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Chen H, Ryu J, Vinyard ME, Lerer A, Pinello L. SIMBA: single-cell embedding along with features. Nat Methods 2024; 21:1003-1013. [PMID: 37248389 PMCID: PMC11166568 DOI: 10.1038/s41592-023-01899-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Most current single-cell analysis pipelines are limited to cell embeddings and rely heavily on clustering, while lacking the ability to explicitly model interactions between different feature types. Furthermore, these methods are tailored to specific tasks, as distinct single-cell problems are formulated differently. To address these shortcomings, here we present SIMBA, a graph embedding method that jointly embeds single cells and their defining features, such as genes, chromatin-accessible regions and DNA sequences, into a common latent space. By leveraging the co-embedding of cells and features, SIMBA allows for the study of cellular heterogeneity, clustering-free marker discovery, gene regulation inference, batch effect removal and omics data integration. We show that SIMBA provides a single framework that allows diverse single-cell problems to be formulated in a unified way and thus simplifies the development of new analyses and extension to new single-cell modalities. SIMBA is implemented as a comprehensive Python library ( https://simba-bio.readthedocs.io ).
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Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jayoung Ryu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael E Vinyard
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Adam Lerer
- Facebook AI Research, New York, NY, USA.
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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2
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Hua X, Hongbing R, Juan X, Jizan L, Beibei Y. Dysregulation of TNF-induced protein 3 and CCAAT/enhancer-binding protein β in alveolar macrophages: Implications for systemic sclerosis-associated interstitial lung disease. Int J Rheum Dis 2024; 27:e15174. [PMID: 38720423 DOI: 10.1111/1756-185x.15174] [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: 01/02/2024] [Revised: 03/26/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024]
Abstract
OBJECTIVES This study investigates the role of TNF-induced protein 3 (TNFAIP3) and CCAAT/enhancer-binding protein β (C/EBPβ) in alveolar macrophages (AMs) of patients with systemic sclerosis-associated interstitial lung disease (SSc-ILD) and their influence on pulmonary fibrosis. METHODS Transfection of HEK293T cells and AMs with plasmids carrying TNFAIP3 and C/EBPβ was performed, followed by co-culturing AMs with pulmonary fibroblasts. Immunoblotting analysis was then utilized to assess the expression of TNFAIP3, C/EBPβ, and collagen type 1 (Col1). Quantitative PCR analysis was conducted to quantify the mRNA levels of C/EBPβ, IL-10, and TGF-β1. STRING database analysis, and immunoprecipitation assays were employed to investigate the interactions between TNFAIP3 and C/EBPβ. RESULTS TNFAIP3 expression was significantly reduced in SSc-ILD AMs, correlating with increased Col1 production in fibroblasts. Overexpression of TNFAIP3 inhibited this pro-fibrotic activity. Conversely, C/EBPβ expression was elevated in SSc-ILD AMs, and its reduction through TNFAIP3 restoration decreased pro-fibrotic cytokines IL-10 and TGFβ1 levels. Protein-protein interaction studies confirmed the regulatory relationship between TNFAIP3 and C/EBPβ. CONCLUSIONS This study highlights the important role of TNFAIP3 in regulating pulmonary fibrosis in SSc-ILD by modulating C/EBPβ expression in AMs. These findings suggest that targeting TNFAIP3 could be a potential therapeutic strategy for managing SSc-ILD patients.
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Affiliation(s)
- Xiao Hua
- Department of Rheumatology and immulology, The First Affiliated Hospital of FuJian Medical University, Fuzhou, China
- Department of Rheumatology and immulology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Rheumatology and immulology, The First Peoples' Hospital of Chenzhou, ChenZhou, Hunan, China
| | - Rui Hongbing
- Department of Rheumatology and immulology, The First Affiliated Hospital of FuJian Medical University, Fuzhou, China
- Department of Rheumatology and immulology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xue Juan
- Department of Rheumatology and immulology, The First Affiliated Hospital of FuJian Medical University, Fuzhou, China
- Department of Rheumatology and immulology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Liu Jizan
- Department of Rheumatology and immulology, The First Affiliated Hospital of FuJian Medical University, Fuzhou, China
- Department of Rheumatology and immulology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Beibei
- Department of Dermatology, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), College of Clinical Medicine for Obstetrics&Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
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3
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Karpurapu M, Kakarala KK, Chung S, Nie Y, Koley A, Dougherty P, Christman JW. Epigallocatechin gallate regulates the myeloid-specific transcription factor PU.1 in macrophages. PLoS One 2024; 19:e0301904. [PMID: 38662666 PMCID: PMC11045095 DOI: 10.1371/journal.pone.0301904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Our previous research demonstrated that PU.1 regulates expression of the genes involved in inflammation in macrophages. Selective knockdown of PU.1 in macrophages ameliorated LPS-induced acute lung injury (ALI) in bone marrow chimera mice. Inhibitors that block the transcriptional activity of PU.1 in macrophages have the potential to mitigate the pathophysiology of LPS-induced ALI. However, complete inactivation of PU.1 gene disrupts normal myelopoiesis. Although the green tea polyphenol Epigallocatechin gallate (EGCG) has been shown to regulate inflammatory genes in various cell types, it is not known if EGCG alters the transcriptional activity of PU.1 protein. Using Schrodinger Glide docking, we have identified that EGCG binds with PU.1 protein, altering its DNA-binding and self-dimerization activity. In silico analysis shows that EGCG forms Hydrogen bonds with Glutamic Acid 209, Leucine 250 in DNA binding and Lysine 196, Tryptophan 193, and Leucine 182 in the self-dimerization domain of the PU.1 protein. Experimental validation using mouse bone marrow-derived macrophages (BMDM) confirmed that EGCG inhibits both DNA binding by PU.1 and self-dimerization. Importantly, EGCG had no impact on expression of the total PU.1 protein levels but significantly reduced expression of various inflammatory genes and generation of ROS. In summary, we report that EGCG acts as an inhibitor of the PU.1 transcription factor in macrophages.
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Affiliation(s)
- Manjula Karpurapu
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | | | - Sangwoon Chung
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - Yunjuan Nie
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
- Department of Basic Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P.R. China
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - Patrick Dougherty
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - John W. Christman
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
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4
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Lian T, Guan R, Zhou BR, Bai Y. Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. Nat Struct Mol Biol 2024; 31:633-643. [PMID: 38267599 DOI: 10.1038/s41594-023-01189-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 11/23/2023] [Indexed: 01/26/2024]
Abstract
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
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Affiliation(s)
- Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Balak CD, Han CZ, Glass CK. Deciphering microglia phenotypes in health and disease. Curr Opin Genet Dev 2024; 84:102146. [PMID: 38171044 DOI: 10.1016/j.gde.2023.102146] [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: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
Microglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent transcription factors interact to select and regulate the ensembles of enhancers that determine microglia development and function. We then highlight recent findings that advance these concepts and conclude with a consideration of open questions that represent some of the major hurdles to be addressed in the future.
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Affiliation(s)
- Christopher D Balak
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA; Biomedical Sciences Graduate Program, University of California, San Diego, USA
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, USA; Department of Medicine, University of California, San Diego, USA.
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6
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Guo K, Machlus KR, Camacho V. The many faces of the megakaryocytes and their biological implications. Curr Opin Hematol 2024; 31:1-5. [PMID: 37910197 PMCID: PMC10842450 DOI: 10.1097/moh.0000000000000793] [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: 11/03/2023]
Abstract
PURPOSE OF REVIEW Single-cell RNA sequencing studies have revealed transcriptional heterogeneity within the megakaryocytic lineage and the identified unique subsets. In this review, we discuss the functional and phenotypic plasticity of these subpopulations as well as the impacts on health and disease. RECENT FINDINGS Megakaryocytes (MKs) can be transcriptionally categorized into platelet generating, niche supporting, immune, and cycling cells, which are distinguished by their unique gene expression patterns and cellular markers. Additionally, a significant population of these cells has been established to reside in the nonhematopoietic tissues and they display enhanced immune-related characteristics. Combined with the location in which the megakaryocytes exist, these cells can play unique roles dictated by their current environment and biological needs, including responding to changes in pathogen exposure. SUMMARY Advances in megakaryocyte research has elucidated the existence of multiple subpopulations of MKs that serve different functions. These subpopulations implicate a greater potential for MKs to be regulators of health and suggest new avenues for treatments and therapies in related diseases.
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Affiliation(s)
- Karen Guo
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kellie R. Machlus
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Virginia Camacho
- Vascular Biology Program, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Nagel S, Haake J, Pommerenke C, Meyer C, MacLeod RAF. Establishment of the Myeloid TBX-Code Reveals Aberrant Expression of T-Box Gene TBX1 in Chronic Myeloid Leukemia. Int J Mol Sci 2023; 25:32. [PMID: 38203204 PMCID: PMC10778679 DOI: 10.3390/ijms25010032] [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: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
T-box genes encode transcription factors, which control developmental processes and promote cancer if deregulated. Recently, we described the lymphoid TBX-code, which collates T-box gene activities in normal lymphopoiesis, enabling identification of members deregulated in lymphoid malignancies. Here, we have extended this analysis to cover myelopoiesis, compiling the myeloid TBX-code and, thus, highlighting which of these genes might be deregulated in myeloid tumor types. We analyzed public T-box gene expression datasets bioinformatically for normal and malignant cells. Candidate T-box-gene-expressing model cell lines were identified and examined by RQ-PCR, Western Blotting, genomic profiling, and siRNA-mediated knockdown combined with RNA-seq analysis and live-cell imaging. The established myeloid TBX-code comprised 10 T-box genes, including progenitor-cell-restricted TBX1. Accordingly, we detected aberrant expression of TBX1 in 10% of stem/progenitor-cell-derived chronic myeloid leukemia (CML) patients. The classic CML cell line K-562 expressed TBX1 at high levels and served as a model to identify TBX1 activators, including transcription factor GATA1 and genomic amplification of the TBX1 locus at 22q11; inhibitors, including BCR::ABL1 fusion and downregulated GNAI2, as well as BMP, FGF2, and WNT signaling; and the target genes CDKN1A, MIR17HG, NAV1, and TMEM38A. The establishment of the myeloid TBX-code permitted identification of aberrant TBX1 expression in subsets of CML patients and cell lines. TBX1 forms an integral part of an oncogenic regulatory network impacting proliferation, survival, and differentiation. Thus, the data spotlight novel diagnostic markers and potential therapeutic targets for this malignancy.
