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Yin Y, Wang Y, Yu X, Li Y, Zhao Y, Liu Z. Overactivation of XBP1 in plasma cells implies worse survival through innate immunity in esophageal squamous cell carcinoma. Cancer Lett 2024:217045. [PMID: 38871246 DOI: 10.1016/j.canlet.2024.217045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
To maintain protein homeostasis, X-box binding protein 1 (XBP1) undergoes splicing following the activation of the unfolded protein response (UPR) in response to endoplasmic reticulum (ER) stress. Although targeting ER stress represents a promising therapeutic strategy, a comprehensive understanding of XBP1 at the cellular level and the link between XBP1 and the innate nervous system is lacking. Here, TCGA pancancer datasets from 33 cancer types, scRNA pancancer datasets from 454 patients and bulk RNA-seq datasets from 155 paired esophageal squamous cell carcinoma (ESCC) patients were analyzed. To cope with ER stress, plasma cells tend to activate XBP1 after undergoing bacterial infection and inflammatory signaling from the innate immune system. Patients with high XBP1 expression in their plasma cells have a higher tumor grade and worse survival. However, activation of the innate immune system with increased XBP1 expression in plasma cells correlates with an increased lymphocyte ratio, indicative of a more robust immune response. Moreover, XBP1 activation appears to initiate leukocyte migration at the transcriptional level. Our study revealed that the XBP1-induced UPR could mediate the crosstalk between optimal acquired humoral immune responses and innate immunity in ESCC.
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Affiliation(s)
- Yin Yin
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuhao Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiao Yu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yang Li
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yahui Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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2
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Nguyen H, Nguyen H, Tran D, Draghici S, Nguyen T. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges. Nucleic Acids Res 2024; 52:4761-4783. [PMID: 38619038 PMCID: PMC11109966 DOI: 10.1093/nar/gkae267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).
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Affiliation(s)
- Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Ha Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Duc Tran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
- Advaita Bioinformatics, Ann Arbor, MI, USA
| | - Tin Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
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3
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Xu L, Saunders K, Huang SP, Knutsdottir H, Martinez-Algarin K, Terrazas I, Chen K, McArthur HM, Maués J, Hodgdon C, Reddy SM, Roussos Torres ET, Xu L, Chan IS. A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response. Cell Rep Med 2024; 5:101511. [PMID: 38614094 PMCID: PMC11148512 DOI: 10.1016/j.xcrm.2024.101511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/20/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage this resource for multiple analyses of immune and cancer epithelial cell heterogeneity. We define natural killer (NK) cell heterogeneity through six subsets in the breast TME. Because NK cell heterogeneity correlates with epithelial cell heterogeneity, we characterize epithelial cells at the level of single-gene expression, molecular subtype, and 10 categories reflecting intratumoral transcriptional heterogeneity. We develop InteractPrint, which considers how cancer epithelial cell heterogeneity influences cancer-immune interactions. We use T cell InteractPrint to predict response to immune checkpoint inhibition (ICI) in two breast cancer clinical trials testing neoadjuvant anti-PD-1 therapy. T cell InteractPrint was predictive of response in both trials versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This resource enables additional high-resolution investigations of the breast TME.
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Affiliation(s)
- Lily Xu
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kaitlyn Saunders
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shao-Po Huang
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Kenneth Martinez-Algarin
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isabella Terrazas
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Heather M McArthur
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | | | - Sangeetha M Reddy
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Evanthia T Roussos Torres
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isaac S Chan
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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4
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Zhou J, Chng WJ. Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing. Front Oncol 2024; 14:1365330. [PMID: 38711849 PMCID: PMC11070491 DOI: 10.3389/fonc.2024.1365330] [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: 01/04/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence of diverse and functionally distinct populations of leukemia cells within the same patient's bone marrow or blood poses a significant challenge in diagnosing and treating AML. A substantial proportion of AML patients demonstrate resistance to induction chemotherapy and a grim prognosis upon relapse. The rapid advance in next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding of AML pathogenesis by enabling high-resolution interrogation of the cellular heterogeneity in the AML ecosystem, and their transcriptional signatures at a single-cell level. New studies have successfully characterized the inextricably intertwined interactions among AML cells, immune cells and bone marrow microenvironment and their contributions to the AML development, therapeutic resistance and relapse. These findings have deepened and broadened our understanding the complexity and heterogeneity of AML, which are difficult to detect with bulk RNA-seq. This review encapsulates the burgeoning body of knowledge generated through scRNA-seq, providing the novel insights and discoveries it has unveiled in AML biology. Furthermore, we discuss the potential implications of scRNA-seq in therapeutic opportunities, focusing on immunotherapy. Finally, we highlight the current limitations and future direction of scRNA-seq in the field.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Singapore
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5
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Tian J, Bai X, Quek C. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy. Int J Mol Sci 2024; 25:4485. [PMID: 38674070 PMCID: PMC11050520 DOI: 10.3390/ijms25084485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.
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Affiliation(s)
| | | | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.T.); (X.B.)
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6
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Su Y, Yu Z, Yang Y, Wong KC, Li X. Distribution-Agnostic Deep Learning Enables Accurate Single-Cell Data Recovery and Transcriptional Regulation Interpretation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307280. [PMID: 38380499 DOI: 10.1002/advs.202307280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/16/2024] [Indexed: 02/22/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a robust method for studying gene expression at the single-cell level, but accurately quantifying genetic material is often hindered by limited mRNA capture, resulting in many missing expression values. Existing imputation methods rely on strict data assumptions, limiting their broader application, and lack reliable supervision, leading to biased signal recovery. To address these challenges, authors developed Bis, a distribution-agnostic deep learning model for accurately recovering missing sing-cell gene expression from multiple platforms. Bis is an optimal transport-based autoencoder model that can capture the intricate distribution of scRNA-seq data while addressing the characteristic sparsity by regularizing the cellular embedding space. Additionally, they propose a module using bulk RNA-seq data to guide reconstruction and ensure expression consistency. Experimental results show Bis outperforms other models across simulated and real datasets, showcasing superiority in various downstream analyses including batch effect removal, clustering, differential expression analysis, and trajectory inference. Moreover, Bis successfully restores gene expression levels in rare cell subsets in a tumor-matched peripheral blood dataset, revealing developmental characteristics of cytokine-induced natural killer cells within a head and neck squamous cell carcinoma microenvironment.
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Affiliation(s)
- Yanchi Su
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Zhuohan Yu
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Changchun, 130012, China
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7
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Liu W, Zhu M, Li G, Xi Y. The KIR2DL family serves as prognostic biomarkers and correlates with immune infiltrates in acute myeloid leukaemia. J Cell Mol Med 2024; 28:e18256. [PMID: 38527290 PMCID: PMC10963068 DOI: 10.1111/jcmm.18256] [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: 04/01/2023] [Revised: 02/16/2024] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
Acute myeloid leukaemia (AML) is a prevalent haematological malignancy in which various immune and stromal cells in the bone marrow microenvironment have instrumental roles and substantially influence its progression. KIR2DL is a member of the immunoglobulin-like receptor family and a natural killer (NK) cell surface-specific receptor. However, its impact on immune infiltration regarding AML has not been addressed. We aimed to explore molecular markers associated with the immune microenvironment and prognosis of AML with a particular focus on KIR2DL family members. Analysis of data from The Cancer Genome Atlas and Genotype-Tissue Expression databases revealed that KIR2DL1, KIR2DL3 and KIR2DL4 expression were significantly upregulated in AML and associated with decreased overall survival (OS). Moreover, univariate Cox analysis implicated KIR2DL genes as independent prognostic markers of OS. Functional enrichment analysis revealed that KIR2DL genes were associated with immune cells, the immune microenvironment and NK cell-mediated cytotoxicity. Additionally, immune infiltration analyses revealed that KIR2DL upregulation was associated with stronger immune infiltration. Finally, we performed drug sensitivity profiling of KIR2DL genes using the Cellminer database. Collectively, our findings suggest that KIR2DL1, KIR2DL3 and KIR2DL4 have critical roles in AML and may represent novel biomarker genes for disease prognosis and immune infiltration.
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Affiliation(s)
- Wenling Liu
- The First Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Mingming Zhu
- Affiliated Hospital of Qinghai UniversityXiningChina
| | - Ganggang Li
- The Fifth People's Hospital of Qinghai ProvinceXiningChina
| | - Yaming Xi
- The First Clinical Medical College of Lanzhou UniversityLanzhouChina
- Department of HematologyThe First Hospital of Lanzhou UniversityLanzhouChina
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8
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Zhang L, Sun Y, Xue CE, Wang S, Xu X, Zheng C, Chen C, Kong D. Uncovering the cellular and omics characteristics of natural killer cells in the bone marrow microenvironment of patients with acute myeloid leukemia. Cancer Cell Int 2024; 24:106. [PMID: 38481242 PMCID: PMC10938822 DOI: 10.1186/s12935-024-03300-w] [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: 12/26/2023] [Accepted: 03/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a highly heterogeneous hematologic malignancy and the most frequently acute leukemia of stem cell precursors and the myeloid derivatives in adult. Longitudinal studies have indicated the therapeutic landscape and drug resistance for patients with AML are still intractable, which largely attribute to the deficiency of detailed information upon the pathogenesis. METHODS In this study, we compared the cellular phenotype of resident NK cells (rAML-NKs, rHD-NKs) and expanded NK cells (eAML-NKs, eHD-NKs) from bone marrow of AML patients (AML) and healthy donors (HD). Then, we took advantage of the co-culture strategy for the evaluation of the in vitro cytotoxicity of NK cells upon diverse tumor cell lines (e.g., K562, Nalm6, U937). With the aid of RNA-sequencing (RNA-SEQ) and bioinformatics analyses (e.g., GOBP analysis, KEGG analysis, GSEA, volcano plot), we verified the similarities and differences of the omics features between eAML-NKs and eHD-NKs. RESULTS Herein, we verified the sharp decline in the content of total resident NK cells (CD3-CD56+) in rAML-NKs compared to rHD-NKs. Differ from the expanded eHD-NKs, eAML-NKs revealed decline in diverse NK cell subsets (NKG2D+, CD25+, NKp44+, NKp46+) and alterations in cellular vitality but conservations in cytotoxicity. According to transcriptomic analysis, AML-NKs and HD-NKs showed multifaceted distinctions in gene expression profiling and genetic variations. CONCLUSIONS Collectively, our data revealed the variations in the cytobiological and transcriptomic features between AML-NKs and HD-NKs in bone marrow environment. Our findings would benefit the further development of novel biomarkers for AML diagnosis and NK cell-based cytotherapy in future.
