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Bataclan M, Leoni C, Moro SG, Pecoraro M, Wong EH, Heissmeyer V, Monticelli S. Crosstalk between Regnase-1 and -3 shapes mast cell survival and cytokine expression. Life Sci Alliance 2024; 7:e202402784. [PMID: 38830770 PMCID: PMC11147952 DOI: 10.26508/lsa.202402784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Post-transcriptional regulation of immune-related transcripts by RNA-binding proteins (RBPs) impacts immune cell responses, including mast cell functionality. Despite their importance in immune regulation, the functional role of most RBPs remains to be understood. By manipulating the expression of specific RBPs in murine mast cells, coupled with mass spectrometry and transcriptomic analyses, we found that the Regnase family of proteins acts as a potent regulator of mast cell physiology. Specifically, Regnase-1 is required to maintain basic cell proliferation and survival, whereas both Regnase-1 and -3 cooperatively regulate the expression of inflammatory transcripts upon activation, with Tnf being a primary target in both human and mouse cells. Furthermore, Regnase-3 directly interacts with Regnase-1 in mast cells and is necessary to restrain Regnase-1 expression through the destabilization of its transcript. Overall, our study identifies protein interactors of endogenously expressed Regnase factors, characterizes the regulatory interplay between Regnase family members in mast cells, and establishes their role in the control of mast cell homeostasis and inflammatory responses.
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Affiliation(s)
- Marian Bataclan
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Cristina Leoni
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Simone G Moro
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Matteo Pecoraro
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Elaine H Wong
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Monticelli
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
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2
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Bai X, Gao J, Guan X, Narum DE, Fornis LB, Griffith DE, Gao B, Sandhaus RA, Huang H, Chan ED. Analysis of alpha-1-antitrypsin (AAT)-regulated, glucocorticoid receptor-dependent genes in macrophages reveals a novel host defense function of AAT. Physiol Rep 2024; 12:e16124. [PMID: 39016119 PMCID: PMC11252833 DOI: 10.14814/phy2.16124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Alpha-1-antitrypsin (AAT) plays a homeostatic role in attenuating excessive inflammation and augmenting host defense against microbes. We demonstrated previously that AAT binds to the glucocorticoid receptor (GR) resulting in significant anti-inflammatory and antimycobacterial consequences in macrophages. Our current investigation aims to uncover AAT-regulated genes that rely on GR in macrophages. We incubated control THP-1 cells (THP-1control) and THP-1 cells knocked down for GR (THP-1GR-KD) with AAT, performed bulk RNA sequencing, and analyzed the findings. In THP-1control cells, AAT significantly upregulated 408 genes and downregulated 376 genes. Comparing THP-1control and THP-1GR-KD cells, 125 (30.6%) of the AAT-upregulated genes and 154 (41.0%) of the AAT-downregulated genes were significantly dependent on GR. Among the AAT-upregulated, GR-dependent genes, CSF-2 that encodes for granulocyte-monocyte colony-stimulating factor (GM-CSF), known to be host-protective against nontuberculous mycobacteria, was strongly upregulated by AAT and dependent on GR. We further quantified the mRNA and protein of several AAT-upregulated, GR-dependent genes in macrophages and the mRNA of several AAT-downregulated, GR-dependent genes. We also discussed the function(s) of selected AAT-regulated, GR-dependent gene products largely in the context of mycobacterial infections. In conclusion, AAT regulated several genes that are dependent on GR and play roles in host immunity against mycobacteria.
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Affiliation(s)
- Xiyuan Bai
- Department of MedicineRocky Mountain Regional Veterans Affairs Medical CenterAuroraColoradoUSA
- Department of Academic AffairsNational Jewish HealthDenverColoradoUSA
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Junfeng Gao
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
| | - Xiaoyu Guan
- Department of Biostatistics and InformaticsUniversity of Colorado School of Public Health Anschutz Medical CampusAuroraColoradoUSA
| | - Drew E. Narum
- Department of Academic AffairsNational Jewish HealthDenverColoradoUSA
| | | | - David E. Griffith
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of MedicineNational Jewish HealthDenverColoradoUSA
| | - Bifeng Gao
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Robert A. Sandhaus
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
- Department of MedicineNational Jewish HealthDenverColoradoUSA
| | - Hua Huang
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
- Department of Immunology and MicrobiologyUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Edward D. Chan
- Department of MedicineRocky Mountain Regional Veterans Affairs Medical CenterAuroraColoradoUSA
- Department of Academic AffairsNational Jewish HealthDenverColoradoUSA
- Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
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3
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Zhang M, Yang J, Yuan Y, Zhou Y, Wang Y, Cui R, Maliu Y, Xu F, Wu X. Recruitment or activation of mast cells in the liver aggravates the accumulation of fibrosis in carbon tetrachloride-induced liver injury. Mol Immunol 2024; 170:60-75. [PMID: 38626622 DOI: 10.1016/j.molimm.2024.04.009] [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: 12/14/2023] [Revised: 03/31/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Abstract
Liver diseases caused by viral infections, alcoholism, drugs, or chemical poisons are a significant health problem: Liver diseases are a leading contributor to mortality, with approximately 2 million deaths per year worldwide. Liver fibrosis, as a common liver disease characterized by excessive collagen deposition, is associated with high morbidity and mortality, and there is no effective treatment. Numerous studies have shown that the accumulation of mast cells (MCs) in the liver is closely associated with liver injury caused by a variety of factors. This study investigated the relationship between MCs and carbon tetrachloride (CCl4)-induced liver fibrosis in rats and the effects of the MC stabilizers sodium cromoglycate (SGC) and ketotifen (KET) on CCl4-induced liver fibrosis. The results showed that MCs were recruited or activated during CCl4-induced liver fibrosis. Coadministration of SCG or KET alleviated the liver fibrosis by decreasing SCF/c-kit expression, inhibiting the TGF-β1/Smad2/3 pathway, depressing the HIF-1a/VEGF pathway, activating Nrf2/HO-1 pathway, and increasing the hepatic levels of GSH, GSH-Px, and GR, thereby reducing hepatic oxidative stress. Collectively, recruitment or activation of MCs is linked to liver fibrosis and the stabilization of MCs may provide a new approach to the prevention of liver fibrosis.