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Affiliation(s)
- Stefan Nagel
- Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
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8
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Salken I, Provencio JJ, Coulibaly AP. A potential therapeutic target: The role of neutrophils in the central nervous system. Brain Behav Immun Health 2023; 33:100688. [PMID: 37767236 PMCID: PMC10520304 DOI: 10.1016/j.bbih.2023.100688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Neutrophils play a critical role in immune defense as the first recruited and most abundant leukocytes in the innate immune system. As such, regulation of neutrophil effector functions have strong implications on immunity. These cells display a wide heterogeneity of function, including both inflammatory and immunomodulatory roles. Neutrophils commonly infiltrate the central nervous system (CNS) in response to varied pathological conditions. There is still little understanding of the role these cells play in the CNS in such conditions. In the present review, we will summarize what is known of neutrophil's role in cancer and Alzheimer's disease (AD), with a focus on highlighting the gaps in our understanding.
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Affiliation(s)
- Isabel Salken
- College of Arts and Science, University of Virginia, USA
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9
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Khayati S, Dehnavi S, Sadeghi M, Tavakol Afshari J, Esmaeili SA, Mohammadi M. The potential role of miRNA in regulating macrophage polarization. Heliyon 2023; 9:e21615. [PMID: 38027572 PMCID: PMC10665754 DOI: 10.1016/j.heliyon.2023.e21615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Macrophage polarization is a dynamic process determining the outcome of various physiological and pathological situations through inducing pro-inflammatory responses or resolving inflammation via exerting anti-inflammatory effects. The miRNAs are epigenetic regulators of different biologic pathways that target transcription factors and signaling molecules to promote macrophage phenotype transition and regulate immune responses. Modulating the macrophage activation, differentiation, and polarization by miRNAs is crucial for immune responses in response to microenvironmental signals and under various physiological and pathological conditions. In term of clinical significance, regulating macrophage polarization via miRNAs could be utilized for inflammation control. Also, understanding the role of miRNAs in macrophage polarization can provide insights into diagnostic strategies associated with dysregulated miRNAs and for developing macrophage-centered therapeutic methods. In this case, targeting miRNAs to further regulate of macrophage polarization may become an efficient strategy for treating immune-associated disorders. The current review investigated and categorized various miRNAs directly or indirectly involved in macrophage polarization by targeting different transcription factors and signaling pathways. In addition, prospects for regulating macrophage polarization via miRNA as a therapeutic choice that could be implicated in various pathological conditions, including cancer or inflammation-mediated injuries, were discussed.
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Affiliation(s)
- Shaho Khayati
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Dehnavi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahvash Sadeghi
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mojgan Mohammadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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10
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Zhao Y, Zhao C, Guo H, Zhang Z, Xu H, Shi M, Xu Y, Wei D, Zhao Y. mTORC2 orchestrates monocytic and granulocytic lineage commitment by an ATF5-mediated pathway. iScience 2023; 26:107540. [PMID: 37649699 PMCID: PMC10462862 DOI: 10.1016/j.isci.2023.107540] [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: 02/07/2023] [Revised: 06/12/2023] [Accepted: 07/27/2023] [Indexed: 09/01/2023] Open
Abstract
Myeloid hematopoiesis is a finely controlled consecutive developmental process, which is essential to maintain peripheral innate immune homeostasis. Herein, we found that Rictor deletion caused the remarkable reduction of granulocyte-monocyte progenitors (GMPs), monocytes, and macrophages, while the levels of neutrophils were unaffected. Adoptive transfer of Rictor-deleted GMPs or common myeloid progenitors (CMPs) in syngeneic mice showed poor re-constitution of monocytes compared to wild-type GMPs or CMPs. In addition to decreasing the proliferation of CMPs/GMPs, Rictor deletion preferentially inhibited Ly6C+ monocyte differentiation, while enhancing neutrophil differentiation, as determined by colony formation assays. mTORC2 promotes monocyte development by downregulation of the AKT-Foxo4-activating transcription factor 5 (ATF5)-mitochondrial unfolded protein response (mtUPR) pathway. Genetic overexpression of ATF5 or exposure to ethidium bromide significantly rescued monocyte/macrophage differentiation defects of Rictor-deficient myeloid progenitors. Therefore, Rictor is required for CMP/GMP proliferation and acts as an important switch to balance monocytic and granulocytic lineage commitment in bone marrow.
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Affiliation(s)
- Yang Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxu Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huawen Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingpu Shi
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Xu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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11
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Thompson B, Lu S, Revilla J, Uddin MJ, Oakland DN, Brovero S, Keles S, Bresnick EH, Petri WA, Burgess SL. Secondary bile acids function through the vitamin D receptor in myeloid progenitors to promote myelopoiesis. Blood Adv 2023; 7:4970-4982. [PMID: 37276450 PMCID: PMC10463201 DOI: 10.1182/bloodadvances.2022009618] [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: 12/23/2022] [Revised: 04/20/2023] [Accepted: 05/14/2023] [Indexed: 06/07/2023] Open
Abstract
Metabolic products of the microbiota can alter hematopoiesis. However, the contribution and site of action of bile acids is poorly understood. Here, we demonstrate that the secondary bile acids, deoxycholic acid (DCA) and lithocholic acid (LCA), increase bone marrow myelopoiesis. Treatment of bone marrow cells with DCA and LCA preferentially expanded immunophenotypic and functional colony-forming unit-granulocyte and macrophage (CFU-GM) granulocyte-monocyte progenitors (GMPs). DCA treatment of sorted hematopoietic stem and progenitor cells (HSPCs) increased CFU-GMs, indicating that direct exposure of HSPCs to DCA sufficed to increase GMPs. The vitamin D receptor (VDR) was required for the DCA-induced increase in CFU-GMs and GMPs. Single-cell RNA sequencing revealed that DCA significantly upregulated genes associated with myeloid differentiation and proliferation in GMPs. The action of DCA on HSPCs to expand GMPs in a VDR-dependent manner suggests microbiome-host interactions could directly affect bone marrow hematopoiesis and potentially the severity of infectious and inflammatory disease.
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Affiliation(s)
- Brandon Thompson
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Shan Lu
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Julio Revilla
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Md Jashim Uddin
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - David N. Oakland
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Savannah Brovero
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Sunduz Keles
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - William A. Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
| | - Stacey L. Burgess
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA
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12
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Li WA, Efendizade A, Ding Y. The role of microRNA in neuronal inflammation and survival in the post ischemic brain: a review. Neurol Res 2023; 45:1-9. [PMID: 28552032 DOI: 10.1080/01616412.2017.1327505] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/15/2017] [Indexed: 12/21/2022]
Abstract
Each year, more than 790 000 people in the United States suffer from a stroke. Although progress has been made in diagnosis and treatment of ischemic stroke (IS), new therapeutic interventions to protect the brain during an ischemic insult is highly needed. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression post-transcriptionally. Growing evidence suggests that miRNAs have a profound impact on ischemic stroke progression and are potential targets of novel treatments. Notably, inflammatory pathways play an important role in the pathogenesis of ischemic stroke and its pathophysiologic progression. Experimental and clinical studies have illustrated that inflammatory molecular events collaboratively contribute to neuronal and glial cell survival, edema formation and regression, and vascular integrity. In the present review, we examine recent discoveries regarding miRNAs and their roles in post-ischemic stroke neuropathogenesis.
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Affiliation(s)
- William A Li
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
| | - Aslan Efendizade
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
| | - Yuchuan Ding
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
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13
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Lian T, Guan R, Zhou BR, Bai Y. Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554718. [PMID: 37790476 PMCID: PMC10542146 DOI: 10.1101/2023.08.25.554718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remain elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
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Affiliation(s)
- Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- These authors equally contributed to this work
| | - Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- These authors equally contributed to this work
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Stephens R, Grainger JR, Smith CJ, Allan SM. Systemic innate myeloid responses to acute ischaemic and haemorrhagic stroke. Semin Immunopathol 2023; 45:281-294. [PMID: 36346451 PMCID: PMC9641697 DOI: 10.1007/s00281-022-00968-y] [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: 07/11/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
Abstract
Acute ischaemic and haemorrhagic stroke account for significant disability and morbidity burdens worldwide. The myeloid arm of the peripheral innate immune system is critical in the immunological response to acute ischaemic and haemorrhagic stroke. Neutrophils, monocytes, and dendritic cells (DC) contribute to the evolution of pathogenic local and systemic inflammation, whilst maintaining a critical role in ongoing immunity protecting against secondary infections. This review aims to summarise the key alterations to myeloid immunity in acute ischaemic stroke, intracerebral haemorrhage (ICH), and subarachnoid haemorrhage (SAH). By integrating clinical and preclinical research, we discover how myeloid immunity is affected across multiple organ systems including the brain, blood, bone marrow, spleen, and lung, and evaluate how these perturbations associate with real-world outcomes including infection. These findings are placed in the context of the rapidly developing field of human immunology, which offers a wealth of opportunity for further research.
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Affiliation(s)
- Ruth Stephens
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - John R Grainger
- Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Immunology, Immunity to Infection and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Craig J Smith
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Clinical Neurosciences, Northern Care Alliance NHS Foundation Trust, Salford, UK
| | - Stuart M Allan
- Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Foundation Trust, University of Manchester, Manchester, UK.
- Lydia Becker Institute of Immunology and Inflammation, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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15
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Chambers C, Cermakova K, Chan YS, Kurtz K, Wohlan K, Lewis AH, Wang C, Pham A, Dejmek M, Sala M, Loeza Cabrera M, Aguilar R, Nencka R, Lacorazza HD, Rau RE, Hodges HC. SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia. Cancer Res 2023; 83:983-996. [PMID: 36662812 PMCID: PMC10071820 DOI: 10.1158/0008-5472.can-22-2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/09/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
In acute myeloid leukemia (AML), SWI/SNF chromatin remodeling complexes sustain leukemic identity by driving high levels of MYC. Previous studies have implicated the hematopoietic transcription factor PU.1 (SPI1) as an important target of SWI/SNF inhibition, but PU.1 is widely regarded to have pioneer-like activity. As a result, many questions have remained regarding the interplay between PU.1 and SWI/SNF in AML as well as normal hematopoiesis. Here we found that PU.1 binds to most of its targets in a SWI/SNF-independent manner and recruits SWI/SNF to promote accessibility for other AML core regulatory factors, including RUNX1, LMO2, and MEIS1. SWI/SNF inhibition in AML cells reduced DNA accessibility and binding of these factors at PU.1 sites and redistributed PU.1 to promoters. Analysis of nontumor hematopoietic cells revealed that similar effects also impair PU.1-dependent B-cell and monocyte populations. Nevertheless, SWI/SNF inhibition induced profound therapeutic response in an immunocompetent AML mouse model as well as in primary human AML samples. In vivo, SWI/SNF inhibition promoted leukemic differentiation and reduced the leukemic stem cell burden in bone marrow but also induced leukopenia. These results reveal a variable therapeutic window for SWI/SNF blockade in AML and highlight important off-tumor effects of such therapies in immunocompetent settings. SIGNIFICANCE Disruption of PU.1-directed enhancer programs upon SWI/SNF inhibition causes differentiation of AML cells and induces leukopenia of PU.1-dependent B cells and monocytes, revealing the on- and off-tumor effects of SWI/SNF blockade.
