201
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Song G, Shi Y, Zhang M, Goswami S, Afridi S, Meng L, Ma J, Chen Y, Lin Y, Zhang J, Liu Y, Jin Z, Yang S, Rao D, Zhang S, Ke A, Wang X, Cao Y, Zhou J, Fan J, Zhang X, Xi R, Gao Q. Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression. Cell Discov 2020; 6:90. [PMID: 33298893 PMCID: PMC7721904 DOI: 10.1038/s41421-020-00214-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Diverse immune cells in the tumor microenvironment form a complex ecosystem, but our knowledge of their heterogeneity and dynamics within hepatocellular carcinoma (HCC) still remains limited. To assess the plasticity and phenotypes of immune cells within HBV/HCV-related HCC microenvironment at single-cell level, we performed single-cell RNA sequencing on 41,698 immune cells from seven pairs of HBV/HCV-related HCC tumors and non-tumor liver tissues. We combined bio-informatic analyses, flow cytometry, and multiplex immunohistochemistry to assess the heterogeneity of different immune cell subsets in functional characteristics, transcriptional regulation, phenotypic switching, and interactions. We identified 29 immune cell subsets of myeloid cells, NK cells, and lymphocytes with unique transcriptomic profiles in HCC. A highly complex immunological network was shaped by diverse immune cell subsets that can transit among different states and mutually interact. Notably, we identified a subset of M2 macrophage with high expression of CCL18 and transcription factor CREM that was enriched in advanced HCC patients, and potentially participated in tumor progression. We also detected a new subset of activated CD8+ T cells highly expressing XCL1 that correlated with better patient survival rates. Meanwhile, distinct transcriptomic signatures, cytotoxic phenotypes, and evolution trajectory of effector CD8+ T cells from early-stage to advanced HCC were also identified. Our study provides insight into the immune microenvironment in HBV/HCV-related HCC and highlights novel macrophage and T-cell subsets that could be further exploited in future immunotherapy.
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Affiliation(s)
- Guohe Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Yang Shi
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Meiying Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shyamal Goswami
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Saifullah Afridi
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Biological Sciences (DBS), National University of Medical Sciences (NUMS), Secretariat c/o Military Hospital, Adjacent to Armed Force Institute of Cardiology, The Mall Rawalpindi, Rawalpindi 46000, Pakistan
| | - Lu Meng
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqiang Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Chen
- Department of Laboratory Medicine, Nantong First People's Hospital, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Juan Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Yuming Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Zijie Jin
- School of Mathematical Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Shuaixi Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Aiwu Ke
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan 410078, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China.
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, China. .,Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China. .,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
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202
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Cózar B, Greppi M, Carpentier S, Narni-Mancinelli E, Chiossone L, Vivier E. Tumor-Infiltrating Natural Killer Cells. Cancer Discov 2020; 11:34-44. [PMID: 33277307 DOI: 10.1158/2159-8290.cd-20-0655] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/03/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
Because of their potent antitumor activity and their proinflammatory role, natural killer (NK) cells are at the forefront of efforts to develop immuno-oncologic treatments. NK cells participate in immune responses to tumors by killing target cells and producing cytokines. However, in the immunosuppressive tumor microenvironment, NK cells become dysfunctional through exposure to inhibitory molecules produced by cancer cells, leading to tumor escape. We provide an overview of what is known about NK tumor infiltration and surveillance and about the mechanisms by which NK cells become dysfunctional. SIGNIFICANCE: The functions of tumor-infiltrating NK cells may be impaired. This review aims to describe the various mechanisms by which tumors alter NK-cell functions.
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Affiliation(s)
- Beatriz Cózar
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France
| | - Marco Greppi
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France.,Center of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | | | | | - Laura Chiossone
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France
| | - Eric Vivier
- Innate Pharma Research Laboratories, Innate Pharma, Marseille, France. .,Aix Marseille University, CNRS, INSERM, CIML, Marseille, France.,APHM, Hôpital de la Timone, Service d'Immunologie, Marseille-Immunopôle, Marseille, France
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203
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Schwane V, Huynh-Tran VH, Vollmers S, Yakup VM, Sauter J, Schmidt AH, Peine S, Altfeld M, Richert L, Körner C. Distinct Signatures in the Receptor Repertoire Discriminate CD56bright and CD56dim Natural Killer Cells. Front Immunol 2020; 11:568927. [PMID: 33335526 PMCID: PMC7736243 DOI: 10.3389/fimmu.2020.568927] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/20/2020] [Indexed: 01/01/2023] Open
Abstract
NK cells are phenotypically and functionally diverse lymphocytes due to variegated expression of a large array of receptors. NK-cell activity is tightly regulated through integration of receptor-derived inhibitory and activating signals. Thus, the receptor profile of each NK cell ultimately determines its ability to sense aberrant cells and subsequently mediate anti-viral or anti-tumor responses. However, an in-depth understanding of how different receptor repertoires enable distinct immune functions of NK cells is lacking. Therefore, we investigated the phenotypic diversity of primary human NK cells by performing extensive phenotypic characterization of 338 surface molecules using flow cytometry (n = 18). Our results showed that NK cells express at least 146 receptors on their surface. Of those, 136 (>90%) exhibited considerable inter-donor variability. Moreover, comparative analysis of CD56bright and CD56dim NK cells identified 70 molecules with differential expression between the two major NK-cell subsets and allowed discrimination of these subsets via unsupervised hierarchical clustering. These receptors were associated with a broad range of NK-cell functions and multiple molecules were not previously associated with predominant expression on either subset (e.g. CD82 and CD147). Altogether, our study contributes to an improved understanding of the phenotypic diversity of NK cells and its potential functional implications on a cellular and population level. While the identified distinct signatures in the receptor repertoires provide a molecular basis for the differential immune functions exerted by CD56bright and CD56dim NK cells, the observed inter-individual differences in the receptor repertoire of NK cells may contribute to a diverging ability to control certain diseases.
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Affiliation(s)
- Vera Schwane
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Van Hung Huynh-Tran
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR1219 and Inria, team SISTM, Bordeaux, France
| | - Sarah Vollmers
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Vivien Maria Yakup
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Alexander H. Schmidt
- DKMS gemeinnützige GmbH, Tübingen, Germany
- DKMS Life Science Lab, Dresden, Germany
| | - Sven Peine
- Institute for Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Department of Immunology, University Hospital Eppendorf (UKE), Hamburg, Germany
| | - Laura Richert
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR1219 and Inria, team SISTM, Bordeaux, France
| | - Christian Körner
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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204
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Cao Y, Qiu Y, Tu G, Yang C. Single-cell RNA Sequencing in Immunology. Curr Genomics 2020; 21:564-575. [PMID: 33414678 PMCID: PMC7770633 DOI: 10.2174/1389202921999201020203249] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
The complex immune system is involved in multiple pathological processes. Single-cell RNA sequencing (scRNA-seq) is able to analyze complex cell mixtures correct to a single cell and single molecule, thus is qualified to analyze immune reactions in several diseases. In recent years, scRNA-seq has been applied in many researching fields and has presented many innovative results. In this review, we intend to provide an overview of single-cell RNA sequencing applications in immunology and a prospect of future directions.
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Affiliation(s)
| | | | - Guowei Tu
- Address correspondence to these authors at the Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Tel: +86-21-64041990; E-mails: ; and Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Tel: +86-21-64041990;, E-mail:
| | - Cheng Yang
- Address correspondence to these authors at the Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Tel: +86-21-64041990; E-mails: ; and Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Tel: +86-21-64041990;, E-mail:
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205
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Yang C, Malarkannan S. Transcriptional Regulation of NK Cell Development by mTOR Complexes. Front Cell Dev Biol 2020; 8:566090. [PMID: 33240877 PMCID: PMC7683515 DOI: 10.3389/fcell.2020.566090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022] Open
Abstract
The mechanistic target of Rapamycin (mTOR) is essential for multiple cellular processes. The unique roles of mTOR complex 1 (mTORC1) or mTOR2 in regulating immune functions are emerging. NK cells are the major lymphocyte subset of innate immunity, and their development and effector functions require metabolic reprogramming. Recent studies demonstrate that in NK cells, conditionally disrupting the formation of mTORC1 or mTOR complex 2 (mTORC2) alters their development significantly. Transcriptomic profiling of NK cells at the single-cell level demonstrates that mTORC1 was critical for the early developmental progression, while mTORC2 regulated the terminal maturation. In this review, we summarize the essential roles of mTOR complexes in NK development and functions.
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Affiliation(s)
- Chao Yang
- Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, WI, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, WI, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
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206
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Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemia. Cell Mol Immunol 2020; 18:1290-1304. [PMID: 33239726 PMCID: PMC8093261 DOI: 10.1038/s41423-020-00574-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells are innate cytotoxic lymphoid cells (ILCs) involved in the killing of infected and tumor cells. Among human and mouse NK cells from the spleen and blood, we previously identified by single-cell RNA sequencing (scRNAseq) two similar major subsets, NK1 and NK2. Using the same technology, we report here the identification, by single-cell RNA sequencing (scRNAseq), of three NK cell subpopulations in human bone marrow. Pseudotime analysis identified a subset of resident CD56bright NK cells, NK0 cells, as the precursor of both circulating CD56dim NK1-like NK cells and CD56bright NK2-like NK cells in human bone marrow and spleen under physiological conditions. Transcriptomic profiles of bone marrow NK cells from patients with acute myeloid leukemia (AML) exhibited stress-induced repression of NK cell effector functions, highlighting the profound impact of this disease on NK cell heterogeneity. Bone marrow NK cells from AML patients exhibited reduced levels of CD160, but the CD160high group had a significantly higher survival rate.