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Affiliation(s)
- Mingkang Zhang
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Jinru Yang
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yufan Yuan
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Yan Zhou
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Yazhi Wang
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Ruirui Cui
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Yimai Maliu
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Fen Xu
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China
| | - Xin'an Wu
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou 730000, China; School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Engineering Research Centre of Prevention and Control for Clinical Medication Risk, Gansu Province, China.
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4
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Miyake K, Ito J, Karasuyama H. Novel insights into the ontogeny of basophils. FRONTIERS IN ALLERGY 2024; 5:1402841. [PMID: 38803659 PMCID: PMC11128600 DOI: 10.3389/falgy.2024.1402841] [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: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024] Open
Abstract
Basophils are the least common granulocytes, accounting for <1% of peripheral blood leukocytes. In the last 20 years, analytical tools for mouse basophils have been developed, and we now recognize that basophils play critical roles in various immune reactions, including the development of allergic inflammation and protective immunity against parasites. Moreover, the combined use of flow cytometric analyses and knockout mice has uncovered several progenitor cells committed to basophils in mice. Recently, advancements in single-cell RNA sequencing (scRNA-seq) technologies have challenged the classical view of the differentiation of various hematopoietic cell lineages. This is also true for basophil differentiation, and studies using scRNA-seq analysis have provided novel insights into basophil differentiation, including the association of basophil differentiation with that of erythrocyte/megakaryocyte and the discovery of novel basophil progenitor cells in the mouse bone marrow. In this review, we summarize the recent findings of basophil ontogeny in both mice and humans, mainly focusing on studies using scRNA-seq analyses.
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Affiliation(s)
- Kensuke Miyake
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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5
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Park SY, Lee YY, Kim MH, Kim CE. Deciphering the Systemic Impact of Herbal Medicines on Allergic Rhinitis: A Network Pharmacological Approach. Life (Basel) 2024; 14:553. [PMID: 38792575 PMCID: PMC11122645 DOI: 10.3390/life14050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Allergic rhinitis (AR) is a systemic allergic disease that has a considerable impact on patients' quality of life. Current treatments include antihistamines and nasal steroids; however, their long-term use often causes undesirable side effects. In this context, traditional Asian medicine (TAM), with its multi-compound, multi-target herbal medicines (medicinal plants), offers a promising alternative. However, the complexity of these multi-compound traits poses challenges in understanding the overall mechanisms and efficacy of herbal medicines. Here, we demonstrate the efficacy and underlying mechanisms of these multi-compound herbal medicines specifically used for AR at a systemic level. We utilized a modified term frequency-inverse document frequency method to select AR-specific herbs and constructed an herb-compound-target network using reliable databases and computational methods, such as the Quantitative Estimate of Drug-likeness for compound filtering, STITCH database for compound-target interaction prediction (with a high confidence score threshold of 0.7), and DisGeNET and CTD databases for disease-gene association analysis. Through this network, we conducted AR-related targets and pathway analyses, as well as clustering analysis based on target-level information of the herbs. Gene ontology enrichment analysis was conducted using a protein-protein interaction network. Our research identified 14 AR-specific herbs and analyzed whether AR-specific herbs are highly related to previously known AR-related genes and pathways. AR-specific herbs were found to target several genes related to inflammation and AR pathogenesis, such as PTGS2, HRH1, and TBXA2R. Pathway analysis revealed that AR-specific herbs were associated with multiple AR-related pathways, including cytokine signaling, immune response, and allergic inflammation. Additionally, clustering analysis based on target similarity identified three distinct subgroups of AR-specific herbs, corroborated by a protein-protein interaction network. Group 1 herbs were associated with the regulation of inflammatory responses to antigenic stimuli, while Group 2 herbs were related to the detection of chemical stimuli involved in the sensory perception of bitter taste. Group 3 herbs were distinctly associated with antigen processing and presentation and NIK/NF-kappa B signaling. This study decodes the principles of TAM herbal configurations for AR using a network pharmacological approach, providing a holistic understanding of drug effects beyond specific pathways.
