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Rytkönen KT, Adossa N, Zúñiga Norman S, Lönnberg T, Poutanen M, Elo LL. Gene Regulatory Network Analysis of Decidual Stromal Cells and Natural Killer Cells. Reprod Sci 2024:10.1007/s43032-024-01653-1. [PMID: 39090334 DOI: 10.1007/s43032-024-01653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Abstract
Human reproductive success relies on the proper differentiation of the uterine endometrium to facilitate implantation, formation of the placenta, and pregnancy. This process involves two critical types of decidual uterine cells: endometrial/decidual stromal cells (dS) and uterine/decidual natural killer (dNK) cells. To better understand the transcription factors governing the in vivo functions of these cells, we analyzed single-cell transcriptomics data from first-trimester terminations of pregnancy, and for the first time conducted gene regulatory network analysis of dS and dNK cell subpopulations. Our analysis revealed stromal cell populations that corresponded to previously described in vitro decidualized cells and senescent decidual cells. We discovered new decidualization driving transcription factors of stromal cells for early pregnancy, including DDIT3 and BRF2, which regulate oxidative stress protection. For dNK cells, we identified transcription factors involved in the immunotolerant (dNK1) subpopulation, including IRX3 and RELB, which repress the NFKB pathway. In contrast, for the less immunotolerant (dNK3) population we predicted TBX21 (T-bet) and IRF2-mediated upregulation of the interferon pathway. To determine the clinical relevance of our findings, we tested the overrepresentation of the predicted transcription factors target genes among cell type-specific regulated genes from pregnancy disorders, such as recurrent pregnancy loss and preeclampsia. We observed that the predicted decidualized stromal and dNK1-specific transcription factor target genes were enriched with the genes downregulated in pregnancy disorders, whereas the predicted dNK3-specific targets were enriched with genes upregulated in pregnancy disorders. Our findings emphasize the importance of stress tolerance pathways in stromal cell decidualization and immunotolerance promoting regulators in dNK differentiation.
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Affiliation(s)
- Kalle T Rytkönen
- Turku Bioscience Centre, University of Turku, Åbo Akademi University, Turku, Finland.
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Nigatu Adossa
- Turku Bioscience Centre, University of Turku, Åbo Akademi University, Turku, Finland
| | - Sebastián Zúñiga Norman
- Turku Bioscience Centre, University of Turku, Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku, Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku, Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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2
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Gao ZX, He T, Zhang P, Hu X, Ge M, Xu YQ, Wang P, Pan HF. Epigenetic regulation of immune cells in systemic lupus erythematosus: insight from chromatin accessibility. Expert Opin Ther Targets 2024; 28:637-649. [PMID: 38943564 DOI: 10.1080/14728222.2024.2375372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/28/2024] [Indexed: 07/01/2024]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a multi-dimensional autoimmune disease involving numerous tissues throughout the body. The chromatin accessibility landscapes in immune cells play a pivotal role in governing their activation, function, and differentiation. Aberrant modulation of chromatin accessibility in immune cells is intimately associated with the onset and progression of SLE. AREAS COVERED In this review, we described the chromatin accessibility landscapes in immune cells, summarized the recent evidence of chromatin accessibility related to the pathogenesis of SLE, and discussed the potential of chromatin accessibility as a valuable option to identify novel therapeutic targets for this disease. EXPERT OPINION Dynamic changes in chromatin accessibility are intimately related to the pathogenesis of SLE and have emerged as a new direction for exploring its epigenetic mechanisms. The differently accessible chromatin regions in immune cells often contain binding sites for transcription factors (TFs) and cis-regulatory elements such as enhancers and promoters, which may be potential therapeutic targets for SLE. Larger scale cohort studies and integrating epigenomic, transcriptomic, and metabolomic data can provide deeper insights into SLE chromatin biology in the future.
