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McNitt SA, Dick JK, Hernandez Castaneda M, Sangala JA, Pierson M, Macchietto M, Burrack KS, Crompton PD, Seydel KB, Hamilton SE, Hart GT. Phenotype and function of IL-10 producing NK cells in individuals with malaria experience. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593687. [PMID: 38798324 PMCID: PMC11118352 DOI: 10.1101/2024.05.11.593687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Plasmodium falciparum infection can trigger high levels of inflammation that lead to fever and sometimes severe disease. People living in malaria-endemic areas gradually develop resistance to symptomatic malaria and control both parasite numbers and the inflammatory response. We previously found that adaptive natural killer (NK) cells correlate with reduced parasite load and protection from symptoms. We also previously found that murine NK cell production of IL-10 can protect mice from experimental cerebral malaria. Human NK cells can also secrete IL-10, but it was unknown what NK cell subsets produce IL-10 and if this is affected by malaria experience. We hypothesize that NK cell immunoregulation may lower inflammation and reduce fever induction. Here, we show that NK cells from subjects with malaria experience make significantly more IL-10 than subjects with no malaria experience. We then determined the proportions of NK cells that are cytotoxic and produce interferon gamma and/or IL-10 and identified a signature of adaptive and checkpoint molecules on IL-10-producing NK cells. Lastly, we find that co-culture with primary monocytes, Plasmodium -infected RBCs, and antibody induces IL-10 production by NK cells. These data suggest that NK cells may contribute to protection from malaria symptoms via IL-10 production.
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2
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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3
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Li JH, Zhou A, Lee CD, Shah SN, Ji JH, Senthilkumar V, Padilla ET, Ball AB, Feng Q, Bustillos CG, Riggan L, Greige A, Divakaruni AS, Annese F, Cooley Coleman JA, Skinner SA, Cowan CW, O'Sullivan TE. MEF2C regulates NK cell effector functions through control of lipid metabolism. Nat Immunol 2024; 25:778-789. [PMID: 38589619 DOI: 10.1038/s41590-024-01811-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/12/2024] [Indexed: 04/10/2024]
Abstract
Natural killer (NK) cells are a critical first line of defense against viral infection. Rare mutations in a small subset of transcription factors can result in decreased NK cell numbers and function in humans, with an associated increased susceptibility to viral infection. However, our understanding of the specific transcription factors governing mature human NK cell function is limited. Here we use a non-viral CRISPR-Cas9 knockout screen targeting genes encoding 31 transcription factors differentially expressed during human NK cell development. We identify myocyte enhancer factor 2C (MEF2C) as a master regulator of human NK cell functionality ex vivo. MEF2C-haploinsufficient patients and mice displayed defects in NK cell development and effector function, with an increased susceptibility to viral infection. Mechanistically, MEF2C was required for an interleukin (IL)-2- and IL-15-mediated increase in lipid content through regulation of sterol regulatory element-binding protein (SREBP) pathways. Supplementation with oleic acid restored MEF2C-deficient and MEF2C-haploinsufficient patient NK cell cytotoxic function. Therefore, MEF2C is a critical orchestrator of NK cell antiviral immunity by regulating SREBP-mediated lipid metabolism.
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Affiliation(s)
- Joey H Li
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Adalia Zhou
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Cassidy D Lee
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Siya N Shah
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jeong Hyun Ji
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Vignesh Senthilkumar
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Eddie T Padilla
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Qinyan Feng
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Christian G Bustillos
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Luke Riggan
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alain Greige
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Fran Annese
- Greenwood Genetic Center, Greenwood, SC, USA
| | | | | | - Christopher W Cowan
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Timothy E O'Sullivan
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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4
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Wang H, An N, Pei A, Sun Y, Li S, Chen S, Zhang N. Exploration of signature based on T cell-related genes in stomach adenocarcinoma by analysis of single cell sequencing data. Aging (Albany NY) 2024; 16:6035-6053. [PMID: 38536020 PMCID: PMC11042963 DOI: 10.18632/aging.205687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/29/2023] [Indexed: 04/23/2024]
Abstract
BACKGROUND Gastric cancer (GC) is a leading reason for the death of cancer around the world. The immune microenvironment counts a great deal in immunotherapy of advanced tumors, in which T cells exert an indispensable function. METHODS Single-cell RNA sequencing data were utilized to characterize the expression profile of T cells, followed by T cell-related genes (TCRGs) to construct signature and measure differences in survival time, enrichment pathways, somatic mutation status, immune status, and immunotherapy between groups. RESULTS The complex tumor microenvironment was analyzed by scRNA-seq data of GC patients. We screened for these T cell signature expression genes and the TCRGs-based signature was successfully constructed and relied on the riskscore grouping. In gene set enrichment analysis, it was shown that pro-tumor and suppressive immune pathways were more abundant in the higher risk group. We also found different infiltration of immune cells in two groups, and that the higher risk samples had a poorer response to immunotherapy. CONCLUSION Our study established a prognostic model, in which different groups had different prognosis, immune status, and enriched features. These results have provided additional insights into prognostic evaluation and the development of highly potent immunotherapies in GC.
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Affiliation(s)
- Huimei Wang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Nan An
- Department of Gastric Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Aiyue Pei
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Yongxiao Sun
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Shuo Li
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Si Chen
- Department of Colorectal and Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Nan Zhang
- Department of Gastroenterology, The First Hospital of Jilin University, Changchun, China
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5
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Vickridge E, Faraco CCF, Lo F, Rahimian H, Liu Z, Tehrani P, Djerir B, Ramdzan ZM, Leduy L, Maréchal A, Gingras AC, Nepveu A. The function of BCL11B in base excision repair contributes to its dual role as an oncogene and a haplo-insufficient tumor suppressor gene. Nucleic Acids Res 2024; 52:223-242. [PMID: 37956270 PMCID: PMC10783527 DOI: 10.1093/nar/gkad1037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Genetic studies in mice and human cancers established BCL11B as a haploinsufficient tumor suppressor gene. Paradoxically, BCL11B is overexpressed in some human cancers where its knockdown is synthetic lethal. We identified the BCL11B protein in a proximity-dependent biotinylation screen performed with the DNA glycosylase NTHL1. In vitro DNA repair assays demonstrated that both BCL11B and a small recombinant BCL11B213-560 protein lacking transcription regulation potential can stimulate the enzymatic activities of two base excision repair (BER) enzymes: NTHL1 and Pol β. In cells, BCL11B is rapidly recruited to sites of DNA damage caused by laser microirradiation. BCL11B knockdown delays, whereas ectopic expression of BCL11B213-560 accelerates, the repair of oxidative DNA damage. Inactivation of one BCL11B allele in TK6 lymphoblastoid cells causes an increase in spontaneous and radiation-induced mutation rates. In turn, ectopic expression of BCL11B213-560 cooperates with the RAS oncogene in cell transformation by reducing DNA damage and cellular senescence. These findings indicate that BCL11B functions as a BER accessory factor, safeguarding normal cells from acquiring mutations. Paradoxically, it also enables the survival of cancer cells that would otherwise undergo senescence or apoptosis due to oxidative DNA damage resulting from the elevated production of reactive oxygen species.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Camila C F Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Fanny Lo
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Hedyeh Rahimian
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Zi Yang Liu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Payman S Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
| | - Billel Djerir
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Zubaidah M Ramdzan
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
| | - Alexandre Maréchal
- Department of Biology and Cancer Research Institute, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
- Department of Oncology, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada
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6
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Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity 2023; 56:2816-2835.e13. [PMID: 38091953 DOI: 10.1016/j.immuni.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.
