1
|
Sun J, Ruiz Daniels R, Balic A, Andresen AMS, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SAM, Fosse JH, Taylor RS, Macqueen DJ. Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109358. [PMID: 38176627 DOI: 10.1016/j.fsi.2024.109358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. We identified clusters of nuclei representing the expected major cell types, namely T cells, B cells, natural killer-like cells, granulocytes, mononuclear phagocytes, endothelial cells, mesenchymal cells, erythrocytes and thrombocytes. We discovered heterogeneity within several immune lineages, providing evidence for resident macrophages and melanomacrophages, infiltrating monocytes, several candidate dendritic cell subpopulations, and B cells at distinct stages of differentiation, including plasma cells and an igt + subset. We provide evidence for twelve candidate T cell subsets, including cd4+ T helper and regulatory T cells, one cd8+ subset, three γδT subsets, and populations double negative for cd4 and cd8. The number of genes showing differential expression during the early stages of Aeromonas infection was highly variable across immune cell types, with the largest changes observed in macrophages and infiltrating monocytes, followed by resting mature B cells. Our analysis provides evidence for a local inflammatory response to infection alongside B cell maturation in the spleen, and upregulation of ccr9 genes in igt + B cells, T helper and cd8+ cells, and monocytes, consistent with the recruitment of immune cell populations to the gut to deal with Aeromonas infection. Overall, this study provides a new cell-resolved perspective of the immune actions of Atlantic salmon spleen, highlighting extensive heterogeneity hidden to bulk transcriptomics. We further provide a large catalogue of cell-specific marker genes that can be leveraged to further explore the function and structural organization of the salmonid immune system.
Collapse
Affiliation(s)
- Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Håvard Bjørgen
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Erling Olaf Koppang
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
| |
Collapse
|
2
|
Wang Y, Li Y, Wang C, Lio CWJ, Ma Q, Liu B. CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq. Brief Bioinform 2023; 25:bbad505. [PMID: 38189539 PMCID: PMC10772951 DOI: 10.1093/bib/bbad505] [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: 09/22/2023] [Revised: 11/21/2023] [Accepted: 12/03/2023] [Indexed: 01/09/2024] Open
Abstract
Sequence motif discovery algorithms enhance the identification of novel deoxyribonucleic acid sequences with pivotal biological significance, especially transcription factor (TF)-binding motifs. The advent of assay for transposase-accessible chromatin using sequencing (ATAC-seq) has broadened the toolkit for motif characterization. Nonetheless, prevailing computational approaches have focused on delineating TF-binding footprints, with motif discovery receiving less attention. Herein, we present Cis rEgulatory Motif Influence using de Bruijn Graph (CEMIG), an algorithm leveraging de Bruijn and Hamming distance graph paradigms to predict and map motif sites. Assessment on 129 ATAC-seq datasets from the Cistrome Data Browser demonstrates CEMIG's exceptional performance, surpassing three established methodologies on four evaluative metrics. CEMIG accurately identifies both cell-type-specific and common TF motifs within GM12878 and K562 cell lines, demonstrating its comparative genomic capabilities in the identification of evolutionary conservation and cell-type specificity. In-depth transcriptional and functional genomic studies have validated the functional relevance of CEMIG-identified motifs across various cell types. CEMIG is available at https://github.com/OSU-BMBL/CEMIG, developed in C++ to ensure cross-platform compatibility with Linux, macOS and Windows operating systems.
Collapse
Affiliation(s)
- Yizhong Wang
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Yang Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Chan-Wang Jerry Lio
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, 250100, China
| |
Collapse
|
3
|
Zezulin AU, Yen D, Ye D, Howell ED, Bresciani E, Diemer J, Ren JG, Ahmad MH, Castilla LH, Touw IP, Minn AJ, Tong W, Liu PP, Tan K, Yu W, Speck NA. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. Genes Dev 2023; 37:605-620. [PMID: 37536952 PMCID: PMC10499021 DOI: 10.1101/gad.350418.123] [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: 01/09/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
The transcription factor RUNX1 is mutated in familial platelet disorder with associated myeloid malignancy (FPDMM) and in sporadic myelodysplastic syndrome and leukemia. RUNX1 was shown to regulate inflammation in multiple cell types. Here we show that RUNX1 is required in granulocyte-monocyte progenitors (GMPs) to epigenetically repress two inflammatory signaling pathways in neutrophils: Toll-like receptor 4 (TLR4) and type I interferon (IFN) signaling. RUNX1 loss in GMPs augments neutrophils' inflammatory response to the TLR4 ligand lipopolysaccharide through increased expression of the TLR4 coreceptor CD14. RUNX1 binds Cd14 and other genes encoding proteins in the TLR4 and type I IFN signaling pathways whose chromatin accessibility increases when RUNX1 is deleted. Transcription factor footprints for the effectors of type I IFN signaling-the signal transducer and activator of transcription (STAT1::STAT2) and interferon regulatory factors (IRFs)-were enriched in chromatin that gained accessibility in both GMPs and neutrophils when RUNX1 was lost. STAT1::STAT2 and IRF motifs were also enriched in the chromatin of retrotransposons that were derepressed in RUNX1-deficient GMPs and neutrophils. We conclude that a major direct effect of RUNX1 loss in GMPs is the derepression of type I IFN and TLR4 signaling, resulting in a state of fixed maladaptive innate immunity.