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Affiliation(s)
- Sa-Yoon Park
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Yoon Yeol Lee
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea
| | - Min Hee Kim
- Department of Ophthalmology, Otolaryngology, and Dermatology, Kyung Hee University College of Korean Medicine, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea
| | - Chang-Eop Kim
- Department of Physiology, College of Korean Medicine, Gachon University, Seongnam 13120, Republic of Korea
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6
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Ammons DT, Hopkins LS, Cronise KE, Kurihara J, Regan DP, Dow S. Single-cell RNA sequencing reveals the cellular and molecular heterogeneity of treatment-naïve primary osteosarcoma in dogs. Commun Biol 2024; 7:496. [PMID: 38658617 PMCID: PMC11043452 DOI: 10.1038/s42003-024-06182-w] [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: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Osteosarcoma (OS) is a heterogeneous, aggressive malignancy of the bone that disproportionally affects children and adolescents. Therapeutic interventions for OS are limited, which is in part due to the complex tumor microenvironment (TME). As such, we used single-cell RNA sequencing (scRNA-seq) to describe the cellular and molecular composition of the TME in 6 treatment-naïve dogs with spontaneously occurring primary OS. Through analysis of 35,310 cells, we identified 41 transcriptomically distinct cell types including the characterization of follicular helper T cells, mature regulatory dendritic cells (mregDCs), and 8 tumor-associated macrophage (TAM) populations. Cell-cell interaction analysis predicted that mregDCs and TAMs play key roles in modulating T cell mediated immunity. Furthermore, we completed cross-species cell type gene signature homology analysis and found a high degree of similarity between human and canine OS. The data presented here act as a roadmap of canine OS which can be applied to advance translational immuno-oncology research.
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Affiliation(s)
- Dylan T Ammons
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Leone S Hopkins
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kathryn E Cronise
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jade Kurihara
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Daniel P Regan
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven Dow
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
- Flint Animal Cancer Center, Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
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7
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Toennesen B, Schmid JM, Sørensen BS, Fricker M, Hoffmann HJH. A five-gene qPCR signature can classify type 2 asthma comparably to microscopy of induced sputum from severe asthma patients. Eur Clin Respir J 2023; 11:2293318. [PMID: 38178813 PMCID: PMC10763913 DOI: 10.1080/20018525.2023.2293318] [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: 08/14/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024] Open
Abstract
Asthma is a heterogenous disease characterized by airway inflammation and variable expiratory airflow limitation resulting in variable respiratory symptoms. Characterization of airway inflammation is important to choose the optimal treatment for severe asthma patients eligible for biological treatment. However, counting cells in induced sputum samples are a time-consuming process, highly dependent on personal skills. Replacing eosinophil and neutrophil cell counting with qPCR for transcripts of selected mast cell, and basophil genes may provide more reproducible results. Aims The objective of this study was to compare qPCR with microscopy in asthma endotyping. Methods A qPCR method measuring five mast cell/basophil genes was applied on induced sputum samples from 30 severe asthma patients and compared with microscopy. Target gene Ct-values (CPA3, GATA2, HDC, MS4A2, TPSAB1/TPSB2) were referenced to household β-actin Ct values as a measure of relative mRNA abundance of the target in each sample. Target/β-actin-ratios in eosinophilic and non-eosinophilic groups determined by microscopy with an eosinophil threshold of 3% in 400 cells were compared using Mann-Whitney U Test. Spearman´s correlations were used to test for correlation between targets vs. FENO and targets vs. blood eosinophil counts. Results The study demonstrated a statistical difference in relative mRNA abundance for four mast cell/basophil specific genes. CPA3, GATA2, HDC and MS4A2 were elevated in eosinophilic asthma versus non-eosinophilic asthma patients. The study found that GATA2, CPA3, MS4A2 and TPSAB1/TPSB2 transcripts are positively correlated with FENO. Neither the five mast cell genes nor the five-gene signature correlated with blood eosinophils. The five-gene signature with a target/β-actin-ratio cut-off ≥2 generated sensitivity = 87%, specificity = 94%, NPV = 88% and PPV = 92% compared to microscopy. Conclusion This study confirms the contribution of mast cells in the pathogenesis of EA and suggests that mast cell mRNA markers could be one of the biomarkers used to identify EA.