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Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Sara Gandolfi
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Olga Dashevsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Hanna Duàn
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Khalid Saeed
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Petra Nygren
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jonas Bouhlal
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Anna Näätänen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Bishwa R Ghimire
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Tiina Hannunen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Hanna Lähteenmäki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Pauliina Rumm
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Jason Theodoropoulos
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland
| | - Essi Laajala
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland
| | - Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Merja Heinäniemi
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Maija Hollmén
- Medicity Research Laboratory, University of Turku, 20014 Turku, Finland
| | - Shizuka Yamano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ryosuke Shirasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rizwan Romee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150 Espoo, Finland
| | - Dean A Lee
- Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ricardo De Matos Simoes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland
| | - Constantine S Mitsiades
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
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7
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Santosa EK, Sun JC. Cardinal features of immune memory in innate lymphocytes. Nat Immunol 2023; 24:1803-1812. [PMID: 37828377 PMCID: PMC10998651 DOI: 10.1038/s41590-023-01607-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/28/2023] [Indexed: 10/14/2023]
Abstract
The ability of vertebrates to 'remember' previous infections had once been attributed exclusively to adaptive immunity. We now appreciate that innate lymphocytes also possess memory properties akin to those of adaptive immune cells. In this Review, we draw parallels from T cell biology to explore the key features of immune memory in innate lymphocytes, including quantity, quality, and location. We discuss the signals that trigger clonal or clonal-like expansion in innate lymphocytes, and highlight recent studies that shed light on the complex cellular and molecular crosstalk between metabolism, epigenetics, and transcription responsible for differentiating innate lymphocyte responses towards a memory fate. Additionally, we explore emerging evidence that activated innate lymphocytes relocate and establish themselves in specific peripheral tissues during infection, which may facilitate an accelerated response program akin to those of tissue-resident memory T cells.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA.
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8
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Santosa EK, Kim H, Rückert T, Le Luduec JB, Abbasi AJ, Wingert CK, Peters L, Frost JN, Hsu KC, Romagnani C, Sun JC. Control of nutrient uptake by IRF4 orchestrates innate immune memory. Nat Immunol 2023; 24:1685-1697. [PMID: 37697097 PMCID: PMC11098052 DOI: 10.1038/s41590-023-01620-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Natural killer (NK) cells are innate cytotoxic lymphocytes with adaptive immune features, including antigen specificity, clonal expansion and memory. As such, NK cells share many transcriptional and epigenetic programs with their adaptive CD8+ T cell siblings. Various signals ranging from antigen, co-stimulation and proinflammatory cytokines are required for optimal NK cell responses in mice and humans during virus infection; however, the integration of these signals remains unclear. In this study, we identified that the transcription factor IRF4 integrates signals to coordinate the NK cell response during mouse cytomegalovirus infection. Loss of IRF4 was detrimental to the expansion and differentiation of virus-specific NK cells. This defect was partially attributed to the inability of IRF4-deficient NK cells to uptake nutrients required for survival and memory generation. Altogether, these data suggest that IRF4 is a signal integrator that acts as a secondary metabolic checkpoint to orchestrate the adaptive response of NK cells during viral infection.
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Affiliation(s)
- Endi K Santosa
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Hyunu Kim
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | | | - Aamna J Abbasi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire K Wingert
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lila Peters
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joe N Frost
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katharine C Hsu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Leibniz-Science Campus Chronic Inflammation, Berlin, Germany
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA.
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9
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Zhi L, Wang X, Gao Q, He W, Shang C, Guo C, Niu Z, Zhu W, Zhang X. Intrinsic and extrinsic factors determining natural killer cell fate: Phenotype and function. Biomed Pharmacother 2023; 165:115136. [PMID: 37453199 DOI: 10.1016/j.biopha.2023.115136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023] Open
Abstract
Natural killer (NK) cells are derived from hematopoietic stem cells. They belong to the innate lymphoid cell family, which is an important part of innate immunity. This family plays a role in the body mainly through the release of perforin, granzyme, and various cytokines and is involved in cytotoxicity and cytokine-mediated immune regulation. NK cells involved in normal immune regulation and the tumor microenvironment (TME) can exhibit completely different states. Here, we discuss the growth, development, and function of NK cells in regard to intrinsic and extrinsic factors. Intrinsic factors are those that influence NK cells to promote cell maturation and exert their effector functions under the control of internal metabolism and self-related genes. Extrinsic factors include the metabolism of the TME and the influence of related proteins on the "fate" of NK cells. This review targets the potential of NK cell metabolism, cellular molecules, regulatory genes, and other mechanisms involved in immune regulation. We further discuss immune-mediated tumor therapy, which is the trend of current research.
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Affiliation(s)
- Lingtong Zhi
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Xing Wang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Qing Gao
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Wenhui He
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Chongye Shang
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Changjiang Guo
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Zhiyuan Niu
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China
| | - Wuling Zhu
- Henan Province Engineering Research Center of Innovation for Synthetic Biology, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, PR China.
| | - Xuan Zhang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
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10
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Luo D, Li L, Wu Y, Yang Y, Ye Y, Hu J, Gao Y, Zeng N, Fei X, Li N, Jiang L. Mitochondria-related genes and metabolic profiles of innate and adaptive immune cells in primary Sjögren's syndrome. Front Immunol 2023; 14:1156774. [PMID: 37497211 PMCID: PMC10366690 DOI: 10.3389/fimmu.2023.1156774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Background Primary Sjogren's syndrome (pSS) is a prototypical systemic autoimmune disease characterised by lymphocyte infiltration and immune-complex deposition in multiple organs. The specific distribution of immune cell populations and their relationship with mitochondria remain unknown. Methods Histological analysis was performed to assess the specific distribution of innate and adaptive immune cell populations in labial salivary gland (LSG) samples from 30 patients with pSS and 13 patients with non-pSS. The ultrastructural morphometric features of mitochondria within immune cells were observed under the transmission electron microscope (TEM). RNA sequencing was performed on LSG samples from 40 patients with pSS and 7 non-pSS patients. The Single-sample Gene Set Enrichment Analysis (ssGSEA), ESTIMATE, and CIBERSORT algorithms and Pearson correlation coefficients were used to examine the relationship between mitochondria-related genes and immune infiltration. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify the mitochondria-specific genes and the related pathways based on the immune cell types. Results HE staining revealed a massive infiltration of plasma cells with abundant immunoglobulin protein distributed around phenotypically normal-appearing acinar and ductal tissues of patients with pSS. Immunohistochemical analyses revealed that innate immune cells (macrophages, eosinophils and NK cells) were distributed throughout the glandular tissue. Dominant adaptive immune cell infiltration composed of B cells, CD4+T cells and CD8+ T cells or ectopic lymphoid follicle-like structures were observed in the LSGs of patients with pSS. TEM validated the swelling of mitochondria with disorganised cristae in some lymphocytes that had invaded the glandular tissue. Subsequently, bioinformatic analysis revealed that innate and adaptive immune cells were associated with different mitochondrial metabolism pathways. Mitochondrial electron transport and respiratory chain complexes in the glandular microenvironment were positively correlated with innate immune cells, whereas amino acid and nucleic acid metabolism were negatively correlated with adaptive immune cells. In addition, mitochondrial biogenesis and mitochondrial apoptosis in the glandular microenvironment were closely associated with adaptive immune cells. Conclusion Innate and adaptive immune cells have distinct distribution profiles in the salivary gland tissues of patients with pSS and are associated with different mitochondrial metabolic pathways, which may contribute to disease progression.
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Affiliation(s)
- Danyang Luo
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Li
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yicheng Wu
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Yang
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yulin Ye
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiawei Hu
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Yiming Gao
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Naiyan Zeng
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Li
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
| | - Liting Jiang
- Department of Stomatology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
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11
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Wong P, Foltz JA, Chang L, Neal CC, Yao T, Cubitt CC, Tran J, Kersting-Schadek S, Palakurty S, Jaeger N, Russler-Germain DA, Marin ND, Gang M, Wagner JA, Zhou AY, Jacobs MT, Foster M, Schappe T, Marsala L, McClain E, Pence P, Becker-Hapak M, Fisk B, Petti AA, Griffith OL, Griffith M, Berrien-Elliott MM, Fehniger TA. T-BET and EOMES sustain mature human NK cell identity and antitumor function. J Clin Invest 2023; 133:e162530. [PMID: 37279078 PMCID: PMC10313375 DOI: 10.1172/jci162530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET- and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor-like (ILCP-like) profile with increased expression of the ILC-3-associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity.