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207
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Tufa DM, Yingst AM, Trahan GD, Shank T, Jones D, Shim S, Lake J, Winkler K, Cobb L, Woods R, Jones K, Verneris MR. Human innate lymphoid cell precursors express CD48 that modulates ILC differentiation through 2B4 signaling. Sci Immunol 2020; 5:eaay4218. [PMID: 33219153 PMCID: PMC8294935 DOI: 10.1126/sciimmunol.aay4218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 06/15/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Innate lymphoid cells (ILCs) develop from common lymphoid progenitors (CLPs), which further differentiate into the common ILC progenitor (CILP) that can give rise to both ILCs and natural killer (NK) cells. Murine ILC intermediates have recently been characterized, but the human counterparts and their developmental trajectories have not yet been identified, largely due to the lack of homologous surface receptors in both organisms. Here, we show that human CILPs (CD34+CD117+α4β7+Lin-) acquire CD48 and CD52, which define NK progenitors (NKPs) and ILC precursors (ILCPs). Two distinct NK cell subsets were generated in vitro from CD34+CD117+α4β7+Lin-CD48-CD52+ and CD34+CD117+α4β7+Lin-CD48+CD52+ NKPs, respectively. Independent of NKPs, ILCPs exist in the CD34+CD117+α4β7+Lin-CD48+CD52+ subset and give rise to ILC1s, ILC2s, and NCR+ ILC3s, whereas CD34+CD117+α4β7+Lin-CD48+CD52- ILCPs give rise to a distinct subset of ILC3s that have lymphoid tissue inducer (LTi)-like properties. In addition, CD48-expressing CD34+CD117+α4β7+Lin- precursors give rise to tissue-associated ILCs in vivo. We also observed that the interaction of 2B4 with CD48 induced differentiation of ILC2s, and together, these findings show that expression of CD48 by human ILCPs modulates ILC differentiation.
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Affiliation(s)
- Dejene M Tufa
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Ashley M Yingst
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - George Devon Trahan
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Tyler Shank
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Dallas Jones
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Seonhui Shim
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Jessica Lake
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Kevin Winkler
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Laura Cobb
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Renee Woods
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Kenneth Jones
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA
| | - Michael R Verneris
- Department of Pediatric, Division of Children's Cancer and Blood Disorders, University of Colorado and Children's Hospital of Colorado, Research Complex 1, North Tower, 12800 E. 19th Ave., Mail Stop 8302, Room P18-4108, Aurora, CO 80045, USA.
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208
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Niu J, Huang Y, Liu X, Zhang Z, Tang J, Wang B, Lu Y, Cai J, Jian J. Single-cell RNA-seq reveals different subsets of non-specific cytotoxic cells in teleost. Genomics 2020; 112:5170-5179. [DOI: 10.1016/j.ygeno.2020.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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209
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Cook ME, Jarjour NN, Lin CC, Edelson BT. Transcription Factor Bhlhe40 in Immunity and Autoimmunity. Trends Immunol 2020; 41:1023-1036. [PMID: 33039338 DOI: 10.1016/j.it.2020.09.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023]
Abstract
The basic helix-loop-helix transcription factor (TF) Bhlhe40 is emerging as a key regulator of immunity during infection, autoimmunity, and inflammatory conditions. We describe the roles of Bhlhe40 in the circulating and tissue-resident arms of the immune system, with emphasis on recent work on the regulation of cytokine production and proliferation. We explore the mechanisms behind these functions in mouse models and human cells, including interactions with other TFs, and propose that Bhlhe40 is a central mediator of both inflammation and pathogen control, as well as a crucial regulator of a growing number of tissue-resident leukocyte populations. Finally, we suggest areas for further study that may advance our understanding of immunity and disease.
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Affiliation(s)
- Melissa E Cook
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas N Jarjour
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Chih-Chung Lin
- Genetics and Aging Research Unit, Mass General Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Brian T Edelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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210
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Niu J, Liu X, Zhang Z, Huang Y, Tang J, Wang B, Lu Y, Cai J, Jian J. A tandem-repeat galectin-4 from Nile tilapia (Oreochromis niloticus) is involved in immune response to bacterial infection via mediating pathogen recognition and opsonization. Mol Immunol 2020; 127:67-77. [PMID: 32927166 DOI: 10.1016/j.molimm.2020.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/23/2022]
Abstract
Galectins are the family of carbohydrate-binding proteins that participate in host-pathogen interaction. In this study, a galectin-4 homolog (OnGal-4) from Nile tilapia (Oreochromis niloticus) was characterized. The open reading frame of OnGal-4 was 1194 bp, encoding a peptide of 397 amino including two CRD regions and two carbohydrate recognition sites. OnGal-4 mRNA was expressed in all examined tissues with the highest level in spleen. After Streptococcus agalactiae (S.agalactiae) challenge, the OnGal-4 expression was up-regulated in the spleen, head kidney, brain, and monocytes/macrophages (Mo/MΦ). The in vitro experiments showed that recombinant OnGal-4 (rOnGal-4) protein could bind and agglutinate S.agalactiae and A.hydrophila. Also, rOnGal-4 could induce cytokines expressions and increased bactericidal activity of Mo/MΦ. Further in vivo analysis indicated that OnGal-4 overexpression could protect O.niloticus from S.agalactiae infection through modulating inflammation response. Our study suggested that OnGal-4 could improve immune response against bacterial infection by mediating pathogen recognition and opsonization.
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Affiliation(s)
- Jinzhong Niu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China
| | - Xinchao Liu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China
| | - Zhiqiang Zhang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China
| | - Yu Huang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China
| | - Jufen Tang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China
| | - Bei Wang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China
| | - Yishan Lu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China
| | - Jia Cai
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China; Guangxi Key Lab for Marine Natural Products and Combinational Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Centre, Guangxi Academy of Sciences, Nanning, China.
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, GD, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong ProvincialEngineeringResearchCenter for AquaticAnimalHealthAssessment, Shenzhen, 518120, China.
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211
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Nguyen R, Patel AG, Griffiths LM, Dapper J, Stewart EA, Houston J, Johnson M, Akers WJ, Furman WL, Dyer MA. Next-generation humanized patient-derived xenograft mouse model for pre-clinical antibody studies in neuroblastoma. Cancer Immunol Immunother 2020; 70:721-732. [PMID: 32915319 DOI: 10.1007/s00262-020-02713-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/31/2020] [Indexed: 12/16/2022]
Abstract
Faithful tumor mouse models are fundamental research tools to advance the field of immuno-oncology (IO). This is particularly relevant in diseases with low incidence, as in the case of pediatric malignancies, that rely on pre-clinical therapeutic development. However, conventional syngeneic and genetically engineered mouse models fail to recapitulate the tumor heterogeneity and microenvironmental complexity of human pathology that are essential determinants of cancer-directed immunity. Here, we characterize a novel mouse model that supports human natural killer (NK) cell development and engraftment of neuroblastoma orthotopic patient-derived xenograft (O-PDX) for pre-clinical antibody and cytokine testing. Using cytotoxicity assays, single-cell RNA-sequencing, and multi-color flow cytometry, we demonstrate that NK cells that develop in the humanized mice are fully licensed to execute NK cell cytotoxicity, permit human tumor engraftment, but can be therapeutically redirected to induce antibody-dependent cell-mediated cytotoxicity (ADCC). Although these cells share phenotypic and molecular features with healthy controls, we noted that they lacked an NK cell subset, termed activated NK cells, that is characterized by differentially expressed genes that are induced by cytokine activation. Because this subset of genes is also downregulated in patients with neuroblastoma compared to healthy controls, we hypothesize that this finding could be due to tumor-mediated suppressive effects. Thus, despite its technical complexity, this humanized patient-derived xenograft mouse model could serve as a faithful system for future testing of IO applications and studies of underlying immunologic processes.
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Affiliation(s)
- Rosa Nguyen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD, USA.
| | - Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lyra M Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason Dapper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth A Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jim Houston
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Melissa Johnson
- Center for In Vivo Imaging and Therapeutics (CIVIT), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walter J Akers
- Center for In Vivo Imaging and Therapeutics (CIVIT), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wayne L Furman
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
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212
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Russick J, Torset C, Hemery E, Cremer I. NK cells in the tumor microenvironment: Prognostic and theranostic impact. Recent advances and trends. Semin Immunol 2020; 48:101407. [PMID: 32900565 DOI: 10.1016/j.smim.2020.101407] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/02/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022]
Abstract
NK cells orchestrate the tumor destruction and control metastasis in a coordinated way with other immune cells of the tumor microenvironment. However, NK cell infiltration in the tumor microenvironment is limited, and tumor cells have developed numerous mechanisms to escape NK cell attack. As a result, NK cells that have been able to infiltrate the tumors are exhausted, and metabolically and functionally impaired. Depending this impairment the prognostic and theranostic values of NK cells differ depending on the studies, the type of cancer, the stage of tumor and the nature of the tumor microenvironment. Extensive studies have been done to investigate different strategies to improve the NK cell function, and nowadays, a battery of therapeutic tools are being tested, with promising results.
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Affiliation(s)
- Jules Russick
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team Inflammation, Complement and Cancer, F-75006, Paris, France
| | - Carine Torset
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team Inflammation, Complement and Cancer, F-75006, Paris, France
| | - Edouard Hemery
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team Inflammation, Complement and Cancer, F-75006, Paris, France
| | - Isabelle Cremer
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Team Inflammation, Complement and Cancer, F-75006, Paris, France.
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213
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Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Pinaud S, Nicholls A, Ros XR, Su J, Eldridge MD, Riedel A, Serrao EM, Rodewald HR, Mack M, Shields JD, Cohen ES, McKenzie ANJ, Goodwin RJA, Brindle KM, Marioni JC, Halim TYF. ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung. Nat Immunol 2020; 21:998-1009. [PMID: 32747815 PMCID: PMC7116357 DOI: 10.1038/s41590-020-0745-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 06/23/2020] [Indexed: 12/23/2022]
Abstract
Metastasis constitutes the primary cause of cancer-related deaths, with the lung being a commonly affected organ. We found that activation of lung-resident group 2 innate lymphoid cells (ILC2s) orchestrated suppression of natural killer (NK) cell-mediated innate antitumor immunity, leading to increased lung metastases and mortality. Using multiple models of lung metastasis, we show that interleukin (IL)-33-dependent ILC2 activation in the lung is involved centrally in promoting tumor burden. ILC2-driven innate type 2 inflammation is accompanied by profound local suppression of interferon-γ production and cytotoxic function of lung NK cells. ILC2-dependent suppression of NK cells is elaborated via an innate regulatory mechanism, which is reliant on IL-5-induced lung eosinophilia, ultimately limiting the metabolic fitness of NK cells. Therapeutic targeting of IL-33 or IL-5 reversed NK cell suppression and alleviated cancer burden. Thus, we reveal an important function of IL-33 and ILC2s in promoting tumor metastasis via their capacity to suppress innate type 1 immunity.