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Affiliation(s)
- B. Toennesen
- Department of Clinical Medicine, Aarhus University & Department of Respiratory Diseases and Allergy, Aarhus, Denmark
| | - J. M. Schmid
- Department of Clinical Medicine, Aarhus University & Department of Respiratory Diseases and Allergy, Aarhus, Denmark
| | - B. S. Sørensen
- Department of Clinical Medicine, Aarhus University & Department of Clinical Biochemistry, Aarhus, Denmark
| | - M. Fricker
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, NSW, Australia & Hunter Medical Research Institute, New Lambton Heights, NSW, Australia, Newcastle, Australia
| | - H. J. H. Hoffmann
- Department of Clinical Medicine, Aarhus University & Department of Respiratory Diseases and Allergy, Aarhus, Denmark
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8
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Schaefer MA, Roy P, Chava S, Meyerson A, Duncan AL, Chee L, Hewitt KJ. Physiological and regenerative functions of sterile-α motif protein-14 in hematopoiesis. Exp Hematol 2023; 128:38-47. [PMID: 37722652 PMCID: PMC10947990 DOI: 10.1016/j.exphem.2023.09.003] [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: 08/29/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Sterile α-motif domain-14 (Samd14) protein expression increases the regenerative capacity of the erythroid system. Samd14 is transcriptionally upregulated and promotes cell signaling via the receptor tyrosine kinase Kit in a critical window of acute erythroid regeneration. We generated a hematopoietic-specific conditional Samd14 knockout mouse model (Samd14-CKO) to study the role of Samd14 in hematopoiesis. The Samd14-CKO mouse was viable and exhibited no steady-state hematopoietic phenotype. Samd14-CKO mice were hypersensitive to 5-fluorouracil, resulting in more severe anemia during recovery and impaired erythroid progenitor colony formation. Ex vivo, Samd14-CKO hematopoietic progenitors were defective in their ability to form mast cells. Samd14-CKO mast cells exhibited altered Kit/stem cell factor (SCF), IL-3/IL-3R signaling, and less granularity than Samd14-FL/FL cells. Our findings indicate that Samd14 promotes both erythroid and mast cell functions. The Samd14-CKO mouse phenotype exhibits striking similarities to the KitW/W-v mice, which carry Kit mutations resulting in reduced tyrosine kinase-dependent signaling, causing mast cell and erythroid abnormalities. The Samd14-CKO mouse model is a new tool for studying hematologic pathologies involving Kit signaling.
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Affiliation(s)
- Meg A Schaefer
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Pooja Roy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Srinivas Chava
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Ainsley Meyerson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Andrew L Duncan
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Linda Chee
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE
| | - Kyle J Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE.
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9
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Gao J, Li Y, Guan X, Mohammed Z, Gomez G, Hui Y, Zhao D, Oskeritzian CA, Huang H. IL-33 priming and antigenic stimulation synergistically promote the transcription of proinflammatory cytokine and chemokine genes in human skin mast cells. BMC Genomics 2023; 24:592. [PMID: 37798647 PMCID: PMC10557204 DOI: 10.1186/s12864-023-09702-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Antigenic stimulation through cross-linking the IgE receptor and epithelial cell-derived cytokine IL-33 are potent stimuli of mast cell (MC) activation. Moreover, IL-33 primes a variety of cell types, including MCs to respond more vigorously to external stimuli. However, target genes induced by the combined IL-33 priming and antigenic stimulation have not been investigated in human skin mast cells (HSMCs) in a genome-wide manner. Furthermore, epigenetic changes induced by the combined IL-33 priming and antigenic stimulation have not been evaluated. RESULTS We found that IL-33 priming of HSMCs enhanced their capacity to promote transcriptional synergy of the IL1B and CXCL8 genes by 16- and 3-fold, respectively, in response to combined IL-33 and antigen stimulation compared to without IL-33 priming. We identified the target genes in IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation using RNA sequencing (RNA-seq). We found that the majority of genes synergistically upregulated in the IL-33-primed HSMCs in response to the combined IL-33 and antigenic stimulation were predominantly proinflammatory cytokine and chemokine genes. Moreover, the combined IL-33 priming and antigenic stimulation increase chromatin accessibility in the synergy target genes but not synergistically. Transcription factor binding motif analysis revealed more binding sites for NF-κB, AP-1, GABPA, and RAP1 in the induced or increased chromatin accessible regions of the synergy target genes. CONCLUSIONS Our study demonstrates that IL-33 priming greatly potentiates MCs' ability to transcribe proinflammatory cytokine and chemokine genes in response to antigenic stimulation, shining light on how epithelial cell-derived cytokine IL-33 can cause exacerbation of skin MC-mediated allergic inflammation.
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Affiliation(s)
- Junfeng Gao
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Yapeng Li
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Xiaoyu Guan
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Zahraa Mohammed
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
- College of Medicine, AI-Mustansiriyah University, Baghdad, Iraq
| | - Gregorio Gomez
- Department of Biomedical Sciences, University of Houston College of Medicine, Houston, TX, USA
| | - Yvonne Hui
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Dianzheng Zhao
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
| | - Carole A Oskeritzian
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA.
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, CO, USA.
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10
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Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, John Wherry E, Sidoli S, Maillard I, Vahedi G. Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. Nat Immunol 2023; 24:1698-1710. [PMID: 37592014 PMCID: PMC10919931 DOI: 10.1038/s41590-023-01599-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 08/19/2023]
Abstract
In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.
