonal expansion of highly active CD8+ T cells, and depletion of Tregs by activation-induced cell death. Control of tumor growth was associated with the presence of an expanded population of highly activated, tumor-infiltrating, oligoclonal CD8+ T cells that led to a diminished TCR repertoire. Our studies show that the combination of CTX and GITR agonism is a rational chemoimmunotherapeutic approach that warrants further clinical investigation.
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Affiliation(s)
- Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Allison Betof Warner
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Rachana Maniyar
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Levi Mb Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Adam D Cohen
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and
| | - Linda Hamadene
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Gabrielle A Rizzuto
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Nathan Suek
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Cailian Liu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Alan N Houghton
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Jedd D Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
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10
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Foroutan M, Molania R, Pfefferle A, Behrenbruch C, Scheer S, Kallies A, Speed TP, Cursons J, Huntington ND. The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome. Cancer Immunol Res 2021; 9:1125-1140. [PMID: 34413087 DOI: 10.1158/2326-6066.cir-21-0137] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/14/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
Immunotherapy success in colorectal cancer is mainly limited to patients whose tumors exhibit high microsatellite instability (MSI). However, there is variability in treatment outcomes within this group, which is in part driven by the frequency and characteristics of tumor-infiltrating immune cells. Indeed, the presence of specific infiltrating immune-cell subsets has been shown to correlate with immunotherapy response and is in many cases prognostic of treatment outcome. Tumor-infiltrating lymphocytes (TIL) can undergo distinct differentiation programs, acquiring features of tissue-residency or exhaustion, a process during which T cells upregulate inhibitory receptors, such as PD-1, and lose functionality. Although residency and exhaustion programs of CD8+ T cells are relatively well studied, these programs have only recently been appreciated in CD4+ T cells and remain largely unknown in tumor-infiltrating natural killer (NK) cells. In this study, we used single-cell RNA sequencing (RNA-seq) data to identify signatures of residency and exhaustion in colorectal cancer-infiltrating lymphocytes, including CD8+, CD4+, and NK cells. We then tested these signatures in independent single-cell data from tumor and normal tissue-infiltrating immune cells. Furthermore, we used versions of these signatures designed for bulk RNA-seq data to explore tumor-intrinsic mutations associated with residency and exhaustion from TCGA data. Finally, using two independent transcriptomic datasets from patients with colon adenocarcinoma, we showed that combinations of these signatures, in particular combinations of NK-cell activity signatures, together with tumor-associated signatures, such as TGFβ signaling, were associated with distinct survival outcomes in patients with colon adenocarcinoma.
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Affiliation(s)
- Momeneh Foroutan
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
| | - Ramyar Molania
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Aline Pfefferle
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,oNKo-innate Pty Ltd., Moonee Ponds, Victoria, Australia
| | - Corina Behrenbruch
- University of Melbourne Centre for Cancer Research, Parkville, Victoria, Australia
| | - Sebastian Scheer
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Terence P Speed
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,School of Mathematics & Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Joseph Cursons
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. .,oNKo-innate Pty Ltd., Moonee Ponds, Victoria, Australia
| | - Nicholas D Huntington
- Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. .,oNKo-innate Pty Ltd., Moonee Ponds, Victoria, Australia
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11
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Sun G, Li Z, Rong D, Zhang H, Shi X, Yang W, Zheng W, Sun G, Wu F, Cao H, Tang W, Sun Y. Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges. Mol Ther Oncolytics 2021; 21:183-206. [PMID: 34027052 PMCID: PMC8131398 DOI: 10.1016/j.omto.2021.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.