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Affiliation(s)
- Pamela Wong
- Department of Medicine, Division of Oncology
| | | | - Lily Chang
- Department of Medicine, Division of Oncology
| | | | - Tony Yao
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | | | | | | | | | | | | | - Mark Foster
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | - Bryan Fisk
- Department of Medicine, Division of Oncology
| | | | | | | | | | - Todd A. Fehniger
- Department of Medicine, Division of Oncology
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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12
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Helm EY, Zelenka T, Cismasiu VB, Islam S, Silvane L, Zitti B, Holmes TD, Drashansky TT, Kwiatkowski AJ, Tao C, Dean J, Obermayer AN, Chen X, Keselowsky BG, Zhang W, Huo Z, Zhou L, Sheridan BS, Conejo-Garcia JR, Shaw TI, Bryceson YT, Avram D. Bcl11b sustains multipotency and restricts effector programs of intestinal-resident memory CD8 + T cells. Sci Immunol 2023; 8:eabn0484. [PMID: 37115913 DOI: 10.1126/sciimmunol.abn0484] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The networks of transcription factors (TFs) that control intestinal-resident memory CD8+ T (TRM) cells, including multipotency and effector programs, are poorly understood. In this work, we investigated the role of the TF Bcl11b in TRM cells during infection with Listeria monocytogenes using mice with post-activation, conditional deletion of Bcl11b in CD8+ T cells. Conditional deletion of Bcl11b resulted in increased numbers of intestinal TRM cells and their precursors as well as decreased splenic effector and circulating memory cells and precursors. Loss of circulating memory cells was in part due to increased intestinal homing of Bcl11b-/- circulating precursors, with no major alterations in their programs. Bcl11b-/- TRM cells had altered transcriptional programs, with diminished expression of multipotent/multifunctional (MP/MF) program genes, including Tcf7, and up-regulation of the effector program genes, including Prdm1. Bcl11b also limits the expression of Ahr, another TF with a role in intestinal CD8+ TRM cell differentiation. Deregulation of TRM programs translated into a poor recall response despite TRM cell accumulation in the intestine. Reduced expression of MP/MF program genes in Bcl11b-/- TRM cells was linked to decreased chromatin accessibility and a reduction in activating histone marks at these loci. In contrast, the effector program genes displayed increased activating epigenetic status. These findings demonstrate that Bcl11b is a frontrunner in the tissue residency program of intestinal memory cells upstream of Tcf1 and Blimp1, promoting multipotency and restricting the effector program.
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Affiliation(s)
- Eric Y Helm
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Tomas Zelenka
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Valeriu B Cismasiu
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Shamima Islam
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Leonardo Silvane
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Beatrice Zitti
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
| | - Tim D Holmes
- Broegelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, N-5021 Bergen, Norway
| | - Theodore T Drashansky
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Alexander J Kwiatkowski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Christine Tao
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Joseph Dean
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Alyssa N Obermayer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Xianghong Chen
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Benjamin G Keselowsky
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- UF Health Cancer Center, Gainesville, FL 32610, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, College of Public Health & Health Professions, University of Florida, Gainesville, FL 32611, USA
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Brian S Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Timothy I Shaw
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
| | - Yenan T Bryceson
- Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-14186 Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Sciences, University of Bergen, N-5021 Bergen, Norway
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, S-14186 Stockholm, Sweden
| | - Dorina Avram
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr., Tampa, FL 33612, USA
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13
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Yang L, Lang Y, Wu H, Xiang K, Wang Y, Yu M, Liu Y, Yang B, He L, Lu G, Ni Q, Chen X, Zhang L. Engineered Toll-like Receptor Nanoagonist Binding to Extracellular Matrix Elicits Safe and Robust Antitumor Immunity. ACS NANO 2023; 17:5340-5353. [PMID: 36913671 DOI: 10.1021/acsnano.2c08429] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cancer immunotherapy, such as the Toll-like receptor (TLR) agonist including CpG oligodeoxynucleotide, has shown potency in clinical settings. However, it is still confronted with multiple challenges, which include the limited efficacy and severe adverse events caused by the rapid clearance and systemic diffusion of CpG. Here we report an improved CpG-based immunotherapy approach composed of a synthetic extracellular matrix (ECM)-anchored DNA/peptide hybrid nanoagonist (EaCpG) via (1) a tailor designed DNA template that encodes tetramer CpG and additional short DNA moieties, (2) generation of elongated multimeric CpG through rolling circle amplification (RCA), (3) self-assembly of densely packaged CpG particles composed of tandem CpG building blocks and magnesium pyrophosphate, and (4) incorporation of multiple copies of ECM binding peptide through hybridization to short DNA moieties. The structurally well-defined EaCpG shows dramatically increased intratumoral retention and marginal systemic dissemination through peritumoral administration, leading to potent antitumor immune response and subsequent tumor elimination, with minimal treatment-related toxicity. Combined with conventional standard-of-care therapies, peritumor administration of EaCpG generates systemic immune responses that lead to a curative abscopal effect on distant untreated tumors in multiple cancer models, which is superior to the unmodified CpG. Taken together, EaCpG provides a facile and generalizable strategy to simultaneously potentiate the potency and safety of CpG for combinational cancer immunotherapies.
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Affiliation(s)
- Liu Yang
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Yue Lang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Haoguang Wu
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Kaiyan Xiang
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Yuanzheng Wang
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Mengqi Yu
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Yu Liu
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Bowei Yang
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Liangcan He
- School of Medicine and Health, Harbin Institute of Technology, Harbin 150080, China
| | - Guangming Lu
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
| | - Qianqian Ni
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Xiaoyuan Chen
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Longjiang Zhang
- Department of Radiology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002 Jiangsu, China
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14
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Ty M, Sun S, Callaway PC, Rek J, Press KD, van der Ploeg K, Nideffer J, Hu Z, Klemm S, Greenleaf W, Donato M, Tukwasibwe S, Arinaitwe E, Nankya F, Musinguzi K, Andrew D, de la Parte L, Mori DM, Lewis SN, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Blish C, Utz PJ, Khatri P, Dorsey G, Kamya M, Boyle M, Feeney M, Ssewanyana I, Jagannathan P. Malaria-driven expansion of adaptive-like functional CD56-negative NK cells correlates with clinical immunity to malaria. Sci Transl Med 2023; 15:eadd9012. [PMID: 36696483 PMCID: PMC9976268 DOI: 10.1126/scitranslmed.add9012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Natural killer (NK) cells likely play an important role in immunity to malaria, but the effect of repeated malaria on NK cell responses remains unclear. Here, we comprehensively profiled the NK cell response in a cohort of 264 Ugandan children. Repeated malaria exposure was associated with expansion of an atypical, CD56neg population of NK cells that differed transcriptionally, epigenetically, and phenotypically from CD56dim NK cells, including decreased expression of PLZF and the Fc receptor γ-chain, increased histone methylation, and increased protein expression of LAG-3, KIR, and LILRB1. CD56neg NK cells were highly functional and displayed greater antibody-dependent cellular cytotoxicity than CD56dim NK cells. Higher frequencies of CD56neg NK cells were associated with protection against symptomatic malaria and high parasite densities. After marked reductions in malaria transmission, frequencies of these cells rapidly declined, suggesting that continuous exposure to Plasmodium falciparum is required to maintain this modified, adaptive-like NK cell subset.
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Affiliation(s)
- Maureen Ty
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Shenghuan Sun
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Perri C Callaway
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | - Jason Nideffer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Zicheng Hu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Michele Donato
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Dean Andrew
- Queensland Institute for Medical Research, Queensland, Australia
| | | | | | | | - Saki Takahashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Catherine Blish
- Department of Medicine, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - P J Utz
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Medicine, Makerere University, Kampala, Uganda
| | - Michelle Boyle
- Queensland Institute for Medical Research, Queensland, Australia
| | - Margaret Feeney
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
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15
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Roa-Bautista A, López-Duarte M, Paz-Gandiaga N, San Segundo Arribas D, Ocejo-Vinyals JG. Deletion in the BCL11B Gene and Intellectual Developmental Disorder with Speech Delay, Dysmorphic Facies, and T-cell Abnormalities - a Case Report. EJIFCC 2022; 33:325-333. [PMID: 36605301 PMCID: PMC9768616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Herein we described a retrospective analysis of a 13-year-old female patient with facial dysmorphia and immune disorder caused by BCL11B gene mutation. The patient upon physical examination presented a particular face (thin eyebrows, small mandible, and widened eye distance), delayed language and motor development. Supplementary examination showed expansion of CD8+, absence of type 2 Innate Lymphoid Cells, increased IgG and altered distribution of T cells. Genetic testing revealed a heterozygous frameshift variation in exon 4 of the BCL11B gene; c.1887_c.1893delCGGCGGG (p.Gly630Glyfs*91). Finally, a BCL11B gene mutation could lead to abnormal development of the nervous and immune systems, therefore, it is necessary to consider this syndrome in patients with the clinical and immunological phenotype described below.