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Affiliation(s)
- Naomi Goldman
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Isabelle Johnson
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Matthew A Sullivan
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Ashley Vanderbeck
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Atishay Jay
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Yeqiao Zhou
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Emily K Ferrari
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Leland Mayne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Jennifer Aguilan
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA
- New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA
| | - Robert B Faryabi
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA
| | - Ivan Maillard
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
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Ammons D, Hopkins L, Cronise K, Kurihara J, Regan D, Dow S. Single-cell RNA sequencing reveals the cellular and molecular heterogeneity of treatment-naïve primary osteosarcoma in dogs. RESEARCH SQUARE 2023:rs.3.rs-3232360. [PMID: 37609233 PMCID: PMC10441479 DOI: 10.21203/rs.3.rs-3232360/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Osteosarcoma (OS) is a heterogeneous, aggressive malignancy of the bone that disproportionally affects children and adolescents. Therapeutic interventions for OS are limited, which is in part due to the complex tumor microenvironment (TME) that has proven to be refractory to immunotherapies. Thus, there is a need to better define the complexity of the OS TME. To address this need, we used single-cell RNA sequencing (scRNA-seq) to describe the cellular and molecular composition of the TME in 6 treatment-naïve dogs with spontaneously occurring primary OS. Through analysis of 35,310 cells, we identified 30 distinct immune cell types, 9 unique tumor populations, 1 cluster of fibroblasts, and 1 cluster of endothelial cells. Independent reclustering of major cell types revealed the presence of follicular helper T cells, mature regulatory dendritic cells (mregDCs), and 8 transcriptomically distinct macrophage/monocyte populations. Cell-cell interaction inference analysis predicted that mregDCs and tumor-associated macrophages (TAMs) play key roles in modulating T cell mediate immunity. Furthermore, we used publicly available human OS scRNA-seq data to complete a cross-species cell type gene signature homology analysis. The analysis revealed a high degree of cell type gene signature homology between species, suggesting the cellular composition of OS is largely conserved between humans and dogs. Our findings provide key new insights into the biology of canine OS and highlight the conserved features of OS across species. Generally, the data presented here acts as a cellular and molecular roadmap of canine OS which can be applied to advance the translational immuno-oncology research field.
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12
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Yang X, Zhang Q, Li S, Devarajan R, Luo B, Tan Z, Wang Z, Giannareas N, Wenta T, Ma W, Li Y, Yang Y, Manninen A, Wu S, Wei GH. GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression. J Exp Clin Cancer Res 2023; 42:198. [PMID: 37550764 PMCID: PMC10408074 DOI: 10.1186/s13046-023-02745-7] [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: 01/21/2023] [Accepted: 06/30/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Aberrant somatic genomic alteration including copy number amplification is a hallmark of cancer genomes. We previously profiled genomic landscapes of prostate cancer (PCa), yet the underlying causal genes with prognostic potential has not been defined. It remains unclear how a somatic genomic event cooperates with inherited germline variants contribute to cancer predisposition and progression. METHODS We applied integrated genomic and clinical data, experimental models and bioinformatic analysis to identify GATA2 as a highly prevalent metastasis-associated genomic amplification in PCa. Biological roles of GATA2 in PCa metastasis was determined in vitro and in vivo. Global chromatin co-occupancy and co-regulation of GATA2 and SMAD4 was investigated by coimmunoprecipitation, ChIP-seq and RNA-seq assays. Tumor cellular assays, qRT-PCR, western blot, ChIP, luciferase assays and CRISPR-Cas9 editing methods were performed to mechanistically understand the cooperation of GATA2 with SMAD4 in promoting TGFβ1 and AR signaling and mediating inherited PCa risk and progression. RESULTS In this study, by integrated genomics and experimental analysis, we identified GATA2 as a prevalent metastasis-associated genomic amplification to transcriptionally augment its own expression in PCa. Functional experiments demonstrated that GATA2 physically interacted and cooperated with SMAD4 for genome-wide chromatin co-occupancy and co-regulation of PCa genes and metastasis pathways like TGFβ signaling. Mechanistically, GATA2 was cooperative with SMAD4 to enhance TGFβ and AR signaling pathways, and activated the expression of TGFβ1 via directly binding to a distal enhancer of TGFβ1. Strinkingly, GATA2 and SMAD4 globally mediated inherited PCa risk and formed a transcriptional complex with HOXB13 at the PCa risk-associated rs339331/6q22 enhancer, leading to increased expression of the PCa susceptibility gene RFX6. CONCLUSIONS Our study prioritizes causal genomic amplification genes with prognostic values in PCa and reveals the pivotal roles of GATA2 in transcriptionally activating the expression of its own and TGFβ1, thereby co-opting to TGFβ1/SMAD4 signaling and RFX6 at 6q22 to modulate PCa predisposition and progression.
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Affiliation(s)
- Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Shuxuan Li
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Raman Devarajan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Binjie Luo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zixian Wang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tomasz Wenta
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wenlong Ma
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China.
- Institute of Urology, South China Hospital of Shenzhen University, Shenzhen, China.
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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13
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Li Y, Gao J, Zhao D, Guan X, Morris SC, Finkelman FD, Huang H. The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis. J Allergy Clin Immunol 2023; 152:195-204.e3. [PMID: 36804390 PMCID: PMC10330076 DOI: 10.1016/j.jaci.2023.01.031] [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: 06/30/2022] [Revised: 12/06/2022] [Accepted: 01/09/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Histamine is a critical mediator of anaphylaxis, a neurotransmitter, and a regulator of gastric acid secretion. Histidine decarboxylase is a rate-limiting enzyme for histamine synthesis. However, in vivo regulation of Hdc, the gene that encodes histidine decarboxylase, is poorly understood. OBJECTIVE We sought to investigate how enhancers regulate Hdc gene transcription and histamine synthesis in resting conditions and in a mouse model of anaphylaxis. METHODS H3K27 acetylation histone modification and chromatin accessibility were used to identify candidate enhancers. The enhancer activity of candidate enhancers was measured in a reporter gene assay, and the function enhancers were validated by CRISPR deletion. RESULTS Deletion of the GC box, which binds to zinc finger transcription factors, in the proximal Hdc enhancer reduced Hdc gene transcription and histamine synthesis in mouse and human mast cell lines. Mast cells, basophils, brain cells, and stomach cells from GC box-deficient mice transcribed the Hdc gene much less than similar cells from wild-type mice, and Hdc GC box-deficient mice failed to develop anaphylaxis. CONCLUSION The HDC GC box within the proximal enhancer in the mouse and human HDC gene is essential for Hdc gene transcription, histamine synthesis, and histamine-mediated anaphylaxis in vitro and in vivo.