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Affiliation(s)
| | - Shaun Png
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Arianne C Richard
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Anastasia Tsyben
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gregory Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Julie Stockis
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Celine Garcia
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Silvain Pinaud
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ashley Nicholls
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Xavier Romero Ros
- Bioscience Asthma, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jing Su
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Angela Riedel
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Eva M Serrao
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Mack
- Department of Internal Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - E Suzanne Cohen
- Bioscience Asthma, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Richard J A Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Kevin M Brindle
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - John C Marioni
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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214
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van Eeden C, Khan L, Osman MS, Cohen Tervaert JW. Natural Killer Cell Dysfunction and Its Role in COVID-19. Int J Mol Sci 2020; 21:E6351. [PMID: 32883007 PMCID: PMC7503862 DOI: 10.3390/ijms21176351] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/15/2022] Open
Abstract
When facing an acute viral infection, our immune systems need to function with finite precision to enable the elimination of the pathogen, whilst protecting our bodies from immune-related damage. In many instances however this "perfect balance" is not achieved, factors such as ageing, cancer, autoimmunity and cardiovascular disease all skew the immune response which is then further distorted by viral infection. In SARS-CoV-2, although the vast majority of COVID-19 cases are mild, as of 24 August 2020, over 800,000 people have died, many from the severe inflammatory cytokine release resulting in extreme clinical manifestations such as acute respiratory distress syndrome (ARDS) and hemophagocytic lymphohistiocytosis (HLH). Severe complications are more common in elderly patients and patients with cardiovascular diseases. Natural killer (NK) cells play a critical role in modulating the immune response and in both of these patient groups, NK cell effector functions are blunted. Preliminary studies in COVID-19 patients with severe disease suggests a reduction in NK cell number and function, resulting in decreased clearance of infected and activated cells, and unchecked elevation of tissue-damaging inflammation markers. SARS-CoV-2 infection skews the immune response towards an overwhelmingly inflammatory phenotype. Restoration of NK cell effector functions has the potential to correct the delicate immune balance required to effectively overcome SARS-CoV-2 infection.
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Affiliation(s)
| | | | | | - Jan Willem Cohen Tervaert
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada; (C.v.E.); (L.K.); (M.S.O.)
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215
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Aass KR, Kastnes MH, Standal T. Molecular interactions and functions of IL-32. J Leukoc Biol 2020; 109:143-159. [PMID: 32869391 DOI: 10.1002/jlb.3mr0620-550r] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
IL-32 is a multifaceted cytokine associated with several diseases and inflammatory conditions. Its expression is induced in response to cellular stress such as hypoxia, infections, and pro-inflammatory cytokines. IL-32 can be secreted from cells and can induce the production of pro-inflammatory cytokines from several cell types but are also described to have anti-inflammatory functions. The intracellular form of IL-32 is shown to play an important role in various cellular processes, including the defense against intracellular bacteria and viruses and in modulation of cell metabolism. In this review, we discuss current literature on molecular interactions of IL-32 with other proteins. We also review data on the role of intracellular IL-32 as a metabolic regulator and its role in antimicrobial host defense.
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Affiliation(s)
- Kristin Roseth Aass
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway
| | - Martin H Kastnes
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway
| | - Therese Standal
- Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research (CEMIR), Trondheim, Norway.,Department of Hematology, St. Olavs Hospital, Trondheim, Norway
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216
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Abstract
Natural killer (NK) cells are innate lymphocytes specialized in immune surveillance against tumors and infections. To reach their optimal functional status, NK cells must undergo a process of maturation from immature to mature NK cells. Genetically modified mice, as well as in vivo and in vitro NK cell differentiation assays, have begun to reveal the landscape of the regulatory network involved in NK cell maturation, in which a balance of cytokine signaling pathways leads to an optimal coordination of transcription factor activity. An increased understanding of NK cell maturation will greatly promote the development and application of NK cell-based clinical therapy. Thus, in this review, we summarize the dynamics of NK cell maturation, describe recently identified factors involved in the regulation of the NK cell maturation process, including cytokines and transcription factors, and discuss the importance of NK cell maturation in health and disease.
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Affiliation(s)
- Jiacheng Bi
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuefu Wang
- Anhui Provincial Laboratory of Inflammatory and Immunity Disease, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
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217
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Wu SY, Fu T, Jiang YZ, Shao ZM. Natural killer cells in cancer biology and therapy. Mol Cancer 2020; 19:120. [PMID: 32762681 PMCID: PMC7409673 DOI: 10.1186/s12943-020-01238-x] [Citation(s) in RCA: 357] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The tumor microenvironment is highly complex, and immune escape is currently considered an important hallmark of cancer, largely contributing to tumor progression and metastasis. Named for their capability of killing target cells autonomously, natural killer (NK) cells serve as the main effector cells toward cancer in innate immunity and are highly heterogeneous in the microenvironment. Most current treatment options harnessing the tumor microenvironment focus on T cell-immunity, either by promoting activating signals or suppressing inhibitory ones. The limited success achieved by T cell immunotherapy highlights the importance of developing new-generation immunotherapeutics, for example utilizing previously ignored NK cells. Although tumors also evolve to resist NK cell-induced cytotoxicity, cytokine supplement, blockade of suppressive molecules and genetic engineering of NK cells may overcome such resistance with great promise in both solid and hematological malignancies. In this review, we summarized the fundamental characteristics and recent advances of NK cells within tumor immunometabolic microenvironment, and discussed potential application and limitations of emerging NK cell-based therapeutic strategies in the era of presicion medicine.
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Affiliation(s)
- Song-Yang Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Tong Fu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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218
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Cantoni C, Granata S, Bruschi M, Spaggiari GM, Candiano G, Zaza G. Recent Advances in the Role of Natural Killer Cells in Acute Kidney Injury. Front Immunol 2020; 11:1484. [PMID: 32903887 PMCID: PMC7438947 DOI: 10.3389/fimmu.2020.01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 01/18/2023] Open
Abstract
Growing evidence is revealing a central role for natural killer (NK) cells, cytotoxic cells belonging to the broad family of innate lymphoid cells (ILCs), in acute and chronic forms of renal disease. NK cell effector functions include both the recognition and elimination of virus-infected and tumor cells and the capability of sensing pathogens through Toll-like receptor (TLR) engagement. Notably, they also display immune regulatory properties, exerted thanks to their ability to secrete cytokines/chemokines and to establish interactions with different innate and adaptive immune cells. Therefore, because of their multiple functions, NK cells may have a major pathogenic role in acute kidney injury (AKI), and a better understanding of the molecular mechanisms driving NK cell activation in AKI and their downstream interactions with intrinsic renal cells and infiltrating immune cells could help to identify new potential biomarkers and to select clinically valuable novel therapeutic targets. In this review, we discuss the current literature regarding the potential involvement of NK cells in AKI.
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Affiliation(s)
- Claudia Cantoni
- Laboratory of Clinical and Experimental Immunology, Integrated Department of Services and Laboratories, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Experimental Medicine (DIMES) and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Simona Granata
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Grazia Maria Spaggiari
- Department of Experimental Medicine (DIMES) and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
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219
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Yao T, Shooshtari P, Haeryfar SMM. Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies. Front Immunol 2020; 11:1691. [PMID: 32849590 PMCID: PMC7413026 DOI: 10.3389/fimmu.2020.01691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Mucosa-associated invariant T (MAIT) cells are unconventional, innate-like T lymphocytes that recognize vitamin B metabolites of microbial origin among other antigens displayed by the monomorphic molecule MHC class I-related protein 1 (MR1). Abundant in human tissues, reactive to local inflammatory cues, and endowed with immunomodulatory and cytolytic functions, MAIT cells are likely to play key roles in human malignancies. They accumulate in various tumor microenvironments (TMEs) where they often lose some of their functional capacities. However, the potential roles of MAIT cells in anticancer immunity or cancer progression and their significance in shaping clinical outcomes remain largely unknown. In this study, we analyzed publicly available bulk and single-cell tumor transcriptomic datasets to investigate the tissue distribution, phenotype, and prognostic significance of MAIT cells across several human cancers. We found that expanded MAIT cell clonotypes were often shared between the blood, tumor tissue and adjacent healthy tissue of patients with colorectal, hepatocellular, and non-small cell lung carcinomas. Gene expression comparisons between tumor-infiltrating and healthy tissue MAIT cells revealed the presence of activation and/or exhaustion programs within the TMEs of primary hepatocellular and colorectal carcinomas. Interestingly, in basal and squamous cell carcinomas of the skin, programmed cell death-1 (PD-1) blockade upregulated the expression of several effector genes in tumor-infiltrating MAIT cells. We derived a signature comprising stable and specific MAIT cell gene markers across several tissue compartments and cancer types. By applying this signature to estimate MAIT cell abundance in pan-cancer gene expression data, we demonstrate that a heavier intratumoral MAIT cell presence is positively correlated with a favorable prognosis in esophageal carcinoma but predicts poor overall survival in colorectal and squamous cell lung carcinomas. Finally, in colorectal carcinoma and four other cancer types, we found a positive correlation between MR1 expression and estimated MAIT cell abundance. Collectively, our findings indicate that MAIT cells serve important but diverse roles in human cancers. Our work provides useful models and resources that employ gene expression data platforms to enable future studies in the realm of MAIT cell biology.
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Affiliation(s)
- Tony Yao
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Parisa Shooshtari
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Lawson Health Research Institute, London Health Sciences Centre, London, ON, Canada
| | - S M Mansour Haeryfar
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Lawson Health Research Institute, London Health Sciences Centre, London, ON, Canada.,Division of Clinical Immunology and Allergy, Department of Medicine, Western University, London, ON, Canada.,Division of General Surgery, Department of Surgery, Western University, London, ON, Canada.,Centre for Human Immunology, Western University, London, ON, Canada
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220
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Murin CD. Considerations of Antibody Geometric Constraints on NK Cell Antibody Dependent Cellular Cytotoxicity. Front Immunol 2020; 11:1635. [PMID: 32849559 PMCID: PMC7406664 DOI: 10.3389/fimmu.2020.01635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/18/2020] [Indexed: 12/31/2022] Open
Abstract
It has been well-established that antibody isotype, glycosylation, and epitope all play roles in the process of antibody dependent cellular cytotoxicity (ADCC). For natural killer (NK) cells, these phenotypes are linked to cellular activation through interaction with the IgG receptor FcγRIIIa, a single pass transmembrane receptor that participates in cytoplasmic signaling complexes. Therefore, it has been hypothesized that there may be underlying spatial and geometric principles that guide proper assembly of an activation complex within the NK cell immune synapse. Further, synergy of antibody phenotypic properties as well as allosteric changes upon antigen binding may also play an as-of-yet unknown role in ADCC. Understanding these facets, however, remains hampered by difficulties associated with studying immune synapse dynamics using classical approaches. In this review, I will discuss relevant NK cell biology related to ADCC, including the structural biology of Fc gamma receptors, and how the dynamics of the NK cell immune synapse are being studied using innovative microscopy techniques. I will provide examples from the literature demonstrating the effects of spatial and geometric constraints on the T cell receptor complex and how this relates to intracellular signaling and the molecular nature of lymphocyte activation complexes, including those of NK cells. Finally, I will examine how the integration of high-throughput and "omics" technologies will influence basic NK cell biology research moving forward. Overall, the goal of this review is to lay a basis for understanding the development of drugs and therapeutic antibodies aimed at augmenting appropriate NK cell ADCC activity in patients being treated for a wide range of illnesses.