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Affiliation(s)
- Leisheng Zhang
- Science and Technology Innovation Center, The Fourth People's Hospital of Jinan, The Teaching Hospital of Shandong First Medical University, 50 Shifan Road, Tianqiao District, Jinan, 250031, Shandong, China.
- National Health Commission (NHC) Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.
| | - Yunyan Sun
- Department of Hematology, Peking University Cancer Hospital Yunnan, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Chun-E Xue
- Department of Hematology, Langfang City Hospital of Traditional Chinese Medicine, Langfang, 065000, China
| | - Shuling Wang
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Xianghong Xu
- Department of Hematology, Peking University Cancer Hospital Yunnan, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650118, China
| | - Chengyun Zheng
- Department of Hematology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, China
| | - Cunrong Chen
- Department of Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, 350001, China.
| | - Dexiao Kong
- Department of Hematology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, China.
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9
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Liu X, Zuo F, Song J, Tang L, Wang X, Liu X, Zhang H, Yang Z, Jing J, Ma X, Shi H. Immune checkpoints HLA-E:CD94-NKG2A and HLA-C:KIR2DL1 complementarily shield circulating tumor cells from NK-mediated immune surveillance. Cell Discov 2024; 10:16. [PMID: 38336855 PMCID: PMC10858264 DOI: 10.1038/s41421-024-00646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/07/2024] [Indexed: 02/12/2024] Open
Affiliation(s)
- Xiaowei Liu
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fengli Zuo
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinen Song
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Leyi Tang
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyan Wang
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xinyu Liu
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hao Zhang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhankun Yang
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, Hebei, China
| | - Jing Jing
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xuelei Ma
- Department of Biotherapy, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China.
| | - Hubing Shi
- Institute for Breast Health Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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10
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Hu X, Cao D, Zhou Z, Wang Z, Zeng J, Hong WX. Single-cell transcriptomic profiling reveals immune cell heterogeneity in acute myeloid leukaemia peripheral blood mononuclear cells after chemotherapy. Cell Oncol (Dordr) 2024; 47:97-112. [PMID: 37615858 PMCID: PMC10899424 DOI: 10.1007/s13402-023-00853-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2023] [Indexed: 08/25/2023] Open
Abstract
PURPOSE Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by the rapid clonal expansion of abnormally differentiated myeloid progenitor cells residing in a complex microenvironment. However, the immune cell types, status, and genome profile of the peripheral blood mononuclear cell (PBMC) microenvironment in AML patients after chemotherapy are poorly understood. In order to explore the immune microenvironment of AML patients after chemotherapy, we conducted this study for providing insights into precision medicine and immunotherapy of AML. METHODS In this study, we used single-cell RNA sequencing (scRNA-seq) to analyse the PBMC microenvironment from five AML patients treated with different chemotherapy regimens and six healthy donors. We compared the cell compositions in AML patients and healthy donors, and performed gene set enrichment analysis (GSEA), CellPhoneDB, and copy number variation (CNV) analysis. RESULTS Using scRNA-seq technology, 91,772 high quality cells of 44,950 PBMCs from AML patients and 46,822 PBMCs from healthy donors were classified as 14 major cell clusters. Our study revealed the sub-cluster diversity of T cells, natural killer (NK) cells, monocytes, dendritic cells (DCs), and haematopoietic stem cell progenitors (HSC-Prog) in AML patients under chemotherapy. NK cells and monocyte-DCs showed significant changes in transcription factor expression and chromosome copy number variation (CNV). We also observed significant heterogeneity in CNV and intercellular interaction networks in HSC-Prog cells. CONCLUSION Our results elucidated the PBMC single-cell landscape and provided insights into precision medicine and immunotherapy for treating AML.
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Affiliation(s)
- Xuqiao Hu
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China.
| | - Dongyan Cao
- Department of Biliary-Pancreatic Surgery, the Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhenru Zhou
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Zhaoyang Wang
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Jieying Zeng
- Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, China
| | - Wen-Xu Hong
- Shenzhen Center for Chronic Disease Control and Prevention, Shenzhen Institute of Dermatology, Shenzhen, China.
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11
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Wu Y, Li Y, Gao Y, Zhang P, Jing Q, Zhang Y, Jin W, Wang Y, Du J, Wu G. Immunotherapies of acute myeloid leukemia: Rationale, clinical evidence and perspective. Biomed Pharmacother 2024; 171:116132. [PMID: 38198961 DOI: 10.1016/j.biopha.2024.116132] [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: 09/30/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is a prevalent hematological malignancy that exhibits a wide array of molecular abnormalities. Although traditional treatment modalities such as chemotherapy and allogeneic stem cell transplantation (HSCT) have become standard therapeutic approaches, a considerable number of patients continue to face relapse and encounter a bleak prognosis. The emergence of immune escape, immunosuppression, minimal residual disease (MRD), and other contributing factors collectively contribute to this challenge. Recent research has increasingly highlighted the notable distinctions between AML tumor microenvironments and those of healthy individuals. In order to investigate the potential therapeutic mechanisms, this study examines the intricate transformations occurring between leukemic cells and their surrounding cells within the tumor microenvironment (TME) of AML. This review classifies immunotherapies into four distinct categories: cancer vaccines, immune checkpoint inhibitors (ICIs), antibody-based immunotherapies, and adoptive T-cell therapies. The results of numerous clinical trials strongly indicate that the identification of optimal combinations of novel agents, either in conjunction with each other or with chemotherapy, represents a crucial advancement in this field. In this review, we aim to explore the current and emerging immunotherapeutic methodologies applicable to AML patients, identify promising targets, and emphasize the crucial requirement to augment patient outcomes. The application of these strategies presents substantial therapeutic prospects within the realm of precision medicine for AML, encompassing the potential to ameliorate patient outcomes.
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Affiliation(s)
- Yunyi Wu
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China; Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yanchun Li
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Yan Gao
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ping Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Qiangan Jing
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yinhao Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Weidong Jin
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ying Wang
- Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
| | - Jing Du
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Gongqiang Wu
- Department of Hematology, Dongyang Hospitai Affiliated to Wenzhou Medical University, Dongyang People's Hospital, Dongyang, Zhejiang, China.
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12
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Yamakawa M, Rexach JE. Cell States and Interactions of CD8 T Cells and Disease-Enriched Microglia in Human Brains with Alzheimer's Disease. Biomedicines 2024; 12:308. [PMID: 38397909 PMCID: PMC10886701 DOI: 10.3390/biomedicines12020308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
Alzheimer's disease (AD) is a multi-stage neurodegenerative disorder characterized by beta-amyloid accumulation, hyperphosphorylated Tau deposits, neurodegeneration, neuroinflammation, and cognitive impairment. Recent studies implicate CD8 T cells as neuroimmune responders to the accumulation of AD pathology in the brain and potential contributors to toxic neuroinflammation. However, more evidence is needed to understand lymphocytes in disease, including their functional states, molecular mediators, and interacting cell types in diseased brain tissue. The scarcity of lymphocytes in brain tissue samples has limited the unbiased profiling of disease-associated cell types, cell states, drug targets, and relationships to common AD genetic risk variants based on transcriptomic analyses. However, using recent large-scale, high-quality single-nuclear sequencing datasets from over 84 Alzheimer's disease and control cases, we leverage single-nuclear RNAseq data from 800 lymphocytes collected from 70 individuals to complete unbiased molecular profiling. We demonstrate that effector memory CD8 T cells are the major lymphocyte subclass enriched in the brain tissues of individuals with AD dementia. We define disease-enriched interactions involving CD8 T cells and multiple brain cell subclasses including two distinct microglial disease states that correlate, respectively, to beta-amyloid and tau pathology. We find that beta-amyloid-associated microglia are a major hub of multicellular cross-talk gained in disease, including interactions involving both vulnerable neuronal subtypes and CD8 T cells. We reproduce prior reports that amyloid-response microglia are depleted in APOE4 carriers. Overall, these human-based studies provide additional support for the potential relevance of effector memory CD8 T cells as a lymphocyte population of interest in AD dementia and provide new candidate interacting partners and drug targets for further functional study.
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Affiliation(s)
| | - Jessica E. Rexach
- Department of Neurology, University of California Los Angeles, Los Angeles, CA 90095, USA;
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13
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Wu WC, Shiu C, Tong TK, Leung SO, Hui CW. Suppression of NK Cell Activation by JAK3 Inhibition: Implication in the Treatment of Autoimmune Diseases. J Immunol Res 2023; 2023:8924603. [PMID: 38106519 PMCID: PMC10723930 DOI: 10.1155/2023/8924603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
Natural killer (NK) cell is an essential cytotoxic lymphocyte in our innate immunity. Activation of NK cells is of paramount importance in defending against pathogens, suppressing autoantibody production and regulating other immune cells. Common gamma chain (γc) cytokines, including IL-2, IL-15, and IL-21, are defined as essential regulators for NK cell homeostasis and development. However, it is inconclusive whether γc cytokine-driven NK cell activation plays a protective or pathogenic role in the development of autoimmunity. In this study, we investigate and correlate the differential effects of γc cytokines in NK cell expansion and activation. IL-2 and IL-15 are mainly responsible for NK cell activation, while IL-21 preferentially stimulates NK cell proliferation. Blockade of Janus tyrosine kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway by either JAK inhibitors or antibodies targeting γc receptor subunits reverses the γc cytokine-induced NK cell activation, leading to suppression of its autoimmunity-like phenotype in vitro. These results underline the mechanisms of how γc cytokines trigger autoimmune phenotype in NK cells as a potential target to autoimmune diseases.