Collapse
Affiliation(s)
- Alexandra U Zezulin
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel Yen
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Darwin Ye
- Department of Radiation Oncology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth D Howell
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jamie Diemer
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jian-Gang Ren
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mohd Hafiz Ahmad
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Lucio H Castilla
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Ivo P Touw
- Department of Hematology, Erasmus Medical College, Rotterdam 3015CN, the Netherlands
| | - Andy J Minn
- Department of Radiation Oncology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wei Tong
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Oncology and Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Wenbao Yu
- Department of Pediatrics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Division of Oncology and Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Nancy A Speck
- Department of Cell and Developmental Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| |
Collapse
|
4
|
Li W, Liu Z, Wang P, Di R, Wang X, Liu Y, Chu M. The transcription factor RUNX1 affects the maturation of porcine oocytes via the BMP15/TGF-β signaling pathway. Int J Biol Macromol 2023; 238:124026. [PMID: 36933589 DOI: 10.1016/j.ijbiomac.2023.124026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
Bone morphogenetic protein 15 (BMP15) is specifically expressed in oocytes in pigs at all stages from early stages to ovulation and has an important role in oocyte maturation. However, there are few reports on the molecular mechanisms by which BMP15 affects oocyte maturation. In this study, we identified the core promoter region of BMP15 using a dual luciferase activity assay and successfully predicted the DNA binding motif of the transcription factor RUNX1. The effect of BMP15 and RUNX1 on oocyte maturation was examined using the first polar body extrusion rate, a reactive oxygen species (ROS) assay and total glutathione (GSH) content at three time points of 12, 24 and 48 h of in vitro culture of porcine isolated oocytes. Subsequently, the effect of the transcription factor RUNX1 on the TGF-β signaling pathway (BMPR1B and ALK5) was further verified using RT-qPCR and Western blotting. We found that the overexpression of BMP15 significantly increased the first polar body extrusion rate (P < 0.01) and total glutathione content of oocytes cultured in vitro for 24 h and decreased reactive oxygen levels (P < 0.01), whereas interference with BMP15 decreased the first polar body extrusion rate (P < 0.01), increased reactive oxygen levels in oocytes cultured in vitro for 24 h (P < 0.01), and decreased glutathione content (P < 0.01). The dual luciferase activity assay and online software prediction showed that RUNX1 is a potential transcription factor binding to the core promoter region (-1203/-1423 bp) of BMP15. Overexpression of RUNX1 significantly increased the expression of BMP15 and oocyte maturation rate, while inhibition of RUNX1 decreased the expression of BMP15 and the oocyte maturation rate. Moreover, the expression of BMPR1B and ALK5 in the TGF-β signaling pathway increased significantly after overexpression of RUNX1, whereas their expression decreased after inhibition of RUNX1. Overall, our results suggest that the transcription factor RUNX1 positively regulates the expression of BMP15 and influences oocyte maturation through the TGF-β signaling pathway. This study provides a theoretical basis for further complementing the BMP15/TGF-β signaling pathway to regulate mammalian oocyte maturation.