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Affiliation(s)
- Charles D. Murin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, United States
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221
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Bald T, Krummel MF, Smyth MJ, Barry KC. The NK cell-cancer cycle: advances and new challenges in NK cell-based immunotherapies. Nat Immunol 2020; 21:835-847. [PMID: 32690952 DOI: 10.1038/s41590-020-0728-z] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells belong to the innate immune system and contribute to protecting the host through killing of infected, foreign, stressed or transformed cells. Additionally, via cellular cross-talk, NK cells orchestrate antitumor immune responses. Hence, significant efforts have been undertaken to exploit the therapeutic properties of NK cells in cancer. Current strategies in preclinical and clinical development include adoptive transfer therapies, direct stimulation, recruitment of NK cells into the tumor microenvironment (TME), blockade of inhibitory receptors that limit NK cell functions, and therapeutic modulation of the TME to enhance antitumor NK cell function. In this Review, we introduce the NK cell-cancer cycle to highlight recent advances in NK cell biology and to discuss the progress and problems of NK cell-based cancer immunotherapies.
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Affiliation(s)
- Tobias Bald
- Oncology and Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Matthew F Krummel
- Department of Pathology, ImmunoX Initiative, and Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA
| | - Mark J Smyth
- Immunology of Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Kevin C Barry
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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222
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Human peripheral blood DNAM-1 neg NK cells are a terminally differentiated subset with limited effector functions. Blood Adv 2020; 3:1681-1694. [PMID: 31167820 DOI: 10.1182/bloodadvances.2018030676] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/25/2019] [Indexed: 01/03/2023] Open
Abstract
Natural killer (NK) cells are a heterogeneous population of innate lymphocytes whose potent anticancer properties make them ideal candidates for cellular therapeutic application. However, our lack of understanding of the role of NK cell diversity in antitumor responses has hindered advances in this area. In this study, we describe a new CD56dim NK cell subset characterized by the lack of expression of DNAX accessory molecule-1 (DNAM-1). Compared with CD56bright and CD56dimDNAM-1pos NK cell subsets, CD56dimDNAM-1neg NK cells displayed reduced motility, poor proliferation, lower production of interferon-γ, and limited killing capacities. Soluble factors secreted by CD56dimDNAM-1neg NK cells impaired CD56dimDNAM-1pos NK cell-mediated killing, indicating a potential inhibitory role for the CD56dimDNAM-1neg NK cell subset. Transcriptome analysis revealed that CD56dimDNAM-1neg NK cells constitute a new mature NK cell subset with a specific gene signature. Upon in vitro cytokine stimulation, CD56dimDNAM-1neg NK cells were found to differentiate from CD56dimDNAM-1pos NK cells. Finally, we report a dysregulation of NK cell subsets in the blood of patients diagnosed with Hodgkin lymphoma and diffuse large B-cell lymphoma, characterized by decreased CD56dimDNAM-1pos/CD56dimDNAM-1neg NK cell ratios and reduced cytotoxic activity of CD56dimDNAM-1pos NK cells. Altogether, our data offer a better understanding of human peripheral blood NK cell populations and have important clinical implications for the design of NK cell-targeting therapies.
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223
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Möbus L, Rodriguez E, Harder I, Stölzl D, Boraczynski N, Gerdes S, Kleinheinz A, Abraham S, Heratizadeh A, Handrick C, Haufe E, Werfel T, Schmitt J, Weidinger S. Atopic dermatitis displays stable and dynamic skin transcriptome signatures. J Allergy Clin Immunol 2020; 147:213-223. [PMID: 32615169 DOI: 10.1016/j.jaci.2020.06.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Skin transcriptome studies in atopic dermatitis (AD) showed broad dysregulation as well as "improvement" under therapy. These observations were mainly made in trials and based on microarray data. OBJECTIVES Our aim was to explore the skin transcriptome and the impact of systemic treatment in patients of the TREATgermany registry. METHODS Biopsy specimens from 59 patients with moderate-to-severe AD before and 30 patients 12 weeks after start of systemic treatment (dupilumab [n = 22] or cyclosporine [n = 8]) and from 31 healthy controls were subjected to mRNA sequencing. Differential expression, pathway enrichment, correlation, and coexpression network analysis were conducted. RESULTS Both lesional and nonlesional skin showed a stable "core" signature characterized by disturbed epidermal differentiation and activation of IL-31/IL-1 signaling. A second dynamic signature showed progressive enrichment for type 2 inflammation, TH17 signaling, and natural killer cell function. Markers correlated with disease activity have functions in epidermal barrier properties and immune modulation. IL4RA was among the top 3 central dysregulated genes. Cyclosporine led to a more pronounced global transcriptome reversion and normalized TH17 cell/IL23 signaling, whereas dupilumab led to a stronger increase in level of epidermal differentiation markers. Both treatments strongly decreased levels of type 2 markers, but overall the residual profile was still profoundly different from that of healthy skin. Lower levels of IL4RA and IL13 and high IL36A expression were related to a stronger clinical response to dupilumab. CONCLUSION The AD core signature is characterized by dysregulation of genes related to keratinocyte differentiation and itch signaling. A dynamic signature reflects progressive immune responses dominated by type 2 cytokines with an additional role of TH17 and natural killer cell signaling.
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Affiliation(s)
- Lena Möbus
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Elke Rodriguez
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inken Harder
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dora Stölzl
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nicole Boraczynski
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sascha Gerdes
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Susanne Abraham
- University Allergy Centre, Carl Gustav Carus University Medical Centre, TU Dresden, Dresden, Germany
| | - Annice Heratizadeh
- Division of Immunodermatology and Allergy Research, Department of Dermatology, Allergy, and Venereology, Hannover Medical School, Hannover, Germany
| | - Christiane Handrick
- Practice for Dermatology and Venereology, Christiane Handrick, MD, Berlin, Germany
| | - Eva Haufe
- Center for Evidence-Based Health Care, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Thomas Werfel
- Division of Immunodermatology and Allergy Research, Department of Dermatology, Allergy, and Venereology, Hannover Medical School, Hannover, Germany
| | - Jochen Schmitt
- Center for Evidence-Based Health Care, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Stephan Weidinger
- Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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224
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Niu J, Huang Y, Liu X, Wu F, Tang J, Wang B, Lu Y, Cai J, Jian J. Fish Galectin8-Like Exerts Positive Regulation on Immune Response Against Bacterial Infection. Front Immunol 2020; 11:1140. [PMID: 32676073 PMCID: PMC7333315 DOI: 10.3389/fimmu.2020.01140] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Galectin-8 is a member of the galectin family that is involved in immune response against pathogens. However, the roles of fish galectin-8 during pathogen infection require comprehensive studies. In this study, a galectin-8 homolog (OnGal8-like, OnGal8-L) was characterized from Nile tilapia (Oreochromis niloticus), and its roles in response to bacterial infection were analyzed. The OnGal8-L contains an open reading frame of 891 bp, encoding a peptide of 296 amino acids with two CRD regions of tandem-repeat galectin and two carbohydrate recognition sites. The OnGal8-L protein shares 46.42% identities with reported Oreochromis niloticus galectin-8 protein. Transcriptional expression analysis revealed that OnGal8-L was constitutively expressed in all examined tissues and was highly expressed in spleen. The transcript levels of OnGal8-L were up-regulated in the spleen, head kidney, and brain, following Streptococcus agalactiae (S. agalactiae) challenge. Further in vitro analysis indicated that the recombinant protein of OnGal8-L (rOnGal8L) could agglutinate erythrocyte, S. agalactiae, and A. hydrophila and bind S. agalactiae, A. hydrophila, and various PAMPs (lipopolysaccharides, lipoteichoic acid, poly I:C, peptidoglycan, galactose, mannose, and maltose). Also, rOnGal8L could regulate inflammatory-related gene expression, phagocytosis, and a respiratory burst of monocytes/macrophages. Moreover, in vivo analysis showed that OnGal8-L overexpression could protect O. niloticus from S. agalactiae infection through modulating serum antibacterial activity (AKP, ACP, and LZM), antioxidant capacity (CAT, POD, and SOD), and monocyte/macrophage proliferation and cytokine expression, as well as reducing bacterial burden and decreasing tissue damage. Our results collectively indicate that OnGal8-L plays important regulatory roles in immune response against bacterial infection.
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Affiliation(s)
- Jinzhong Niu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Yu Huang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Xinchao Liu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Fenglei Wu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China
| | - Jufen Tang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Yishan Lu
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
| | - Jia Cai
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.,Guangxi Key Lab for Marine Natural Products and Combinational Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Jichang Jian
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, College of Fishery, Guangdong Ocean University, Zhanjiang, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
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225
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Qian J, Olbrecht S, Boeckx B, Vos H, Laoui D, Etlioglu E, Wauters E, Pomella V, Verbandt S, Busschaert P, Bassez A, Franken A, Bempt MV, Xiong J, Weynand B, van Herck Y, Antoranz A, Bosisio FM, Thienpont B, Floris G, Vergote I, Smeets A, Tejpar S, Lambrechts D. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res 2020; 30:745-762. [PMID: 32561858 PMCID: PMC7608385 DOI: 10.1038/s41422-020-0355-0] [Citation(s) in RCA: 359] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells, which are profoundly moulded by cancer cells. An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs. Here, we profile 233,591 single cells from patients with lung, colorectal, ovary and breast cancer (n = 36) and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies. We identify 68 stromal cell populations, of which 46 are shared between cancer types and 22 are unique. We also characterise each population phenotypically by highlighting its marker genes, transcription factors, metabolic activities and tissue-specific expression differences. Resident cell types are characterised by substantial tissue specificity, while tumor-infiltrating cell types are largely shared across cancer types. Finally, by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naïve CD4+ T-cell phenotype predictive of response to checkpoint immunotherapy, we illustrate how it can serve as a guide to interpret scRNA-seq data. In conclusion, by providing a comprehensive blueprint through an interactive web server, we generate the first panoramic view on the shared complexity of stromal cells in different cancers.