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Affiliation(s)
- Guangshun Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig Maximilians University, Munich, Germany
| | - Dawei Rong
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Hao Zhang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xuesong Shi
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weijun Yang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Yangbai Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
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12
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Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, Yu X, Shi S. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol 2021; 14:91. [PMID: 34108022 PMCID: PMC8190846 DOI: 10.1186/s13045-021-01105-2] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Single-cell sequencing, including genomics, transcriptomics, epigenomics, proteomics and metabolomics sequencing, is a powerful tool to decipher the cellular and molecular landscape at a single-cell resolution, unlike bulk sequencing, which provides averaged data. The use of single-cell sequencing in cancer research has revolutionized our understanding of the biological characteristics and dynamics within cancer lesions. In this review, we summarize emerging single-cell sequencing technologies and recent cancer research progress obtained by single-cell sequencing, including information related to the landscapes of malignant cells and immune cells, tumor heterogeneity, circulating tumor cells and the underlying mechanisms of tumor biological behaviors. Overall, the prospects of single-cell sequencing in facilitating diagnosis, targeted therapy and prognostic prediction among a spectrum of tumors are bright. In the near future, advances in single-cell sequencing will undoubtedly improve our understanding of the biological characteristics of tumors and highlight potential precise therapeutic targets for patients.
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Affiliation(s)
- Yalan Lei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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13
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Chen P, Zhou L, Chen J, Lu Y, Cao C, Lv S, Wei Z, Wang L, Chen J, Hu X, Wu Z, Zhou X, Su D, Deng X, Zeng C, Wang H, Pu Z, Diao R, Mou L. The Immune Atlas of Human Deciduas With Unexplained Recurrent Pregnancy Loss. Front Immunol 2021; 12:689019. [PMID: 34168655 PMCID: PMC8218877 DOI: 10.3389/fimmu.2021.689019] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 02/05/2023] Open
Abstract
Recurrent pregnancy loss (RPL) is a common fertility problem that affects 1%-2% of couples all over the world. Despite exciting discoveries regarding the important roles of the decidual natural killer cell (dNK) and regulatory T cell in pregnancy, the immune heterogeneity in patients with unexplained recurrent pregnancy loss (URPL) remains elusive. Here, we profiled the transcriptomes of 13,953 CD45+ cells from three normal and three URPL deciduas. Based on our data, the cellular composition revealed three major populations of immune cells including dNK cell, T cell, and macrophage, and four minor populations including monocytes, dendritic cell (DC), mast cell, and B cell. Especially, we identified a subpopulation of CSF1+ CD59+ KIRs-expressing dNK cells in normal deciduas, while the proportion of this subpopulation was decreased in URPL deciduas. We also identified a small subpopulation of activated dDCs that were accumulated mainly in URPL deciduas. Furthermore, our data revealed that in decidua at early pregnancy, CD8+ T cells exhibited cytotoxic properties. The decidual macrophages expressed high levels of both M1 and M2 feature genes, which made them unique to the conventional M1/M2 classification. Our single-cell data revealed the immune heterogeneity in decidua and the potentially pathogenic immune variations in URPL.
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Affiliation(s)
- Pengfei Chen
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Shenzhen, China.,Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Liying Zhou
- Department of Gynaecology, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Jiying Chen
- Department of Gynaecology, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Ying Lu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Chaoxia Cao
- Department of Gynaecology, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Shuangli Lv
- Department of Gynaecology, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Zhihong Wei
- Department of Gynaecology, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.,Department of Gynaecology, Shenzhen Baoan People's Hospital (Group), Shenzhen, China
| | - Liping Wang
- Centre of Reproductive Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jiao Chen
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Xinglin Hu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Zijing Wu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Xiaohua Zhou