Collapse
Affiliation(s)
- Wentao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ziyi Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Peng Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
5
|
Zezulin AU, Ye D, Howell E, Yen D, Bresciani E, Diemer J, Ren JG, Ahmad MH, Castilla LH, Touw IP, Minn AJ, Tong W, Liu PP, Tan K, Yu W, Speck NA. RUNX1 is required in granulocyte-monocyte progenitors to attenuate inflammatory cytokine production by neutrophils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525911. [PMID: 36747636 PMCID: PMC9900925 DOI: 10.1101/2023.01.27.525911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The transcription factor RUNX1 is mutated in familial platelet disorder with associated myeloid malignancies (FPDMM) and in sporadic myelodysplastic syndrome and leukemia. RUNX1 regulates inflammation in multiple cell types. Here we show that RUNX1 is required in granulocyte-monocyte progenitors (GMPs) to restrict the inflammatory response of neutrophils to toll-like receptor 4 (TLR4) signaling. Loss of RUNX1 in GMPs increased the TLR4 coreceptor CD14 on neutrophils, which contributed to neutrophils’ increased inflammatory cytokine production in response to the TLR4 ligand lipopolysaccharide. RUNX1 loss increased the chromatin accessibility of retrotransposons in GMPs and neutrophils and induced a type I interferon signature characterized by enriched footprints for signal transducer and activator of transcription (STAT1::STAT2) and interferon regulatory factors (IRF) in opened chromatin, and increased expression of interferon-stimulated genes. The overproduction of inflammatory cytokines by neutrophils was reversed by inhibitors of type I IFN signaling. We conclude that RUNX1 restrains the chromatin accessibility of retrotransposons in GMPs and neutrophils, and that loss of RUNX1 increases proinflammatory cytokine production by elevating tonic type I interferon signaling.
Collapse
|
6
|
Jahanimoghadam A, Abdolahzadeh H, Rad NK, Zahiri J. Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: An Integrated Bioinformatics Analysis. J Mol Neurosci 2022; 72:2326-2337. [PMID: 36301487 PMCID: PMC9607846 DOI: 10.1007/s12031-022-02068-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has emerged since December 2019 and was later characterized as a pandemic by WHO, imposing a major public health threat globally. Our study aimed to identify common signatures from different biological levels to enlighten the current unclear association between COVID-19 and Parkinson's disease (PD) as a number of possible links, and hypotheses were reported in the literature. We have analyzed transcriptome data from peripheral blood mononuclear cells (PBMCs) of both COVID-19 and PD patients, resulting in a total of 81 common differentially expressed genes (DEGs). The functional enrichment analysis of common DEGs are mostly involved in the complement system, type II interferon gamma (IFNG) signaling pathway, oxidative damage, microglia pathogen phagocytosis pathway, and GABAergic synapse. The protein-protein interaction network (PPIN) construction was carried out followed by hub detection, revealing 10 hub genes (MX1, IFI27, C1QC, C1QA, IFI6, NFIX, C1S, XAF1, IFI35, and ELANE). Some of the hub genes were associated with molecular mechanisms such as Lewy bodies-induced inflammation, microglia activation, and cytokine storm. We investigated regulatory elements of hub genes at transcription factor and miRNA levels. The major transcription factors regulating hub genes are SOX2, XAF1, RUNX1, MITF, and SPI1. We propose that these events may have important roles in the onset or progression of PD. To sum up, our analysis describes possible mechanisms linking COVID-19 and PD, elucidating some unknown clues in between.
Collapse
Affiliation(s)
- Aria Jahanimoghadam
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, Würzburg, Germany
| | - Hadis Abdolahzadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Niloofar Khoshdel Rad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Javad Zahiri
- Department of Neuroscience, University of California San Diego, La Jolla, San Diego, CA, USA.
| |
Collapse
|
7
|
Genetic dissection of TLR9 reveals complex regulatory and cryptic proinflammatory roles in mouse lupus. Nat Immunol 2022; 23:1457-1469. [PMID: 36151396 PMCID: PMC9561083 DOI: 10.1038/s41590-022-01310-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 08/08/2022] [Indexed: 02/04/2023]
Abstract
In lupus, Toll-like receptor 7 (TLR7) and TLR9 mediate loss of tolerance to RNA and DNA, respectively. Yet, TLR7 promotes disease, while TLR9 protects from disease, implying differences in signaling. To dissect this 'TLR paradox', we generated two TLR9 point mutants (lacking either ligand (TLR9K51E) or MyD88 (TLR9P915H) binding) in lupus-prone MRL/lpr mice. Ameliorated disease of Tlr9K51E mice compared to Tlr9-/- controls revealed a TLR9 'scaffold' protective function that is ligand and MyD88 independent. Unexpectedly, Tlr9P915H mice were more protected than both Tlr9K51E and Tlr9WT mice, suggesting that TLR9 also possesses ligand-dependent, but MyD88-independent, regulatory signaling and MyD88-mediated proinflammatory signaling. Triple-mixed bone marrow chimeras showed that TLR9-MyD88-independent regulatory roles were B cell intrinsic and restrained differentiation into pathogenic age-associated B cells and plasmablasts. These studies reveal MyD88-independent regulatory roles of TLR9, shedding light on the biology of endosomal TLRs.
Collapse
|