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Affiliation(s)
- Yapeng Li
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colo
| | - Junfeng Gao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colo
| | - Dianzheng Zhao
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colo
| | - Xiaoyu Guan
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colo
| | - Suzanne C Morris
- Department of Medicine, Division of Immunology, Allergy, and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Fred D Finkelman
- Department of Medicine, Division of Immunology, Allergy, and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colo; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colo.
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14
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Tang RY, Yin L, Yao L, Zhang QF, Chen XP. A Co-Expressed Natural Antisense RNA FCER1A-AS Controls IgE-Dependent Immunity by Promoting Expression of FcεRIα. Microbiol Spectr 2023; 11:e0073323. [PMID: 37154775 PMCID: PMC10269606 DOI: 10.1128/spectrum.00733-23] [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: 02/17/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
As the α-subunit of the high-affinity receptor for the Fc portion of immunoglobulin E (FcεRIα), FcεRIα plays a central role in IgE-mediated allergic disorders and in the immunity and immunopathology of some parasitic infections. FcεRIα is specifically expressed on basophils and mast cells, but the mechanism that controls FcεRIα expression in these cells is poorly understood. In this study, we found that the natural antisense transcript (NAT) of FcεRIα (FCER1A-AS) is co-expressed with the sense transcript (FCER1A-S) in both interleukin (IL)-3-induced FcεRIα-expressing cells and in the high FcεRIα-expressing cell line MC/9. When FCER1A-AS is selectively knocked down by the CRISPR/RfxCas13d (CasRx) approach in MC/9 cells, the expression of both FCER1A-S mRNA and proteins is markedly decreased. Furthermore, FCER1A-AS deficiency was also found to be associated with a lack of FCER1A-S expression in vivo. Correspondingly, homozygous mice deficient in FCER1A-AS demonstrated a similar phenotype to FCER1A knockout mice in Schistosoma japonicum infection and in IgE-FcεRIα-mediated cutaneous anaphylaxis. Thus, we uncovered a novel pathway for the control of FcεRIα expression by its co-expressed natural antisense transcript. IMPORTANCE FcεRIα is responsible for high-affinity binding with the Fc portion of IgE, which is critical for IgE-dependent disease responses such as allergy responses and anti-parasite immunity. FcεRIα is expressed on a few cell types, including mast cells and basophils. Although the expression of FcεRIα is known to be promoted by the IL-3-GATA-2 pathway during its differentiation, the mechanism by which FcεRIα expression is maintained remains unknown. In this study, we discovered that a natural antisense transcript, FCER1A-AS, is co-expressed with the sense transcript. The presence of FCER1A-AS is essential for sense transcript expression in mast cells and basophils, but not for the differentiation of these cells through cis-regulation. Like FcεRIα knockout mice, mice lacking FCER1A-AS also exhibit reduced survival after Schistosoma japonicum infection and a lack of IgE-mediated cutaneous anaphylaxis. Thus, a novel pathway for regulating IgE-mediated allergic diseases through noncoding RNAs has been revealed.
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Affiliation(s)
- Ruo-yu Tang
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Lan Yin
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Liang Yao
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Qing-Feng Zhang
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
| | - Xiao-Ping Chen
- Department of Microbiology and Immunology, School of Medicine, Tongji University, Shanghai, China
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15
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Yuan XQ, Zhou N, Wang JP, Yang XZ, Wang S, Zhang CY, Li GC, Peng L. Anchoring super-enhancer-driven oncogenic lncRNAs for anti-tumor therapy in hepatocellular carcinoma. Mol Ther 2023; 31:1756-1774. [PMID: 36461633 PMCID: PMC10277835 DOI: 10.1016/j.ymthe.2022.11.013] [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: 08/18/2021] [Revised: 10/19/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Super-enhancer (SE) plays a vital role in the determination of cell identity and fate. Up-regulated expression of coding genes is frequently associated with SE. However, the transcription dysregulation driven by SE, from the viewpoint of long non-coding RNA (lncRNA), remains unclear. Here, SE-associated lncRNAs in HCC are comprehensively outlined for the first time. This study integrally screens and identifies several novel SE-associated lncRNAs that are highly abundant and sensitive to JQ1. Especially, HSAL3 is identified as an uncharacterized SE-driven oncogenic lncRNA, which is activated by transcription factors HCFC1 and HSF1 via its super-enhancer. HSAL3 interference negatively regulates NOTCH signaling, implying the potential mechanism of its tumor-promoting role. The expression of HSAL3 is increased in HCC samples, and higher HSAL3 expression indicates an inferior overall survival of HCC patients. Furthermore, siHSAL3 loaded nanoparticles exert anti-tumor effect on HCC in vitro and in vivo. In conclusion, this is the first comprehensive survey of SE-associated lncRNAs in HCC. HSAL3 is a novel SE-driven oncogenic lncRNA, and siHSAL3 loaded nanoparticles are therapeutic candidates for HCC. This work sheds lights on the merit of anchoring SE-driven oncogenic lncRNAs for HCC treatment.