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Affiliation(s)
- Zhao-Xing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tian He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao Hu
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Man Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-Qing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Peng Wang
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
- Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
- Department of Epidemiology, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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3
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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4
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Kirschenbaum D, Xie K, Ingelfinger F, Katzenelenbogen Y, Abadie K, Look T, Sheban F, Phan TS, Li B, Zwicky P, Yofe I, David E, Mazuz K, Hou J, Chen Y, Shaim H, Shanley M, Becker S, Qian J, Colonna M, Ginhoux F, Rezvani K, Theis FJ, Yosef N, Weiss T, Weiner A, Amit I. Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma. Cell 2024; 187:149-165.e23. [PMID: 38134933 DOI: 10.1016/j.cell.2023.11.032] [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: 05/02/2023] [Revised: 09/15/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023]
Abstract
Deciphering the cell-state transitions underlying immune adaptation across time is fundamental for advancing biology. Empirical in vivo genomic technologies that capture cellular dynamics are currently lacking. We present Zman-seq, a single-cell technology recording transcriptomic dynamics across time by introducing time stamps into circulating immune cells, tracking them in tissues for days. Applying Zman-seq resolved cell-state and molecular trajectories of the dysfunctional immune microenvironment in glioblastoma. Within 24 hours of tumor infiltration, cytotoxic natural killer cells transitioned to a dysfunctional program regulated by TGFB1 signaling. Infiltrating monocytes differentiated into immunosuppressive macrophages, characterized by the upregulation of suppressive myeloid checkpoints Trem2, Il18bp, and Arg1, over 36 to 48 hours. Treatment with an antagonistic anti-TREM2 antibody reshaped the tumor microenvironment by redirecting the monocyte trajectory toward pro-inflammatory macrophages. Zman-seq is a broadly applicable technology, enabling empirical measurements of differentiation trajectories, which can enhance the development of more efficacious immunotherapies.
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Affiliation(s)
- Daniel Kirschenbaum
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ken Xie
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Florian Ingelfinger
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | | | - Kathleen Abadie
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Thomas Look
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Fadi Sheban
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Truong San Phan
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Baoguo Li
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Pascale Zwicky
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ido Yofe
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eyal David
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Kfir Mazuz
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jinchao Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yun Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Soeren Becker
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jiawen Qian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Florent Ginhoux
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore 138648, Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore 138648, Singapore
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Assaf Weiner
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ido Amit
- Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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5
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Lu X, Luo Y, Nie X, Zhang B, Wang X, Li R, Liu G, Zhou Q, Liu Z, Fan L, Hotaling JM, Zhang Z, Bo H, Guo J. Single-cell multi-omics analysis of human testicular germ cell tumor reveals its molecular features and microenvironment. Nat Commun 2023; 14:8462. [PMID: 38123589 PMCID: PMC10733385 DOI: 10.1038/s41467-023-44305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Seminoma is the most common malignant solid tumor in 14 to 44 year-old men. However, its molecular features and tumor microenvironment (TME) is largely unexplored. Here, we perform a series of studies via genomics profiling (single cell multi-omics and spatial transcriptomics) and functional examination using seminoma samples and a seminoma cell line. We identify key gene expression programs share between seminoma and primordial germ cells, and further characterize the functions of TFAP2C in promoting tumor invasion and migration. We also identify 15 immune cell subtypes in TME, and find that subtypes with exhaustion features were located closer to the tumor region through combined spatial transcriptome analysis. Furthermore, we identify key pathways and genes that may facilitate seminoma disseminating beyond the seminiferous tubules. These findings advance our knowledge of seminoma tumorigenesis and produce a multi-omics atlas of in situ human seminoma microenvironment, which could help discover potential therapy targets for seminoma.
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Affiliation(s)
- Xiaojian Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanwei Luo
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xichen Nie
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bailing Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ran Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guangmin Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Qianyin Zhou
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zhizhong Liu
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Liqing Fan
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Zhe Zhang
- Department of Urology, Peking University Third Hospital, Beijing, China.
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China.
| | - Hao Bo
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, Hunan, China.
| | - Jingtao Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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6
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Schnoegl D, Hiesinger A, Huntington ND, Gotthardt D. AP-1 transcription factors in cytotoxic lymphocyte development and antitumor immunity. Curr Opin Immunol 2023; 85:102397. [PMID: 37931499 DOI: 10.1016/j.coi.2023.102397] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023]
Abstract
The proper functioning of cytotoxic lymphocytes, such as natural killer and CD8+ T cells, is essential for effective cancer-immunity and immunotherapy responses. The differentiation of these cells is controlled by several transcription factors (TFs), including members of the activator protein (AP)-1 family. The activity of AP-1 family members is regulated by various immune signaling pathways, which can be triggered by activating or inhibitory receptors as well as cytokines. The target genes controlled by AP-1 TFs are central to generate immunity to pathogens or malignancies. Here, we provide an overview of the current understanding of how AP-1 TFs regulate cytotoxic lymphocytes.