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Affiliation(s)
- Junbin Qian
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Siel Olbrecht
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hanne Vos
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Damya Laoui
- Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Emre Etlioglu
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Els Wauters
- Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospital KU Leuven, Leuven, Belgium.,Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Verbandt
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ayse Bassez
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Amelie Franken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jieyi Xiong
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | | | - Asier Antoranz
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Francesca Maria Bosisio
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ann Smeets
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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226
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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227
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Zhang Y, Fung ITH, Sankar P, Chen X, Robison LS, Ye L, D'Souza SS, Salinero AE, Kuentzel ML, Chittur SV, Zhang W, Zuloaga KL, Yang Q. Depletion of NK Cells Improves Cognitive Function in the Alzheimer Disease Mouse Model. THE JOURNAL OF IMMUNOLOGY 2020; 205:502-510. [PMID: 32503894 DOI: 10.4049/jimmunol.2000037] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022]
Abstract
Despite mounting evidence suggesting the involvement of the immune system in regulating brain function, the specific role of immune and inflammatory cells in neurodegenerative diseases remain poorly understood. In this study, we report that depletion of NK cells, a type of innate lymphocytes, alleviates neuroinflammation, stimulates neurogenesis, and improves cognitive function in a triple-transgenic Alzheimer disease (AD) mouse model. NK cells in the brains of triple-transgenic AD mouse model (3xTg-AD) mice exhibited an enhanced proinflammatory profile. Depletion of NK cells by anti-NK1.1 Abs drastically improved cognitive function of 3xTg-AD mice. NK cell depletion did not affect amyloid β concentrations but enhanced neurogenesis and reduced neuroinflammation. Notably, in 3xTg-AD mice depleted of NK cells, microglia demonstrated a homeostatic-like morphology, decreased proliferative response and reduced expression of neurodestructive proinflammatory cytokines. Together, our results suggest a proinflammatory role for NK cells in 3xTg-AD mice and indicate that targeting NK cells might unlock novel strategies to combat AD.
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Affiliation(s)
- Yuanyue Zhang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Ivan Ting Hin Fung
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Poornima Sankar
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Xiangyu Chen
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Lisa S Robison
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Longyun Ye
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Shanti S D'Souza
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208
| | - Abigail E Salinero
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Marcy L Kuentzel
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY 12144; and
| | - Sridar V Chittur
- Center for Functional Genomics, University at Albany-SUNY, Rensselaer, NY 12144; and
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY 12208
| | - Kristen L Zuloaga
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208;
| | - Qi Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208;
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228
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Single-Cell RNA Sequencing of Tumor-Infiltrating NK Cells Reveals that Inhibition of Transcription Factor HIF-1α Unleashes NK Cell Activity. Immunity 2020; 52:1075-1087.e8. [PMID: 32445619 DOI: 10.1016/j.immuni.2020.05.001] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/19/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022]
Abstract
Enhancing immune cell functions in tumors remains a major challenge in cancer immunotherapy. Hypoxia is a common feature of solid tumors, and cells adapt by upregulating the transcription factor HIF-1α. Here, we defined the transcriptional landscape of mouse tumor-infiltrating natural killer (NK) cells by using single-cell RNA sequencing. Conditional deletion of Hif1a in NK cells resulted in reduced tumor growth, elevated expression of activation markers, effector molecules, and an enriched NF-κB pathway in tumor-infiltrating NK cells. Interleukin-18 (IL-18) from myeloid cells was required for NF-κB activation and the enhanced anti-tumor activity of Hif1a-/- NK cells. Extended culture with an HIF-1α inhibitor increased human NK cell responses. Low HIF1A expression was associated with high expression of IFNG in human tumor-infiltrating NK cells, and an enriched NK-IL18-IFNG signature in solid tumors correlated with increased overall patient survival. Thus, inhibition of HIF-1α unleashes NK cell anti-tumor activity and could be exploited for cancer therapy.
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229
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Abstract
One of the hallmarks of the vertebrate adaptive immune system is the prolific expansion of individual cell clones that encounter their cognate antigen. More recently, however, there is growing evidence for the clonal expansion of innate lymphocytes, particularly in the context of pathogen challenge. Clonal expansion not only serves to amplify the number of specific lymphocytes to mount a robust protective response to the pathogen at hand but also results in selection and differentiation of the responding lymphocytes to generate a multitude of cell fates. Here, we summarize the evidence for clonal expansion in innate lymphocytes, which has primarily been observed in natural killer (NK) cells responding to cytomegalovirus infection, and consider the requirements for such a response in NK cells in light of those for T cells. Furthermore, we discuss multiple aspects of heterogeneity that both contribute to and result from the fundamental immunological process of clonal expansion, highlighting the parallels between innate and adaptive lymphocytes, with a particular focus on NK cells and CD8+ T cells.
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230
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Collins KS, Cheng YH, Ferreira RM, Gao H, Dollins MD, Janosevic D, Khan NA, White C, Dagher PC, Eadon MT. Interindividual Variability in Lymphocyte Stimulation and Transcriptomic Response Predicts Mycophenolic Acid Sensitivity in Healthy Volunteers. Clin Transl Sci 2020; 13:1137-1149. [PMID: 32415749 PMCID: PMC7719379 DOI: 10.1111/cts.12795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/23/2020] [Indexed: 11/30/2022] Open
Abstract
Mycophenolic acid (MPA) is an immunosuppressant commonly used to prevent renal transplant rejection and treat glomerulonephritis. MPA inhibits IMPDH2 within stimulated lymphocytes, reducing guanosine synthesis. Despite the widespread use of MPA, interindividual variability in response remains with rates of allograft rejection up to 15% and approximately half of individuals fail to achieve complete remission to lupus nephritis. We sought to identify contributors to interindividual variability in MPA response, hypothesizing that the HPRT1 salvage guanosine synthesis contributes to variability. MPA sensitivity was measured in 40 healthy individuals using an ex vivo lymphocyte viability assay. Measurement of candidate gene expression (n ± 40) and single‐cell RNA‐sequencing (n ± 6) in lymphocytes was performed at baseline, poststimulation, and post‐MPA treatment. After stimulation, HPRT1 expression was 2.1‐fold higher in resistant individuals compared with sensitive individuals (P ± 0.049). Knockdown of HPRT1 increased MPA sensitivity (12%; P ± 0.003), consistent with higher expression levels in resistant individuals. Sensitive individuals had higher IMPDH2 expression and 132% greater stimulation. In lymphocyte subpopulations, differentially expressed genes between sensitive and resistant individuals included KLF2 and LTB. Knockdown of KLF2 and LTB aligned with the predicted direction of effect on proliferation. In sensitive individuals, more frequent receptor‐ligand interactions were observed after stimulation (P ± 0.0004), but fewer interactions remained after MPA treatment (P ± 0.0014). These data identify a polygenic transcriptomic signature in lymphocyte subpopulations predictive of MPA response. The degree of lymphocyte stimulation, HPRT1, KLF2, and LTB expression may serve as markers of MPA efficacy.
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Affiliation(s)
- Kimberly S Collins
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ying-Hua Cheng
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ricardo M Ferreira
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Matthew D Dollins
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Danielle Janosevic
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nida A Khan
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chloe White
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Pierre C Dagher
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael T Eadon
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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231
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Yang C, Siebert JR, Burns R, Zheng Y, Mei A, Bonacci B, Wang D, Urrutia RA, Riese MJ, Rao S, Carlson KS, Thakar MS, Malarkannan S. Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature. eLife 2020; 9:51339. [PMID: 32406817 PMCID: PMC7255804 DOI: 10.7554/elife.51339] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 05/08/2020] [Indexed: 12/26/2022] Open
Abstract
The transcriptional activation and repression during NK cell ontology are poorly understood. Here, using single-cell RNA-sequencing, we reveal a novel role for T-bet in suppressing the immature gene signature during murine NK cell development. Based on transcriptome, we identified five distinct NK cell clusters and define their relative developmental maturity in the bone marrow. Transcriptome-based machine-learning classifiers revealed that half of the mTORC2-deficient NK cells belongs to the least mature NK cluster. Mechanistically, loss of mTORC2 results in an increased expression of signature genes representing immature NK cells. Since mTORC2 regulates the expression of T-bet through AktS473-FoxO1 axis, we further characterized the T-bet-deficient NK cells and found an augmented immature transcriptomic signature. Moreover, deletion of Foxo1 restores the expression of T-bet and corrects the abnormal expression of immature NK genes. Collectively, our study reveals a novel role for mTORC2-AktS473-FoxO1-T-bet axis in suppressing the transcriptional signature of immature NK cells.
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Affiliation(s)
- Chao Yang
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, United States
| | - Jason R Siebert
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, United States
| | - Robert Burns
- Bioinfomatics Core, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Yongwei Zheng
- Laboratory of B-Cell Lymphopoiesis, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Ao Mei
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, United States
| | - Benedetta Bonacci
- Flow Cytometry Core, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Demin Wang
- Laboratory of B-Cell Lymphopoiesis, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, United States
| | - Matthew J Riese
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, United States.,Laboratory of Lymphocyte Biology, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Medicine, Medical College of Wisconsin, Milwaukee, United States
| | - Sridhar Rao
- Laboratory of Stem Cell Transcriptional Regulation, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Karen-Sue Carlson
- Department of Medicine, Medical College of Wisconsin, Milwaukee, United States.,Laboratory of Coagulation Biology, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States
| | - Monica S Thakar
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, United States
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, Blood Center of Wisconsin, Milwaukee, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, United States.,Department of Medicine, Medical College of Wisconsin, Milwaukee, United States.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, United States
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232
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Pfefferle A, Jacobs B, Haroun-Izquierdo A, Kveberg L, Sohlberg E, Malmberg KJ. Deciphering Natural Killer Cell Homeostasis. Front Immunol 2020; 11:812. [PMID: 32477340 PMCID: PMC7235169 DOI: 10.3389/fimmu.2020.00812] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/08/2020] [Indexed: 12/23/2022] Open
Abstract
Natural killer (NK) cells have a central role within the innate immune system, eliminating virally infected, foreign and transformed cells through their natural cytotoxic capacity. Release of their cytotoxic granules is tightly controlled through the balance of a large repertoire of inhibitory and activating receptors, and it is the unique combination of these receptors expressed by individual cells that confers immense diversity both in phenotype and functionality. The diverse, yet unique, NK cell repertoire within an individual is surprisingly stable over time considering the constant renewal of these cells at steady state. Here we give an overview of NK cell differentiation and discuss metabolic requirements, intra-lineage plasticity and transcriptional reprogramming during IL-15-driven homeostatic proliferation. New insights into the regulation of NK cell differentiation and homeostasis could pave the way for the successful implementation of NK cell-based immunotherapy against cancer.