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Affiliation(s)
- Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, P. R. China
| | - Nan Zhou
- Department of Research, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou 510370, P. R. China
| | - Jun-Pu Wang
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha 410008, P. R. China; Department of Pathology, School of Basic Medicine, Central South University, Changsha 410013, P. R. China
| | - Xian-Zhu Yang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
| | - Shan Wang
- Department of Pathology, Xiang-ya Hospital, Central South University, Changsha 410008, P. R. China; Department of Pathology, School of Basic Medicine, Central South University, Changsha 410013, P. R. China
| | - Chao-Yang Zhang
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Guan-Cheng Li
- Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, Central South University, Changsha 410078, P. R. China; Cancer Research Institute, Central South University, Changsha 410078, P. R. China
| | - Li Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China; Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China.
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16
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Li G, Kang Y, Feng X, Wang G, Yuan Y, Li Z, Du L, Xu B. Dynamic changes of enhancer and super enhancer landscape in degenerated nucleus pulposus cells. Life Sci Alliance 2023; 6:e202201854. [PMID: 37012048 PMCID: PMC10070812 DOI: 10.26508/lsa.202201854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Inflammatory cascade and extracellular matrix remodeling have been identified as pivotal pathological factors in the progression of intervertebral disc degeneration (IDD), but the mechanisms underlying the aberrant activation of transcription during nucleus pulposus (NP) cell degeneration remain elusive. Super-enhancers (SEs) are large clusters of adjacent lone enhancers, which control expression modes of cellular fate and pathogenic genes. Here, we showed that SEs underwent tremendous remodeling during NP cell degeneration and that SE-related transcripts were most abundant in inflammatory cascade and extracellular matrix remodeling processes. Inhibition of cyclin-dependent kinase 7, a transcriptional kinase-mediated transcriptional initiation in trans-acting SE complex, constricted the transcription of inflammatory cascades, and extracellular matrix remodeling-related genes such as IL1β and MMP3 in NP cells, meanwhile, also restrained the transcription of Mmp16, Tnfrsf21, and Il11ra1 to retard IDD in rats. In summary, our findings clarify SEs control the transcription of genes associated with inflammatory cascade and extracellular matrix remodeling during NP cell degeneration and identify inhibition of the cyclin-dependent kinase 7, required for SE-mediated transcriptional activation, as a therapeutic option for IDD.
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Affiliation(s)
- Guowang Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yuxiang Kang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Guohua Wang
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Yue Yuan
- Graduate School of Tianjin Medical University, Tianjin, China
| | - Zhenhua Li
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Lilong Du
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
| | - Baoshan Xu
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin, China
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17
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Chia SL, Kapoor S, Carvalho C, Bajénoff M, Gentek R. Mast cell ontogeny: From fetal development to life-long health and disease. Immunol Rev 2023; 315:31-53. [PMID: 36752151 PMCID: PMC10952628 DOI: 10.1111/imr.13191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mast cells (MCs) are evolutionarily ancient innate immune cells with important roles in protective immunity against bacteria, parasites, and venomous animals. They can be found in most organs of the body, where they also contribute to normal tissue functioning, for example by engaging in crosstalk with nerves. Despite this, they are most widely known for their detrimental roles in allergy, anaphylaxis, and atopic disease. Just like macrophages, mast cells were conventionally thought to originate from the bone marrow. However, they are already present in fetal tissues before the onset of bone marrow hematopoiesis, questioning this dogma. In recent years, our view of myeloid cell ontogeny has been revised. We now know that the first mast cells originate from progenitors made in the extra-embryonic yolk sac, and later get supplemented with mast cells produced from subsequent waves of hematopoiesis. In most connective tissues, sizeable populations of fetal-derived mast cells persist into adulthood, where they self-maintain largely independently from the bone marrow. These developmental origins are highly reminiscent of macrophages, which are known to have critical functions in development. Mast cells too may thus support healthy development. Their fetal origins and longevity also make mast cells susceptible to genetic and environmental perturbations, which may render them pathological. Here, we review our current understanding of mast cell biology from a developmental perspective. We first summarize how mast cell populations are established from distinct hematopoietic progenitor waves, and how they are subsequently maintained throughout life. We then discuss what functions mast cells may normally have at early life stages, and how they may be co-opted to cause, worsen, or increase susceptibility to disease.