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Affiliation(s)
- Diana Schnoegl
- Institute for Rheumatology and Immunology, Medical University of Graz, Austria; Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Angela Hiesinger
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | | | - Dagmar Gotthardt
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria.
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7
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Garofalo S, Cocozza G, Mormino A, Bernardini G, Russo E, Ielpo D, Andolina D, Ventura R, Martinello K, Renzi M, Fucile S, Laffranchi M, Mortari EP, Carsetti R, Sciumè G, Sozzani S, Santoni A, Tremblay ME, Ransohoff RM, Limatola C. Natural killer cells and innate lymphoid cells 1 tune anxiety-like behavior and memory in mice via interferon-γ and acetylcholine. Nat Commun 2023; 14:3103. [PMID: 37248289 DOI: 10.1038/s41467-023-38899-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/18/2023] [Indexed: 05/31/2023] Open
Abstract
The mechanisms of communication between the brain and the immune cells are still largely unclear. Here, we characterize the populations of resident natural killer (NK) cells and innate lymphoid cells (ILC) 1 in the meningeal dura layer of adult mice. We describe that ILC1/NK cell-derived interferon-γ and acetylcholine can contribute to the modulation of brain homeostatic functions, shaping synaptic neuronal transmission and neurotransmitter levels with effects on mice behavior. In detail, the interferon-γ plays a role in the formation of non-spatial memory, tuning the frequency of GABAergic neurotransmission on cortical pyramidal neurons, while the acetylcholine is a mediator involved in the modulation of brain circuitries that regulate anxiety-like behavior. These findings disclose mechanisms of immune-to-brain communication that modulate brain functions under physiological conditions.
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Affiliation(s)
- Stefano Garofalo
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy.
| | - Germana Cocozza
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Alessandro Mormino
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | | | - Eleonora Russo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Donald Ielpo
- Department of Psychology and Centre for Research in Neurobiology D. Bovet, Sapienza University of Rome, Rome, Italy
| | - Diego Andolina
- Department of Psychology and Centre for Research in Neurobiology D. Bovet, Sapienza University of Rome, Rome, Italy
| | - Rossella Ventura
- Department of Psychology and Centre for Research in Neurobiology D. Bovet, Sapienza University of Rome, Rome, Italy
| | | | - Massimiliano Renzi
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Sergio Fucile
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Mattia Laffranchi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Eva Piano Mortari
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Carsetti
- B Cell Unit, Immunology Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Silvano Sozzani
- IRCCS Neuromed, Pozzilli, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Angela Santoni
- IRCCS Neuromed, Pozzilli, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Marie-Eve Tremblay
- Centre de Recherche CHU de Quebec-Université Laval, Quebec City, QC, Canada
| | | | - Cristina Limatola
- IRCCS Neuromed, Pozzilli, Italy.
- Department of Physiology and Pharmacology, Sapienza University, Laboratory affiliated to Istituto Pasteur, Rome, Italy.