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Affiliation(s)
- Courtney Chambers
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Yuen San Chan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Kristen Kurtz
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
| | - Andrew Henry Lewis
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Christiana Wang
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Anh Pham
- Department of Bioengineering, Rice University, Houston, Texas
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mario Loeza Cabrera
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Rogelio Aguilar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - H. Daniel Lacorazza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Rachel E. Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - H. Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Abstract
Alzheimer's disease (AD) is a debilitating age-related neurodegenerative condition. Unbiased genetic studies have implicated a central role for microglia, the resident innate immune cells of the central nervous system, in AD pathogenesis. On-going efforts are clarifying the biology underlying these associations and the microglial pathways that are dysfunctional in AD. Several genetic risk factors converge to decrease the function of activating microglial receptors and increase the function of inhibitory receptors, resulting in a seemingly dampened microglial phenotype in AD. Moreover, many of these microglial proteins that are genetically associated with AD appear to interact and share pathways or regulatory mechanisms, presenting several points of convergence that may be strategic targets for therapeutic intervention. Here, we review some of these studies and their implications for microglial participation in AD pathogenesis.
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17
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Peng H, Lin Y, Hu F, Lv C, Wu B, Weng Q, Liu L, Xia C, Liu X, Zhao Y, Zhang Q, Geng Y, Zhang M, Wang J. Prolonged generation of multi-lineage blood cells in wild-type animals from pluripotent stem cells. Stem Cell Reports 2023; 18:720-735. [PMID: 36801005 PMCID: PMC10031304 DOI: 10.1016/j.stemcr.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Regenerating prolonged multi-lineage hematopoiesis from pluripotent stem cells (PSCs), an unlimited cell source, is a crucial aim of regenerative hematology. In this study, we used a gene-edited PSC line and revealed that simultaneous expression of three transcription factors, Runx1, Hoxa9, and Hoxa10, drove the robust emergence of induced hematopoietic progenitor cells (iHPCs). The iHPCs engrafted successfully in wild-type animals and repopulated abundant and complete myeloid-, B-, and T-lineage mature cells. The generative multi-lineage hematopoiesis distributed normally in multiple organs, persisted over 6 months, and eventually declined over time with no leukemogenesis. Transcriptome characterization of generative myeloid, B, and T cells at the single-cell resolution further projected their identities to natural cell counterparts. Thus, we provide evidence that co-expression of exogenous Runx1, Hoxa9, and Hoxa10 simultaneously leads to long-term reconstitution of myeloid, B, and T lineages using PSC-derived iHPCs as the cell source.
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Affiliation(s)
- Huan Peng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunqing Lin
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangxiao Hu
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100083, China
| | - Cui Lv
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Bingyan Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qitong Weng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijuan Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengxiang Xia
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100083, China
| | - Xiaofei Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalan Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Qi Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Geng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengyun Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China.
| | - Jinyong Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100083, China.
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18
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In Vitro Human Haematopoietic Stem Cell Expansion and Differentiation. Cells 2023; 12:cells12060896. [PMID: 36980237 PMCID: PMC10046976 DOI: 10.3390/cells12060896] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
The haematopoietic system plays an essential role in our health and survival. It is comprised of a range of mature blood and immune cell types, including oxygen-carrying erythrocytes, platelet-producing megakaryocytes and infection-fighting myeloid and lymphoid cells. Self-renewing multipotent haematopoietic stem cells (HSCs) and a range of intermediate haematopoietic progenitor cell types differentiate into these mature cell types to continuously support haematopoietic system homeostasis throughout life. This process of haematopoiesis is tightly regulated in vivo and primarily takes place in the bone marrow. Over the years, a range of in vitro culture systems have been developed, either to expand haematopoietic stem and progenitor cells or to differentiate them into the various haematopoietic lineages, based on the use of recombinant cytokines, co-culture systems and/or small molecules. These approaches provide important tractable models to study human haematopoiesis in vitro. Additionally, haematopoietic cell culture systems are being developed and clinical tested as a source of cell products for transplantation and transfusion medicine. This review discusses the in vitro culture protocols for human HSC expansion and differentiation, and summarises the key factors involved in these biological processes.
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19
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Ahmadzadeh K, Pereira M, Vanoppen M, Bernaerts E, Ko J, Mitera T, Maksoudian C, Manshian BB, Soenen S, Rose CD, Matthys P, Wouters C, Behmoaras J. Multinucleation resets human macrophages for specialized functions at the expense of their identity. EMBO Rep 2023; 24:e56310. [PMID: 36597777 PMCID: PMC9986822 DOI: 10.15252/embr.202256310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Macrophages undergo plasma membrane fusion and cell multinucleation to form multinucleated giant cells (MGCs) such as osteoclasts in bone, Langhans giant cells (LGCs) as part of granulomas or foreign-body giant cells (FBGCs) in reaction to exogenous material. How multinucleation per se contributes to functional specialization of mature mononuclear macrophages remains poorly understood in humans. Here, we integrate comparative transcriptomics with functional assays in purified mature mononuclear and multinucleated human osteoclasts, LGCs and FBGCs. Strikingly, in all three types of MGCs, multinucleation causes a pronounced downregulation of macrophage identity. We show enhanced lysosome-mediated intracellular iron homeostasis promoting MGC formation. The transition from mononuclear to multinuclear state is accompanied by cell specialization specific to each polykaryon. Enhanced phagocytic and mitochondrial function associate with FBGCs and osteoclasts, respectively. Moreover, human LGCs preferentially express B7-H3 (CD276) and can form granuloma-like clusters in vitro, suggesting that their multinucleation potentiates T cell activation. These findings demonstrate how cell-cell fusion and multinucleation reset human macrophage identity as part of an advanced maturation step that confers MGC-specific functionality.
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Affiliation(s)
- Kourosh Ahmadzadeh
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Marie Pereira
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
| | - Margot Vanoppen
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Eline Bernaerts
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Jeong‐Hun Ko
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
| | - Tania Mitera
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Christy Maksoudian
- NanoHealth and Optical Imaging Group, Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Bella B Manshian
- Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Stefaan Soenen
- NanoHealth and Optical Imaging Group, Translational Cell and Tissue Research Unit, Department of Imaging and PathologyKU LeuvenLeuvenBelgium
| | - Carlos D Rose
- Division of Pediatric Rheumatology Nemours Children's HospitalThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Patrick Matthys
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
| | - Carine Wouters
- Laboratory of Immunobiology, Department Microbiology, Immunology and Transplantation, Rega InstituteKU Leuven—University of LeuvenLeuvenBelgium
- Division Pediatric RheumatologyUZ LeuvenLeuvenBelgium
- European Reference Network for Rare ImmunodeficiencyAutoinflammatory and Autoimmune Diseases (RITA) at University Hospital LeuvenLeuvenBelgium
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Hammersmith HospitalImperial College LondonLondonUK
- Programme in Cardiovascular and Metabolic Disorders and Centre for Computational BiologyDuke‐NUS Medical School SingaporeSingaporeSingapore
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20
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MicroRNA Modulation during Orthodontic Tooth Movement: A Promising Strategy for Novel Diagnostic and Personalized Therapeutic Interventions. Int J Mol Sci 2022; 23:ijms232415501. [PMID: 36555142 PMCID: PMC9779831 DOI: 10.3390/ijms232415501] [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: 11/04/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The Orthodontic Tooth Movement (OTM) is allowed through a mediated cell/tissue mechanism performed by applying a force or a pair of forces on the dental elements, and the tooth movement is a fundamental requirement during any orthodontic treatment. In this regard, it has been widely shown that each orthodontic treatment has a minimum duration required concerning numerous factors (age, patient compliance, type of technique used, etc.). In this regard, the aim of the following revision of the literature is to give readers a global vision of principal microRNAs (miRNAs) that are most frequently associated with OTM and their possible roles. Previously published studies of the last 15 years have been considered in the PubMed search using "OTM" and "miRNA" keywords for the present review article. In vitro and in vivo studies and clinical trials were mainly explored. Correlation between OTM and modulation of several miRNAs acting through post-transcriptional regulation on target genes was observed in the majority of previous studied. The expression analysis of miRNAs in biological samples, such as gingival crevicular fluid (GCF), can be considered a useful tool for novel diagnostic and/or prognostic approaches and for new personalized orthodontic treatments able to achieve a better clinical response rate. Although only a few studies have been published, the data obtained until now encourage further investigation of the role of miRNA modulation during orthodontic treatment. The aim of this study is to update the insights into the role and impact of principal micro-RNAs (miRNAs) that are most frequently associated during OTM.
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21
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Feng F, Jiao P, Wang J, Li Y, Bao B, Luoreng Z, Wang X. Role of Long Noncoding RNAs in the Regulation of Cellular Immune Response and Inflammatory Diseases. Cells 2022; 11:cells11223642. [PMID: 36429069 PMCID: PMC9688074 DOI: 10.3390/cells11223642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered genetic regulatory molecules that regulate immune responses and are closely associated with the occurrence and development of various diseases, including inflammation, in humans and animals. Under specific physiological conditions, lncRNA expression varies at the cell or tissue level, and lncRNAs can bind to specific miRNAs, target mRNAs, and target proteins to participate in certain processes, such as cell differentiation and inflammatory responses, via the corresponding signaling pathways. This review article summarizes the regulatory role of lncRNAs in macrophage polarization, dendritic cell differentiation, T cell differentiation, and endothelial and epithelial inflammation. In addition, it describes the molecular mechanism of lncRNAs in acute kidney injury, hepatitis, inflammatory injury of the lung, osteoarthritis, mastitis, and neuroinflammation to provide a reference for the molecular regulatory network as well as the genetic diagnosis and treatment of inflammatory diseases in humans and animals.