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Affiliation(s)
- Adriel Roa-Bautista
- Division of Immunology, Marques de Valdecilla University Hospital, University of Cantabria, IDIVAL, Santander, Cantabria, Spain,Corresponding author: Adriel Roa-Bautista, MD, MHSc Division of Immunology Marques de Valdecilla University Hospital University of Cantabria IDIVAL, Santander, Cantabria (39008) Spain Phone: +34 640 55 57 65 E-mail:
| | - Mónica López-Duarte
- Division of Hematology, Marques de Valdecilla University Hospital, University of Cantabria, IDIVAL, Santander, Cantabria, Spain
| | - Nerea Paz-Gandiaga
- Division of Genetics, Marques de Valdecilla University Hospital, University of Cantabria, IDIVAL, Santander, Cantabria, Spain
| | - David San Segundo Arribas
- Division of Immunology, Marques de Valdecilla University Hospital, University of Cantabria, IDIVAL, Santander, Cantabria, Spain
| | - J. Gonzalo Ocejo-Vinyals
- Division of Immunology, Marques de Valdecilla University Hospital, University of Cantabria, IDIVAL, Santander, Cantabria, Spain
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16
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Forkel H, Grabarczyk P, Depke M, Troschke-Meurer S, Simm S, Hammer E, Michalik S, Hentschker C, Corleis B, Loyal L, Zumpe M, Siebert N, Dorhoi A, Thiel A, Lode H, Völker U, Schmidt CA. BCL11B depletion induces the development of highly cytotoxic innate T cells out of IL-15 stimulated peripheral blood αβ CD8+ T cells. Oncoimmunology 2022; 11:2148850. [PMID: 36507091 PMCID: PMC9728472 DOI: 10.1080/2162402x.2022.2148850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BCL11B, an essential transcription factor for thymopoiesis, regulates also vital processes in post-thymic lymphocytes. Increased expression of BCL11B was recently correlated with the maturation of NK cells, whereas reduced BCL11B levels were observed in native and induced T cell subsets displaying NK cell features. We show that BCL11B-depleted CD8+ T cells stimulated with IL-15 acquired remarkable innate characteristics. These induced innate CD8+ (iiT8) cells expressed multiple innate receptors like NKp30, CD161, and CD16 as well as factors regulating migration and tissue homing while maintaining their T cell phenotype. The iiT8 cells effectively killed leukemic cells spontaneously and neuroblastoma spheroids in the presence of a tumor-specific monoclonal antibody mediated by CD16 receptor activation. These iiT8 cells integrate the innate natural killer cell activity with adaptive T cell longevity, promising an interesting therapeutic potential. Our study demonstrates that innate T cells, albeit of limited clinical applicability given their low frequency, can be efficiently generated from peripheral blood and applied for adoptive transfer, CAR therapy, or combined with therapeutic antibodies.
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Affiliation(s)
- Hannes Forkel
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Piotr Grabarczyk
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Maren Depke
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
| | - Sascha Troschke-Meurer
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Björn Corleis
- Institute for Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Lucie Loyal
- Si-M/“Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Maxi Zumpe
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Nikolai Siebert
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Anca Dorhoi
- Institute for Immunology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Andreas Thiel
- Si-M/“Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Holger Lode
- Department of Pediatric Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian A. Schmidt
- Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany,CONTACT Christian A. Schmidt Internal Medicine Clinic C, University Medicine Greifswald, Greifswald, Germany
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17
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Imianowski CJ, Whiteside SK, Lozano T, Evans AC, Benson JD, Courreges CJ, Sadiyah F, Lau CM, Zandhuis ND, Grant FM, Schuijs MJ, Vardaka P, Kuo P, Soilleux EJ, Yang J, Sun JC, Kurosaki T, Okkenhaug K, Halim TY, Roychoudhuri R. BACH2 restricts NK cell maturation and function, limiting immunity to cancer metastasis. J Exp Med 2022; 219:e20211476. [PMID: 36178457 PMCID: PMC9529614 DOI: 10.1084/jem.20211476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/11/2021] [Accepted: 08/26/2022] [Indexed: 11/04/2022] Open
Abstract
Natural killer (NK) cells are critical to immune surveillance against infections and cancer. Their role in immune surveillance requires that NK cells are present within tissues in a quiescent state. Mechanisms by which NK cells remain quiescent in tissues are incompletely elucidated. The transcriptional repressor BACH2 plays a critical role within the adaptive immune system, but its function within innate lymphocytes has been unclear. Here, we show that BACH2 acts as an intrinsic negative regulator of NK cell maturation and function. BACH2 is expressed within developing and mature NK cells and promotes the maintenance of immature NK cells by restricting their maturation in the presence of weak stimulatory signals. Loss of BACH2 within NK cells results in accumulation of activated NK cells with unrestrained cytotoxic function within tissues, which mediate augmented immune surveillance to pulmonary cancer metastasis. These findings establish a critical function of BACH2 as a global negative regulator of innate cytotoxic function and tumor immune surveillance by NK cells.
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Affiliation(s)
- Charlotte J. Imianowski
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Sarah K. Whiteside
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Teresa Lozano
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | | | - Jayme D. Benson
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Firas Sadiyah
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Colleen M. Lau
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
- Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Nordin D. Zandhuis
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Francis M. Grant
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Martijn J. Schuijs
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Panagiota Vardaka
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Paula Kuo
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | | | - Jie Yang
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | - Rahul Roychoudhuri
- Department of Pathology, University of Cambridge, Cambridge, UK
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, Cambridgeshire, UK
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18
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To kill or not to kill - The role of the tumor microenvironment in shaping group 1 ILC functions. Semin Immunol 2022; 61-64:101670. [PMID: 36372017 PMCID: PMC7613863 DOI: 10.1016/j.smim.2022.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Group 1 innate lymphoid cells (ILC) comprise two major IFN-γ producing populations, namely Natural Killer (NK) cells, and ILC1s. Recent studies have revealed a complex and diverse composition of group 1 ILC subsets infiltrating different tumors. In this review, we will outline the commonalities and differences between group 1 ILC subsets in both mice and humans, discuss how the tissue and tumor microenvironment shapes their phenotype and functions, as well as describe their contrasting roles in the response to different cancers.
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19
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Shemesh A, Su Y, Calabrese DR, Chen D, Arakawa-Hoyt J, Roybal KT, Heath JR, Greenland JR, Lanier LL. Diminished cell proliferation promotes natural killer cell adaptive-like phenotype by limiting FcεRIγ expression. J Exp Med 2022; 219:e20220551. [PMID: 36066491 PMCID: PMC9448639 DOI: 10.1084/jem.20220551] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/14/2022] [Accepted: 08/05/2022] [Indexed: 12/20/2022] Open
Abstract
Human adaptive-like natural killer (NK) cells express low levels of FcεRIγ (FcRγ-/low) and are reported to accumulate during COVID-19 infection; however, the mechanism underlying and regulating FcRγ expression in NK cells has yet to be fully defined. We observed lower FcRγ protein expression in NK cell subsets from lung transplant patients during rapamycin treatment, suggesting a link with reduced mTOR activity. Further, FcRγ-/low NK cell subsets from healthy donors displayed reduced mTOR activity. We discovered that FcRγ upregulation is dependent on cell proliferation progression mediated by IL-2, IL-15, or IL-12, is sensitive to mTOR suppression, and is inhibited by TGFβ or IFNα. Accordingly, the accumulation of adaptive-like FcRγ-/low NK cells in COVID-19 patients corresponded to increased TGFβ and IFNα levels and disease severity. Our results show that an adaptive-like NK cell phenotype is induced by diminished cell proliferation and has an early prognostic value for increased TGFβ and IFNα levels in COVID-19 infection associated with disease severity.