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8
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Herrera-Uribe J, Lim KS, Byrne KA, Daharsh L, Liu H, Corbett RJ, Marco G, Schroyen M, Koltes JE, Loving CL, Tuggle CK. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Front Genet 2023; 14:1107462. [PMID: 37287538 PMCID: PMC10242145 DOI: 10.3389/fgene.2023.1107462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea
| | - Kristen A. Byrne
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Ryan J. Corbett
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gianna Marco
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Crystal L. Loving
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
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9
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Liu N, Chen L, Yan M, Tao Q, Wu J, Chen J, Chen X, Zhang W, Peng C. Eubacterium rectale Improves the Efficacy of Anti-PD1 Immunotherapy in Melanoma via l-Serine-Mediated NK Cell Activation. RESEARCH (WASHINGTON, D.C.) 2023; 6:0127. [PMID: 37223471 PMCID: PMC10202379 DOI: 10.34133/research.0127] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/02/2023] [Indexed: 05/25/2023]
Abstract
Natural killer (NK) cells, as key immune cells, play essential roles in tumor cell immune escape and immunotherapy. Accumulating evidence has demonstrated that the gut microbiota community affects the efficacy of anti-PD1 immunotherapy and that remodeling the gut microbiota is a promising strategy to enhance anti-PD1 immunotherapy responsiveness in advanced melanoma patients; however, the details of the mechanism remain elusive. In this study, we found that Eubacterium rectale was significantly enriched in melanoma patients who responded to anti-PD1 immunotherapy and that a high E. rectale abundance was related to longer survival in melanoma patients. Furthermore, administration of E. rectale remarkably improved the efficacy of anti-PD1 therapy and increased the overall survival of tumor-bearing mice; moreover, application of E. rectale led to a significant accumulation of NK cells in the tumor microenvironment. Interestingly, conditioned medium isolated from an E. rectale culture system dramatically enhanced NK cell function. Gas chromatography-mass spectrometry/ultrahigh performance liquid chromatography-tandem mass spectrometry-based metabolomic analysis showed that l-serine production was significantly decreased in the E. rectale group; moreover, administration of an l-serine synthesis inhibitor dramatically increased NK cell activation, which enhanced anti-PD1 immunotherapy effects. Mechanistically, supplementation with l-serine or application of an l-serine synthesis inhibitor affected NK cell activation through Fos/Fosl. In summary, our findings reveal the role of bacteria-modulated serine metabolic signaling in NK cell activation and provide a novel therapeutic strategy to improve the efficacy of anti-PD1 immunotherapy in melanoma.
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Affiliation(s)
- Nian Liu
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Lihui Chen
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Mingjie Yan
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Qian Tao
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
| | - Jie Wu
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
| | - Jing Chen
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
| | - Xiang Chen
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
| | - Cong Peng
- Department of Clinical Pharmacology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Department of Dermatology, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- Furong Laboratory, Xiangya Hospital,
Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital,
Central South University, Changsha, Hunan, China
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10
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Wang P, Liang T, Zhan H, Zhu M, Wu M, Qian L, Zhou Y, Ni F. Unique metabolism and protein expression signature in human decidual NK cells. Front Immunol 2023; 14:1136652. [PMID: 36936959 PMCID: PMC10020942 DOI: 10.3389/fimmu.2023.1136652] [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: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Human decidual natural killer (dNK) cells are a unique type of tissue-resident NK cells at the maternal-fetal interface. dNK cells are likely to have pivotal roles during pregnancy, including in maternal-fetal immune tolerance, trophoblast invasion, and fetal development. However, detailed insights into these cells are still lacking. In this study, we performed metabolomic and proteomic analyses on human NK cells derived from decidua and peripheral blood. We found that 77 metabolites were significantly changed in dNK cells. Notably, compared to peripheral blood NK (pNK) cells, 29 metabolites involved in glycerophospholipid and glutathione metabolism were significantly decreased in dNK cells. Moreover, we found that 394 proteins were differentially expressed in dNK cells. Pathway analyses and network enrichment analyses identified 110 differentially expressed proteins involved in focal adhesion, cytoskeleton remodeling, oxidoreductase activity, and fatty acid metabolism in dNK cells. The integrated proteomic and metabolomic analyses revealed significant downregulation in glutathione metabolism in dNK cells compared to pNK cells. Our data indicate that human dNK cells have unique metabolism and protein-expression features, likely regulating their function in pregnancy and immunity.