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Affiliation(s)
- Fen Feng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Peng Jiao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yanxia Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Binwu Bao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
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22
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Zhang Z, Bossila EA, Li L, Hu S, Zhao Y. Central gene transcriptional regulatory networks shaping monocyte development in bone marrow. Front Immunol 2022; 13:1011279. [PMID: 36304450 PMCID: PMC9595600 DOI: 10.3389/fimmu.2022.1011279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The development of monocytes in bone marrow is a complex process with multiple steps. We used RNA-seq data to analyze the transcriptome profiles in developing stages of monocytes, including hematopoietic stem cells (HSCs), common myeloid progenitors (CMPs), granulocyte-monocyte progenitors (GMPs), and monocytes. We found that genes related to potassium and other cation transmembrane activities and ion binding were upregulated during the differentiation of HSCs into CMPs. Protein transport and membrane surface functional molecules were significantly upregulated in the GMP stage. The CD42RAC and proteasome pathways are significantly upregulated during the development of HSCs into monocytes. Transcription factors Ank1, Runx2, Hmga2, Klf1, Nfia, and Bmyc were upregulated during the differentiation of HSCs into CMPs; Gfi1 and Hmgn2 were highly expressed during the differentiation of CMPs into GMPs; Seventeen transcription factors including Foxo1, Cdkn2d, Foxo3, Ep300, Pias1, Nfkb1, Creb1, Bcl6, Ppp3cb, Stat5b, Nfatc4, Mef2a, Stat6, Ifnar2, Irf7, Irf5, and Cebpb were identified as potentially involved in the development of GMPs into monocytes in mice and humans. In metabolism pathway regulation, HSCs have high glucose, lipid, and nucleic acid metabolism activities; CMPs mainly up regulate the TCA cycle related genes; and GMPs have extremely active metabolisms, with significantly elevated pentose phosphate pathway, TCA cycle, histidine metabolism, and purine metabolism. In the monocyte phase, the tricarboxylic acid (TCA) cycle is reduced, and the anaerobic glycolysis process becomes dominated. Overall, our studies offer the kinetics and maps of gene transcriptional expressions and cell metabolisms during monocyte development in bone marrow.
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Affiliation(s)
- Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elhusseny A. Bossila
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Biotechnology Department, Faculty of Agriculture Al-Azhar University, Cairo, Egypt
| | - Ling Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regeneration, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regeneration, Beijing, China
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23
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Hwang N, Huh Y, Bu S, Seo KJ, Kwon SH, Kim JW, Yoon BK, Ahn HS, Fang S. Single-cell sequencing of PBMC characterizes the altered transcriptomic landscape of classical monocytes in BNT162b2-induced myocarditis. Front Immunol 2022; 13:979188. [PMID: 36225942 PMCID: PMC9549039 DOI: 10.3389/fimmu.2022.979188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most dangerous threat to public health worldwide for the last few years, which led to the development of the novel mRNA vaccine (BNT162b2). However, BNT162b2 vaccination is known to be associated with myocarditis. Here, as an attempt to determine the pathogenesis of the disease and to develop biomarkers to determine whether subjects likely proceed to myocarditis after vaccination, we conducted a time series analysis of peripheral blood mononuclear cells of a patient with BNT162b2-induced myocarditis. Single-cell RNA sequence analysis identified monocytes as the cell clusters with the most dynamic changes. To identify distinct gene expression signatures, we compared monocytes of BNT162b2-induced myocarditis with monocytes under various conditions, including SARS-CoV-2 infection, BNT162b2 vaccination, and Kawasaki disease, a disease similar to myocarditis. Representative changes in the transcriptomic profile of classical monocytes include the upregulation of genes related to fatty acid metabolism and downregulation of transcription factor AP-1 activity. This study provides, for the first time, the importance of classical monocytes in the pathogenesis of myocarditis following BNT162b2 vaccination and presents the possibility that vaccination affects monocytes, further inducing their differentiation and infiltration into the heart.
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Affiliation(s)
- Nahee Hwang
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, South Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Yune Huh
- Department of Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seonghyeon Bu
- Divison of Cardiology, Department of Internal medicine, The Catholic University of Korea, Uijeongbu St. Mary’s Hospital, Seoul, South Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Kyung Jin Seo
- Department of Hospital Pathology, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Se Hwan Kwon
- Department of Radiology, Kyung Hee University Medical Center, Seoul, South Korea
| | - Jae-woo Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, South Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
| | - Bo Kyung Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Bo Kyung Yoon, ; Hyo-Suk Ahn, ; Sungsoon Fang,
| | - Hyo-Suk Ahn
- Divison of Cardiology, Department of Internal medicine, The Catholic University of Korea, Uijeongbu St. Mary’s Hospital, Seoul, South Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, South Korea
- *Correspondence: Bo Kyung Yoon, ; Hyo-Suk Ahn, ; Sungsoon Fang,
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, South Korea
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
- *Correspondence: Bo Kyung Yoon, ; Hyo-Suk Ahn, ; Sungsoon Fang,
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24
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Chen ST, Park MD, Del Valle DM, Buckup M, Tabachnikova A, Thompson RC, Simons NW, Mouskas K, Lee B, Geanon D, D'Souza D, Dawson T, Marvin R, Nie K, Zhao Z, LeBerichel J, Chang C, Jamal H, Akturk G, Chaddha U, Mathews K, Acquah S, Brown SA, Reiss M, Harkin T, Feldmann M, Powell CA, Hook JL, Kim-Schulze S, Rahman AH, Brown BD, Beckmann ND, Gnjatic S, Kenigsberg E, Charney AW, Merad M. A shift in lung macrophage composition is associated with COVID-19 severity and recovery. Sci Transl Med 2022; 14:eabn5168. [PMID: 36103512 PMCID: PMC10117220 DOI: 10.1126/scitranslmed.abn5168] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although it has been more than 2 years since the start of the coronavirus disease 2019 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, therapies to treat COVID-19 and other inflammatory diseases remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and mortality to develop tailored immunotherapy strategies to halt disease progression. We assembled the Mount Sinai COVID-19 Biobank, which was composed of almost 600 hospitalized patients followed longitudinally through the peak of the pandemic in 2020. Moderate disease and survival were associated with a stronger antigen presentation and effector T cell signature. In contrast, severe disease and death were associated with an altered antigen presentation signature, increased numbers of inflammatory immature myeloid cells, and extrafollicular activated B cells that have been previously associated with autoantibody formation. In severely ill patients with COVID-19, lung tissue-resident alveolar macrophages not only were drastically depleted but also had an altered antigen presentation signature, which coincided with an influx of inflammatory monocytes and monocyte-derived macrophages. In addition, we found that the size of the alveolar macrophage pool correlated with patient outcome and that alveolar macrophage numbers and functionality were restored to homeostasis in patients who recovered from COVID-19. These data suggest that local and systemic myeloid cell dysregulation are drivers of COVID-19 severity and modulation of alveolar macrophage numbers and activity in the lung may be a viable therapeutic strategy for the treatment of critical inflammatory lung diseases.
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Affiliation(s)
- Steven T Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diane Marie Del Valle
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ryan C Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Nicole W Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Darwin D'Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhen Zhao
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jessica LeBerichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hajra Jamal
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Guray Akturk
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Udit Chaddha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kusum Mathews
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel Acquah
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stacey-Ann Brown
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle Reiss
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy Harkin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Charles A Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaime L Hook
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adeeb H Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian D Brown
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | -
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute of Data Science and Genomics Technology, New York, NY 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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25
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Hu L, Liu S, Peng Y, Ge R, Su R, Senevirathne C, Harada BT, Dai Q, Wei J, Zhang L, Hao Z, Luo L, Wang H, Wang Y, Luo M, Chen M, Chen J, He C. m 6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat Biotechnol 2022; 40:1210-1219. [PMID: 35288668 PMCID: PMC9378555 DOI: 10.1038/s41587-022-01243-z] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/28/2022] [Indexed: 01/28/2023]
Abstract
Functional studies of the RNA N6-methyladenosine (m6A) modification have been limited by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such studies, here, we introduce m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq), a method for quantitative, whole-transcriptome mapping of m6A at single-nucleotide resolution. The method requires only ~30 ng of poly(A) or rRNA-depleted RNA. We mapped m6A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells (HSPCs). We identified numerous cell-state-specific m6A sites whose methylation status was highly dynamic during cell differentiation. We observed changes of m6A stoichiometry as well as expression levels of transcripts encoding or regulated by key transcriptional factors (TFs) critical for HSPC differentiation. m6A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m6A sites in diverse biological processes using limited input RNA.
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Affiliation(s)
- Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Fudan University Institutes of Biomedical Sciences, Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, China.
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Yong Peng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bryan T Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lisheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Liangzhi Luo
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Huanyu Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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26
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Vitamin D Derivatives in Acute Myeloid Leukemia: The Matter of Selecting the Right Targets. Nutrients 2022; 14:nu14142851. [PMID: 35889808 PMCID: PMC9320351 DOI: 10.3390/nu14142851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive and often fatal hematopoietic malignancy. A very attractive way to treat myeloid leukemia, called “differentiation therapy”, was proposed when in vitro studies showed that some compounds are capable of inducing differentiation of AML cell lines. One of the differentiation-inducing agents, all-trans-retinoic acid (ATRA), which can induce granulocytic differentiation in AML cell lines, has been introduced into clinics to treat patients with acute promyelocytic leukemia (APL) in which a PML-RARA fusion protein is generated by a chromosomal translocation. ATRA has greatly improved the treatment of APL. Since 1,25-dihydroxyvitamin D (1,25D) is capable of inducing monocytic differentiation of leukemic cells, the idea of treating other AMLs with vitamin D analogs was widely accepted. However, early clinical trials in which cancer patients were treated either with 1,25D or with analogs did not lead to conclusive results. Recent results have shown that AML types with certain mutations, such as isocitrate dehydrogenase (IDH) mutations, may be the right targets for differentiation therapy using 1,25D, due to upregulation of vitamin D receptor (VDR) pathway.
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27
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Ding P, Tan Q, Wei Z, Chen Q, Wang C, Qi L, Wen L, Zhang C, Yao C. Toll-like receptor 9 deficiency induces osteoclastic bone loss via gut microbiota-associated systemic chronic inflammation. Bone Res 2022; 10:42. [PMID: 35624094 PMCID: PMC9142495 DOI: 10.1038/s41413-022-00210-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/06/2022] [Accepted: 03/13/2022] [Indexed: 02/08/2023] Open
Abstract
Toll-like receptors (TLRs) play pivotal roles in inflammation and provide important links between the immune and skeletal systems. Although the activation of TLRs may affect osteoclast differentiation and bone metabolism, whether and how TLRs are required for normal bone remodeling remains to be fully explored. In the current study, we show for the first time that TLR9-/- mice exhibit a low bone mass and low-grade systemic chronic inflammation, which is characterized by the expansion of CD4+ T cells and increased levels of inflammatory cytokines, including TNFα, RANKL, and IL1β. The increased levels of these cytokines significantly promote osteoclastogenesis and induce bone loss. Importantly, TLR9 deletion alters the gut microbiota, and this dysbiosis is the basis of the systemic inflammation and bone loss observed in TLR9-/- mice. Furthermore, through single-cell RNA sequencing, we identified myeloid-biased hematopoiesis in the bone marrow of TLR9-/- mice and determined that the increase in myelopoiesis, likely caused by the adaptation of hematopoietic stem cells to systemic inflammation, also contributes to inflammation-induced osteoclastogenesis and subsequent bone loss in TLR9-/- mice. Thus, our study provides novel evidence that TLR9 signaling connects the gut microbiota, immune system, and bone and is critical in maintaining the homeostasis of inflammation, hematopoiesis, and bone metabolism under normal conditions.