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Affiliation(s)
- Avishai Shemesh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA
| | - Daniel R. Calabrese
- Department of Medicine, University of California, San Francisco, CA
- Medical Service, Veterans Affairs Health Care System, San Francisco, CA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA
- Department of Microbiology, University of Washington, Seattle, WA
- Department of Informatics, University of Washington, Seattle, WA
| | - Janice Arakawa-Hoyt
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Kole T. Roybal
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
- Gladstone University of California, San Francisco Institute for Genetic Immunology, San Francisco, CA
- University of California, San Francisco Cell Design Institute, San Francisco, CA
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA
- Department of Bioengineering, University of Washington, Seattle, WA
| | - John R. Greenland
- Department of Medicine, University of California, San Francisco, CA
- Medical Service, Veterans Affairs Health Care System, San Francisco, CA
| | - Lewis L. Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA
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20
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Haroun-Izquierdo A, Vincenti M, Netskar H, van Ooijen H, Zhang B, Bendzick L, Kanaya M, Momayyezi P, Li S, Wiiger MT, Hoel HJ, Krokeide SZ, Kremer V, Tjonnfjord G, Berggren S, Wikström K, Blomberg P, Alici E, Felices M, Önfelt B, Höglund P, Valamehr B, Ljunggren HG, Björklund A, Hammer Q, Kveberg L, Cichocki F, Miller JS, Malmberg KJ, Sohlberg E. Adaptive single-KIR +NKG2C + NK cells expanded from select superdonors show potent missing-self reactivity and efficiently control HLA-mismatched acute myeloid leukemia. J Immunother Cancer 2022; 10:jitc-2022-005577. [PMID: 36319065 PMCID: PMC9628692 DOI: 10.1136/jitc-2022-005577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Natural killer (NK) cells hold great promise as a source for allogeneic cell therapy against hematological malignancies, including acute myeloid leukemia (AML). Current treatments are hampered by variability in NK cell subset responses, a limitation which could be circumvented by specific expansion of highly potent single killer immunoglobulin-like receptor (KIR)+NKG2C+ adaptive NK cells to maximize missing-self reactivity. METHODS We developed a GMP-compliant protocol to expand adaptive NK cells from cryopreserved cells derived from select third-party superdonors, that is, donors harboring large adaptive NK cell subsets with desired KIR specificities at baseline. We studied the adaptive state of the cell product (ADAPT-NK) by flow cytometry and mass cytometry as well as cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq). We investigated the functional responses of ADAPT-NK cells against a wide range of tumor target cell lines and primary AML samples using flow cytometry and IncuCyte as well as in a mouse model of AML. RESULTS ADAPT-NK cells were >90% pure with a homogeneous expression of a single self-HLA specific KIR and expanded a median of 470-fold. The ADAPT-NK cells largely retained their adaptive transcriptional signature with activation of effector programs without signs of exhaustion. ADAPT-NK cells showed high degranulation capacity and efficient killing of HLA-C/KIR mismatched tumor cell lines as well as primary leukemic blasts from AML patients. Finally, the expanded adaptive NK cells had preserved robust antibody-dependent cellular cytotoxicity potential and combination of ADAPT-NK cells with an anti-CD16/IL-15/anti-CD33 tri-specific engager led to near-complete killing of resistant CD45dim blast subtypes. CONCLUSIONS These preclinical data demonstrate the feasibility of off-the-shelf therapy with a non-engineered, yet highly specific, NK cell population with full missing-self recognition capability.
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Affiliation(s)
- Alvaro Haroun-Izquierdo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Marianna Vincenti
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Herman Netskar
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanna van Ooijen
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Bin Zhang
- University of Minnesota, Masonic Cancer Center, Minneapolis, Minnesota, USA
| | - Laura Bendzick
- University of Minnesota, Masonic Cancer Center, Minneapolis, Minnesota, USA
| | - Minoru Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Pouria Momayyezi
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Shuo Li
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Merete Thune Wiiger
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanna Julie Hoel
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Silje Zandstra Krokeide
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Veronika Kremer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Geir Tjonnfjord
- Department of Hematology, Oslo University Hospital and K.G. Jebsen Centre for B-cell malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stéphanie Berggren
- Vecura, Karolinska Center for Cell Therapy Clinical Research Center, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Wikström
- Vecura, Karolinska Center for Cell Therapy Clinical Research Center, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Blomberg
- Vecura, Karolinska Center for Cell Therapy Clinical Research Center, Karolinska University Hospital, Stockholm, Sweden
| | - Evren Alici
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Martin Felices
- University of Minnesota, Masonic Cancer Center, Minneapolis, Minnesota, USA
| | - Björn Önfelt
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Petter Höglund
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Björklund
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation, Karolinska University Hospital, Stockholm, Sweden
| | - Quirin Hammer
- 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 and University of Oslo, Oslo, Norway
| | - Frank Cichocki
- University of Minnesota, Masonic Cancer Center, Minneapolis, Minnesota, USA
| | - Jeffrey S Miller
- University of Minnesota, Masonic Cancer Center, Minneapolis, Minnesota, USA
| | - 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 and University of Oslo, Oslo, Norway
| | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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21
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Li S, Bern MD, Miao B, Fan C, Xing X, Inoue T, Piersma SJ, Wang T, Colonna M, Kurosaki T, Yokoyama WM. The transcription factor Bach2 negatively regulates murine natural killer cell maturation and function. eLife 2022; 11:e77294. [PMID: 36190189 PMCID: PMC9560152 DOI: 10.7554/elife.77294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 10/02/2022] [Indexed: 11/13/2022] Open
Abstract
BTB domain And CNC Homolog 2 (Bach2) is a transcription repressor that actively participates in T and B lymphocyte development, but it is unknown if Bach2 is also involved in the development of innate immune cells, such as natural killer (NK) cells. Here, we followed the expression of Bach2 during murine NK cell development, finding that it peaked in immature CD27+CD11b+ cells and decreased upon further maturation. Bach2 showed an organ and tissue-specific expression pattern in NK cells. Bach2 expression positively correlated with the expression of transcription factor TCF1 and negatively correlated with genes encoding NK effector molecules and those involved in the cell cycle. Lack of Bach2 expression caused changes in chromatin accessibility of corresponding genes. In the end, Bach2 deficiency resulted in increased proportions of terminally differentiated NK cells with increased production of granzymes and cytokines. NK cell-mediated control of tumor metastasis was also augmented in the absence of Bach2. Therefore, Bach2 is a key checkpoint protein regulating NK terminal maturation.
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Affiliation(s)
- Shasha Li
- Division of Rheumatology, Department of Medicine, Washington University School of MedicineSt LouisUnited States
| | - Michael D Bern
- Division of Rheumatology, Department of Medicine, Washington University School of MedicineSt LouisUnited States
| | - Benpeng Miao
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt LouisUnited States
| | - Changxu Fan
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt LouisUnited States
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt LouisUnited States
| | - Takeshi Inoue
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka UniversityOsakaJapan
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of MedicineSt LouisUnited States
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt LouisUnited States
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of MedicineSt LouisUnited States
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka UniversityOsakaJapan
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of MedicineSt LouisUnited States
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22
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Cord Blood-Derived Natural Killer Cell Exploitation in Immunotherapy Protocols: More Than a Promise? Cancers (Basel) 2022; 14:cancers14184439. [PMID: 36139598 PMCID: PMC9496735 DOI: 10.3390/cancers14184439] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary NK cell anti-tumor activity against hematological malignancies is well-established and many studies support their role in the control of solid tumor growth and metastasis generation. However, tumor microenvironment may affect NK cell function. Ongoing studies are aimed to design novel immunotherapeutic protocols to combine NK cell-based immunotherapy with other therapeutic strategies to improve the anti-tumor NK cell response. In this context, UCB is one of the main sources of both mature NK cells and of CD34+ HSPC that can generate NK cells, both in-vivo and in-vitro. UCB-derived NK cells represent a valuable tool to perform in-vitro and preclinical analyses and are already used in several clinical settings, particularly against hematological malignancies. The present review describes the characteristics of different types of UCB-derived NK cells and the in-vitro models to expand them, both for research and clinical purposes in the context of cancer immunotherapy. Abstract In the last 20 years, Natural Killer (NK) cell-based immunotherapy has become a promising approach to target various types of cancer. Indeed, NK cells play a pivotal role in the first-line defense against tumors through major histocompatibility complex-independent immunosurveillance. Their role in the control of leukemia relapse has been clearly established and, moreover, the presence of NK cells in the tumor microenvironment (TME) generally correlates with good prognosis. However, it has also been observed that, often, NK cells poorly infiltrate the tumor tissue, and, in TME, their functions may be compromised by immunosuppressive factors that contribute to the failure of anti-cancer immune response. Currently, studies are focused on the design of effective strategies to expand NK cells and enhance their cytotoxic activity, exploiting different cell sources, such as peripheral blood (PB), umbilical cord blood (UCB) and NK cell lines. Among them, UCB represents an important source of mature NK cells and CD34+ Hematopoietic Stem and Progenitor Cells (HSPCs), as precursors of NK cells. In this review, we summarize the UCB-derived NK cell activity in the tumor context, review the different in-vitro models to expand NK cells from UCB, and discuss the importance of their exploitation in anti-tumor immunotherapy protocols.