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Affiliation(s)
- Ping Wang
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), The Chinese Academy of Science (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Tingting Liang
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), The Chinese Academy of Science (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Heqin Zhan
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Mingming Zhu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), The Chinese Academy of Science (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Mingming Wu
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), The Chinese Academy of Science (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Lili Qian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fang Ni
- Department of Hematology, The First Affiliated Hospital of University of Science and Technology of China (USTC), The Chinese Academy of Science (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
- *Correspondence: Fang Ni,
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11
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Hayes LN, An K, Carloni E, Li F, Vincent E, Trippaers C, Paranjpe M, Dölen G, Goff LA, Ramos A, Kano SI, Sawa A. Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry. Nature 2022; 610:327-334. [PMID: 36171283 DOI: 10.1038/s41586-022-05274-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/24/2022] [Indexed: 01/12/2023]
Abstract
Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function1,2. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood3,4. Several maternal environmental factors-such as an aberrant microbiome, immune activation and poor nutrition-can influence prenatal brain development5,6. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that, after maternal immune activation (MIA) in mice, microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was accompanied by changes in chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single-cell RNA-sequencing analysis revealed that MIA does not induce a distinct subpopulation but, rather, decreases the contribution to inflammatory microglia states. Prenatal replacement of microglia from MIA offspring with physiological infiltration of naive microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment affect the long-term microglia reactivity and proper striatal circuit development.
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Affiliation(s)
- Lindsay N Hayes
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyongman An
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisa Carloni
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fangze Li
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Vincent
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chloë Trippaers
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Manish Paranjpe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gül Dölen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adriana Ramos
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shin-Ichi Kano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Akira Sawa
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Mental Health, Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Wiedemann GM. Localization Matters: Epigenetic Regulation of Natural Killer Cells in Different Tissue Microenvironments. Front Immunol 2022; 13:913054. [PMID: 35707540 PMCID: PMC9191276 DOI: 10.3389/fimmu.2022.913054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Natural Killer cells (NK cells) are cytotoxic innate lymphoid cells (ILCs), which play a key role in the early protection against viral infection and cancer. In addition to mounting rapid effector responses, NK cells possess the capacity to generate long-lived memory cells in response to certain stimuli, thus blurring the lines between innate and adaptive immunity and making NK cells an ideal candidate for tumor immunotherapy. NK cell development, activation and memory formation are regulated by epigenetic alterations driven by a complex interplay of external and internal signals. These epigenetic modifications can convey long-lasting functional and phenotypic changes and critically modify their response to stimulation. Here, we review how NK cell functionality and plasticity are regulated at the epigenetic level in different tissue microenvironments and within tumor microenvironments. An in-depth understanding of the epigenetic modifications underlying NK cell functional diversity in different environments is an essential step in the development of NK cell-based cancer therapies.
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13
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Barnes SA, Trew I, de Jong E, Foley B. Making a Killer: Selecting the Optimal Natural Killer Cells for Improved Immunotherapies. Front Immunol 2021; 12:765705. [PMID: 34777383 PMCID: PMC8578927 DOI: 10.3389/fimmu.2021.765705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Over the past 20 years natural killer (NK) cell-based immunotherapies have emerged as a safe and effective treatment option for patients with relapsed or refractory leukemia. Unlike T cell-based therapies, NK cells harbor an innate capacity to eliminate malignant cells without prior sensitization and can be adoptively transferred between individuals without the need for extensive HLA matching. A wide variety of therapeutic NK cell sources are currently being investigated clinically, including allogeneic donor-derived NK cells, stem cell-derived NK cells and NK cell lines. However, it is becoming increasingly clear that not all NK cells are endowed with the same antitumor potential. Despite advances in techniques to enhance NK cell cytotoxicity and persistence, the initial identification and utilization of highly functional NK cells remains essential to ensure the future success of adoptive NK cell therapies. Indeed, little consideration has been given to the identification and selection of donors who harbor NK cells with potent antitumor activity. In this regard, there is currently no standard donor selection criteria for adoptive NK cell therapy. Here, we review our current understanding of the factors which govern NK cell functional fate, and propose a paradigm shift away from traditional phenotypic characterization of NK cell subsets towards a functional profile based on molecular and metabolic characteristics. We also discuss previous selection models for NK cell-based immunotherapies and highlight important considerations for the selection of optimal NK cell donors for future adoptive cell therapies.