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Affiliation(s)
- Wai Chung Wu
- SinoMab BioScience Limited, Units 303 and 305 to 307, No. 15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong
| | - Carol Shiu
- SinoMab BioScience Limited, Units 303 and 305 to 307, No. 15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong
| | - Tak Keung Tong
- SinoMab BioScience Limited, Units 303 and 305 to 307, No. 15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong
| | - Shui On Leung
- SinoMab BioScience Limited, Units 303 and 305 to 307, No. 15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong
| | - Chin Wai Hui
- SinoMab BioScience Limited, Units 303 and 305 to 307, No. 15 Science Park West Avenue, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong
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14
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Li H, Rahman MA, Ruesch M, Eisele CD, Anderson EM, Wright PW, Cao J, Ratnayake S, Chen Q, Yan C, Meerzaman D, Abraham RS, Freud AG, Anderson SK. Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination. Cell Rep 2023; 42:113454. [PMID: 37976160 PMCID: PMC10842785 DOI: 10.1016/j.celrep.2023.113454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 10/02/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Previous studies of the murine Ly49 and human KIR gene clusters implicated competing sense and antisense promoters in the control of variegated gene expression. In the current study, an examination of transcription factor genes defines an abundance of convergent and divergent sense/antisense promoter pairs, suggesting that competing promoters may control cell fate determination. Differentiation of CD34+ hematopoietic progenitors in vitro shows that cells with GATA1 antisense transcription have enhanced GATA2 transcription and a mast cell phenotype, whereas cells with GATA2 antisense transcription have increased GATA1 transcripts and an erythroblast phenotype. Detailed analyses of the AHR and RORC genes demonstrate the ability of competing promoters to act as binary switches and the association of antisense transcription with an immature/progenitor cell phenotype. These data indicate that alternative cell fates generated by promoter competition in lineage-determining transcription factors contribute to the programming of cell differentiation.
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Affiliation(s)
- Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Md Ahasanur Rahman
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael Ruesch
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Medical Scientist Training Program, The Ohio State University, Columbus, OH 43210, USA
| | - Caprice D Eisele
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Erik M Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennie Cao
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Shashikala Ratnayake
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qingrong Chen
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chunhua Yan
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Daoud Meerzaman
- Cancer Genomics and Bioinformatics Branch, Center for Biomedical Informatics & Information Technology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43210, USA; Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Aharon G Freud
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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15
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Mälarstig A, Grassmann F, Dahl L, Dimitriou M, McLeod D, Gabrielson M, Smith-Byrne K, Thomas CE, Huang TH, Forsberg SKG, Eriksson P, Ulfstedt M, Johansson M, Sokolov AV, Schiöth HB, Hall P, Schwenk JM, Czene K, Hedman ÅK. Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation. Nat Commun 2023; 14:7680. [PMID: 37996402 PMCID: PMC10667261 DOI: 10.1038/s41467-023-43485-8] [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: 03/28/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Biomarkers for early detection of breast cancer may complement population screening approaches to enable earlier and more precise treatment. The blood proteome is an important source for biomarker discovery but so far, few proteins have been identified with breast cancer risk. Here, we measure 2929 unique proteins in plasma from 598 women selected from the Karolinska Mammography Project to explore the association between protein levels, clinical characteristics, and gene variants, and to identify proteins with a causal role in breast cancer. We present 812 cis-acting protein quantitative trait loci for 737 proteins which are used as instruments in Mendelian randomisation analyses of breast cancer risk. Of those, we present five proteins (CD160, DNPH1, LAYN, LRRC37A2 and TLR1) that show a potential causal role in breast cancer risk with confirmatory results in independent cohorts. Our study suggests that these proteins should be further explored as biomarkers and potential drug targets in breast cancer.
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Affiliation(s)
- Anders Mälarstig
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden.
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany
| | - Leo Dahl
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Marios Dimitriou
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
| | - Dianna McLeod
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Karl Smith-Byrne
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Cecilia E Thomas
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Tzu-Hsuan Huang
- Cancer Immunology Discovery, Pfizer Inc., San Diego, California, USA
| | | | | | | | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Aleksandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Åsa K Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pfizer Worldwide Research Development and Medical, Stockholm, Sweden
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16
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Hou W, Ji Z, Chen Z, Wherry EJ, Hicks SC, Ji H. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nat Commun 2023; 14:7286. [PMID: 37949861 PMCID: PMC10638410 DOI: 10.1038/s41467-023-42841-y] [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: 07/11/2021] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Pseudotime analysis with single-cell RNA-sequencing (scRNA-seq) data has been widely used to study dynamic gene regulatory programs along continuous biological processes. While many methods have been developed to infer the pseudotemporal trajectories of cells within a biological sample, it remains a challenge to compare pseudotemporal patterns with multiple samples (or replicates) across different experimental conditions. Here, we introduce Lamian, a comprehensive and statistically-rigorous computational framework for differential multi-sample pseudotime analysis. Lamian can be used to identify changes in a biological process associated with sample covariates, such as different biological conditions while adjusting for batch effects, and to detect changes in gene expression, cell density, and topology of a pseudotemporal trajectory. Unlike existing methods that ignore sample variability, Lamian draws statistical inference after accounting for cross-sample variability and hence substantially reduces sample-specific false discoveries that are not generalizable to new samples. Using both real scRNA-seq and simulation data, including an analysis of differential immune response programs between COVID-19 patients with different disease severity levels, we demonstrate the advantages of Lamian in decoding cellular gene expression programs in continuous biological processes.
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Affiliation(s)
- Wenpin Hou
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Zhicheng Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zeyu Chen
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephanie C Hicks
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
| | - Hongkai Ji
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
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17
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Hegewisch-Solloa E, Nalin AP, Freud AG, Mace EM. Deciphering the localization and trajectory of human natural killer cell development. J Leukoc Biol 2023; 114:487-506. [PMID: 36869821 DOI: 10.1093/jleuko/qiad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 03/05/2023] Open
Abstract
Innate immune cells represent the first line of cellular immunity, comprised of both circulating and tissue-resident natural killer cells and innate lymphoid cells. These innate lymphocytes arise from a common CD34+ progenitor that differentiates into mature natural killer cells and innate lymphoid cells. The successive stages in natural killer cell maturation are characterized by increased lineage restriction and changes to phenotype and function. Mechanisms of human natural killer cell development have not been fully elucidated, especially the role of signals that drive the spatial localization and maturation of natural killer cells. Cytokines, extracellular matrix components, and chemokines provide maturation signals and influence the trafficking of natural killer cell progenitors to peripheral sites of differentiation. Here we present the latest advances in our understanding of natural killer and innate lymphoid cell development in peripheral sites, including secondary lymphoid tissues (i.e. tonsil). Recent work in the field has provided a model for the spatial distribution of natural killer cell and innate lymphoid cell developmental intermediates in tissue and generated further insights into the developmental niche. In support of this model, future studies using multifaceted approaches seek to fully map the developmental trajectory of human natural killer cells and innate lymphoid cells in secondary lymphoid tissues.
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Affiliation(s)
- Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
| | - Ansel P Nalin
- Biomedical Sciences Graduate Program, Medical Scientist Training Program, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 10th Ave. Columbus, OH 43210, USA
| | - Aharon G Freud
- Department of Pathology, Comprehensive Cancer Center and The James Cancer Hospital and Solove Research Institute, The Ohio State University, 460 W 12th Ave. Columbus, OH 43210, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, 630 W 168th St. New York, NY 10032, USA
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18
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Zhang Z, Deng C, Zhu P, Yao D, Shi J, Zeng T, Huang W, Huang Z, Wu Z, Li J, Xiao M, Fu L. Single-cell RNA-seq reveals a microenvironment and an exhaustion state of T/NK cells in acute myeloid leukemia. Cancer Sci 2023; 114:3873-3883. [PMID: 37591615 PMCID: PMC10551605 DOI: 10.1111/cas.15932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous blood cancer. Effective immunotherapies for AML are hindered by a lack of understanding of the tumor microenvironment (TME). Here, we retrieved published single-cell RNA sequencing data for 128,688 cells derived from 29 bone marrow aspirates, including 21 AML patients and eight healthy donors. We established a global tumor ecosystem including nine main cell types. Myeloid, T, and NK cells were further re-clustered and annotated. Developmental trajectory analysis indicated that exhausted CD8+ T cells might develop via tissue residual memory T cells (TRM) in the AML TME. Significantly higher expression levels of exhaustion molecules in AML TRM cells suggested that these cells were influenced by the TME and entered an exhausted state. Meanwhile, the upregulation of checkpoint molecules and downregulation of granzyme were also observed in AML NK cells, suggesting an exhaustion state. In conclusion, our comprehensive profiling of T/NK subpopulations provides deeper insights into the AML immunosuppressive ecosystem, which is critical for immunotherapies.
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Affiliation(s)
- Zhiyong Zhang
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Medical Innovation Research Division of Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Cong Deng
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
- Department of Clinical LaboratoryThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Pei Zhu
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Danlin Yao
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Jinlong Shi
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Medical Innovation Research Division of Chinese PLA General HospitalBeijingPeople's Republic of China
| | - Tiansheng Zeng
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Wenhui Huang
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Zeyong Huang
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Zhihua Wu
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Junyi Li
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Min Xiao
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
| | - Lin Fu
- Department of HematologyThe Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhouPeople's Republic of China
- Central Laboratory, The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouPeople's Republic of China
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19
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Chen H, Zhao X, Pan W, Xiao H. Integrated genomic and single-cell transcriptomic analyses reveal clonal evolution and immune signature in donor cell leukemia after haploidentical allogeneic hematopoietic stem cell transplantation. Leuk Lymphoma 2023; 64:1681-1688. [PMID: 37424322 DOI: 10.1080/10428194.2023.2232493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
The pathogenesis of donor cell leukemia (DCL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is unclear and likely multifactorial. Leukemic transformation of healthy donor HSCs in recipient's bone marrow microenvironment provides a useful in vivo model for investigating the mechanisms involved in leukemogenesis. Here, we report a rare case of late-onset DCL developing in a recipient. Whole-genome sequencing indicates that donor-derived cells harboring clonal hematopoiesis of indeterminate potential (CHIP)-associated genetic alterations expand and eventually transform to full-blown AML via acquisition of additional somatic mutations within the recipient's bone marrow microenvironment. The 10× single-cell RNA sequencing reveals the abundance of GMP-like cells with a specific transcriptional signature in DCL. Moreover, impaired immune surveillance, including dysfunction of cytotoxic T lymphocytes (CTLs) and decreased number of canonical NK cells, is discovered in DCL. Our data add valuable information to the current understanding of the mechanisms of DCL.