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23
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Morgan RC, Kee BL. Genomic and Transcriptional Mechanisms Governing Innate-like T Lymphocyte Development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:208-216. [PMID: 35821098 DOI: 10.4049/jimmunol.2200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
Innate-like lymphocytes are a subset of lymphoid cells that function as a first line of defense against microbial infection. These cells are activated by proinflammatory cytokines or broadly expressed receptors and are able to rapidly perform their effector functions owing to a uniquely primed chromatin state that is acquired as a part of their developmental program. These cells function in many organs to protect against disease, but they release cytokines and cytotoxic mediators that can also lead to severe tissue pathologies. Therefore, harnessing the capabilities of these cells for therapeutic interventions will require a deep understanding of how these cells develop and regulate their effector functions. In this review we discuss recent advances in the identification of the transcription factors and the genomic regions that guide the development and function of invariant NKT cells and we highlight related mechanisms in other innate-like lymphocytes.
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Affiliation(s)
- Roxroy C Morgan
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL; and
| | - Barbara L Kee
- Cancer Biology and Immunology, Department of Pathology, University of Chicago, Chicago, IL
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24
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Jaiswal SR, Arunachalam J, Saifullah A, Lakhchaura R, Tailor D, Mehta A, Bhagawati G, Aiyer H, Khamar B, Malhotra SV, Chakrabarti S. Impact of an Immune Modulator Mycobacterium-w on Adaptive Natural Killer Cells and Protection Against COVID-19. Front Immunol 2022; 13:887230. [PMID: 35603154 PMCID: PMC9115578 DOI: 10.3389/fimmu.2022.887230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
The kinetics of NKG2C+ adaptive natural killer (ANK) cells and NKG2A+inhibitory NK (iNK) cells with respect to the incidence of SARS-CoV-2 infection were studied for 6 months in a cohort of healthcare workers following the administration of the heat-killed Mycobacterium w (Mw group) in comparison to a control group. In both groups, corona virus disease 2019 (COVID-19) correlated with lower NKG2C+ANK cells at baseline. There was a significant upregulation of NKG2C expression and IFN-γ release in the Mw group (p=0.0009), particularly in those with a lower baseline NKG2C expression, along with the downregulation of iNK cells (p<0.0001). This translated to a significant reduction in the incidence and severity of COVID-19 in the Mw group (incidence risk ratio-0.15, p=0.0004). RNA-seq analysis at 6 months showed an upregulation of the ANK pathway genes and an enhanced ANK-mediated antibody-dependent cellular cytotoxicity (ADCC) signature. Thus, Mw was observed to have a salutary impact on the ANK cell profile and a long-term upregulation of ANK-ADCC pathways, which could have provided protection against COVID-19 in a non-immune high-risk population.
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Affiliation(s)
- Sarita Rani Jaiswal
- Cellular Therapy and Immunology, Manashi Chakrabarti Foundation, New Delhi, India
- Department of Blood and Marrow Transplantation, Dharamshila Narayana Super-Speciality Hospital, New Delhi, India
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, India
| | - Jaganath Arunachalam
- Cellular Therapy and Immunology, Manashi Chakrabarti Foundation, New Delhi, India
| | - Ashraf Saifullah
- Department of Blood and Marrow Transplantation, Dharamshila Narayana Super-Speciality Hospital, New Delhi, India
| | - Rohit Lakhchaura
- Department of Blood and Marrow Transplantation, Dharamshila Narayana Super-Speciality Hospital, New Delhi, India
| | - Dhanir Tailor
- Department of Cell, Development & Cancer Biology and Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Anupama Mehta
- Department of Blood and Marrow Transplantation, Dharamshila Narayana Super-Speciality Hospital, New Delhi, India
| | - Gitali Bhagawati
- Department of Pathology and Microbiology, Dharamshila Narayana Super-speciality Hospital, New Delhi, India
| | - Hemamalini Aiyer
- Department of Pathology and Microbiology, Dharamshila Narayana Super-speciality Hospital, New Delhi, India
| | - Bakulesh Khamar
- Research & Development, Cadila Pharmaceuticals Ltd, Ahmedabad, India
| | - Sanjay V. Malhotra
- Department of Cell, Development & Cancer Biology and Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
| | - Suparno Chakrabarti
- Cellular Therapy and Immunology, Manashi Chakrabarti Foundation, New Delhi, India
- Department of Blood and Marrow Transplantation, Dharamshila Narayana Super-Speciality Hospital, New Delhi, India
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25
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Gao F, Zhou Z, Lin Y, Shu G, Yin G, Zhang T. Biology and Clinical Relevance of HCMV-Associated Adaptive NK Cells. Front Immunol 2022; 13:830396. [PMID: 35464486 PMCID: PMC9022632 DOI: 10.3389/fimmu.2022.830396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Natural killer (NK) cells are an important component of the innate immune system due to their strong ability to kill virally infected or transformed cells without prior exposure to the antigen (Ag). However, the biology of human NK (hNK) cells has largely remained elusive. Recent advances have characterized several novel hNK subsets. Among them, adaptive NK cells demonstrate an intriguing specialized antibody (Ab)-dependent response and several adaptive immune features. Most adaptive NK cells express a higher level of NKG2C but lack an intracellular signaling adaptor, FcϵRIγ (hereafter abbreviated as FcRγ). The specific expression pattern of these genes, with other signature genes, is the result of a specific epigenetic modification. The expansion of adaptive NK cells in vivo has been documented in various viral infections, while the frequency of adaptive NK cells among peripheral blood mononuclear cells correlates with improved prognosis of monoclonal Ab treatment against leukemia. This review summarizes the discovery and signature phenotype of adaptive NK cells. We also discuss the reported association between adaptive NK cells and pathological conditions. Finally, we briefly highlight the application of adaptive NK cells in adoptive cell therapy against cancer.
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Affiliation(s)
- Fei Gao
- Immuno-Oncology Laboratory, Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Zhengwei Zhou
- Immuno-Oncology Laboratory, Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Ying Lin
- Immuno-Oncology Laboratory, Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Guang Shu
- Immuno-Oncology Laboratory, Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Gang Yin
- Immuno-Oncology Laboratory, Department of Pathology, School of Basic Medicine, Central South University, Changsha, China
| | - Tianxiang Zhang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
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26
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Understanding natural killer cell biology from a single cell perspective. Cell Immunol 2022; 373:104497. [DOI: 10.1016/j.cellimm.2022.104497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/26/2022] [Accepted: 02/16/2022] [Indexed: 12/27/2022]
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27
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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28
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Seo S, Mace EM. Diversity of human NK cell developmental pathways defined by single-cell analyses. Curr Opin Immunol 2022; 74:106-111. [PMID: 34861544 PMCID: PMC8901532 DOI: 10.1016/j.coi.2021.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Human natural killer (NK) and innate lymphoid cells (ILCs) include diverse specialized phenotypic and functional subsets that reflect their roles as innate immune effector cells present in tissue and circulation. In recent years, significant advances have been made in better defining their tissue resident phenotypes, developmental pathways, and phenotypic plasticity. Here we offer a brief review of new insights into human NK cell diversity specifically defined by next generation sequencing and single-cell transcriptomic studies and integrate these into our current models of human NK cell developmental trajectories and mature subsets. These studies highlight both a deeper understanding of innate lymphoid cell differentiation and homeostasis and underscore critical questions that remain outstanding in the field.