- Department of Gynaecology, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Danna Su
- Centre of Reproductive Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Xuefeng Deng
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Changchun Zeng
- Department of Traumatic Orthopedics, Shenzhen Longhua District Central Hospital, Shenzhen, China
| | - Huiyun Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zuhui Pu
- Department of Radiology, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Ruiying Diao
- Centre of Reproductive Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center, Institute of Translational Medicine, First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
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14
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Klopfenstein Q, Derangère V, Arnould L, Thibaudin M, Limagne E, Ghiringhelli F, Truntzer C, Ladoire S. Evaluation of tumor immune contexture among intrinsic molecular subtypes helps to predict outcome in early breast cancer. J Immunother Cancer 2021; 9:jitc-2020-002036. [PMID: 34083415 PMCID: PMC8183202 DOI: 10.1136/jitc-2020-002036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 11/09/2022] Open
Abstract
Background The prognosis of early breast cancer is linked to clinic-pathological stage and the molecular characteristics of intrinsic tumor cells. In some patients, the amount and quality of tumor-infiltrating immune cells appear to affect long term outcome. We aimed to propose a new tool to estimate immune infiltrate, and link these factors to patient prognosis according to breast cancer molecular subtypes. Methods We performed in silico analyses in more than 2800 early breast cancer transcriptomes with corresponding clinical annotations. We first developed a new gene expression deconvolution algorithm that accurately estimates the quantity of immune cell populations (tumor immune contexture, TIC) in tumors. Then, we studied associations between these immune profiles and relapse-free and overall survival among the different intrinsic molecular subtypes of breast cancer defined by PAM50 classification. Results TIC estimates the abundance of 15 immune cell subsets. Both myeloid and lymphoid subpopulations show different spread among intrinsic molecular breast cancer subtypes. A high abundance of myeloid cells was associated with poor outcome, while lymphoid cells were associated with favorable prognosis. Unsupervised clustering describing the 15 immune cell subsets revealed four subgroups of breast tumors associated with distinct patient survival, but independent from PAM50. Adding this information to clinical stage and PAM50 strongly improves the prediction of relapse or death. Conclusions Our findings make it possible to refine the survival stratification of early patients with breast cancer by incorporating TIC in addition to PAM50 and clinical tumor burden in a prognostic model validated in training and validation cohorts.
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Affiliation(s)
- Quentin Klopfenstein
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France
| | - Valentin Derangère
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France.,Unit of Pathology, Department of Biology and Pathology of the Tumors, Centre Georges François Leclerc, Dijon, France
| | - Laurent Arnould
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,Unit of Pathology, Department of Biology and Pathology of the Tumors, Centre Georges François Leclerc, Dijon, France
| | - Marion Thibaudin
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France
| | - Emeric Limagne
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France
| | - Francois Ghiringhelli
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France.,Department of Medical Oncology, Centre Georges François Leclerc, Dijon, France
| | - Caroline Truntzer
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France.,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France
| | - Sylvain Ladoire
- Transfer Biology Cancer Platform, Centre Georges-Francois Leclerc, Dijon, France .,GIMI: Genetic and Immunology Medical Institute, Dijon, France, Dijon, France.,University of Burgundy-Franche Comté, France, Dijon, France.,UMR INSERM U1231, Univ Burgundy Franche Comte, Dijon, France.,Department of Medical Oncology, Centre Georges François Leclerc, Dijon, France
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15
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Bhatt D, Kang B, Sawant D, Zheng L, Perez K, Huang Z, Sekirov L, Wolak D, Huang JY, Liu X, DeVoss J, Manzanillo PS, Pierce N, Zhang Z, Symons A, Ouyang W. STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets. J Exp Med 2021; 218:212026. [PMID: 33900375 PMCID: PMC8077174 DOI: 10.1084/jem.20201329] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/18/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/β sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti–PD-1 treatment in MC38 and B16F10 tumor models.