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Affiliation(s)
- Huiqiao Chen
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiujie Zhao
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjue Pan
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haowen Xiao
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
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20
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Lepretre F, Gras D, Chanez P, Duez C. Natural killer cells in the lung: potential role in asthma and virus-induced exacerbation? Eur Respir Rev 2023; 32:230036. [PMID: 37437915 DOI: 10.1183/16000617.0036-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023] Open
Abstract
Asthma is a chronic inflammatory airway disorder whose pathophysiological and immunological mechanisms are not completely understood. Asthma exacerbations are mostly driven by respiratory viral infections and characterised by worsening of symptoms. Despite current therapies, asthma exacerbations can still be life-threatening. Natural killer (NK) cells are innate lymphoid cells well known for their antiviral activity and are present in the lung as circulating and resident cells. However, their functions in asthma and its exacerbations are still unclear. In this review, we will address NK cell activation and functions, which are particularly relevant for asthma and virus-induced asthma exacerbations. Then, the role of NK cells in the lungs at homeostasis in healthy individuals will be described, as well as their functions during pulmonary viral infections, with an emphasis on those associated with asthma exacerbations. Finally, we will discuss the involvement of NK cells in asthma and virus-induced exacerbations and examine the effect of asthma treatments on NK cells.
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Affiliation(s)
- Florian Lepretre
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Delphine Gras
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
| | - Pascal Chanez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
- APHM, Hôpital Nord, Clinique des Bronches, de l'allergie et du sommeil, Marseille, France
| | - Catherine Duez
- Aix-Marseille Université, INSERM, INRAE, C2VN, Marseille, France
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21
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Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
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Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
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22
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Qi C, Liu Q. Natural killer cells in aging and age-related diseases. Neurobiol Dis 2023; 183:106156. [PMID: 37209924 DOI: 10.1016/j.nbd.2023.106156] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023] Open
Abstract
Aging leads to escalated systemic inflammation. As the sentinel of immune system, natural killer (NK) cells are early responders that sense cues and signals from target organs and swiftly orchestrate local inflammation upon their arrival. Emerging evidence indicates a profound role of NK cells in the initiation and evolution of neuroinflammation in aging and age-related diseases. Here we discuss recent advances in NK cell biology and the organ-specific features of NK cells in normal brain aging, Alzheimer's disease, Parkinson's disease and stroke. Our increasing understanding of NK cells and their unique features in aging and age-related diseases may facilitate the future design of immune therapies targeting NK cells to benefit the old population.
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Affiliation(s)
- Caiyun Qi
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin 300052, China; Tianjin Institute of Immunology, Tianjin Medical University, Tianjin 300070, China.
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23
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Iyoda T, Yamasaki S, Ueda S, Shimizu K, Fujii SI. Natural Killer T and Natural Killer Cell-Based Immunotherapy Strategies Targeting Cancer. Biomolecules 2023; 13:biom13020348. [PMID: 36830717 PMCID: PMC9953375 DOI: 10.3390/biom13020348] [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: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Both natural killer T (NKT) and natural killer (NK) cells are innate cytotoxic lymphoid cells that produce inflammatory cytokines and chemokines, and their role in the innate immune response to tumors and microorganisms has been investigated. Especially, emerging evidence has revealed their status and function in the tumor microenvironment (TME) of tumor cells. Some bacteria producing NKT cell ligands have been identified to exert antitumor effects, even in the TME. By contrast, tumor-derived lipids or metabolites may reportedly suppress NKT and NK cells in situ. Since NKT and NK cells recognize stress-inducible molecules or inhibitory molecules on cancer cells, their status or function depends on the balance between inhibitory and activating receptor signals. As a recent strategy in cancer immunotherapy, the mobilization or restoration of endogenous NKT or NK cells by novel vaccines or therapies has become a focus of research. As a new biological evidence, after activation, effector memory-type NKT cells lasted in tumor-bearing models, and NK cell-based immune checkpoint inhibition potentiated the enhancement of NK cell cytotoxicity against cancer cells in preclinical and clinical trials. Furthermore, several new modalities based on the characteristics of NKT and NK cells, including artificial adjuvant vector cells, chimeric antigen receptor-expressing NK or NKT cell therapy, or their combination with immune checkpoint blockade have been developed. This review examines challenges and future directions for improving these therapies.
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Affiliation(s)
- Tomonori Iyoda
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Satoru Yamasaki
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shogo Ueda
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- RIKEN Program for Drug Discovery and Medical Technology Platforms, Yokohama 230-0045, Japan
- Correspondence: (K.S.); (S.F.); Tel.:+ 81-45-503-7062 (S.F.); Fax: +81-45-503-7061 (S.F.)
| | - Shin-ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- RIKEN Program for Drug Discovery and Medical Technology Platforms, Yokohama 230-0045, Japan
- Correspondence: (K.S.); (S.F.); Tel.:+ 81-45-503-7062 (S.F.); Fax: +81-45-503-7061 (S.F.)
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24
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Hirz T, Mei S, Sarkar H, Kfoury Y, Wu S, Verhoeven BM, Subtelny AO, Zlatev DV, Wszolek MW, Salari K, Murray E, Chen F, Macosko EZ, Wu CL, Scadden DT, Dahl DM, Baryawno N, Saylor PJ, Kharchenko PV, Sykes DB. Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nat Commun 2023; 14:663. [PMID: 36750562 PMCID: PMC9905093 DOI: 10.1038/s41467-023-36325-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
The treatment of low-risk primary prostate cancer entails active surveillance only, while high-risk disease requires multimodal treatment including surgery, radiation therapy, and hormonal therapy. Recurrence and development of metastatic disease remains a clinical problem, without a clear understanding of what drives immune escape and tumor progression. Here, we comprehensively describe the tumor microenvironment of localized prostate cancer in comparison with adjacent normal samples and healthy controls. Single-cell RNA sequencing and high-resolution spatial transcriptomic analyses reveal tumor context dependent changes in gene expression. Our data indicate that an immune suppressive tumor microenvironment associates with suppressive myeloid populations and exhausted T-cells, in addition to high stromal angiogenic activity. We infer cell-to-cell relationships from high throughput ligand-receptor interaction measurements within undissociated tissue sections. Our work thus provides a highly detailed and comprehensive resource of the prostate tumor microenvironment as well as tumor-stromal cell interactions.
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Affiliation(s)
- Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Hirak Sarkar
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Youmna Kfoury
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bronte M Verhoeven
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Alexander O Subtelny
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dimitar V Zlatev
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew W Wszolek
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Keyan Salari
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Douglas M Dahl
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Philip J Saylor
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Peter V Kharchenko
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Altos Labs, San Diego, CA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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25
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Mace EM. Human natural killer cells: Form, function, and development. J Allergy Clin Immunol 2023; 151:371-385. [PMID: 36195172 PMCID: PMC9905317 DOI: 10.1016/j.jaci.2022.09.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 02/07/2023]
Abstract
Human natural killer (NK) cells are innate lymphoid cells that mediate important effector functions in the control of viral infection and malignancy. Their ability to distinguish "self" from "nonself" and lyse virally infected and tumorigenic cells through germline-encoded receptors makes them important players in maintaining human health and a powerful tool for immunotherapeutic applications and fighting disease. This review introduces our current understanding of NK cell biology, including key facets of NK cell differentiation and the acquisition and execution of NK cell effector function. Further, it addresses the clinical relevance of NK cells in both primary immunodeficiency and immunotherapy. It is intended to provide an up-to-date and comprehensive overview of this important and interesting innate immune effector cell subset.
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Affiliation(s)
- Emily M Mace
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York.
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26
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Ng CK, Belz GT. Innate lymphoid cells: potential targets for cancer therapeutics. Trends Cancer 2023; 9:158-171. [PMID: 36357314 DOI: 10.1016/j.trecan.2022.10.007] [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: 08/16/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022]
Abstract
Innate lymphoid cells (ILCs) comprise a number of different subsets, including natural killer (NK) cells, ILC1s, ILC2s, ILC3s, and lymphoid tissue-inducer (LTi) cells that express receptors and signaling pathways that are highly responsive to continuously changing microenvironmental cues. In this Review, we highlight the key features of innate cells that define their capacity to respond rapidly to different environments, how this ability can drive both tumor protection (limiting tumor development) or, alternatively, tumor progression, promoting tumor dissemination and resistance to immunotherapy. We discuss how understanding the regulation of ILCs that can detect tumor cells early in a response opens the possibility of exploiting this functional plasticity to develop rational therapeutic strategies to bolster adaptive immune responses and improve patient outcomes.
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Affiliation(s)
- Chun Ki Ng
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Gabrielle T Belz
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia.
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27
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Song P, Cao K, Mao Y, Ai S, Sun F, Hu Q, Liu S, Wang M, Lu X, Guan W, Shen X. Tissue specific imprinting on innate lymphoid cells during homeostasis and disease process revealed by integrative inference of single-cell transcriptomics. Front Immunol 2023; 14:1127413. [PMID: 36960063 PMCID: PMC10028295 DOI: 10.3389/fimmu.2023.1127413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Innate lymphoid cells (ILCs) are key components of the immune system, yet the similarity and distinction of the properties across tissues under homeostasis, inflammation and tumor process remain elusive. Methods Here we performed integrative inference of ILCs to reveal their transcriptional profiles and heterogeneity from single-cell genomics. We collected a large number of ILCs from human six different tissues which can represent unique immune niches (circulation, lymphoid tissue, normal and inflamed mucosa, tumor microenvironment), to systematically address the transcriptional imprinting. Results ILCs are profoundly imprinted by their organ of residence, and tissue-specific distinctions are apparent under pathological conditions. In the hepatocellular carcinoma microenvironment, we identified intermediate c-kit+ ILC2 population, and lin-CD127- NK-like cells that expressed markers of cytotoxicity including CCL5 and IFNG. Additionally, CD127+CD94+ ILC1s were preferentially enriched in inflamed ileum from patients with Crohn's disease. Discussion These analyses depicted a comprehensive characterization of ILC anatomical distribution and subset heterogeneity, and provided a base line for future temporal or spatial studies focused on tissue-specific ILC-mediated immunity.