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Affiliation(s)
- Peng Ding
- Department of Orthopedic Surgery, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China
| | - Qiyuan Tan
- Department of Endocrinology and Metabolism, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China
| | - Zhanying Wei
- Department of Osteoporosis and Skeletal Disorders, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China
| | - Qiyu Chen
- Department of Orthopedic Surgery, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China
| | - Chun Wang
- Department of Osteoporosis and Skeletal Disorders, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China
| | - Luyue Qi
- Department of Endocrinology and Metabolism, Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Wen
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA
| | - Changqing Zhang
- Department of Orthopedic Surgery, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China.
| | - Chen Yao
- Department of Orthopedic Surgery, Shanghai Jiaotong University affiliated Sixth People's Hospital, Shanghai, China.
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28
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Shi W, Ye J, Shi Z, Pan C, Zhang Q, Lin Y, Luo Y, Su W, Zheng Y, Liu Y. Chromatin accessibility analysis reveals regulatory dynamics and therapeutic relevance of Vogt-Koyanagi-Harada disease. Commun Biol 2022; 5:506. [PMID: 35618758 PMCID: PMC9135711 DOI: 10.1038/s42003-022-03430-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/29/2022] [Indexed: 12/19/2022] Open
Abstract
The barrier to curing Vogt-Koyanagi-Harada disease (VKH) is thought to reside in a lack of understanding in the roles and regulations of peripheral inflammatory immune cells. Here we perform a single-cell multi-omic study of 166,149 cells in peripheral blood mononuclear cells from patients with VKH, profile the chromatin accessibility and gene expression in the same blood samples, and uncover prominent cellular heterogeneity. Immune cells in VKH blood are highly activated and pro-inflammatory. Notably, we describe an enrichment of transcription targets for nuclear factor kappa B in conventional dendritic cells (cDCs) that governed inflammation. Integrative analysis of transcriptomic and chromatin maps shows that the RELA in cDCs is related to disease complications and poor prognosis. Ligand-receptor interaction pairs also identify cDC as an important predictor that regulated multiple immune subsets. Our results reveal epigenetic and transcriptional dynamics in auto-inflammation, especially the cDC subtype that might lead to therapeutic strategies in VKH.
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Affiliation(s)
- Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Caineng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yuanting Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China. .,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China.
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.,Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
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29
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DeSouza-Vieira T. The metamorphosis of neutrophil transcriptional program during Leishmania infection. Parasite Immunol 2022; 44:e12922. [PMID: 35437801 DOI: 10.1111/pim.12922] [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: 12/10/2021] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022]
Abstract
The role of neutrophils in the course of Leishmania infection remains controversial, displaying tremendous variability depending on the species of parasite, stage of infection, host genetic background, and methodological discrepancies among studies. Although neutrophils have long been categorized as short-lived cells with limited capacity to express proteins de novo, recent advances have revealed significant plasticity in neutrophil transcriptional programs and intrapopulation heterogeneity, which can be regulated by both intrinsic and extrinsic factors that together determine the profile of neutrophil effector response. In this review, we focus on the current understanding of neutrophil transcriptional plasticity, neutrotime, evidence of Leishmania-mediated alterations in neutrophil transcriptome leading to the rise of subpopulations, and finally, functional implications of those findings to the course of Leishmania infection.
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Affiliation(s)
- Thiago DeSouza-Vieira
- Laboratório de Bioquímica e Biologia Molecular de Proteases, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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30
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Wu S, Zhou T, Tian T. A robust method for designing multistable systems by embedding bistable subsystems. NPJ Syst Biol Appl 2022; 8:10. [PMID: 35338169 PMCID: PMC8956579 DOI: 10.1038/s41540-022-00220-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
Although multistability is an important dynamic property of a wide range of complex systems, it is still a challenge to develop mathematical models for realising high order multistability using realistic regulatory mechanisms. To address this issue, we propose a robust method to develop multistable mathematical models by embedding bistable models together. Using the GATA1-GATA2-PU.1 module in hematopoiesis as the test system, we first develop a tristable model based on two bistable models without any high cooperative coefficients, and then modify the tristable model based on experimentally determined mechanisms. The modified model successfully realises four stable steady states and accurately reflects a recent experimental observation showing four transcriptional states. In addition, we develop a stochastic model, and stochastic simulations successfully realise the experimental observations in single cells. These results suggest that the proposed method is a general approach to develop mathematical models for realising multistability and heterogeneity in complex systems.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Melbourne, VIC, Australia
| | - Tianshou Zhou
- School of Mathematics and Statistics, Sun Yet-Sen University, Guangzhou, China
| | - Tianhai Tian
- School of Mathematics, Monash University, Melbourne, VIC, Australia.
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31
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Chen ST, Park MD, Del Valle DM, Buckup M, Tabachnikova A, Simons NW, Mouskas K, Lee B, Geanon D, D’Souza D, Dawson T, Marvin R, Nie K, Thompson RC, Zhao Z, LeBerichel J, Chang C, Jamal H, Chaddha U, Mathews K, Acquah S, Brown SA, Reiss M, Harkin T, Feldmann M, Powell CA, Hook JL, Kim-Schulze S, Rahman AH, Brown BD, Beckmann ND, Gnjatic S, Kenigsberg E, Charney AW, Merad M. Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.11.475918. [PMID: 35043110 PMCID: PMC8764718 DOI: 10.1101/2022.01.11.475918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoMΦ). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.
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Affiliation(s)
- Steven T. Chen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew D. Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Diane Marie Del Valle
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mark Buckup
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole W. Simons
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Konstantinos Mouskas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Darwin D’Souza
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Marvin
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kai Nie
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan C. Thompson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Zhen Zhao
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jessica LeBerichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hajra Jamal
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Udit Chaddha
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kusum Mathews
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Samuel Acquah
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stacey-Ann Brown
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michelle Reiss
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Timothy Harkin
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marc Feldmann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaime L. Hook
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seunghee Kim-Schulze
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adeeb H. Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Immunai, New York, NY, USA
| | - Brian D. Brown
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | | | - Noam D. Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Sacha Gnjatic
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
| | - Alexander W. Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute of Data Science and Genomics Technology, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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32
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Pons V, Rivest S. Targeting Systemic Innate Immune Cells as a Therapeutic Avenue for Alzheimer Disease. Pharmacol Rev 2022; 74:1-17. [PMID: 34987086 DOI: 10.1124/pharmrev.121.000400] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer disease (AD) is the first progressive neurodegenerative disease worldwide, and the disease is characterized by an accumulation of amyloid in the brain and neurovasculature that triggers cognitive decline and neuroinflammation. The innate immune system has a preponderant role in AD. The last decade, scientists focused their efforts on therapies aiming to modulate innate immunity. The latter is of great interest, since they participate to the inflammation and phagocytose the amyloid in the brain and blood vessels. We and others have developed pharmacological approaches to stimulate these cells using various ligands. These include toll-like receptor 4, macrophage colony stimulating factor, and more recently nucleotide-binding oligomerization domain-containing 2 receptors. This review will discuss the great potential to take advantage of the innate immune system to fight naturally against amyloid β accumulation and prevent its detrimental consequence on brain functions and its vascular system. SIGNIFICANCE STATEMENT: The focus on amyloid β removal from the perivascular space rather than targeting CNS plaque formation and clearance represents a new direction with a great potential. Small molecules able to act at the level of peripheral immunity would constitute a novel approach for tackling aberrant central nervous system biology, one of which we believe would have the potential of generating a lot of interest.
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Affiliation(s)
- Vincent Pons
- Neuroscience Laboratory, CHU de Québec Research Center and Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Boul., Québec City, QC G1V 4G2, Canada
| | - Serge Rivest
- Neuroscience Laboratory, CHU de Québec Research Center and Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Boul., Québec City, QC G1V 4G2, Canada
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33
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Paudel S, Ghimire L, Jin L, Jeansonne D, Jeyaseelan S. Regulation of emergency granulopoiesis during infection. Front Immunol 2022; 13:961601. [PMID: 36148240 PMCID: PMC9485265 DOI: 10.3389/fimmu.2022.961601] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
During acute infectious and inflammatory conditions, a large number of neutrophils are in high demand as they are consumed in peripheral organs. The hematopoietic system rapidly responds to the demand by turning from steady state to emergency granulopoiesis to expedite neutrophil generation in the bone marrow (BM). How the hematopoietic system integrates pathogenic and inflammatory stress signals into the molecular cues of emergency granulopoiesis has been the subject of investigations. Recent studies in the field have highlighted emerging concepts, including the direct sensing of pathogens by BM resident or sentinel hematopoietic stem and progenitor cells (HSPCs), the crosstalk of HSPCs, endothelial cells, and stromal cells to convert signals to granulopoiesis, and the identification of novel inflammatory molecules, such as C/EBP-β, ROS, IL-27, IFN-γ, CXCL1 with direct effects on HSPCs. In this review, we will provide a detailed account of emerging concepts while reassessing well-established cellular and molecular players of emergency granulopoiesis. While providing our views on the discrepant results and theories, we will postulate an updated model of granulopoiesis in the context of health and disease.
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Affiliation(s)
- Sagar Paudel
- Center for Lung Biology and Disease, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Pathobiological Sciences, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Laxman Ghimire
- Center for Lung Biology and Disease, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Pathobiological Sciences, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Liliang Jin
- Center for Lung Biology and Disease, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Pathobiological Sciences, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Duane Jeansonne
- Center for Lung Biology and Disease, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Pathobiological Sciences, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States
| | - Samithamby Jeyaseelan
- Center for Lung Biology and Disease, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Department of Pathobiological Sciences, Louisiana State University (LSU) School of Veterinary Medicine, Baton Rouge, LA, United States.,Section of Pulmonary and Critical Care, Department of Medicine, LSU Health Sciences Center, New Orleans, LA, United States
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34
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Orchard P, Manickam N, Ventresca C, Vadlamudi S, Varshney A, Rai V, Kaplan J, Lalancette C, Mohlke KL, Gallagher K, Burant CF, Parker SCJ. Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits. Genome Res 2021; 31:2258-2275. [PMID: 34815310 PMCID: PMC8647829 DOI: 10.1101/gr.268482.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/16/2021] [Indexed: 12/12/2022]
Abstract
Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 33,862 nuclei and identify seven cell types ranging in abundance from 59.6% to 1.0% of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome-wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells (∼3.5% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types.