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Affiliation(s)
- Dev Bhatt
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Boxi Kang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Deepali Sawant
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Liangtao Zheng
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Kristy Perez
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Zhiyu Huang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Laura Sekirov
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Dan Wolak
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Julie Y Huang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Xian Liu
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Jason DeVoss
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Paolo S Manzanillo
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Nathan Pierce
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Zemin Zhang
- Beijing Advanced Innovation Centre for Genomics, Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing, China
| | - Antony Symons
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
| | - Wenjun Ouyang
- Department of Inflammation and Oncology, Amgen Research, Amgen, South San Francisco, CA
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16
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Woolaver RA, Wang X, Krinsky AL, Waschke BC, Chen SMY, Popolizio V, Nicklawsky AG, Gao D, Chen Z, Jimeno A, Wang XJ, Wang JH. Differences in TCR repertoire and T cell activation underlie the divergent outcomes of antitumor immune responses in tumor-eradicating versus tumor-progressing hosts. J Immunother Cancer 2021; 9:jitc-2020-001615. [PMID: 33414263 PMCID: PMC7797305 DOI: 10.1136/jitc-2020-001615] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Background Antitumor immunity is highly heterogeneous between individuals; however, underlying mechanisms remain elusive, despite their potential to improve personalized cancer immunotherapy. Head and neck squamous cell carcinomas (HNSCCs) vary significantly in immune infiltration and therapeutic responses between patients, demanding a mouse model with appropriate heterogeneity to investigate mechanistic differences. Methods We developed a unique HNSCC mouse model to investigate underlying mechanisms of heterogeneous antitumor immunity. This model system may provide a better control for tumor-intrinsic and host-genetic variables, thereby uncovering the contribution of the adaptive immunity to tumor eradication. We employed single-cell T-cell receptor (TCR) sequencing coupled with single-cell RNA sequencing to identify the difference in TCR repertoire of CD8 tumor-infiltrating lymphocytes (TILs) and the unique activation states linked with different TCR clonotypes. Results We discovered that genetically identical wild-type recipient mice responded heterogeneously to the same squamous cell carcinoma tumors orthotopically transplanted into the buccal mucosa. While tumors initially grew in 100% of recipients and most developed aggressive tumors, ~25% of recipients reproducibly eradicated tumors without intervention. Heterogeneous antitumor responses were dependent on CD8 T cells. Consistently, CD8 TILs in regressing tumors were significantly increased and more activated. Single-cell TCR-sequencing revealed that CD8 TILs from both growing and regressing tumors displayed evidence of clonal expansion compared with splenic controls. However, top TCR clonotypes and TCR specificity groups appear to be mutually exclusive between regressing and growing TILs. Furthermore, many TCRα/TCRβ sequences only occur in one recipient. By coupling single-cell transcriptomic analysis with unique TCR clonotypes, we found that top TCR clonotypes clustered in distinct activation states in regressing versus growing TILs. Intriguingly, the few TCR clonotypes shared between regressors and progressors differed greatly in their activation states, suggesting a more dominant influence from tumor microenvironment than TCR itself on T cell activation status. Conclusions We reveal that intrinsic differences in the TCR repertoire of TILs and their different transcriptional trajectories may underlie the heterogeneous antitumor immune responses in different hosts. We suggest that antitumor immune responses are highly individualized and different hosts employ different TCR specificities against the same tumors, which may have important implications for developing personalized cancer immunotherapy.
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Affiliation(s)
- Rachel A Woolaver
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Xiaoguang Wang
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexandra L Krinsky
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Brittany C Waschke
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Samantha M Y Chen
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Vince Popolizio
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Andrew G Nicklawsky
- Pediatrics, Biostatistics and Informatics, Cancer Center Biostatistics Core, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dexiang Gao
- Pediatrics, Biostatistics and Informatics, Cancer Center Biostatistics Core, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Zhangguo Chen
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Antonio Jimeno
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Xiao-Jing Wang
- Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jing Hong Wang
- Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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17
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Ferrarini I, Rigo A, Visco C, Krampera M, Vinante F. The Evolving Knowledge on T and NK Cells in Classic Hodgkin Lymphoma: Insights into Novel Subsets Populating the Immune Microenvironment. Cancers (Basel) 2020; 12:cancers12123757. [PMID: 33327433 PMCID: PMC7764890 DOI: 10.3390/cancers12123757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 12/24/2022] Open
Abstract
Simple Summary In classic Hodgkin lymphoma, T and NK cells constitute a significant fraction of the reactive microenvironment established by malignant Hodgkin Reed–Sternberg cells. Despite their abundance, T and NK cells remain largely ineffective because of two coordinated levels of immune evasion. The first is based on the acquisition of regulatory properties or exhausted phenotypes that cripple their antitumor activity. The second is represented by their peculiar spatial distribution, with the most immunosuppressive subpopulations lying in close proximity of neoplastic cells. Recent discoveries about the functional role and the spatial orientation of T and NK cells in classic Hodgkin lymphoma are the focus of this review. Abstract Classic Hodgkin lymphoma (cHL) is a unique lymphoid neoplasm characterized by extensive immune infiltrates surrounding rare malignant Hodgkin Reed–Sternberg (HRS) cells. Different subsets of T and NK cells have long been recognized in the cHL microenvironment, yet their distinct contribution to disease pathogenesis has remained enigmatic. Very recently, novel platforms for high dimensional analysis of immune cells, such as single-cell RNA sequencing and mass cytometry, have revealed unanticipated insights into the composition of T- and NK-cell compartments in cHL. Advances in imaging techniques have better defined specific T-helper subpopulations physically interacting with neoplastic cells. In addition, the identification of novel cytotoxic subsets with an exhausted phenotype, typically enriched in cHL milieu, is shedding light on previously unrecognized immune evasion mechanisms. This review examines the immunological features and the functional properties of T and NK subsets recently identified in the cHL microenvironment, highlighting their pathological interplay with HRS cells. We also discuss how this knowledge can be exploited to predict response to immunotherapy and to design novel strategies to improve PD-1 blockade efficacy.