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Affiliation(s)
- Samantha A Barnes
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Isabella Trew
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Emma de Jong
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Bree Foley
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
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14
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Xia M, Wang B, Wang Z, Zhang X, Wang X. Epigenetic Regulation of NK Cell-Mediated Antitumor Immunity. Front Immunol 2021; 12:672328. [PMID: 34017344 PMCID: PMC8129532 DOI: 10.3389/fimmu.2021.672328] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
Natural killer (NK) cells are critical innate lymphocytes that can directly kill target cells without prior immunization. NK cell activation is controlled by the balance of multiple germline-encoded activating and inhibitory receptors. NK cells are a heterogeneous and plastic population displaying a broad spectrum of functional states (resting, activating, memory, repressed, and exhausted). In this review, we present an overview of the epigenetic regulation of NK cell-mediated antitumor immunity, including DNA methylation, histone modification, transcription factor changes, and microRNA expression. NK cell-based immunotherapy has been recognized as a promising strategy to treat cancer. Since epigenetic alterations are reversible and druggable, these studies will help identify new ways to enhance NK cell-mediated antitumor cytotoxicity by targeting intrinsic epigenetic regulators alone or in combination with other strategies.
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Affiliation(s)
- Miaoran Xia
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University, Beijing, China
| | - Bingbing Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University, Beijing, China
| | - Zihan Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University, Beijing, China
| | - Xulong Zhang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xi Wang
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Cancer Invasion and Metastasis Research, Capital Medical University, Beijing, China.,Department of Oncology, Capital Medical University, Beijing, China
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15
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Mukherjee D, Gonzales BJ, Ashwal-Fluss R, Turm H, Groysman M, Citri A. Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice. eLife 2021; 10:65228. [PMID: 33724178 PMCID: PMC8057818 DOI: 10.7554/elife.65228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Drug addiction develops due to brain-wide plasticity within neuronal ensembles, mediated by dynamic gene expression. Though the most common approach to identify such ensembles relies on immediate early gene expression, little is known of how the activity of these genes is linked to modified behavior observed following repeated drug exposure. To address this gap, we present a broad-to-specific approach, beginning with a comprehensive investigation of brain-wide cocaine-driven gene expression, through the description of dynamic spatial patterns of gene induction in subregions of the striatum, and finally address functionality of region-specific gene induction in the development of cocaine preference. Our findings reveal differential cell-type specific dynamic transcriptional recruitment patterns within two subdomains of the dorsal striatum following repeated cocaine exposure. Furthermore, we demonstrate that induction of the IEG Egr2 in the ventrolateral striatum, as well as the cells within which it is expressed, are required for the development of cocaine seeking. The human brain is ever changing, constantly rewiring itself in response to new experiences, knowledge or information from the environment. Addictive drugs such as cocaine can hijack the genetic mechanisms responsible for this plasticity, creating dangerous, obsessive drug-seeking and consuming behaviors. Cocaine-induced plasticity is difficult to apprehend, however, as brain regions or even cell populations can react differently to the compound. For instance, sub-regions in the striatum – the brain area that responds to rewards and helps to plan movement – show distinct responses during progressive exposure to cocaine. And while researchers know that the drug immediately changes how neurons switch certain genes on and off, it is still unclear how these genetic modifications later affect behavior. Mukherjee, Gonzales et al. explored these questions at different scales, first focusing on how progressive cocaine exposure changed the way various gene programs were activated across the entire brain. This revealed that programs in the striatum were the most affected by the drug. Examining this region more closely showed that cocaine switches on genes in specific ‘spiny projection’ neuron populations, depending on where these cells are located and the drug history of the mouse. Finally, Mukherjee, Gonzales et al. used genetically modified mice to piece together cocaine exposure, genetic changes and modifications in behavior. These experiments revealed that the drive to seek cocaine depended on activation of the Egr2 gene in populations of spiny projection neurons in a specific sub-region of the striatum. The gene, which codes for a protein that regulates how genes are switched on and off, was itself strongly activated by cocaine intake. Cocaine addiction can have devastating consequences for individuals. Grasping how this drug alters the brain could pave the way for new treatments, while also providing information on the basic mechanisms underlying brain plasticity.
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Affiliation(s)
- Diptendu Mukherjee
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ben Jerry Gonzales
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reut Ashwal-Fluss
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Hagit Turm
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maya Groysman
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Ami Citri
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Program in Child and Brain Development, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Canada
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