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Affiliation(s)
- Peng Song
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Ke Cao
- Department of Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yonghuan Mao
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Shichao Ai
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Feng Sun
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qiongyuan Hu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Song Liu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Meng Wang
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaofeng Lu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
| | - Xiaofei Shen
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
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28
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Kang G, Zhao X, Sun J, Cheng C, Wang C, Tao L, Zong L, Yin W, Cong J, Li J, Wang X. A2AR limits IL-15-induced generation of CD39 + NK cells with high cytotoxicity. Int Immunopharmacol 2023; 114:109567. [PMID: 36529024 DOI: 10.1016/j.intimp.2022.109567] [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: 09/02/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
CD39-mediated inhibition of natural killer (NK) cell activity has been demonstrated, but the characteristics of CD39+ NK cells in humans are not known. We investigated the characteristics of human circulating CD39+ NK cells. In healthy donors, the proportion of circulating CD39+ NK cells in total NK cells was relatively low compared with that of CD39- NK cells. Nonetheless, a higher proportion of CD39+ NK cells expressed CD107a. Similarly, a higher proportion of CD39+ NK cells expressed CD107a in patients with hepatitis B virus or patients with hepatocellular carcinoma. Stimulation with NK-sensitive K562 cells or interleukin (IL)-12/IL-18 activated CD39+ NK cells to express higher levels of CD107a, IFN-γ and TNF-α, relative to CD39- NK cells. Importantly, IL-15 induced the generation of CD39+ NK cells. In contrast, A2A adenosine receptor (A2AR) ligation suppressed the generation of CD39+ NK cells by inhibiting IL-15 signaling. These data for the first time demonstrated that A2AR counteracts IL-15-induced generation of human CD39+ NK cells, which have a stronger cytotoxicity than CD39- NK cells. IL-15-induced human CD39+ NK cells might be better choice for immunotherapy based on adoptive transfer of NK cells.
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Affiliation(s)
- Guijie Kang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Xueqin Zhao
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Jiafeng Sun
- Dental Department, Health Service Center, Jianghai Community, Guangyi Street, Liangxi District, Wuxi 214000, Jiangsu, China
| | - Chen Cheng
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Cen Wang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China
| | - Longxiang Tao
- Department of Radiology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Lu Zong
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, Anhui, China
| | - Wenwei Yin
- Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jingjing Cong
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China.
| | - Jing Li
- School of Life Sciences, Anhui Medical University, Hefei 230032, China.
| | - Xuefu Wang
- School of Pharmacy, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei 230032, China.
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29
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Subedi N, Verhagen LP, de Jonge P, Van Eyndhoven LC, van Turnhout MC, Koomen V, Baudry J, Eyer K, Dolstra H, Tel J. Single‐Cell Profiling Reveals Functional Heterogeneity and Serial Killing in Human Peripheral and Ex Vivo‐Generated CD34+ Progenitor‐Derived Natural Killer Cells. Adv Biol (Weinh) 2022; 7:e2200207. [PMID: 36517083 DOI: 10.1002/adbi.202200207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Increasing evidence suggests that natural killer (NK) cells are composed of distinct functional subsets. This multifunctional role has made them an attractive choice for anticancer immunotherapy. A functional NK cell repertoire is generated through cellular education, resulting in a heterogeneous NK cell population with distinct capabilities responding to different stimuli. The application of a high-throughput droplet-based microfluidic platform allows monitoring of NK cell-target cell interactions at the single-cell level and in real-time. A variable response of single NK cells toward different target cells is observed, and a distinct population of NK cells (serial killers) capable of inducing multiple target lysis is identified. By assessing the cytotoxic dynamics, it is shown that single umbilical cord blood-derived CD34+ hematopoietic progenitor (HPC)-NK cells display superior antitumor cytotoxicity. With an integrated analysis of cytotoxicity and cytokine secretion, it is shown that target cell interactions augment cytotoxic as well as secretory behavior of NK cells. By providing an integrated assessment of NK cell functions by microfluidics, this study paves the way to further functionally characterize NK cells ultimately aimed to improve cancer immunotherapy.
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Affiliation(s)
- Nikita Subedi
- Laboratory of Immunoengineering Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
- Institute for Complex Molecular Systems Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
| | - Liesbeth Petronella Verhagen
- Laboratory of Immunoengineering Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
- Institute for Complex Molecular Systems Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
| | - Paul de Jonge
- Department of Laboratory Medicine – Laboratory of Hematology Radboud Institute of Molecular Life Sciences Radboud University Medical Center Nijmegen 6525 GA The Netherlands
| | - Laura C. Van Eyndhoven
- Laboratory of Immunoengineering Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
- Institute for Complex Molecular Systems Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
| | - Mark C. van Turnhout
- Soft Tissue Engineering and Mechanobiology Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
| | - Vera Koomen
- Laboratory of Immunoengineering Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés (LCMD) ESPCI Paris PSL Research University CNRS UMR8231 Chimie Biologie Innovation Paris 75005 France
| | - Klaus Eyer
- Laboratoire Colloïdes et Matériaux Divisés (LCMD) ESPCI Paris PSL Research University CNRS UMR8231 Chimie Biologie Innovation Paris 75005 France
- Laboratory for Functional Immune Repertoire Analysis Institute of Pharmaceutical Sciences D‐CHAB, ETH, Zürich Zurich 8093 Switzerland
| | - Harry Dolstra
- Department of Laboratory Medicine – Laboratory of Hematology Radboud Institute of Molecular Life Sciences Radboud University Medical Center Nijmegen 6525 GA The Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering Department of Biomedical Engineering Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
- Institute for Complex Molecular Systems Eindhoven University of Technology Groene Loper 5 Eindhoven 5600 MB The Netherlands
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30
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Liu C, Chen Y, Lu D, Liu B, Zhang T, Deng L, Liu Z, Zhong C, Fu R. Single-cell transcriptomic analysis of PB and BM NK cells from severe aplastic anaemia patients. Clin Transl Med 2022; 12:e1092. [PMID: 36471484 PMCID: PMC9722964 DOI: 10.1002/ctm2.1092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/29/2022] [Accepted: 10/11/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Chunyan Liu
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Yingying Chen
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Dan Lu
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Bingnan Liu
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Tian Zhang
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Ling Deng
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Zixuan Liu
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Congwei Zhong
- Department of HematologyTianjin Medical University General HospitalTianjinChina
| | - Rong Fu
- Department of HematologyTianjin Medical University General HospitalTianjinChina
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31
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Melsen JE, van Ostaijen-ten Dam MM, Schoorl DJA, Schol PJ, van den Homberg DAL, Lankester AC, Lugthart G, Schilham MW. Single-cell transcriptomics in bone marrow delineates CD56 dimGranzymeK + subset as intermediate stage in NK cell differentiation. Front Immunol 2022; 13:1044398. [PMID: 36505452 PMCID: PMC9730327 DOI: 10.3389/fimmu.2022.1044398] [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: 09/14/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56brightCD16+, CD56dimCD16+ and CD69+CXCR6+ lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells.
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32
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Qi C, Liu F, Zhang W, Han Y, Zhang N, Liu Q, Li H. Alzheimer's disease alters the transcriptomic profile of natural killer cells at single-cell resolution. Front Immunol 2022; 13:1004885. [PMID: 36405736 PMCID: PMC9666759 DOI: 10.3389/fimmu.2022.1004885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/12/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer's disease (AD) is the most common dementia without an effective cure at least partially due to incomplete understanding of the disease. Inflammation has emerged as a central player in the onset and progression of AD. As innate lymphoid cells, natural killer (NK) cells orchestrate the initiation and evolution of inflammatory responses. Yet, the transcriptomic features of NK cells in AD remain poorly understood. We assessed the diversity of NK cells using web-based single-cell RNA sequencing data of blood NK cells from patients with AD and control subjects and flow cytometry. We identified a contraction of NK cell compartment in AD, accompanied by a reduction of cytotoxicity. Unbiased clustering revealed four subsets of NK cells in AD, i.e., CD56bright NK cells, CD56dim effector NK cells, adaptive NK cells, and a unique NK cell subset that is expanded and characterized by upregulation of CX3CR1, TBX21, MYOM2, DUSP1, and ZFP36L2, and negatively correlated with cognitive function in AD patients. Pseudo-temporal analysis revealed that this unique NK cell subset was at a late stage of NK cell development and enriched with transcription factors TBX21, NFATC2, and SMAD3. Together, our study identified a distinct NK cell subset and its potential involvement in AD.
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Affiliation(s)
| | | | | | | | - Nan Zhang
- *Correspondence: Qiang Liu, ; Handong Li, ; Nan Zhang,
| | - Qiang Liu
- *Correspondence: Qiang Liu, ; Handong Li, ; Nan Zhang,
| | - Handong Li
- *Correspondence: Qiang Liu, ; Handong Li, ; Nan Zhang,
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Moiseev I, Tcvetkov N, Epifanovskaya O, Babenko E, Parfenenkova A, Bakin E, Yurovskaya K, Morozova E. Landscape of alterations in the checkpoint system in myelodysplastic syndrome and implications for prognosis. PLoS One 2022; 17:e0275399. [PMID: 36282797 PMCID: PMC9595516 DOI: 10.1371/journal.pone.0275399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 11/06/2022] Open
Abstract
The emergence of novel immunotherapies for myelodysplastic syndrome (MDS) calls for a profound characterization of the "immunome" in the bone marrow (BM) and evaluation of prognostic impact of immunological changes. We performed a prospective study of 87 MDS patients who were referred to a tertiary hematological center and of 11 bone marrow donors who were not related to the study cohort. A flow cytometry panel with 48 markers including checkpoint ligands and receptors was used to study lymphoid and myeloid subpopulations in the bone marrow aspirates. The study found that both the healthy donors and the MDS patients have a high proportion of lymphocytes with PD-1 expression (41±18% and 58±25% respectively) and a high proportion of myeloid cells with PD-1L expression (31±23% and 12±7% respectively), indicating a potential physiological role of checkpoint systems in BM. At the same time, complex alterations including PD-1, CTLA-4, LAG-3 and TIM3 pathways accompanied by an increased level of T-reg and myeloid derived suppressor cell populations were identified in the BM of MDS patients. Cluster analysis showed independent prognostic significance of the checkpoint profile for overall survival (HR 1.90, 95%CI 1.01–3.56, p = 0.0471). TIM3-postive NK and CD8 effector cells along with the blast count were the key subpopulations for prognosis. An elevation of blasts in the bone marrow was associated with simultaneous expression of multiple checkpoints on myeloid cells.