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Affiliation(s)
- Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
| | - Emily M. Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center New York NY 10032
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29
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Lau CM, Wiedemann GM, Sun JC. Epigenetic regulation of natural killer cell memory. Immunol Rev 2022; 305:90-110. [PMID: 34908173 PMCID: PMC8955591 DOI: 10.1111/imr.13031] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 01/03/2023]
Abstract
Immunological memory is the underlying mechanism by which the immune system remembers previous encounters with pathogens to produce an enhanced secondary response upon re-encounter. It stands as the hallmark feature of the adaptive immune system and the cornerstone of vaccine development. Classic recall responses are executed by conventional T and B cells, which undergo somatic recombination and modify their receptor repertoire to ensure recognition of a vast number of antigens. However, recent evidence has challenged the dogma that memory responses are restricted to the adaptive immune system, which has prompted a reevaluation of what delineates "immune memory." Natural killer (NK) cells of the innate immune system have been at the forefront of these pushed boundaries, and have proved to be more "adaptable" than previously thought. Like T cells, we now appreciate that their "natural" abilities actually require a myriad of signals for optimal responses. In this review, we discuss the many signals required for effector and memory NK cell responses and the epigenetic mechanisms that ultimately endow their enhanced features.
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Affiliation(s)
- Colleen M. Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gabriela M. Wiedemann
- Department of Internal Medicine II, School of Medicine, Technical University of Munich, Munich, Germany
| | - Joseph C. Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, New York, USA
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30
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Zheng Y, Liu B, Deng X, Chen Y, Huang Y, Zhang Y, Xu Y, Sang L, Liu X, Li Y. Construction and validation of a robust prognostic model based on immune features in sepsis. Front Immunol 2022; 13:994295. [PMID: 36532037 PMCID: PMC9756843 DOI: 10.3389/fimmu.2022.994295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/11/2022] [Indexed: 12/05/2022] Open
Abstract
Purpose Sepsis, with life-threatening organ failure, is caused by the uncontrolled host response to infection. Immune response plays an important role in the pathophysiology of sepsis. Immune-related genes (IRGs) are promising novel biomarkers that have been used to construct the diagnostic and prognostic model. However, an IRG prognostic model used to predict the 28-day mortality in sepsis was still limited. Therefore, the study aimed to develop a prognostic model based on IRGs to identify patients with high risk and predict the 28-day mortality in sepsis. Then, we further explore the circulating immune cell and immunosuppression state in sepsis. Materials and methods The differentially expressed genes (DEGs), differentially expressed immune-related genes (DEIRGs), and differentially expressed transcription factors (DETFs) were obtained from the GEO, ImmPort, and Cistrome databases. Then, the TFs-DEIRGs regulatory network and prognostic prediction model were constructed by Cox regression analysis and Pearson correlation analysis. The external datasets also validated the reliability of the prognostic model. Based on the prognostic DEIRGs, we developed a nomogram and conducted an independent prognosis analysis to explore the relationship between DEIRGs in the prognostic model and clinical features in sepsis. Besides, we further evaluate the circulating immune cells state in sepsis. Results A total of seven datasets were included in our study. Among them, GSE65682 was identified as a discovery cohort. The results of GSEA showed that there is a significant correlation between sepsis and immune response. Then, based on a P value <0.01, 69 prognostic DEIRGs were obtained and the potential molecular mechanisms of DEIRGs were also clarified. According to multivariate Cox regression analysis, 22 DEIRGs were further identified to construct the prognostic model and identify patients with high risk. The Kaplan-Meier survival analysis showed that high-risk groups have higher 28-day mortality than low-risk groups (P=1.105e-13). The AUC value was 0.879 which symbolized that the prognostic model had a better accuracy to predict the 28-day mortality. The external datasets also prove that the prognostic model had an excellent prediction value. Furthermore, the results of correlation analysis showed that patients with Mars1 might have higher risk scores than Mars2-4 (P=0.002). According to the previous study, Mars1 endotype was characterized by immunoparalysis. Thus, the sepsis patients in high-risk groups might exist the immunosuppression. Between the high-risk and low-risk groups, circulating immune cells types were significantly different, and risk score was significantly negatively correlated with naive CD4+ T cells (P=0.019), activated NK cells (P=0.0045), monocytes (P=0.0134), and M1 macrophages (P=0.0002). Conclusions Our study provides a robust prognostic model based on 22 DEIRGs which can predict 28-day mortality and immunosuppression status in sepsis. The higher risk score was positively associated with 28-day mortality and the development of immunosuppression. IRGs are a promising biomarker that might facilitate personalized treatments for sepsis.
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Affiliation(s)
- Yongxin Zheng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Baiyun Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiumei Deng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yubiao Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yongbo Huang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yu Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yonghao Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ling Sang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yimin Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Yimin Li,
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31
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Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nat Immunol 2022; 23:1551-1563. [PMID: 36289449 PMCID: PMC9663309 DOI: 10.1038/s41590-022-01327-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
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32
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Meeths M, Bryceson YT. Genetics and pathophysiology of haemophagocytic lymphohistiocytosis. Acta Paediatr 2021; 110:2903-2911. [PMID: 34192386 DOI: 10.1111/apa.16013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022]
Abstract
Haemophagocytic lymphohistiocytosis (HLH) represents a life-threatening hyperinflammatory syndrome. Familial studies have established autosomal and X-linked recessive causes of HLH, highlighting a pivotal role for lymphocyte cytotoxicity in the control of certain virus infections and immunoregulation. Recently, a more complex etiological framework has emerged, linking HLH predisposition to variants in genes required for metabolism or immunity to intracellular pathogens. We review genetic predisposition to HLH and discuss how molecular insights have provided fundamental knowledge of the immune system as well as detailed pathophysiological understanding of hyperinflammatory diseases, highlighting new treatment strategies.
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Affiliation(s)
- Marie Meeths
- Childhood Cancer Research Unit Department of Women’s and Children’s Health Karolinska Institutet Stockholm Sweden
- Theme of Children’s Health Karolinska University Hospital Stockholm Sweden
| | - Yenan T. Bryceson
- Centre for Hematology and Regenerative Medicine Department of Medicine Karolinska Institute Stockholm Sweden
- Division of Clinical Immunology and Transfusion Medicine Karolinska University Hospital Stockholm Sweden
- Broegelmann Research Laboratory Department of Clinical Sciences University of Bergen Bergen Norway
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33
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Grabarczyk P, Delin M, Rogińska D, Schulig L, Forkel H, Depke M, Link A, Machaliński B, Schmidt CA. Nuclear import of BCL11B is mediated by a classical nuclear localization signal and not the Krüppel-like zinc fingers. J Cell Sci 2021; 134:272659. [PMID: 34714335 DOI: 10.1242/jcs.258655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/24/2021] [Indexed: 11/20/2022] Open
Abstract
The Krüppel-like transcription factor BCL11B is characterized by wide tissue distribution and crucial functions in key developmental and cellular processes and various pathologies including cancer or HIV infection. Although basics of BCL11B activity and relevant interactions with other proteins were uncovered, how this exclusively nuclear protein localizes to its compartment remained unclear. Here, we demonstrate that unlike other KLFs, BCL11B does not require the C-terminal DNA-binding domain to pass through the nuclear envelope but encodes an independent, previously unidentified nuclear localization signal (NLS) which is located distantly from the zinc finger domains and fulfills the essential criteria of an autonomous NLS. First, it can redirect a heterologous cytoplasmic protein to the nucleus. Second, its mutations cause aberrant localization of the protein of origin. Finally, we provide experimental and in silico evidences of the direct interaction with importin alpha. The relative conservation of this motif allows formulating a consensus sequence (K/R)K-X13-14-KR+K++ which can be found in all BCL11B orthologues among vertebrates and in the closely related protein BCL11A.