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Affiliation(s)
- Peter Orchard
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nandini Manickam
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Christa Ventresca
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Arushi Varshney
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vivek Rai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jeremy Kaplan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Katherine Gallagher
- Department of Surgery, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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35
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Tumino N, Weber G, Besi F, Del Bufalo F, Bertaina V, Paci P, Quatrini L, Antonucci L, Sinibaldi M, Quintarelli C, Maggi E, De Angelis B, Locatelli F, Moretta L, Vacca P, Caruana I. Polymorphonuclear myeloid-derived suppressor cells impair the anti-tumor efficacy of GD2.CAR T-cells in patients with neuroblastoma. J Hematol Oncol 2021; 14:191. [PMID: 34772439 PMCID: PMC8588686 DOI: 10.1186/s13045-021-01193-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022] Open
Abstract
The outcome of patients affected by high-risk or metastatic neuroblastoma (NB) remains grim, with ≥ 50% of the children experiencing relapse or progression of the disease despite multimodal, intensive treatment. In order to identify new strategies to improve the overall survival and the quality of life of these children, we recently developed and optimized a third-generation GD2-specific chimeric antigen receptor (CAR) construct, which is currently under evaluation in our Institution in a phase I/II clinical trial (NCT03373097) enrolling patients with relapsed/refractory NB. We observed that our CAR T-cells are able to induce marked tumor reduction and even achieve complete remission with a higher efficiency than that of other CAR T-cells reported in previous studies. However, often responses are not sustained and relapses occur. Here, we demonstrate for the first time a mechanism of resistance to GD2.CAR T-cell treatment, showing how polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) increase in the peripheral blood (PB) of NB patients after GD2.CAR T-cell treatment in case of relapse and loss of response. In vitro, isolated PMN-MDSC demonstrate to inhibit the anti-tumor cytotoxicity of different generations of GD2.CAR T-cells. Gene-expression profiling of GD2.CAR T-cells "conditioned" with PMN-MDSC shows downregulation of genes involved in cell activation, signal transduction, inflammation and cytokine/chemokine secretion. Analysis of NB gene-expression dataset confirms a correlation between expression of these genes and patient outcome. Moreover, in patients treated with GD2.CAR T-cells, the frequency of circulating PMN-MDSC inversely correlates with the levels of GD2.CAR T-cells, resulting more elevated in patients who did not respond or lost response to the treatment. The presence and the frequency of PMN-MDSC in PB of high-risk and metastatic NB represents a useful prognostic marker to predict the response to GD2.CAR T-cells and other adoptive immunotherapy. This study underlines the importance of further optimization of both CAR T-cells and clinical trial in order to target elements of the tumor microenvironment.
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Affiliation(s)
- Nicola Tumino
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy
| | - Gerrit Weber
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy.,Department of Pediatric Hematology, Oncology and Stem Cell Transplantation University Children's Hospital of Würzburg, 97080, Würzburg, Germany
| | - Francesca Besi
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy
| | - Francesca Del Bufalo
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Valentina Bertaina
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Linda Quatrini
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy
| | - Laura Antonucci
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Matilde Sinibaldi
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Concetta Quintarelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Enrico Maggi
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy
| | - Biagio De Angelis
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy. .,Department of Maternal, Infantile, and Urological Sciences, Sapienza University of Rome, Rome, Italy.
| | - Lorenzo Moretta
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy.
| | - Paola Vacca
- Immunology Research Area, IRCCS Bambino Gesù Children's Hospital, Viale San Paolo 15, 00146, Rome, Italy
| | - Ignazio Caruana
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Piazza Sant'Onofrio, 4, 00165, Rome, Italy.,Department of Pediatric Hematology, Oncology and Stem Cell Transplantation University Children's Hospital of Würzburg, 97080, Würzburg, Germany
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36
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Sun S, Jin C, Si J, Lei Y, Chen K, Cui Y, Liu Z, Liu J, Zhao M, Zhang X, Tang F, Rondina MT, Li Y, Wang QF. Single-cell analysis of ploidy and the transcriptome reveals functional and spatial divergency in murine megakaryopoiesis. Blood 2021; 138:1211-1224. [PMID: 34115843 PMCID: PMC8499048 DOI: 10.1182/blood.2021010697] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/26/2021] [Indexed: 11/20/2022] Open
Abstract
Megakaryocytes (MKs), the platelet progenitor cells, play important roles in hematopoietic stem cell (HSC) maintenance and immunity. However, it is not known whether these diverse programs are executed by a single population or by distinct subsets of cells. Here, we manually isolated primary CD41+ MKs from the bone marrow (BM) of mice and human donors based on ploidy (2N-32N) and performed single-cell RNA sequencing analysis. We found that cellular heterogeneity existed within 3 distinct subpopulations that possess gene signatures related to platelet generation, HSC niche interaction, and inflammatory responses. In situ immunostaining of mouse BM demonstrated that platelet generation and the HSC niche-related MKs were in close physical proximity to blood vessels and HSCs, respectively. Proplatelets, which could give rise to platelets under blood shear forces, were predominantly formed on a platelet generation subset. Remarkably, the inflammatory responses subpopulation, consisting generally of low-ploidy LSP1+ and CD53+ MKs (≤8N), represented ∼5% of total MKs in the BM. These MKs could specifically respond to pathogenic infections in mice. Rapid expansion of this population was accompanied by strong upregulation of a preexisting PU.1- and IRF-8-associated monocytic-like transcriptional program involved in pathogen recognition and clearance as well as antigen presentation. Consistently, isolated primary CD53+ cells were capable of engulfing and digesting bacteria and stimulating T cells in vitro. Together, our findings uncover new molecular, spatial, and functional heterogeneity within MKs in vivo and demonstrate the existence of a specialized MK subpopulation that may act as a new type of immune cell.
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Affiliation(s)
- Shu Sun
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chen Jin
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Si
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Lei
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kunying Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueli Cui
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
- Biomedical Institute for Pioneering Investigation via Convergence, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhenbo Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Jiang Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangzhou, China
| | - Xiaohui Zhang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing, China
- National Clinical Research Center for Hematologic Disease, Beijing, China
- Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
- Collaborative Innovation Center of Hematology, Peking University, Beijing, China
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Peking University, Beijing, China
- Biomedical Institute for Pioneering Investigation via Convergence, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Matthew T Rondina
- Department of Internal Medicine and Pathology, and the Molecular Medicine Program, University of Utah, Salt Lake City, UT; and
- Geriatric Research Education and Clinical Center, George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT
| | - Yueying Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian-Fei Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, CAS, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Lin YJ, Wei KC, Chen PY, Lim M, Hwang TL. Roles of Neutrophils in Glioma and Brain Metastases. Front Immunol 2021; 12:701383. [PMID: 34484197 PMCID: PMC8411705 DOI: 10.3389/fimmu.2021.701383] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/19/2021] [Indexed: 12/16/2022] Open
Abstract
Neutrophils, which are the most abundant circulating leukocytes in humans, are the first line of defense against bacterial and fungal infections. Recent studies have reported the role and importance of neutrophils in cancers. Glioma and brain metastases are the most common malignant tumors of the brain. The tumor microenvironment (TME) in the brain is complex and unique owing to the brain-blood barrier or brain-tumor barrier, which may prevent drug penetration and decrease the efficacy of immunotherapy. However, there are limited studies on the correlation between brain cancer and neutrophils. This review discusses the origin and functions of neutrophils. Additionally, the current knowledge on the correlation between neutrophil-to-lymphocyte ratio and prognosis of glioma and brain metastases has been summarized. Furthermore, the implications of tumor-associated neutrophil (TAN) phenotypes and the functions of TANs have been discussed. Finally, the potential effects of various treatments on TANs and the ability of neutrophils to function as a nanocarrier of drugs to the brain TME have been summarized. However, further studies are needed to elucidate the complex interactions between neutrophils, other immune cells, and brain tumor cells.
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Affiliation(s)
- Ya-Jui Lin
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Kuo-Chen Wei
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, Chang Gung Medical Foundation, New Taipei, Taiwan
- School of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Pin-Yuan Chen
- School of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Michael Lim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, Taiwan
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38
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Lemus-Conejo A, Medrano M, Lopez S, Millan-Linares MC, Rosillo MA, Perez-Simon JA, Muriana FJG, Abia R. MUFAs in High-Fat Diets Protect against Obesity-Induced Bias of Hematopoietic Cell Lineages. Mol Nutr Food Res 2021; 65:e2001203. [PMID: 34132459 DOI: 10.1002/mnfr.202001203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/27/2021] [Indexed: 11/08/2022]
Abstract
SCOPE The role of dietary fatty acids in the generation of bone marrow (BM) immune cells and their trafficking to extramedullary compartments in the obesity is not yet fully understood. METHODS AND RESULTS C57BL/6J mice are randomly assigned to isocaloric high-fat diets (HFDs) formulate with dietary fats rich in saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs) or MUFAs fortified with eicosapentaenoic and docosahexaenoic acids for 20 weeks, followed by profiling of the obese metabolic phenotype and immunophenotypic features of immune cells in blood, spleen, and BM. All HFDs induce an obese phenotype, but it becomes largely less disruptive after the HFDs are enriched in MUFAs, which also induce signs of granulopoiesis and an expansion of long-term hematopoietic stem and granulocyte-macrophage progenitor cells in BM. In contrast, a HFD enriched in SFAs disturbs the fitness of medullary lymphocytes and promotes monopoiesis in favor of pro-inflammatory activated subsets. CONCLUSION The reshaping of the fatty acid pools with MUFAs from the diet serves to manipulate the generation and trafficking of immune cells that are biased during obesity. These findings reveal a novel strategy by which dietary MUFAs may be instrumental in combating HFD-induced dysfunctional immune systems.