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Affiliation(s)
- Aline Pfefferle
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Benedikt Jacobs
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lise Kveberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,The KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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233
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Esaulova E, Cantoni C, Shchukina I, Zaitsev K, Bucelli RC, Wu GF, Artyomov MN, Cross AH, Edelson BT. Single-cell RNA-seq analysis of human CSF microglia and myeloid cells in neuroinflammation. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2020; 7:7/4/e732. [PMID: 32371549 PMCID: PMC7217663 DOI: 10.1212/nxi.0000000000000732] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
Objective To identify and characterize myeloid cell populations within the CSF of patients with MS and anti-myelin oligodendrocyte glycoprotein (MOG) disorder by high-resolution single-cell gene expression analysis. Methods Single-cell RNA sequencing (scRNA-seq) was used to profile individual cells of CSF and blood from 2 subjects with relapsing-remitting MS (RRMS) and one with anti-MOG disorder. Publicly available scRNA-seq data from the blood and CSF of 2 subjects with HIV were also analyzed. An informatics pipeline was used to cluster cell populations by transcriptomic profiling. Based on gene expression by CSF myeloid cells, a flow cytometry panel was devised to examine myeloid cell populations from the CSF of 11 additional subjects, including individuals with RRMS, anti-MOG disorder, and control subjects without inflammatory demyelination. Results Common myeloid populations were identified within the CSF of subjects with RRMS, anti-MOG disorder, and HIV. These included monocytes, conventional and plasmacytoid dendritic cells, and cells with a transcriptomic signature matching microglia. Microglia could be discriminated from other myeloid cell populations in the CSF by flow cytometry. Conclusions High-resolution single-cell gene expression analysis clearly distinguishes distinct myeloid cell types present within the CSF of subjects with neuroinflammation. A population of microglia exists within the human CSF, which is detectable by surface protein expression. The function of these cells during immunity and disease requires further investigation.
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Affiliation(s)
- Ekaterina Esaulova
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Claudia Cantoni
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Irina Shchukina
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Konstantin Zaitsev
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Robert C Bucelli
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Gregory F Wu
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia.
| | - Maxim N Artyomov
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Anne H Cross
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia
| | - Brian T Edelson
- From the Department of Pathology and Immunology (E.E., I.S., K.Z., G.F.W., M.N.A., B.T.E.) and Department of Neurology (C.C., R.C.B., G.F.W., A.H.C.), Washington University School of Medicine, St. Louis, MO; and Computer Technologies Department (K.Z.), ITMO University, St. Petersburg, Russia.
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234
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Aid M, Ram DR, Bosinger SE, Barouch DH, Reeves RK. Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections. Front Cell Infect Microbiol 2020; 10:194. [PMID: 32411625 PMCID: PMC7201019 DOI: 10.3389/fcimb.2020.00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/09/2020] [Indexed: 01/25/2023] Open
Abstract
Natural killer (NK) cells are crucial regulators of antiviral and anti-tumor immune responses. Although in humans some NK cell transcriptional programs are relatively well-established, NK cell transcriptional networks in non-human primates (NHP) remain poorly delineated. Here we performed RNA-Seq experiments using purified NK cells from experimentally naïve rhesus macaques, providing the first transcriptional characterization of pure NK cells in any NHP species. This novel NK cell transcriptomic signature (NK RMtsig) overlaps with published human NK signatures, allowing us to identify new key signaling and transcription factor networks underlying NK cell function. Finally, we show that applying NK RMtsig to an unrelated rhesus macaque cohort infected with SIVmac251 or ZIKV can sensitively detect NK cell repertoire perturbations, thus confirming applicability of this approach. In sum, we propose this NHP NK cell signature will serve as a useful resource for future studies involving infection, disease or treatment modalities in NHP.
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Affiliation(s)
- Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Daniel R Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Steven E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
| | - R Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
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235
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Zhao J, Zhang S, Liu Y, He X, Qu M, Xu G, Wang H, Huang M, Pan J, Liu Z, Li Z, Liu L, Zhang Z. Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov 2020; 6:22. [PMID: 32351704 PMCID: PMC7186229 DOI: 10.1038/s41421-020-0157-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
The liver plays a critical role in both immune defense and tolerance in the body. The liver-resident immune cells (LrICs) determine the immune properties, but the unique composition and heterogeneity of these cells are incompletely understood. Here, we dissect the diversity of LrICs by a comprehensive transcriptomic profiling using the unbiased single-cell RNA-sequencing (scRNA-seq). A total of 70, 706 of CD45+ immune cells from the paired liver perfusion, spleen and peripheral blood as references were profiled. We identified more than 30 discrete cell populations comprising 13 of T and NK cell, 7 of B cell, 4 of plasma cell, and 8 of myeloid cell subsets in human liver and donor-paired spleen and blood, and characterized their tissue distribution, gene expression and functional modules. Especially, four of CXCR6+ T and NK cell subsets were found to be present preferentially in the liver, where they manifested heterogeneity, distinct function and prominent homeostatic proliferation. We propose a universal category system of T and NK cells based on distinct chemokine receptors, confirmed subsequently by phenotype, transcriptional factors and functionality. We also identified adaptive changes by the spleen and liver-derived monocyte and macrophage populations. Finally, we give a global glimpse on B cell and plasma cell subsets in human spleen and liver. We, therefore, reveal the heterogeneity and functional diversity of LrICs in human. This study presents comprehensively the landscape of LrICs and will enable further study on their roles in various human diseases.
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Affiliation(s)
- Juanjuan Zhao
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112 China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai, 201058 China
| | - Yang Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112 China
| | - Xiaomeng He
- Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of PLA, Beijing, 100039 China
| | - Mengmeng Qu
- Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of PLA, Beijing, 100039 China
| | - Gang Xu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
| | - Hongbo Wang
- Research Center for Liver Transplantation, Fifth Medical Center for General Hospital of PLA, Beijing, 100039 China
| | - Man Huang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
| | - Jing Pan
- Research Center for Clinical & Translational Medicine, Fifth Medical Center for General Hospital of PLA, Beijing, 100039 China
| | - Zhenwen Liu
- Research Center for Liver Transplantation, Fifth Medical Center for General Hospital of PLA, Beijing, 100039 China
| | - Zhiwei Li
- Deparment for Liver Transplantation, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
| | - Lei Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112 China
| | - Zheng Zhang
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, Guangdong 518112 China
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112 China
- Key Laboratory of Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences; Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436 China
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236
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Abstract
The continuous interactions between host and pathogens during their coevolution have shaped both the immune system and the countermeasures used by pathogens. Natural killer (NK) cells are innate lymphocytes that are considered central players in the antiviral response. Not only do they express a variety of inhibitory and activating receptors to discriminate and eliminate target cells but they can also produce immunoregulatory cytokines to alert the immune system. Reciprocally, several unrelated viruses including cytomegalovirus, human immunodeficiency virus, influenza virus, and dengue virus have evolved a multitude of mechanisms to evade NK cell function, such as the targeting of pathways for NK cell receptors and their ligands, apoptosis, and cytokine-mediated signaling. The studies discussed in this article provide further insights into the antiviral function of NK cells and the pathways involved, their constituent proteins, and ways in which they could be manipulated for host benefit.
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Affiliation(s)
- Mathieu Mancini
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada;,
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec H3A 0C7, Canada;,
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada
- Department of Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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237
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Dege C, Fegan KH, Creamer JP, Berrien-Elliott MM, Luff SA, Kim D, Wagner JA, Kingsley PD, McGrath KE, Fehniger TA, Palis J, Sturgeon CM. Potently Cytotoxic Natural Killer Cells Initially Emerge from Erythro-Myeloid Progenitors during Mammalian Development. Dev Cell 2020; 53:229-239.e7. [PMID: 32197069 PMCID: PMC7185477 DOI: 10.1016/j.devcel.2020.02.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 12/31/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022]
Abstract
Natural killer (NK) cells are a critical component of the innate immune system. However, their ontogenic origin has remained unclear. Here, we report that NK cell potential first arises from Hoxaneg/low Kit+CD41+CD16/32+ hematopoietic-stem-cell (HSC)-independent erythro-myeloid progenitors (EMPs) present in the murine yolk sac. EMP-derived NK cells and primary fetal NK cells, unlike their adult counterparts, exhibit robust degranulation in response to stimulation. Parallel studies using human pluripotent stem cells (hPSCs) revealed that HOXAneg/low CD34+ progenitors give rise to NK cells that, similar to murine EMP-derived NK cells, harbor a potent cytotoxic degranulation bias. In contrast, hPSC-derived HOXA+ CD34+ progenitors, as well as human cord blood CD34+ cells, give rise to NK cells that exhibit an attenuated degranulation response but robustly produce inflammatory cytokines. Collectively, our studies identify an extra-embryonic origin of potently cytotoxic NK cells, suggesting that ontogenic origin is a relevant factor in designing hPSC-derived adoptive immunotherapies.
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Affiliation(s)
- Carissa Dege
- Department of Medicine, Division of Hematology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Katherine H Fegan
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - J Philip Creamer
- Department of Medicine, Division of Hematology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Melissa M Berrien-Elliott
- Department of Medicine, Division of Oncology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Stephanie A Luff
- Department of Medicine, Division of Hematology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Darren Kim
- Department of Medicine, Division of Hematology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Julia A Wagner
- Department of Medicine, Division of Oncology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Paul D Kingsley
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Kathleen E McGrath
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Todd A Fehniger
- Department of Medicine, Division of Oncology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - James Palis
- Center for Pediatric Biomedical Research and Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA.
| | - Christopher M Sturgeon
- Department of Medicine, Division of Hematology, Washington University in St Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St Louis, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University in St Louis, St. Louis, MO 63110, USA.