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Affiliation(s)
- Ivan Moiseev
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
- * E-mail:
| | - Nikolai Tcvetkov
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Olga Epifanovskaya
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Elena Babenko
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Anna Parfenenkova
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Evgenii Bakin
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Ksenia Yurovskaya
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
| | - Elena Morozova
- RM Gorbacheva Research Institute, Pavlov University, Saint-Petersburg, Russian Federation
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Demaria O, Gauthier L, Vetizou M, Blanchard Alvarez A, Vagne C, Habif G, Batista L, Baron W, Belaïd N, Girard-Madoux M, Cesari C, Caratini M, Bosco F, Benac O, Lopez J, Fenis A, Galluso J, Trichard S, Carrette B, Carrette F, Maguer A, Jaubert S, Sansaloni A, Letay-Drouet R, Kosthowa C, Lovera N, Dujardin A, Chanuc F, Le Van M, Bokobza S, Jarmuzynski N, Fos C, Gourdin N, Remark R, Lechevallier E, Fakhry N, Salas S, Deville JL, Le Grand R, Bonnafous C, Vollmy L, Represa A, Carpentier S, Rossi B, Morel A, Cornen S, Perrot I, Morel Y, Vivier E. Antitumor immunity induced by antibody-based natural killer cell engager therapeutics armed with not-alpha IL-2 variant. Cell Rep Med 2022; 3:100783. [PMID: 36260981 PMCID: PMC9589122 DOI: 10.1016/j.xcrm.2022.100783] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/29/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022]
Abstract
Harnessing innate immunity is emerging as a promising therapeutic approach in cancer. We report here the design of tetraspecific molecules engaging natural killer (NK) cell-activating receptors NKp46 and CD16a, the β-chain of the interleukin-2 receptor (IL-2R), and a tumor-associated antigen (TAA). In vitro, these tetraspecific antibody-based natural killer cell engager therapeutics (ANKETs) induce a preferential activation and proliferation of NK cells, and the binding to the targeted TAA triggers NK cell cytotoxicity and cytokine and chemokine production. In vivo, tetraspecific ANKETs induce NK cell proliferation and their accumulation at the tumor bed, as well as the control of local and disseminated tumors. Treatment of non-human primates with CD20-directed tetraspecific ANKET leads to CD20+ circulating B cell depletion, with minimal systemic cytokine release and no sign of toxicity. Tetraspecific ANKETs, thus, constitute a technological platform for harnessing NK cells as next-generation cancer immunotherapies. Tetraspecific ANKETs constitute a technological platform to harness NK cells in cancer Tetraspecific ANKETs target NKp46, CD16a, IL-2Rβ, and a tumor antigen Tetraspecific ANKETs stimulate NK cell proliferation, activation, and antitumor functions In vivo, tetraspecific ANKETs promote NK cell tumor accumulation and antitumor activity
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Eric Lechevallier
- Assistance Publique des Hôpitaux de Marseille, Chirurgie Urologique et Transplantation Rénale, Hôpital de la Conception, Marseille, France
| | - Nicolas Fakhry
- Assistance Publique des Hôpitaux de Marseille, ORL et Chirurgie Cervico-Faciale, Hôpital de la Conception, Marseille, France
| | - Sébastien Salas
- Assistance Publique des Hôpitaux de Marseille, Service d'Oncologie Médicale et de Soins Palliatifs, CHU Timone Adulte, Marseille, France
| | - Jean-Laurent Deville
- Assistance Publique des Hôpitaux de Marseille, Oncologie Médicale, Hôpital de la Timone, Marseille, France
| | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | | | | | | | | | | | | | | | | | | | - Eric Vivier
- Innate Pharma, Marseille, France,Aix Marseille University, CNRS, INSERM, CIML, Marseille, France,Assistance Publique des Hôpitaux de Marseille, Hôpital de la Timone, Marseille-Immunopôle, Marseille, France,Corresponding author
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Bottino C, Della Chiesa M, Sorrentino S, Morini M, Vitale C, Dondero A, Tondo A, Conte M, Garaventa A, Castriconi R. Strategies for Potentiating NK-Mediated Neuroblastoma Surveillance in Autologous or HLA-Haploidentical Hematopoietic Stem Cell Transplants. Cancers (Basel) 2022; 14:cancers14194548. [PMID: 36230485 PMCID: PMC9559312 DOI: 10.3390/cancers14194548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary High-risk neuroblastomas (HR-NB) are malignant tumors of childhood that are treated with a very aggressive and life-threatening approach; this includes autologous hemopoietic stem cell transplantation (HSCT) and the infusion of a mAb targeting the GD2 tumor-associated antigen. Although the current treatment provided benefits, the 5-year overall survival remains below 50% due to relapses and refractoriness to therapy. Thus, there is an urgent need to ameliorate the standard therapeutic protocol, particularly improving the immune-mediated anti-tumor responses. Our review aims at summarizing and critically discussing novel immunotherapeutic strategies in HR-NB, including NK cell-based therapies and HLA-haploidentical HSCT from patients’ family. Abstract High-risk neuroblastomas (HR-NB) still have an unacceptable 5-year overall survival despite the aggressive therapy. This includes standardized immunotherapy combining autologous hemopoietic stem cell transplantation (HSCT) and the anti-GD2 mAb. The treatment did not significantly change for more than one decade, apart from the abandonment of IL-2, which demonstrated unacceptable toxicity. Of note, immunotherapy is a promising therapeutic option in cancer and could be optimized by several strategies. These include the HLA-haploidentical αβT/B-depleted HSCT, and the antibody targeting of novel NB-associated antigens such as B7-H3, and PD1. Other approaches could limit the immunoregulatory role of tumor-derived exosomes and potentiate the low antibody-dependent cell cytotoxicity of CD16 dim/neg NK cells, abundant in the early phase post-transplant. The latter effect could be obtained using multi-specific tools engaging activating NK receptors and tumor antigens, and possibly holding immunostimulatory cytokines in their construct. Finally, treatments also consider the infusion of novel engineered cytokines with scarce side effects, and cell effectors engineered with chimeric antigen receptors (CARs). Our review aims to discuss several promising strategies that could be successfully exploited to potentiate the NK-mediated surveillance of neuroblastoma, particularly in the HSCT setting. Many of these approaches are safe, feasible, and effective at pre-clinical and clinical levels.
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Affiliation(s)
- Cristina Bottino
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
- Correspondence: ; Tel.: +39-01056363855
| | - Mariella Della Chiesa
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
| | | | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Chiara Vitale
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
| | - Alessandra Dondero
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
| | - Annalisa Tondo
- Department of Pediatric Hematology/Oncology and HSCT, Meyer Children’s University Hospital, 50139 Florence, Italy
| | - Massimo Conte
- Pediatric Oncology Unit-IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Alberto Garaventa
- Pediatric Oncology Unit-IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Roberta Castriconi
- Department of Experimental Medicine (DIMES), University of Genoa, 16132 Genoa, Italy
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Sparano C, Solís-Sayago D, Vijaykumar A, Rickenbach C, Vermeer M, Ingelfinger F, Litscher G, Fonseca A, Mussak C, Mayoux M, Friedrich C, Nombela-Arrieta C, Gasteiger G, Becher B, Tugues S. Embryonic and neonatal waves generate distinct populations of hepatic ILC1s. Sci Immunol 2022; 7:eabo6641. [PMID: 36054340 DOI: 10.1126/sciimmunol.abo6641] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Group 1 innate lymphoid cells (ILCs) comprising circulating natural killer (cNK) cells and tissue-resident ILC1s are critical for host defense against pathogens and tumors. Despite a growing understanding of their role in homeostasis and disease, the ontogeny of group 1 ILCs remains largely unknown. Here, we used fate mapping and single-cell transcriptomics to comprehensively investigate the origin and turnover of murine group 1 ILCs. Whereas cNK cells are continuously replaced throughout life, we uncovered tissue-dependent development and turnover of ILC1s. A first wave of ILC1s emerges during embryogenesis in the liver and transiently colonizes fetal tissues. After birth, a second wave quickly replaces ILC1s in most tissues apart from the liver, where they layer with embryonic ILC1s, persist until adulthood, and undergo a specific developmental program. Whereas embryonically derived ILC1s give rise to a cytotoxic subset, the neonatal wave establishes the full spectrum of ILC1s. Our findings uncover key ontogenic features of murine group 1 ILCs and their association with cellular identities and functions.
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Affiliation(s)
- Colin Sparano
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Darío Solís-Sayago
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Anjali Vijaykumar
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Chiara Rickenbach
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| | - Marijne Vermeer
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Florian Ingelfinger
- Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Gioana Litscher
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - André Fonseca
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Caroline Mussak
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Maud Mayoux
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Christin Friedrich
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - César Nombela-Arrieta
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Burkhard Becher
- Inflammation Research, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Sonia Tugues
- Innate Lymphoid Cells and Cancer, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
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37
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Hoekzema RS, Marsh L, Sumray O, Carroll TM, Lu X, Byrne HM, Harrington HA. Multiscale Methods for Signal Selection in Single-Cell Data. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1116. [PMID: 36010781 PMCID: PMC9407339 DOI: 10.3390/e24081116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Analysis of single-cell transcriptomics often relies on clustering cells and then performing differential gene expression (DGE) to identify genes that vary between these clusters. These discrete analyses successfully determine cell types and markers; however, continuous variation within and between cell types may not be detected. We propose three topologically motivated mathematical methods for unsupervised feature selection that consider discrete and continuous transcriptional patterns on an equal footing across multiple scales simultaneously. Eigenscores (eigi) rank signals or genes based on their correspondence to low-frequency intrinsic patterning in the data using the spectral decomposition of the Laplacian graph. The multiscale Laplacian score (MLS) is an unsupervised method for locating relevant scales in data and selecting the genes that are coherently expressed at these respective scales. The persistent Rayleigh quotient (PRQ) takes data equipped with a filtration, allowing the separation of genes with different roles in a bifurcation process (e.g., pseudo-time). We demonstrate the utility of these techniques by applying them to published single-cell transcriptomics data sets. The methods validate previously identified genes and detect additional biologically meaningful genes with coherent expression patterns. By studying the interaction between gene signals and the geometry of the underlying space, the three methods give multidimensional rankings of the genes and visualisation of relationships between them.
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Affiliation(s)
- Renee S. Hoekzema
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Department of Mathematics, Free University of Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Lewis Marsh
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Otto Sumray
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Thomas M. Carroll
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Helen M. Byrne
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Ludwig Institute for Cancer Research, University of Oxford, Oxford OX1 2JD, UK
| | - Heather A. Harrington
- Mathematical Institute, University of Oxford, Oxford OX1 2JD, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX1 2JD, UK
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38
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Medjouel Khlifi H, Guia S, Vivier E, Narni-Mancinelli E. Role of the ITAM-Bearing Receptors Expressed by Natural Killer Cells in Cancer. Front Immunol 2022; 13:898745. [PMID: 35757695 PMCID: PMC9231431 DOI: 10.3389/fimmu.2022.898745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Natural Killer (NK) cells are innate lymphoid cells (ILCs) capable of recognizing and directly killing tumor cells. They also secrete cytokines and chemokines, which participate in the shaping of the adaptive response. NK cells identify tumor cells and are activated through a net positive signal from inhibitory and activating receptors. Several activating NK cell receptors are coupled to adaptor molecules containing an immunoreceptor tyrosine-based activation motif (ITAM). These receptors include CD16 and the natural cytotoxic receptors NKp46, NKp44, NKp30 in humans. The powerful antitumor NK cell response triggered by these activating receptors has made them attractive targets for exploitation in immunotherapy. In this review, we will discuss the different activating receptors associated with ITAM-bearing cell surface receptors expressed on NK cells, their modulations in the tumor context and the various therapeutic tools developed to boost NK cell responses in cancer patients.