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Affiliation(s)
- Ana Lemus-Conejo
- Laboratory of Cellular and Molecular Nutrition, Instituto de la Grasa, The Spanish National Research Council (CSIC), Seville, 41013, Spain
| | - Mayte Medrano
- Department of Haematology, Instituto de Biomedicina de Sevilla (IBiS/CSIC/CIBERONC), Hospital Universitario Virgen del Rocio, University of Seville, Seville, 41012, Spain
| | - Sergio Lopez
- Laboratory of Cellular and Molecular Nutrition, Instituto de la Grasa, The Spanish National Research Council (CSIC), Seville, 41013, Spain
- Department of Cell Biology, Faculty of Biology, University of Seville, Seville, 41012, Spain
- Instituto de Biomedicina de Sevilla (IBiS/CSIC), Hospital Universitario Virgen del Rocio, University of Seville, Seville, 41012, Spain
| | | | - Maria A Rosillo
- Laboratory of Cellular and Molecular Nutrition, Instituto de la Grasa, The Spanish National Research Council (CSIC), Seville, 41013, Spain
| | - Jose A Perez-Simon
- Department of Haematology, Instituto de Biomedicina de Sevilla (IBiS/CSIC/CIBERONC), Hospital Universitario Virgen del Rocio, University of Seville, Seville, 41012, Spain
| | - Francisco J G Muriana
- Laboratory of Cellular and Molecular Nutrition, Instituto de la Grasa, The Spanish National Research Council (CSIC), Seville, 41013, Spain
| | - Rocio Abia
- Laboratory of Cellular and Molecular Nutrition, Instituto de la Grasa, The Spanish National Research Council (CSIC), Seville, 41013, Spain
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39
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Desterke C, Bennaceur-Griscelli A, Turhan AG. EGR1 dysregulation defines an inflammatory and leukemic program in cell trajectory of human-aged hematopoietic stem cells (HSC). Stem Cell Res Ther 2021; 12:419. [PMID: 34294125 PMCID: PMC8296523 DOI: 10.1186/s13287-021-02498-0] [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: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background During aging, hematopoietic stem cells (HSC) lose progressively both their self-renewal and differentiation potential. The precise molecular mechanisms of this phenomenon are not well established. To uncover the molecular events underlying this event, we have performed a bioinformatics analysis of 650 single-cell transcriptomes. Methods Single-cell transcriptome analyses of expression heterogeneity, cell cycle, and cell trajectory in human cell compartment enriched in hematopoietic stem cell compartment were investigated in the bone marrow according to the age of the donors. Identification of aging-related nodules was identified by weighted correlation network analysis in this primitive compartment. Results The analysis of single-cell transcriptomes allowed to uncover a major upregulation of EGR1 in human-aged lineage−CD34+CD38− cells which present cell cycle dysregulation with reduction of G2/M phase according to less expression of CCND2 during S phase. EGR1 upregulation in aging hematopoietic stem cells was found to be independent of cell cycle phases and gender. EGR1 expression trajectory in aged HSC highlighted a signature enriched in hematopoietic and immune disorders with the best induction of AP-1 complex and quiescence regulators such as EGR1, BTG2, JUNB, and NR41A. Sonic Hedgehog-related TMEM107 transmembrane molecule followed also EGR1 cell trajectory. EGR1-dependent gene weighted network analysis in human HSC-associated IER2 target protein-specific regulators of PP2A activity, IL1B, TNFSF10 ligands, and CD69, SELP membrane molecules in old HSC module with immune and leukemogenic signature. In contrast, for young HSC which were found with different cell cycle phase progression, its specific module highlighted upregulation of HIF1A hypoxic factor, PDE4B immune marker, DRAK2 (STK17B) T cell apoptosis regulator, and MYADM myeloid-associated marker. Conclusion EGR1 was found to be connected to the aging of human HSC and highlighted a specific cell trajectory contributing to the dysregulation of an inflammatory and leukemia-related transcriptional program in aged human HSCs. EGR1 and its program were found to be connected to the aging of human HSC with dissociation of quiescence property and cell cycle phase progression in this primitive hematopoietic compartment. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02498-0.
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Affiliation(s)
| | - Annelise Bennaceur-Griscelli
- INSERM UA9, University Paris-Saclay, 94800, Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800, Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, 94800, Villejuif, France.,Faculty of Medicine, University Paris Saclay, 94275, Le Kremlin Bicêtre, France
| | - Ali G Turhan
- INSERM UA9, University Paris-Saclay, 94800, Villejuif, France. .,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800, Villejuif, France. .,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, 94800, Villejuif, France. .,Faculty of Medicine, University Paris Saclay, 94275, Le Kremlin Bicêtre, France.
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40
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Bhatt HK, Song D, Musgrave G, Rao PSS. Cannabinoid-induced changes in the immune system: The role of microRNAs. Int Immunopharmacol 2021; 98:107832. [PMID: 34107381 DOI: 10.1016/j.intimp.2021.107832] [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: 03/11/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring cannabinoids have been used by humans for their medicinal benefits for over several millennia. While the use of cannabinoids has been strictly regulated in the past century, easing of state regulations has been associated with an increase in use of cannabinoids in the United States. The potential therapeutic applications of cannabinoids have been explored and the anti-inflammatory effect of cannabis-derived cannabinoids has been well-documented. The pharmacological effects of cannabinoids are governed by the modulation of cannabinoid receptors, CB1 and CB2, expressed in the central and peripheral tissues. Moreover, growing scientific evidence suggests that the cannabinoid-mediated changes in the immune system involves change in expression of microRNAs (miRNAs). MiRNAs are short non-coding, single-stranded RNA which have the ability to affect post-translational regulation of gene expression. Studies over the past decade have investigated the changes in expression of miRNAs following treatment of various components of the immune system with different chemical modulators of the cannabinoid receptors. Such studies have highlighted the key role played by various miRNAs in driving the observed immunomodulatory effects of cannabinoids. The aim of this review article, therefore, is to summarize the role of miRNAs behind the observed effects of cannabinoids on the overall immune system, rather than focusing on a single disease state.
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Affiliation(s)
- Hirva K Bhatt
- College of Pharmacy, The University of Findlay, Findlay, OH 45840, United States
| | - Dana Song
- College of Pharmacy, The University of Findlay, Findlay, OH 45840, United States
| | - Gyen Musgrave
- Greenleaf Apothecaries, LLC, 15335 Madison Road, Middlefield, OH 44062, United States
| | - P S S Rao
- College of Pharmacy, The University of Findlay, Findlay, OH 45840, United States.
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41
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Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19. Nat Cell Biol 2021; 23:620-630. [PMID: 34108657 PMCID: PMC9105401 DOI: 10.1038/s41556-021-00690-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 04/28/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often causes severe complications and even death. However, asymptomatic infection has also been reported, highlighting the difference in immune responses among individuals. Here we performed single-cell chromatin accessibility and T cell-receptor analyses of peripheral blood mononuclear cells collected from individuals convalescing from COVID-19 and healthy donors. Chromatin remodelling was observed in both innate and adaptive immune cells in the individuals convalescing from COVID-19. Compared with healthy donors, recovered individuals contained abundant TBET-enriched CD16+ and IRF1-enriched CD14+ monocytes with sequential trained and activated epigenomic states. The B-cell lineage in recovered individuals exhibited an accelerated developmental programme from immature B cells to antibody-producing plasma cells. Finally, an integrated analysis of single-cell T cell-receptor clonality with the chromatin accessibility landscape revealed the expansion of putative SARS-CoV-2-specific CD8+ T cells with epigenomic profiles that promote the differentiation of effector or memory cells. Overall, our data suggest that immune cells of individuals convalescing from COVID-19 exhibit global remodelling of the chromatin accessibility landscape, indicative of the establishment of immunological memory.
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42
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Sharma J, Pandey A, Sharma S, Dixit A. Securinine Induces Differentiation of Human Promyelocytic Leukemic HL-60 Cells through JNK-Mediated Signaling Pathway. Nutr Cancer 2021; 74:1122-1137. [PMID: 33998358 DOI: 10.1080/01635581.2021.1925710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Acute myeloid leukemia is characterized by abnormal differentiation of hematopoietic stem cells, leading to the accumulation of immature myeloid cells. Differentiation therapy has been a successful treatment option for acute promyelocytic leukemia but suffers from adverse effects. Therefore, search for novel differentiation-inducing agents with minimal side effects is desirable. Securinine, a naturally-occurring alkaloid, induces differentiation in various leukemic cells and apoptosis in other types of cancers. However, the underlying molecular mechanism(s) remain elusive. Our study aimed to elucidate the possible molecular mechanism(s) and signaling events involved in securinine-induced differentiation of HL-60 cells. Securinine inhibited proliferation in a time- and dose-dependent manner and triggered differentiation. A higher CD14+ population indicated maturation toward monocytic lineage. Securinine caused cell cycle arrest at the G0/G1 phase and enhanced ROS generation. Quantitative gene expression analysis showed significant down-regulation of C/EBP-α, C/EBP-ε, GAΤΑ, and c-myc and up-regulation of the PU.1 gene. The expression of distinct protein kinases Lyn, Chk-2, Yes, FAK, c-Jun, and JNK were enhanced. Use of specific inhibitors of crucial intracellular signaling proteins indicated that JNK and ERK blockade resulted in a significant decline in differentiation. These data thus confirm that securinine induces differentiation through the activation of the JNK-ERK signaling pathway in HL-60 cells.
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Affiliation(s)
- Jeetesh Sharma
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ankita Pandey
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sapna Sharma
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Aparna Dixit
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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43
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Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency. Blood Adv 2021; 4:2656-2670. [PMID: 32556286 DOI: 10.1182/bloodadvances.2019001352] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
Constitutional GATA2 deficiency caused by heterozygous germline GATA2 mutations has a broad spectrum of clinical phenotypes, including systemic infections, lymphedema, cytopenias, and myeloid neoplasms. Genotype-phenotype correlation is not well understood mechanistically in GATA2 deficiency. We performed whole transcriptome sequencing of single hematopoietic stem and progenitor cells from 8 patients, who had pathogenic GATA2 mutations and myelodysplasia. Mapping patients' cells onto normal hematopoiesis, we observed deficiency in lymphoid/myeloid progenitors, also evident from highly constrained gene correlations. HSPCs of patients exhibited distinct patterns of gene expression and coexpression compared with counterparts from healthy donors. Distinct lineages showed differently altered transcriptional profiles. Stem cells in patients had dysregulated gene expression related to apoptosis, cell cycle, and quiescence; increased expression of erythroid/megakaryocytic priming genes; and decreased lymphoid priming genes. The prominent deficiency in lympho-myeloid lineages in GATA2 deficiency appeared at least partly due to the expression of aberrant gene programs in stem cells prior to lineage commitment. We computationally imputed cells with chromosomal abnormalities and determined their gene expression; DNA repair genes were downregulated in trisomy 8 cells, potentially rendering these cells vulnerable to second-hit somatic mutations and additional chromosomal abnormalities. Cells with complex cytogenetic abnormalities showed defects in genes related to multilineage differentiation and cell cycle. Single-cell RNA sequencing is powerful in resolving transcriptomes of cell subpopulations despite a paucity of cells in marrow failure. Our study discloses previously uncharacterized transcriptome signatures of stem cells and progenitors in GATA2 deficiency, providing a broad perspective of potential mechanisms by which germline mutations modulate early hematopoiesis in a human disease. This trial was registered at www.clinicaltrials.gov as NCT01905826, NCT01861106, and NCT00001620.