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238
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Lehmann FM, von Burg N, Ivanek R, Teufel C, Horvath E, Peter A, Turchinovich G, Staehli D, Eichlisberger T, Gomez de Agüero M, Coto-Llerena M, Prchal-Murphy M, Sexl V, Bentires-Alj M, Mueller C, Finke D. Microbiota-induced tissue signals regulate ILC3-mediated antigen presentation. Nat Commun 2020; 11:1794. [PMID: 32286285 PMCID: PMC7156681 DOI: 10.1038/s41467-020-15612-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Although group 3 innate lymphoid cells (ILC3s) are efficient inducers of T cell responses in the spleen, they fail to induce CD4+ T cell proliferation in the gut. The signals regulating ILC3-T cell responses remain unknown. Here, we show that transcripts associated with MHC II antigen presentation are down-modulated in intestinal natural cytotoxicity receptor (NCR)- ILC3s. Further data implicate microbiota-induced IL-23 as a crucial signal for reversible silencing of MHC II in ILC3s, thereby reducing the capacity of ILC3s to present antigen to T cells in the intestinal mucosa. Moreover, IL-23-mediated MHC II suppression is dependent on mTORC1 and STAT3 phosphorylation in NCR- ILC3s. By contrast, splenic interferon-γ induces MHC II expression and CD4+ T cell stimulation by NCR- ILC3s. Our results thus identify biological circuits for tissue-specific regulation of ILC3-dependent T cell responses. These pathways may have implications for inducing or silencing T cell responses in human diseases.
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Affiliation(s)
- Frank Michael Lehmann
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | - Nicole von Burg
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
- Department of Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Robert Ivanek
- Department of Biomedicine, University of Basel, 4056, Basel, Switzerland
- Swiss Institute of Bioinformatics, 4053, Basel, Switzerland
| | - Claudia Teufel
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | - Edit Horvath
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | - Annick Peter
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | - Gleb Turchinovich
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | - Daniel Staehli
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland
| | | | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories, Department for BioMedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, 3010, Bern, Switzerland
| | | | - Michaela Prchal-Murphy
- Institute of Pharmacology and Toxicology, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, Department for Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | - Daniela Finke
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, 4058, Basel, Switzerland.
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239
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Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. Blood Adv 2020; 4:1388-1406. [PMID: 32271902 PMCID: PMC7160259 DOI: 10.1182/bloodadvances.2019000699] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
Human natural killer (NK) cells in peripheral blood perform many functions, and classification of specific subsets has been a longstanding goal. We report single-cell RNA sequencing of NK cells, comparing gene expression in unstimulated and interleukin (IL)-2-activated cells from healthy cytomegalovirus (CMV)-negative donors. Three NK cell subsets resembled well-described populations; CD56brightCD16-, CD56dimCD16+CD57-, and CD56dimCD16+CD57+. CD56dimCD16+CD57- cells subdivided to include a population with higher chemokine mRNA and increased frequency of killer-cell immunoglobulin-like receptor expression. Three novel human blood NK cell populations were identified: a population of type I interferon-responding NK cells that were CD56neg; a population exhibiting a cytokine-induced memory-like phenotype, including increased granzyme B mRNA in response to IL-2; and finally, a small population, with low ribosomal expression, downregulation of oxidative phosphorylation, and high levels of immediate early response genes indicative of cellular activation. Analysis of CMV+ donors established that CMV altered the proportion of NK cells in each subset, especially an increase in adaptive NK cells, as well as gene regulation within each subset. Together, these data establish an unexpected diversity in blood NK cells and provide a new framework for analyzing NK cell responses in health and disease.
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240
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Seo W, Shimizu K, Kojo S, Okeke A, Kohwi-Shigematsu T, Fujii SI, Taniuchi I. Runx-mediated regulation of CCL5 via antagonizing two enhancers influences immune cell function and anti-tumor immunity. Nat Commun 2020; 11:1562. [PMID: 32218434 PMCID: PMC7099032 DOI: 10.1038/s41467-020-15375-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
CCL5 is a unique chemokine with distinct stage and cell-type specificities for regulating inflammation, but how these specificities are achieved and how CCL5 modulates immune responses is not well understood. Here we identify two stage-specific enhancers: the proximal enhancer mediates the constitutive CCL5 expression during the steady state, while the distal enhancer located 1.35 Mb from the promoter induces CCL5 expression in activated cells. Both enhancers are antagonized by RUNX/CBFβ complexes, and SATB1 further mediates the long-distance interaction of the distal enhancer with the promoter. Deletion of the proximal enhancer decreases CCL5 expression and augments the cytotoxic activity of tissue-resident T and NK cells, which coincides with reduced melanoma metastasis in mouse models. By contrast, increased CCL5 expression resulting from RUNX3 mutation is associated with more tumor metastasis in the lung. Collectively, our results suggest that RUNX3-mediated CCL5 repression is critical for modulating anti-tumor immunity. CCL5 is an important chemokine for modulation of inflammatory responses, but how CCL5 expression is regulated is still unclear. Here the authors show that the CCL5 locus contains two enhancers, with the proximal enhancer being responsible for homeostatic expression and the distal enhancer enforcing inducibility, while both enhancers are modulated by RUNX3.
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Affiliation(s)
- Wooseok Seo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan. .,Department of Immunology, Nagoya University Graduate School of Medicine, Showa-ku Tsurumai-Cho 65, Nagoya, 466-8550, Japan.
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Satoshi Kojo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Arinze Okeke
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | | | - Shin-Ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
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241
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Federici C, Shahaj E, Cecchetti S, Camerini S, Casella M, Iessi E, Camisaschi C, Paolino G, Calvieri S, Ferro S, Cova A, Squarcina P, Bertuccini L, Iosi F, Huber V, Lugini L. Natural-Killer-Derived Extracellular Vesicles: Immune Sensors and Interactors. Front Immunol 2020; 11:262. [PMID: 32231660 PMCID: PMC7082405 DOI: 10.3389/fimmu.2020.00262] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/31/2020] [Indexed: 12/20/2022] Open
Abstract
Natural killer (NK) cells contribute to immunosurveillance and first-line defense in the control of tumor growth and metastasis diffusion. NK-cell-derived extracellular vesicles (NKEVs) are constitutively secreted and biologically active. They reflect the protein and genetic repertoire of originating cells, and exert antitumor activity in vitro and in vivo. Cancer can compromise NK cell functions, a status potentially reflected by their extracellular vesicles. Hence, NKEVs could, on the one hand, contribute to improve cancer therapy by interacting with tumor and/or immune cells and on the other hand, sense the actual NK cell status in cancer patients. Here, we investigated the composition of healthy donors' NKEVs, including NK microvesicles and exosomes, and their interaction with uncompromised cells of the immune system. To sense the systemic NK cell status in cancer patients, we developed an immune enzymatic test (NKExoELISA) that measures plasma NK-cell-derived exosomes, captured as tsg101+CD56+ nanovesicles. NKEV mass spectrometry and cytokine analysis showed the expression of NK cell markers, i.e., NKG2D and CD94, perforin, granzymes, CD40L, and other molecules involved in cytotoxicity, homing, cell adhesion, and immune activation, together with EV markers tsg101, CD81, CD63, and CD9 in both NK-derived exosomes and microvesicles. Data are available via Proteome Xchange with identifier PXD014894. Immunomodulation studies revealed that NKEVs displayed main stimulatory functions in peripheral blood mononuclear cells (PBMCs), inducing the expression of human leukocyte antigen DR isotype (HLA-DR) and costimulatory molecules on monocytes and CD25 expression on T cells, which was maintained in the presence of lipopolysaccharide (LPS) and interleukin (IL)-10/transforming growth factor beta (TGFβ), respectively. Furthermore, NKEVs increased the CD56+ NK cell fraction, suggesting that effects mediated by NKEVs might be potentially exploited in support of cancer therapy. The measurement of circulating NK exosomes in the plasma of melanoma patients and healthy donors evidenced lower levels of tsg101+CD56+ exosomes in patients with respect to donors. Likewise, we detected lower frequencies of NK cells in PBMCs of these patients. These data highlight the potential of NKExoELISA to sense alterations of the NK cell immune status.
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Affiliation(s)
- Cristina Federici
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Eriomina Shahaj
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | | | - Elisabetta Iessi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Chiara Camisaschi
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Paolino
- Dermatologic Clinic, La Sapienza University of Rome, Rome, Italy
| | - Stefano Calvieri
- Dermatologic Clinic, La Sapienza University of Rome, Rome, Italy
| | - Simona Ferro
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Agata Cova
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paola Squarcina
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Francesca Iosi
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Veronica Huber
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luana Lugini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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242
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Bähr I, Spielmann J, Quandt D, Kielstein H. Obesity-Associated Alterations of Natural Killer Cells and Immunosurveillance of Cancer. Front Immunol 2020; 11:245. [PMID: 32231659 PMCID: PMC7082404 DOI: 10.3389/fimmu.2020.00245] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
Obesity is accompanied by a systemic chronic low-grade inflammation as well as dysfunctions of several innate and adaptive immune cells. Recent findings emphasize an impaired functionality and phenotype of natural killer (NK) cells under obese conditions. This review provides a detailed overview on research related to overweight and obesity with a particular focus on NK cells. We discuss obesity-associated alterations in subsets, distribution, phenotype, cytotoxicity, cytokine secretion, and signaling cascades of NK cells investigated in vitro as well as in animal and human studies. In addition, we provide recent insights into the effects of physical activity and obesity-associated nutritional factors as well as the reduction of body weight and fat mass on NK cell functions of obese individuals. Finally, we highlight the impact of impaired NK cell physiology on obesity-associated diseases, focusing on the elevated susceptibility for viral infections and increased risk for cancer development and impaired treatment response.
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Affiliation(s)
- Ina Bähr
- Institute of Anatomy and Cell Biology, Medical Faculty of Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Julia Spielmann
- Institute of Anatomy and Cell Biology, Medical Faculty of Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Dagmar Quandt
- Institute of Anatomy and Cell Biology, Medical Faculty of Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.,Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
| | - Heike Kielstein
- Institute of Anatomy and Cell Biology, Medical Faculty of Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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243
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Zheng Z, Chen E, Lu W, Mouradian G, Hodges M, Liang M, Liu P, Lu Y. Single-Cell Transcriptomic Analysis. Compr Physiol 2020; 10:767-783. [PMID: 32163201 DOI: 10.1002/cphy.c190037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-cell sequencing measures the sequence information from individual cells using optimized single-cell isolation protocols and next-generation sequencing technologies. Recent advancement in single-cell sequencing has transformed biomedical research, providing insights into diverse biological processes such as mammalian development, immune system function, cellular diversity and heterogeneity, and disease pathogenesis. In this article, we introduce and describe popular commercial platforms for single-cell RNA sequencing, general workflow for data analysis, repositories and databases, and applications for these approaches in biomedical research. © 2020 American Physiological Society. Compr Physiol 10:767-783, 2020.