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Affiliation(s)
- Isacco Ferrarini
- Section of Hematology, Department of Medicine, University of Verona, 37134 Verona, Italy; (A.R.); (C.V.); (M.K.); (F.V.)
- Cancer Research and Cell Biology Laboratory, Department of Medicine, University of Verona, 37134 Verona, Italy
- Correspondence: ; Tel.: +39-045-812-8411
| | - Antonella Rigo
- Section of Hematology, Department of Medicine, University of Verona, 37134 Verona, Italy; (A.R.); (C.V.); (M.K.); (F.V.)
- Cancer Research and Cell Biology Laboratory, Department of Medicine, University of Verona, 37134 Verona, Italy
| | - Carlo Visco
- Section of Hematology, Department of Medicine, University of Verona, 37134 Verona, Italy; (A.R.); (C.V.); (M.K.); (F.V.)
| | - Mauro Krampera
- Section of Hematology, Department of Medicine, University of Verona, 37134 Verona, Italy; (A.R.); (C.V.); (M.K.); (F.V.)
| | - Fabrizio Vinante
- Section of Hematology, Department of Medicine, University of Verona, 37134 Verona, Italy; (A.R.); (C.V.); (M.K.); (F.V.)
- Cancer Research and Cell Biology Laboratory, Department of Medicine, University of Verona, 37134 Verona, Italy
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18
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Yu X, Zhang L, Chaudhry A, Rapaport AS, Ouyang W. Unravelling the heterogeneity and dynamic relationships of tumor-infiltrating T cells by single-cell RNA sequencing analysis. J Leukoc Biol 2020; 107:917-932. [PMID: 32272497 PMCID: PMC7317876 DOI: 10.1002/jlb.6mr0320-234r] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
T cells are crucial for the success of immune-based cancer therapy. Reinvigorating antitumor T cell activity by blocking checkpoint inhibitory receptors has provided clinical benefits for many cancer patients. However, the efficacy of these treatments varies in cancer patients and the mechanisms underlying these diverse responses remain elusive. The density and status of tumor-infiltrating T cells have been shown to positively correlate with patient response to checkpoint blockades. Therefore, further understanding of the heterogeneity, clonal expansion, migration, and effector functions of tumor-infiltrating T cells will provide fundamental insights into antitumor immune responses. To this end, recent advances in single-cell RNA sequencing technology have enabled profound and extensive characterization of intratumoral immune cells and have improved our understanding of their dynamic relationships. Here, we summarize recent progress in single-cell RNA sequencing technology and current strategies to uncover heterogeneous tumor-infiltrating T cell subsets. In particular, we discuss how the coupling of deep transcriptome information with T cell receptor (TCR)-based lineage tracing has furthered our understanding of intratumoral T cell populations. We also discuss the functional implications of various T cell subsets in tumors and highlight the identification of novel T cell markers with therapeutic or prognostic potential.
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Affiliation(s)
- Xin Yu
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Lei Zhang
- Beijing Advanced Innovation Center for GenomicsPeking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Ashutosh Chaudhry
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Aaron S. Rapaport
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
| | - Wenjun Ouyang
- Department of Inflammation and OncologyAmgen Research, Amgen Inc.South San FranciscoCaliforniaUSA
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