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Zhang Y, Hu L, Ren G, Zeng Y, Zhao X, Zhong C. Distinct regulatory machineries underlying divergent chromatin landscapes distinguish innate lymphoid cells from T helper cells. Front Immunol 2023; 14:1271879. [PMID: 38106414 PMCID: PMC10722145 DOI: 10.3389/fimmu.2023.1271879] [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: 08/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Innate lymphoid cells (ILCs), as the innate counterpart of CD4+ T helper (Th) cells, play crucial roles in maintaining tissue homeostasis. While the ILC subsets and their corresponding Th subsets demonstrate significant similarities in core programming related to effector function and regulatory mechanisms, their principal distinctions, given their innate and adaptive lymphocyte nature, remain largely unknown. In this study, we have employed an integrative analysis of 294 bulk RNA-sequencing results across all ILC and Th subsets, using scRNA-seq algorithms. Consequently, we identify two genesets that predominantly differentiate ILCs from Th cells, as well as three genesets that distinguish various immune responses. Furthermore, through chromatin accessibility analysis, we find that the ILC geneset tends to rely on specific transcriptional regulation at promoter regions compared with the Th geneset. Additionally, we observe that ILCs and Th cells are under differential transcriptional regulation. For example, ILCs are under stronger regulation by multiple transcription factors, including RORα, GATA3, and NF-κB. Otherwise, Th cells are under stronger regulation by AP-1. Thus, our findings suggest that, despite the acknowledged similarities in effector functions between ILC subsets and corresponding Th subsets, the underlying regulatory machineries still exhibit substantial distinctions. These insights provide a comprehensive understanding of the unique roles played by each cell type during immune responses.
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Affiliation(s)
- Yime Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Luni Hu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Guanqun Ren
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
| | - Yanyu Zeng
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xingyu Zhao
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Chao Zhong
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Key National Health Commission Laboratory of Medical Immunology, Peking University, Beijing, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, China
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Hu L, Han M, Deng Y, Gong J, Hou Z, Zeng Y, Zhang Y, He J, Zhong C. Genetic distinction between functional tissue-resident and conventional natural killer cells. iScience 2023; 26:107187. [PMID: 37404378 PMCID: PMC10316664 DOI: 10.1016/j.isci.2023.107187] [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] [Received: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Tissue-residential natural killer (trNK) cells act as pioneering responders during infectious challenges. However, their discrimination with conventional NK (cNK) cells is still an issue. Through an integrative transcriptome comparison of the two NK subgroups from different tissues, we have defined two genesets capable of efficiently distinguishing them. Based on the two genesets, a fundamental difference between the activation of trNK and cNK is identified and further confirmed. Mechanistically, we have discovered a particular role of chromatin landscape in regulating the trNK activation. In addition, IL-21R and IL-18R are respectively highly expressed by trNK and cNK, indicating a role of cytokine milieu in determining their differential activation. Indeed, IL-21 is particularly critical in accessorily promoting trNK activation using a bunch of bifunctional transcription factors. Together, this study sheds light on the bona fide difference between trNK and cNK, which will further expand our knowledge about their distinct functionalities during immune responses.
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Affiliation(s)
- Luni Hu
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Mengwei Han
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yichen Deng
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jingjing Gong
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China
| | - Zhiyuan Hou
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China
| | - Yanyu Zeng
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yime Zhang
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jing He
- Department of Rheumatology and Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis, Peking University People’s Hospital, Beijing, China
| | - Chao Zhong
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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Song N, Xu Y, Paust HJ, Panzer U, de Las Noriega MM, Guo L, Renné T, Huang J, Meng X, Zhao M, Thaiss F. IKK1 aggravates ischemia-reperfusion kidney injury by promoting the differentiation of effector T cells. Cell Mol Life Sci 2023; 80:125. [PMID: 37074502 PMCID: PMC10115737 DOI: 10.1007/s00018-023-04763-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/20/2023]
Abstract
Ischemia-reperfusion injury (IRI) is one of the major causes of acute kidney injury (AKI), and experimental work has revealed detailed insight into the inflammatory response in the kidney. T cells and NFκB pathway play an important role in IRI. Therefore, we examined the regulatory role and mechanisms of IkappaB kinase 1 (IKK1) in CD4+T lymphocytes in an experimental model of IRI. IRI was induced in CD4cre and CD4IKK1Δ mice. Compared to control mice, conditional deficiency of IKK1 in CD4+T lymphocyte significantly decreased serum creatinine, blood urea nitrogen (BUN) level, and renal tubular injury score. Mechanistically, lack in IKK1 in CD4+T lymphocytes reduced the ability of CD4 lymphocytes to differentiate into Th1/Th17 cells. Similar to IKK1 gene ablation, pharmacological inhibition of IKK also protected mice from IRI. Together, lymphocyte IKK1 plays a pivotal role in IRI by promoting T cells differentiation into Th1/Th17 and targeting lymphocyte IKK1 may be a novel therapeutic strategy for IRI.
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Affiliation(s)
- Ning Song
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Yang Xu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Hans-Joachim Paust
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Ulf Panzer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | | | - Linlin Guo
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, 55131, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, 20246, Germany
| | - Xianglin Meng
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Mingyan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Youzheng St 23, Harbin, 150001, China.
- Heilongjiang Provincial Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
| | - Friedrich Thaiss
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, Hamburg, 20246, Germany.
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