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Affiliation(s)
- Zhihong Zheng
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Enguo Chen
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China
| | - Weiguo Lu
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Gary Mouradian
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Matthew Hodges
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mingyu Liang
- Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China.,Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yan Lu
- Department of Gynecologic Oncology, Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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244
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Kee BL, Morman RE, Sun M. Transcriptional regulation of natural killer cell development and maturation. Adv Immunol 2020; 146:1-28. [PMID: 32327150 DOI: 10.1016/bs.ai.2020.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Natural killer cells are lymphocytes that respond rapidly to intracellular pathogens or cancer/stressed cells by producing pro-inflammatory cytokines or chemokines and by killing target cells through direct cytolysis. NK cells are distinct from B and T lymphocytes in that they become activated through a series of broadly expressed germ line encoded activating and inhibitory receptors or through the actions of inflammatory cytokines. They are the founding member of the innate lymphoid cell family, which mirror the functions of T lymphocytes, with NK cells being the innate counterpart to CD8 T lymphocytes. Despite the functional relationship between NK cells and CD8 T cells, the mechanisms controlling their specification, differentiation and maturation are distinct, with NK cells emerging from multipotent lymphoid progenitors in the bone marrow under the control of a unique transcriptional program. Over the past few years, substantial progress has been made in understanding the developmental pathways and the factors involved in generating mature and functional NK cells. NK cells have immense therapeutic potential and understanding how to acquire large numbers of functional cells and how to endow them with potent activity to control hematopoietic and non-hematopoietic malignancies and autoimmunity is a major clinical goal. In this review, we examine basic aspects of conventional NK cell development in mice and humans and discuss multiple transcription factors that are known to guide the development of these cells.
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Affiliation(s)
- Barbara L Kee
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States.
| | - Rosmary E Morman
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States
| | - Mengxi Sun
- Department of Pathology and Committee on Immunology, The University of Chicago, Chicago, IL, United States
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245
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Regis S, Dondero A, Caliendo F, Bottino C, Castriconi R. NK Cell Function Regulation by TGF-β-Induced Epigenetic Mechanisms. Front Immunol 2020; 11:311. [PMID: 32161594 PMCID: PMC7052483 DOI: 10.3389/fimmu.2020.00311] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
TGF-β is a potent immunosuppressive cytokine that severely affects the function of NK cells. Tumor cells can take advantage of this ability, enriching their surrounding microenvironment with TGF-β. TGF-β can alter the expression of effector molecules and of activating and chemokine receptors, influence metabolism, induce the NK cell conversion toward the less cytolytic ILC1s. These and other changes possibly occur by the induction of complex gene expression programs, involving epigenetic mechanisms. While most of these programs are at present unexplored, the role of certain transcription factors, microRNAs and chromatin changes determined by TGF-β in NK cells start to be elucidated in human and/or mouse NK cells. The deep understanding of these mechanisms will be useful to design therapies contributing to restore the full NK function.
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Affiliation(s)
- Stefano Regis
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Fabio Caliendo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Cristina Bottino
- Laboratory of Clinical and Experimental Immunology, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Roberta Castriconi
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Centre of Excellence for Biomedical Research, CEBR, University of Genoa, Genoa, Italy
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246
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Davies AJ, Rinaldi S, Costigan M, Oh SB. Cytotoxic Immunity in Peripheral Nerve Injury and Pain. Front Neurosci 2020; 14:142. [PMID: 32153361 PMCID: PMC7047751 DOI: 10.3389/fnins.2020.00142] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/04/2020] [Indexed: 12/13/2022] Open
Abstract
Cytotoxicity and consequent cell death pathways are a critical component of the immune response to infection, disease or injury. While numerous examples of inflammation causing neuronal sensitization and pain have been described, there is a growing appreciation of the role of cytotoxic immunity in response to painful nerve injury. In this review we highlight the functions of cytotoxic immune effector cells, focusing in particular on natural killer (NK) cells, and describe the consequent action of these cells in the injured nerve as well as other chronic pain conditions and peripheral neuropathies. We describe how targeted delivery of cytotoxic factors via the immune synapse operates alongside Wallerian degeneration to allow local axon degeneration in the absence of cell death and is well-placed to support the restoration of homeostasis within the nerve. We also summarize the evidence for the expression of endogenous ligands and receptors on injured nerve targets and infiltrating immune cells that facilitate direct neuro-immune interactions, as well as modulation of the surrounding immune milieu. A number of chronic pain and peripheral neuropathies appear comorbid with a loss of function of cellular cytotoxicity suggesting such mechanisms may actually help to resolve neuropathic pain. Thus while the immune response to peripheral nerve injury is a major driver of maladaptive pain, it is simultaneously capable of directing resolution of injury in part through the pathways of cellular cytotoxicity. Our growing knowledge in tuning immune function away from inflammation toward recovery from nerve injury therefore holds promise for interventions aimed at preventing the transition from acute to chronic pain.
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Affiliation(s)
- Alexander J. Davies
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Simon Rinaldi
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Michael Costigan
- Department of Anesthesia, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Neurobiology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Seog Bae Oh
- Department of Brain and Cognitive Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
- Dental Research Institute and Department of Neurobiology & Physiology, School of Dentistry, Seoul National University, Seoul, South Korea
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247
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Donovan MKR, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants. Nat Commun 2020; 11:955. [PMID: 32075962 PMCID: PMC7031340 DOI: 10.1038/s41467-020-14561-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022] Open
Abstract
The Genotype-Tissue Expression (GTEx) resource has provided insights into the regulatory impact of genetic variation on gene expression across human tissues; however, thus far has not considered how variation acts at the resolution of the different cell types. Here, using gene expression signatures obtained from mouse cell types, we deconvolute bulk RNA-seq samples from 28 GTEx tissues to quantify cellular composition, which reveals striking heterogeneity across these samples. Conducting eQTL analyses for GTEx liver and skin samples using cell composition estimates as interaction terms, we identify thousands of genetic associations that are cell-type-associated. The skin cell-type associated eQTLs colocalize with skin diseases, indicating that variants which influence gene expression in distinct skin cell types play important roles in traits and disease. Our study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners.
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Affiliation(s)
- Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Matteo D'Antonio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Kelly A Frazer
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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248
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Efremova M, Vento-Tormo R, Park JE, Teichmann SA, James KR. Immunology in the Era of Single-Cell Technologies. Annu Rev Immunol 2020; 38:727-757. [PMID: 32075461 DOI: 10.1146/annurev-immunol-090419-020340] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immune cells are characterized by diversity, specificity, plasticity, and adaptability-properties that enable them to contribute to homeostasis and respond specifically and dynamically to the many threats encountered by the body. Single-cell technologies, including the assessment of transcriptomics, genomics, and proteomics at the level of individual cells, are ideally suited to studying these properties of immune cells. In this review we discuss the benefits of adopting single-cell approaches in studying underappreciated qualities of immune cells and highlight examples where these technologies have been critical to advancing our understanding of the immune system in health and disease.
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Affiliation(s)
- Mirjana Efremova
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Jong-Eun Park
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; , .,Theory of Condensed Matter, Department of Physics, University of Cambridge, Cambridgeshire CB3 0HE, United Kingdom.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Kylie R James
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom; ,
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249
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Reyes M, Filbin MR, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N. An immune-cell signature of bacterial sepsis. Nat Med 2020; 26:333-340. [PMID: 32066974 DOI: 10.1038/s41591-020-0752-4] [Citation(s) in RCA: 229] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 12/17/2022]
Abstract
Dysregulation of the immune response to bacterial infection can lead to sepsis, a condition with high mortality. Multiple whole-blood gene-expression studies have defined sepsis-associated molecular signatures, but have not resolved changes in transcriptional states of specific cell types. Here, we used single-cell RNA-sequencing to profile the blood of people with sepsis (n = 29) across three clinical cohorts with corresponding controls (n = 36). We profiled total peripheral blood mononuclear cells (PBMCs, 106,545 cells) and dendritic cells (19,806 cells) across all subjects and, on the basis of clustering of their gene-expression profiles, defined 16 immune-cell states. We identified a unique CD14+ monocyte state that is expanded in people with sepsis and validated its power in distinguishing these individuals from controls using public transcriptomic data from subjects with different disease etiologies and from multiple geographic locations (18 cohorts, n = 1,467 subjects). We identified a panel of surface markers for isolation and quantification of the monocyte state and characterized its epigenomic and functional phenotypes, and propose a model for its induction from human bone marrow. This study demonstrates the utility of single-cell genomics in discovering disease-associated cytologic signatures and provides insight into the cellular basis of immune dysregulation in bacterial sepsis.
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Affiliation(s)
- Miguel Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael R Filbin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Emergency Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Roby P Bhattacharyya
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | | | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rebecca M Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Marcia B Goldberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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250
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Dogra P, Rancan C, Ma W, Toth M, Senda T, Carpenter DJ, Kubota M, Matsumoto R, Thapa P, Szabo PA, Li Poon MM, Li J, Arakawa-Hoyt J, Shen Y, Fong L, Lanier LL, Farber DL. Tissue Determinants of Human NK Cell Development, Function, and Residence. Cell 2020; 180:749-763.e13. [PMID: 32059780 DOI: 10.1016/j.cell.2020.01.022] [Citation(s) in RCA: 230] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/09/2019] [Accepted: 01/15/2020] [Indexed: 12/15/2022]
Abstract
Immune responses in diverse tissue sites are critical for protective immunity and homeostasis. Here, we investigate how tissue localization regulates the development and function of human natural killer (NK) cells, innate lymphocytes important for anti-viral and tumor immunity. Integrating high-dimensional analysis of NK cells from blood, lymphoid organs, and mucosal tissue sites from 60 individuals, we identify tissue-specific patterns of NK cell subset distribution, maturation, and function maintained across age and between individuals. Mature and terminally differentiated NK cells with enhanced effector function predominate in blood, bone marrow, spleen, and lungs and exhibit shared transcriptional programs across sites. By contrast, precursor and immature NK cells with reduced effector capacity populate lymph nodes and intestines and exhibit tissue-resident signatures and site-specific adaptations. Together, our results reveal anatomic control of NK cell development and maintenance as tissue-resident populations, whereas mature, terminally differentiated subsets mediate immunosurveillance through diverse peripheral sites. VIDEO ABSTRACT.
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Affiliation(s)
- Pranay Dogra
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Chiara Rancan
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wenji Ma
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Marta Toth
- Department of Immunology, Faculty of Medicine, University of Debrecen and Doctoral School of Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Takashi Senda
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Dustin J Carpenter
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Masaru Kubota
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Rei Matsumoto
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA
| | - Puspa Thapa
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Peter A Szabo
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Maya Meimei Li Poon
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacky Li
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Janice Arakawa-Hoyt
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Lawrence Fong
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lewis L Lanier
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Surgery, Columbia University Medical Center, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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