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44
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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45
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Leylek R, Alcántara-Hernández M, Granja JM, Chavez M, Perez K, Diaz OR, Li R, Satpathy AT, Chang HY, Idoyaga J. Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity. Cell Rep 2021; 32:108180. [PMID: 32966789 PMCID: PMC7546547 DOI: 10.1016/j.celrep.2020.108180] [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: 03/19/2020] [Revised: 06/18/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin accessibility profiles across resting and stimulated human DC subsets by means of the assay for transposase-accessible chromatin using sequencing (ATAC-seq). We uncover specific regions of chromatin accessibility for each subset and transcriptional regulators of DC function. By comparing plasmacytoid DC responses to IFN-I-producing and non-IFN-I-producing conditions, we identify genetic programs related to their function. Finally, by intersecting chromatin accessibility with genome-wide association studies, we recognize DC subset-specific enrichment of heritability in autoimmune diseases. Our results unravel the basis of human DC subset heterogeneity and provide a framework for their analysis in disease pathogenesis. Human dendritic cells (DCs) orchestrate immune responses by a division of labor between functionally specialized subsets; however, the transcriptional basis of this heterogeneity is poorly understood. Using ATAC-seq, Leylek et al. profile the chromatin landscape of human DC subsets, providing insight into the underlying regulatory mechanisms that modulate their function.
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Affiliation(s)
- Rebecca Leylek
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly Perez
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oscar R Diaz
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Identification of Potential Key lncRNAs in the Context of Mouse Myeloid Differentiation by Systematic Transcriptomics Analysis. Genes (Basel) 2021; 12:genes12050630. [PMID: 33922442 PMCID: PMC8146222 DOI: 10.3390/genes12050630] [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: 02/20/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
Hematopoietic differentiation is a well-orchestrated process by many regulators such as transcription factor and long non-coding RNAs (lncRNAs). However, due to the large number of lncRNAs and the difficulty in determining their roles, the study of lncRNAs is a considerable challenge in hematopoietic differentiation. Here, through gene co-expression network analysis over RNA-seq data generated from representative types of mouse myeloid cells, we obtained a catalog of potential key lncRNAs in the context of mouse myeloid differentiation. Then, employing a widely used in vitro cell model, we screened a novel lncRNA, named Gdal1 (Granulocytic differentiation associated lncRNA 1), from this list and demonstrated that Gdal1 was required for granulocytic differentiation. Furthermore, knockdown of Cebpe, a principal transcription factor of granulocytic differentiation regulation, led to down-regulation of Gdal1, but not vice versa. In addition, expression of genes involved in myeloid differentiation and its regulation, such as Cebpa, were influenced in Gdal1 knockdown cells with differentiation blockage. We thus systematically identified myeloid differentiation associated lncRNAs and substantiated the identification by investigation of one of these lncRNAs on cellular phenotype and gene regulation levels. This study promotes our understanding of the regulation of myeloid differentiation and the characterization of roles of lncRNAs in hematopoietic system.
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De G, Chen A, Zhao Q, Xie R, Wang C, Li M, Zhao H, Gu X, McCarl LH, Zhang F, Cai W, Yang M, Lin P, Liu S, Bian B. A multi-herb-combined remedy to overcome hyper-inflammatory response by reprogramming transcription factor profile and shaping monocyte subsets. Pharmacol Res 2021; 169:105617. [PMID: 33872811 DOI: 10.1016/j.phrs.2021.105617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022]
Abstract
Traditional Chinese multi-herb-combined prescriptions usually show better performance than a single agent since a group of effective compounds interfere multiple disease-relevant targets simultaneously. Huang-Lian-Jie-Du decoction is a remedy made of four herbs that are widely used to treat oral ulcers, gingivitis, and periodontitis. However, the active ingredients and underlying mechanisms are not clear. To address these questions, we prepared a water extract solution of Huang-Lian-Jie-Du decoction (HLJDD), called it as WEH (Water Extract Solution of HLJDD), and used it to treat LPS-induced systemic inflammation in mice. We observed that WEH attenuated inflammatory responses including reducing production of cytokines, chemokines and interferons (IFNs), further attenuating emergency myelopoiesis, and preventing mice septic lethality. Upon LPS stimulation, mice pretreated with WEH increased circulating Ly6C- patrolling and splenic Ly6C+ inflammatory monocytes. The acute myelopoiesis related transcriptional factor profile was rearranged by WEH. Mechanistically we confirmed that WEH interrupted LPS/TLR4/CD14 signaling-mediated downstream signaling pathways through its nine principal ingredients, which blocked LPS stimulated divergent signaling cascades, such as activation of NF-κB, p38 MAPK, and ERK1/2. We conclude that the old remedy blunts LPS-induced "danger" signal recognition and transduction process at multiple sites. To translate our findings into clinical applications, we refined the crude extract into a pure multicomponent drug by directly mixing these nine chemical entities, which completely reproduced the effect of protecting mice from lethal septic shock. Finally, we reduced a large number of compounds within a multi-herb water extract to seven-chemical combination that exhibited superior therapeutic efficacy compared with WEH.
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Affiliation(s)
- Gejing De
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China.
| | - Apeng Chen
- Department of Neurological Surgery, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Qinghe Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Ran Xie
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Chaoxi Wang
- First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Meng Li
- Berry Genomics Corp., Beijing, Science & Technology Park, Changping District, Beijing 102299, China
| | - Haiyu Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Xinru Gu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Lauren H McCarl
- Department of Neurological Surgery, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Fangbo Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Weiyan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Miyi Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China
| | - Peihui Lin
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Baolin Bian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongcheng District, Beijing 100700, China.
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48
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Choi J, Lysakovskaia K, Stik G, Demel C, Söding J, Tian TV, Graf T, Cramer P. Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 2021; 10:e65381. [PMID: 33770473 PMCID: PMC8004103 DOI: 10.7554/elife.65381] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/14/2021] [Indexed: 12/18/2022] Open
Abstract
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrophages. Putative enhancers are established by binding of the pioneer factor C/EBPα followed by chromatin opening and enhancer RNA (eRNA) synthesis from H3K4-monomethylated regions. Using eRNA synthesis as a proxy for enhancer activity, we find that most putative enhancers cooperate in an additive way to regulate transcription of assigned target genes. However, transcription from 136 target genes depends exponentially on the summed activity of its putative paired enhancers, indicating that these enhancers cooperate synergistically. The target genes are cell type-specific, suggesting that enhancer synergy can contribute to cell fate determination. Enhancer synergy appears to depend on cell type-specific transcription factors, and such interacting enhancers are not predicted from occupancy or accessibility data that are used to detect superenhancers.
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Affiliation(s)
- Jinmi Choi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Kseniia Lysakovskaia
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Gregoire Stik
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Carina Demel
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
| | - Johannes Söding
- Max Planck Institute for Biophysical Chemistry, Quantitative Biology and BioinformaticsGöttingenGermany
| | - Tian V Tian
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG)BarcelonaSpain
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular BiologyGöttingenGermany
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The epigenetic pioneer EGR2 initiates DNA demethylation in differentiating monocytes at both stable and transient binding sites. Nat Commun 2021; 12:1556. [PMID: 33692344 PMCID: PMC7946903 DOI: 10.1038/s41467-021-21661-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
The differentiation of human blood monocytes (MO), the post-mitotic precursors of macrophages (MAC) and dendritic cells (moDC), is accompanied by the active turnover of DNA methylation, but the extent, consequences and mechanisms of DNA methylation changes remain unclear. Here, we profile and compare epigenetic landscapes during IL-4/GM-CSF-driven MO differentiation across the genome and detect several thousand regions that are actively demethylated during culture, both with or without accompanying changes in chromatin accessibility or transcription factor (TF) binding. We further identify TF that are globally associated with DNA demethylation processes. While interferon regulatory factor 4 (IRF4) is found to control hallmark dendritic cell functions with less impact on DNA methylation, early growth response 2 (EGR2) proves essential for MO differentiation as well as DNA methylation turnover at its binding sites. We also show that ERG2 interacts with the 5mC hydroxylase TET2, and its consensus binding sequences show a characteristic DNA methylation footprint at demethylated sites with or without detectable protein binding. Our findings reveal an essential role for EGR2 as epigenetic pioneer in human MO and suggest that active DNA demethylation can be initiated by the TET2-recruiting TF both at stable and transient binding sites. DNA methylation turnover is an essential epigenetic process during development. Here, the authors look at the changes in DNA methylation during the differentiation of post-mitotic human monocytes (MO), and find that EGR2 interacts with TET2 and is required for DNA demethylation at its binding sites; revealing EGR2 as an epigenetic pioneer factor in human MO.
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50
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Martínez de Paz A, Josefowicz SZ. Signaling-to-chromatin pathways in the immune system. Immunol Rev 2021; 300:37-53. [PMID: 33644906 PMCID: PMC8548991 DOI: 10.1111/imr.12955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 02/01/2023]
Abstract
Complex organisms are able to respond to diverse environmental cues by rapidly inducing specific transcriptional programs comprising a few dozen genes among thousands. The highly complex environment within the nucleus-a crowded milieu containing large genomes tightly condensed with histone proteins in the form of chromatin-makes inducible transcription a challenge for the cell, akin to the proverbial needle in a haystack. The different signaling pathways and transcription factors involved in the transmission of information from the cell surface to the nucleus have been readily explored, but not so much the specific mechanisms employed by the cell to ultimately instruct the chromatin changes necessary for a fast and robust transcription activation. Signaling pathways rely on cascades of protein kinases that, in addition to activating transcription factors can also activate the chromatin template by phosphorylating histone proteins, what we refer to as "signaling-to-chromatin." These pathways appear to be selectively employed and especially critical for driving inducible transcription in macrophages and likely in diverse other immune cell populations. Here, we discuss signaling-to-chromatin pathways with potential relevance in diverse immune cell populations together with chromatin related mechanisms that help to "solve" the needle in a haystack challenge of robust chromatin activation and inducible transcription.
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Affiliation(s)
- Alexia Martínez de Paz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Steven Zvi Josefowicz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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