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Affiliation(s)
- Hakim Medjouel Khlifi
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France
| | - Sophie Guia
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France
| | - Eric Vivier
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France.,Innate Pharma Research Laboratories, Marseille, France.,APHM, Hôpital de la Timone, Marseille-Immunopôle, Marseille, France
| | - Emilie Narni-Mancinelli
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France
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Rahmani S, Yazdanpanah N, Rezaei N. Natural killer cells and acute myeloid leukemia: promises and challenges. Cancer Immunol Immunother 2022; 71:2849-2867. [PMID: 35639116 DOI: 10.1007/s00262-022-03217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
Acute myeloid leukemia (AML) is considered as one of the most malignant conditions of the bone marrow. Over the past few decades, despite substantial progresses in the management of AML, relapse remission remains a major problem. Natural killer cells (NK cells) are known as a unique component of the innate immune system. Due to swift tumor detection, distinct cytotoxic action, and extensive immune interaction, NK cells have been used in various cancer settings for decades. It has been a growing knowledge of therapeutic magnitudes ranging from adoptive NK cell transfer to chimeric antigen receptor NK cells, aiming to achieve better therapeutic responses in patients with AML. In this article, the potentials of NK cells for treatment of AML are highlighted, and challenges for such therapeutic methods are discussed. In addition, the clinical application of NK cells, mainly in patients with AML, is pictured according to the existing evidence.
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Affiliation(s)
- Shayan Rahmani
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Niloufar Yazdanpanah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Dr. Qarib St, Keshavarz Blvd, Tehran, 14194, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center Hospital, Tehran University of Medical Sciences, Dr. Qarib St, Keshavarz Blvd, Tehran, 14194, Iran. .,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran. .,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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40
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Busà R, Bulati M, Badami E, Zito G, Maresca DC, Conaldi PG, Ercolano G, Ianaro A. Tissue-Resident Innate Immune Cell-Based Therapy: A Cornerstone of Immunotherapy Strategies for Cancer Treatment. Front Cell Dev Biol 2022; 10:907572. [PMID: 35757002 PMCID: PMC9221069 DOI: 10.3389/fcell.2022.907572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/03/2022] [Indexed: 11/18/2022] Open
Abstract
Cancer immunotherapy has led to impressive advances in cancer treatment. Unfortunately, in a high percentage of patients is difficult to consistently restore immune responses to eradicate established tumors. It is well accepted that adaptive immune cells, such as B lymphocytes, CD4+ helper T lymphocytes, and CD8+ cytotoxic T-lymphocytes (CTLs), are the most effective cells able to eliminate tumors. However, it has been recently reported that innate immune cells, including natural killer cells (NK), dendritic cells (DC), macrophages, myeloid-derived suppressor cells (MDSCs), and innate lymphoid cells (ILCs), represent important contributors to modulating the tumor microenvironment and shaping the adaptive tumor response. In fact, their role as a bridge to adaptive immunity, make them an attractive therapeutic target for cancer treatment. Here, we provide a comprehensive overview of the pleiotropic role of tissue-resident innate immune cells in different tumor contexts. In addition, we discuss how current and future therapeutic approaches targeting innate immune cells sustain the adaptive immune system in order to improve the efficacy of current tumor immunotherapies.
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Affiliation(s)
- Rosalia Busà
- Research Department, Mediterranean Institute for Transplantation and Advanced Specialized Therapies (IRCCS ISMETT), Palermo, Italy
| | - Matteo Bulati
- Research Department, Mediterranean Institute for Transplantation and Advanced Specialized Therapies (IRCCS ISMETT), Palermo, Italy
| | - Ester Badami
- Research Department, Mediterranean Institute for Transplantation and Advanced Specialized Therapies (IRCCS ISMETT), Palermo, Italy
- Ri.MED Foundation, Palermo, Italy
| | - Giovanni Zito
- Research Department, Mediterranean Institute for Transplantation and Advanced Specialized Therapies (IRCCS ISMETT), Palermo, Italy
| | | | - Pier Giulio Conaldi
- Research Department, Mediterranean Institute for Transplantation and Advanced Specialized Therapies (IRCCS ISMETT), Palermo, Italy
| | - Giuseppe Ercolano
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
- *Correspondence: Giuseppe Ercolano,
| | - Angela Ianaro
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Naples, Italy
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41
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Sugimura R, Chao Y. Deciphering Innate Immune Cell-Tumor Microenvironment Crosstalk at a Single-Cell Level. Front Cell Dev Biol 2022; 10:803947. [PMID: 35646915 PMCID: PMC9140036 DOI: 10.3389/fcell.2022.803947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
The tumor microenvironment encompasses various innate immune cells which regulate tumor progression. Exploiting innate immune cells is a new frontier of cancer immunotherapy. However, the classical surface markers for cell-type classification cannot always well-conclude the phenotype, which will further hinge our understanding. The innate immune cells include dendritic cells, monocytes/macrophages, natural killer cells, and innate lymphoid cells. They play important roles in tumor growth and survival, in some cases promoting cancer, in other cases negating cancer. The precise characterization of innate immune cells at the single-cell level will boost the potential of cancer immunotherapy. With the development of single-cell RNA sequencing technology, the transcriptome of each cell in the tumor microenvironment can be dissected at a single-cell level, which paves a way for a better understanding of the cell type and its functions. Here, we summarize the subtypes and functions of innate immune cells in the tumor microenvironment based on recent literature on single-cell technology. We provide updates on recent achievements and prospects for how to exploit novel functions of tumor-associated innate immune cells and target them for cancer immunotherapy.
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Single-cell transcriptomics reveal a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19. Genome Med 2022; 14:46. [PMID: 35501841 PMCID: PMC9060844 DOI: 10.1186/s13073-022-01049-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/15/2022] [Indexed: 12/22/2022] Open
Abstract
Background Natural killer (NK) cells are innate lymphoid cells that mediate antitumour and antiviral responses. However, very little is known about how ageing influences human NK cells, especially at the single-cell level. Methods We applied single-cell sequencing (scRNA-seq) to human lymphocytes and NK cells from 4 young and 4 elderly individuals and then analysed the transcriptome data using Seurat. We detected the proportion and phenotype of NK cell subsets in peripheral blood samples from a total of 62 young and 52 elderly healthy donors by flow cytometry. We also used flow cytometry to examine the effector functions of NK cell subsets upon IFN-α/IL-12+IL-15/K562/IL-2 stimulation in vitro in peripheral blood samples from a total of 64 young and 63 elderly healthy donors. We finally studied and integrated single-cell transcriptomes of NK cells from 15 young and 41 elderly COVID-19 patients with those from 12 young and 6 elderly healthy control individuals to investigate the impacts of ageing on NK cell subsets in COVID-19 disease. Results We discovered a memory-like NK subpopulation (NK2) exhibiting the largest distribution change between elderly and young individuals among lymphocytes. Notably, we discovered a unique NK subset that was predominantly CD52+ NK2 cells (NK2.1). These memory-like NK2.1 cells accumulated with age, exhibited proinflammatory characteristics, and displayed a type I interferon response state. Integrative analyses of a large-cohort COVID-19 dataset and our datasets revealed that NK2.1 cells from elderly COVID-19 patients are enriched for type I interferon signalling, which is positively correlated with disease severity in COVID-19. Conclusions We identified a unique memory-like NK cell subset that accumulates with ageing and correlates with disease severity in COVID-19. Our results identify memory-like NK2.1 cells as a potential target for developing immunotherapies for infectious diseases and for addressing age-related dysfunctions of the immune system. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01049-3.
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Single-cell RNA sequencing analysis of human bone-marrow-derived mesenchymal stem cells and functional subpopulation identification. Exp Mol Med 2022; 54:483-492. [PMID: 35365767 PMCID: PMC9076886 DOI: 10.1038/s12276-022-00749-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 12/02/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are a common kind of multipotent cell in vivo, but their heterogeneity limits their further applications. To identify MSC subpopulations and clarify their relationships, we performed cell mapping of bone-marrow-derived MSCs through single-cell RNA (scRNA) sequencing. In our study, three main subpopulations, namely, the stemness subpopulation, functional subpopulation, and proliferative subpopulation, were identified using marker genes and further bioinformatic analyses. Developmental trajectory analysis showed that the stemness subpopulation was the root and then became either the functional subpopulation or the proliferative subpopulation. The functional subpopulation showed stronger immunoregulatory and osteogenic differentiation abilities but lower proliferation and adipogenic differentiation. MSCs at different passages or isolated from different donors exhibited distinct cell mapping profiles, which accounted for their corresponding different functions. This study provides new insight into the biological features and clinical use of MSCs at the single-cell level, which may contribute to expanding their application in the clinic.
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44
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Rethacker L, Boy M, Bisio V, Roussin F, Denizeau J, Vincent-Salomon A, Borcoman E, Sedlik C, Piaggio E, Toubert A, Dulphy N, Caignard A. Innate lymphoid cells: NK and cytotoxic ILC3 subsets infiltrate metastatic breast cancer lymph nodes. Oncoimmunology 2022; 11:2057396. [PMID: 35371620 PMCID: PMC8973349 DOI: 10.1080/2162402x.2022.2057396] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Innate lymphoid cells (ILCs) – which include cytotoxic Natural Killer (NK) cells and helper-type ILC – are important regulators of tissue immune homeostasis, with possible roles in tumor surveillance. We analyzed ILC and their functionality in human lymph nodes (LN). In LN, NK cells and ILC3 were the prominent subpopulations. Among the ILC3s, we identified a CD56+/ILC3 subset with a phenotype close to ILC3 but also expressing cytotoxicity genes shared with NK. In tumor-draining LNs (TD-LNs) and tumor samples from breast cancer (BC) patients, NK cells were prominent, and proportions of ILC3 subsets were low. In tumors and TD-LN, NK cells display reduced levels of NCR (Natural cytotoxicity receptors), despite high transcript levels and included a small subset CD127− CD56− NK cells with reduced function. Activated by cytokines CD56+/ILC3 cells from donor and patients LN acquired cytotoxic capacity and produced IFNg. In TD-LN, all cytokine activated ILC populations produced TNFα in response to BC cell line. Analyses of cytotoxic and helper ILC indicate a switch toward NK cells in TD-LN. The local tumor microenvironment inhibited NK cell functions through downregulation of NCR, but cytokine stimulation restored their functionality.