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Affiliation(s)
- Piotr Grabarczyk
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Martin Delin
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Dorota Rogińska
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lukas Schulig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Hannes Forkel
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Maren Depke
- Clinic of Hematology and Oncology, University Medicine Greifswald, Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Bogusław Machaliński
- Department of General Pathology, Pomeranian Medical University, Szczecin, Poland
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34
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Perturbed NK Cell Homeostasis Associated with Disease Severity in Chronic Neutropenia. Blood 2021; 139:704-716. [PMID: 34699594 DOI: 10.1182/blood.2021013233] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/24/2021] [Indexed: 11/20/2022] Open
Abstract
Neutrophils have been suggested to play a critical role in terminal differentiation of NK cells. Whether this is a direct effect or a consequence of global immune changes with effects on NK cell homeostasis remains unknown. Here, we used high-resolution flow- and mass cytometry to examine NK cell repertoires in 64 patients with neutropenia and 27 healthy age- and gender-matched donors. A subgroup of patients with chronic neutropenia showed severely disrupted NK cell homeostasis manifested as increased frequencies of CD56bright NK cells and a lack of mature CD56dim NK cells. These immature NK cell repertoires were characterized by expression of proliferation/exhaustion markers Ki-67, Tim-3 and TIGIT and displayed blunted tumor target cell responses. Systems-level immune mapping revealed that the changes in immunophenotypes were confined to NK cells, leaving T cell differentiation intact. RNA sequencing of NK cells from these patients showed upregulation of a network of genes, including TNFSF9, CENPF, MKI67 and TOP2A, associated with apoptosis and the cell cycle, different from conventional CD56bright signatures. Profiling of 249 plasma proteins showed a coordinated enrichment of pathways related to apoptosis and cell turnover, which correlated with immature NK cell repertoires. Notably, most of these patients exhibited severe-grade neutropenia, suggesting that the profoundly altered NK cell homeostasis was connected to the severity of their underlying etiology. Hence, although our data suggests that neutrophils are dispensable for NK cell development and differentiation, some patients displayed a specific gap in the NK repertoire, associated with poor cytotoxic function and more severe disease manifestations.
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35
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Sottile R, Panjwani MK, Lau CM, Daniyan AF, Tanaka K, Barker JN, Brentjens RJ, Sun JC, Le Luduec JB, Hsu KC. Human cytomegalovirus expands a CD8 + T cell population with loss of BCL11B expression and gain of NK cell identity. Sci Immunol 2021; 6:eabe6968. [PMID: 34559552 DOI: 10.1126/sciimmunol.abe6968] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Rosa Sottile
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kazim Panjwani
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Colleen M Lau
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony F Daniyan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kento Tanaka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juliet N Barker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renier J Brentjens
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Jean-Benoît Le Luduec
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katharine C Hsu
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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36
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Xue S, Ma M, Bei S, Li F, Wu C, Li H, Hu Y, Zhang X, Qian Y, Qin Z, Jiang J, Feng L. Identification and Validation of the Immune Regulator CXCR4 as a Novel Promising Target for Gastric Cancer. Front Immunol 2021; 12:702615. [PMID: 34322132 PMCID: PMC8311657 DOI: 10.3389/fimmu.2021.702615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/10/2021] [Indexed: 12/24/2022] Open
Abstract
Immune checkpoint blockade has attracted a lot of attention in the treatment of human malignant tumors. We are trying to establish a prognostic model of gastric cancer (GC) based on the expression profile of immunoregulatory factor-related genes. Based on the TCGA database, we identified 234 differentially expressed immunoregulatory factors. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) conducted enrichment analysis to clarify the biological functions of differential expression of immunoregulatory factors. STRING database predicted the interaction network between 234 differently expressed immune regulatory factors. The expression of 11 immunoregulatory factors was significantly related to the overall survival of gastric cancer patients. Univariate Cox regression analysis, Kaplan–Meier analysis and multivariate Cox regression analysis found that immunomodulatory factors were involved in the progression of gastric cancer and promising biomarkers for predicting prognosis. Among them, CXCR4 was related to the low survival of GC patients and a key immunomodulatory factor in GC. Based on TCGA data, the high expression of CXCR4 in GC was positively correlated with the advanced stage and grade of gastric cancer and related to poor prognosis. Univariate analysis and multivariate analysis indicated that CXCR4 was an independent prognostic indicator for TCGA gastric cancer patients. In vitro functional studies had shown that CXCR4 promoted the proliferation, migration, and invasion of gastric cancer cells. In summary, this study has determined the prognostic value of 11 immunomodulatory factors in gastric cancer. CXCR4 is an independent prognostic indicator for gastric cancer patients, which may help to improve the individualized prognostic prediction of GC and provide candidates for the diagnosis and treatment of GC.
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Affiliation(s)
- Shuai Xue
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Ming Ma
- Department of Gastroenterology, Minhang Hospital, Fudan University, Shanghai, China
| | - Songhua Bei
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Fan Li
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Chenqu Wu
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Huanqing Li
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Yanling Hu
- Institute of Fudan Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaohong Zhang
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - YanQing Qian
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Zhe Qin
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Jun Jiang
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Li Feng
- Endoscopy Center, Minhang Hospital, Fudan University, Shanghai, China
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37
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Drashansky TT, Helm EY, Curkovic N, Cooper J, Cheng P, Chen X, Gautam N, Meng L, Kwiatkowski AJ, Collins WO, Keselowsky BG, Sant'Angelo D, Huo Z, Zhang W, Zhou L, Avram D. BCL11B is positioned upstream of PLZF and RORγt to control thymic development of mucosal-associated invariant T cells and MAIT17 program. iScience 2021; 24:102307. [PMID: 33870128 PMCID: PMC8042176 DOI: 10.1016/j.isci.2021.102307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/02/2020] [Accepted: 03/10/2021] [Indexed: 12/25/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells recognize microbial riboflavin metabolites presented by MR1 and play role in immune responses to microbial infections and tumors. We report here that absence of the transcription factor (TF) Bcl11b in mice alters predominantly MAIT17 cells in the thymus and further in the lung, both at steady state and following Salmonella infection. Transcriptomics and ChIP-seq analyses show direct control of TCR signaling program and position BCL11B upstream of essential TFs of MAIT17 program, including RORγt, ZBTB16 (PLZF), and MAF. BCL11B binding at key MAIT17 and at TCR signaling program genes in human MAIT cells occurred mostly in regions enriched for H3K27Ac. Unexpectedly, in human MAIT cells, BCL11B also bound at MAIT1 program genes, at putative active enhancers, although this program was not affected in mouse MAIT cells in the absence of Bcl11b. These studies endorse BCL11B as an essential TF for MAIT cells both in mice and humans. BCL11B controls MAIT cell development in mice, predominantly MAIT17 lineage BCL11B sustains MAIT17 and TCR signaling programs at steady state and in infection BCL11B binds at MAIT17 and TCR program genes in human MAIT cells Many BCL11B binding sites at MAIT17 and TCR genes are at putative active enhancers
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Affiliation(s)
- Theodore T Drashansky
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Eric Y Helm
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nina Curkovic
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jaimee Cooper
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Pingyan Cheng
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Xianghong Chen
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Namrata Gautam
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA
| | - Lingsong Meng
- Department of Biostatistics, College of Medicine, College of Public Health & Health Professions, University of Florida, Gainesville, FL 32611, USA
| | - Alexander J Kwiatkowski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - William O Collins
- Department of Otolaryngology, College of Medicine, University of Florida, Gainesville, FL 32605, USA
| | - Benjamin G Keselowsky
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Derek Sant'Angelo
- Department of Pediatrics, The Child Health Institute of NJ, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine, College of Public Health & Health Professions, University of Florida, Gainesville, FL 32611, USA
| | - Weizhou Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, Gainesville, FL 32610, USA
| | - Liang Zhou
- UF Health Cancer Center, Gainesville, FL 32610, USA.,Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Dr, Tampa, FL 33612, USA.,UF Health Cancer Center, Gainesville, FL 32610, USA
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38
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Rückert T, Romagnani C. A natural killer's hike through epigenetic landscapes. Sci Immunol 2021; 6:6/57/eabf8019. [PMID: 33712474 DOI: 10.1126/sciimmunol.abf8019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 11/02/2022]
Abstract
The transcription factor BCL11B guides NK cells along their differentiation trajectory (see the related Research Article by Holmes et al.).
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Affiliation(s)
- Timo Rückert
- Innate Immunity, German Rheumatism Research Centre - a Leibniz Institute, Berlin, Germany
| | - Chiara Romagnani
- Innate Immunity, German Rheumatism Research Centre - a Leibniz Institute, Berlin, Germany. .,Medical Department I, Charité University Medicine Berlin, Berlin, Germany.,Leibniz-Science Campus Chronic Inflammation, Berlin, Germany
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