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Affiliation(s)
- Louise Rethacker
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
| | - Maxime Boy
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
| | - Valeria Bisio
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
| | - France Roussin
- Service d’Anesthésie-Réanimation, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Jordan Denizeau
- INSERM U932, Département de Recherche Translationelle, Institut Curie, Université de Recherche Paris Sciences & Lettres (PSL), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
| | - Anne Vincent-Salomon
- Diagnostic and Theranostic Medicine Division, Institut Curie, PSL Research University, Paris, France
| | - Edith Borcoman
- Department of Medical Oncology, Institut Curie, Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
| | - Christine Sedlik
- INSERM U932, Département de Recherche Translationelle, Institut Curie, Université de Recherche Paris Sciences & Lettres (PSL), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
| | - Eliane Piaggio
- INSERM U932, Département de Recherche Translationelle, Institut Curie, Université de Recherche Paris Sciences & Lettres (PSL), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
| | - Antoine Toubert
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
- Assistance Publique–Hôpitaux de Paris (AP–HP), Hôpital Saint-Louis, Laboratoire d’Immunologie et Histocompatibilité, Paris, France
| | - Nicolas Dulphy
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
- Assistance Publique–Hôpitaux de Paris (AP–HP), Hôpital Saint-Louis, Laboratoire d’Immunologie et Histocompatibilité, Paris, France
| | - Anne Caignard
- INSERM U1160, Institut de Recherche Saint-Louis, Hôpital Saint Louis, Paris, France
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45
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Wolf D, Barreras H, Copsel SN, Komanduri KV, Levy RB. Improved NK cell recovery following the use of PTCy or Treg expanded donors in experimental MHC-matched allogeneic BMT. Transplant Cell Ther 2022; 28:303.e1-303.e7. [DOI: 10.1016/j.jtct.2022.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
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46
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Understanding natural killer cell biology from a single cell perspective. Cell Immunol 2022; 373:104497. [DOI: 10.1016/j.cellimm.2022.104497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/26/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022]
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47
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Seo S, Mace EM. Diversity of human NK cell developmental pathways defined by single-cell analyses. Curr Opin Immunol 2022; 74:106-111. [PMID: 34861544 PMCID: PMC8901532 DOI: 10.1016/j.coi.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Human natural killer (NK) and innate lymphoid cells (ILCs) include diverse specialized phenotypic and functional subsets that reflect their roles as innate immune effector cells present in tissue and circulation. In recent years, significant advances have been made in better defining their tissue resident phenotypes, developmental pathways, and phenotypic plasticity. Here we offer a brief review of new insights into human NK cell diversity specifically defined by next generation sequencing and single-cell transcriptomic studies and integrate these into our current models of human NK cell developmental trajectories and mature subsets. These studies highlight both a deeper understanding of innate lymphoid cell differentiation and homeostasis and underscore critical questions that remain outstanding in the field.
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Affiliation(s)
- Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
| | - Emily M. Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
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48
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Bou-Tayeh B, Laletin V, Salem N, Just-Landi S, Fares J, Leblanc R, Balzano M, Kerdiles YM, Bidaut G, Hérault O, Olive D, Aurrand-Lions M, Walzer T, Nunès JA, Fauriat C. Chronic IL-15 Stimulation and Impaired mTOR Signaling and Metabolism in Natural Killer Cells During Acute Myeloid Leukemia. Front Immunol 2021; 12:730970. [PMID: 34975835 PMCID: PMC8718679 DOI: 10.3389/fimmu.2021.730970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022] Open
Abstract
Natural Killer (NK) cells are potent anti-leukemic immune effectors. However, they display multiple defects in acute myeloid leukemia (AML) patients leading to reduced anti-tumor potential. Our limited understanding of the mechanisms underlying these defects hampers the development of strategies to restore NK cell potential. Here, we have used a mouse model of AML to gain insight into these mechanisms. We found that leukemia progression resulted in NK cell maturation defects and functional alterations. Next, we assessed NK cell cytokine signaling governing their behavior. We showed that NK cells from leukemic mice exhibit constitutive IL-15/mTOR signaling and type I IFN signaling. However, these cells failed to respond to IL-15 stimulation in vitro as illustrated by reduced activation of the mTOR pathway. Moreover, our data suggest that mTOR-mediated metabolic responses were reduced in NK cells from AML-bearing mice. Noteworthy, the reduction of mTOR-mediated activation of NK cells during AML development partially rescued NK cell metabolic and functional defects. Altogether, our data strongly suggest that NK cells from leukemic mice are metabolically and functionally exhausted as a result of a chronic cytokine activation, at least partially IL-15/mTOR signaling. NK cells from AML patients also displayed reduced IL-2/15Rβ expression and showed cues of reduced metabolic response to IL-15 stimulation in vitro, suggesting that a similar mechanism might occur in AML patients. Our study pinpoints the dysregulation of cytokine stimulation pathways as a new mechanism leading to NK cell defects in AML.
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Affiliation(s)
- Berna Bou-Tayeh
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Vladimir Laletin
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Nassim Salem
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Sylvaine Just-Landi
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
- IBiSA Immunomonitoring Platform, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Joanna Fares
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Raphael Leblanc
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Marielle Balzano
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Yann M. Kerdiles
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'Immunologie de Marseille-Luminy (CIML), Marseille, France
| | - Ghislain Bidaut
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
- Cibi Technological Platform, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Olivier Hérault
- Centre National de la Recherche Scientifique (CNRS) UMR 7292, LNOx Team, François Rabelais University, Tours, France
| | - Daniel Olive
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
- IBiSA Immunomonitoring Platform, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Michel Aurrand-Lions
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon, France
| | - Jacques A. Nunès
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
| | - Cyril Fauriat
- Aix-Marseille Université UM105, Centre National de la Recherche Scientifique (CNRS) UMR7258, Inserm UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille (CRCM), Marseille, France
- *Correspondence: Cyril Fauriat,
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49
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Zeng X, Yao D, Liu L, Zhang Y, Lai J, Zhong J, Zha X, Lu Y, Jin Z, Chen S, Li Y, Xu L. Terminal differentiation of bone marrow NK cells and increased circulation of TIGIT + NK cells may be related to poor outcome in acute myeloid leukemia. Asia Pac J Clin Oncol 2021; 18:456-464. [PMID: 34811925 DOI: 10.1111/ajco.13723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
AIM In order to further understand the feature of natural killer cell (NK) dysfunction in acute myeloid leukemia (AML), The distribution of NK cell subset the expression of the inhibitory receptors immunoglobulin and ITIM domain (TIGIT), killer cell lectin-like receptor (KLRG1), and the expression of maturation marker CD57 in NK cell subsets and their correlation with patient outcomes were analyzed in this study. METHODS We collected peripheral blood (PB) and bone marrow (BM) samples from de novo AML (AML-DN) patients, patients who achieved complete remission after chemotherapy (AML-CR), and healthy individuals. An eight-color flow cytometry panel was used to identify different NK subsets and their expression of TIGIT, CD57 and KLRG1. RESULTS Decreased percentage of CD56dim CD16+ NK cells was found only in the PB of AML-DN and AML-CR patients but not in the BM. The expression frequency of TIGIT and KLRG1 was elevated on NK cells from the PB of AML-DN patients, while it was recovered in AML-CR patients. Moreover, a higher percentage of CD57+ CD56dim CD16+ NK cells, representing a terminally differentiated NK subset with strong cytotoxic capacity but defective replication potential, was detected in the BM of AML-DN patients and predicted sub-optimal survival for patients. CONCLUSION The results indicated that the NK cell subsets in the PB of AML patients had an exhaustion phenotype, while the BM NK cells had a terminally differentiated phenotype, which correlated with short survival for AML patients.
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Affiliation(s)
- Xiangbo Zeng
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Danlin Yao
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Lian Liu
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Yikai Zhang
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Jing Lai
- Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Jun Zhong
- Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Xianfeng Zha
- Department of clinical laboratory, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Yuhong Lu
- Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Zhenyi Jin
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China
| | - Shaohua Chen
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China
| | - Yangqiu Li
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
| | - Ling Xu
- Key Laboratory for Regenerative Medicine of Ministry of Education; Institute of Hematology, School of Medicine; Jinan University, Guangzhou, 510632, China.,Department of Hematology; First Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510632, China
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50
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Barnes SA, Trew I, de Jong E, Foley B. Making a Killer: Selecting the Optimal Natural Killer Cells for Improved Immunotherapies. Front Immunol 2021; 12:765705. [PMID: 34777383 PMCID: PMC8578927 DOI: 10.3389/fimmu.2021.765705] [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] [Received: 08/27/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Over the past 20 years natural killer (NK) cell-based immunotherapies have emerged as a safe and effective treatment option for patients with relapsed or refractory leukemia. Unlike T cell-based therapies, NK cells harbor an innate capacity to eliminate malignant cells without prior sensitization and can be adoptively transferred between individuals without the need for extensive HLA matching. A wide variety of therapeutic NK cell sources are currently being investigated clinically, including allogeneic donor-derived NK cells, stem cell-derived NK cells and NK cell lines. However, it is becoming increasingly clear that not all NK cells are endowed with the same antitumor potential. Despite advances in techniques to enhance NK cell cytotoxicity and persistence, the initial identification and utilization of highly functional NK cells remains essential to ensure the future success of adoptive NK cell therapies. Indeed, little consideration has been given to the identification and selection of donors who harbor NK cells with potent antitumor activity. In this regard, there is currently no standard donor selection criteria for adoptive NK cell therapy. Here, we review our current understanding of the factors which govern NK cell functional fate, and propose a paradigm shift away from traditional phenotypic characterization of NK cell subsets towards a functional profile based on molecular and metabolic characteristics. We also discuss previous selection models for NK cell-based immunotherapies and highlight important considerations for the selection of optimal NK cell donors for future adoptive cell therapies.
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Affiliation(s)
- Samantha A Barnes
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Isabella Trew
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Emma de Jong
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Bree Foley
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
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