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Affiliation(s)
- Shin Li Chia
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Simran Kapoor
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Cyril Carvalho
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Marc Bajénoff
- Centre d'Immunologie de Marseille‐Luminy (CIML)MarseilleFrance
| | - Rebecca Gentek
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
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18
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CREB Is Activated by the SCF/KIT Axis in a Partially ERK-Dependent Manner and Orchestrates Survival and the Induction of Immediate Early Genes in Human Skin Mast Cells. Int J Mol Sci 2023; 24:ijms24044135. [PMID: 36835547 PMCID: PMC9966046 DOI: 10.3390/ijms24044135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/27/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
cAMP response element binding protein (CREB) functions as a prototypical stimulus-inducible transcription factor (TF) that initiates multiple cellular changes in response to activation. Despite pronounced expression in mast cells (MCs), CREB function is surprisingly ill-defined in the lineage. Skin MCs (skMCs) are critical effector cells in acute allergic and pseudo-allergic settings, and they contribute to various chronic dermatoses such as urticaria, atopic dermatitis, allergic contact dermatitis, psoriasis, prurigo, rosacea and others. Using MCs of skin origin, we demonstrate herein that CREB is rapidly phosphorylated on serine-133 upon SCF-mediated KIT dimerization. Phosphorylation initiated by the SCF/KIT axis required intrinsic KIT kinase activity and partially depended on ERK1/2, but not on other kinases such as p38, JNK, PI3K or PKA. CREB was constitutively nuclear, where phosphorylation occurred. Interestingly, ERK did not translocate to the nucleus upon SCF activation of skMCs, but a fraction was present in the nucleus at baseline, and phosphorylation was prompted in the cytoplasm and nucleus in situ. CREB was required for SCF-facilitated survival, as demonstrated with the CREB-selective inhibitor 666-15. Knock-down of CREB by RNA interference duplicated CREB's anti-apoptotic function. On comparison with other modules (PI3K, p38 and MEK/ERK), CREB was equal or more potent at survival promotion. SCF efficiently induces immediate early genes (IEGs) in skMCs (FOS, JUNB and NR4A2). We now demonstrate that CREB is an essential partaker in this induction. Collectively, the ancient TF CREB is a crucial component of skMCs, where it operates as an effector of the SCF/KIT axis, orchestrating IEG induction and lifespan.
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Abstract
Mast cells originate from the CD34+/CD117+ hematopoietic progenitors in the bone marrow, migrate into circulation, and ultimately mature and reside in peripheral tissues. Microbiota/metabolites and certain immune cells (e.g., Treg cells) play a key role in maintaining immune tolerance. Cross-linking of allergen-specific IgE on mast cells activates the high-affinity membrane-bound receptor FcεRI, thereby initiating an intracellular signal cascade, leading to degranulation and release of pro-inflammatory mediators. The intracellular signal transduction is intricately regulated by various kinases, transcription factors, and cytokines. Importantly, multiple signal components in the FcεRI-mast cell–mediated allergic cascade can be targeted for therapeutic purposes. Pharmacological interventions that include therapeutic antibodies against IgE, FcεRI, and cytokines as well as inhibitors/activators of several key intracellular signaling molecues have been used to inhibit allergic reactions. Other factors that are not part of the signal pathway but can enhance an individual’s susceptibility to allergen stimulation are referred to as cofactors. Herein, we provide a mechanistic overview of the FcεRI-mast cell–mediated allergic signaling. This will broaden our scope and visions on specific preventive and therapeutic strategies for the clinical management of mast cell–associated hypersensitivity reactions.
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Babina M, Franke K, Bal G. How "Neuronal" Are Human Skin Mast Cells? Int J Mol Sci 2022; 23:ijms231810871. [PMID: 36142795 PMCID: PMC9505265 DOI: 10.3390/ijms231810871] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Mast cells are evolutionarily old cells and the principal effectors in allergic responses and inflammation. They are seeded from the yolk sac during embryogenesis or are derived from hematopoietic progenitors and are therefore related to other leukocyte subsets, even though they form a separate clade in the hematopoietic system. Herein, we systematically bundle information from several recent high-throughput endeavors, especially those comparing MCs with other cell types, and combine such information with knowledge on the genes’ functions to reveal groups of neuronal markers specifically expressed by MCs. We focus on recent advances made regarding human tissue MCs, but also refer to studies in mice. In broad terms, genes hyper-expressed in MCs, but largely inactive in other myelocytes, can be classified into subcategories such as traffic/lysosomes (MLPH and RAB27B), the dopamine system (MAOB, DRD2, SLC6A3, and SLC18A2), Ca2+-related entities (CALB2), adhesion molecules (L1CAM and NTM) and, as an overall principle, the transcription factors and modulators of transcriptional activity (LMO4, PBX1, MEIS2, and EHMT2). Their function in MCs is generally unknown but may tentatively be deduced by comparison with other systems. MCs share functions with the nervous system, as they express typical neurotransmitters (histamine and serotonin) and a degranulation machinery that shares features with the neuronal apparatus at the synapse. Therefore, selective overlaps are plausible, and they further highlight the uniqueness of MCs within the myeloid system, as well as when compared with basophils. Apart from investigating their functional implications in MCs, a key question is whether their expression in the lineage is due to the specific reactivation of genes normally silenced in leukocytes or whether the genes are not switched off during mastocytic development from early progenitors.
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Affiliation(s)
- Magda Babina
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
- Correspondence:
| | - Kristin Franke
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Gürkan Bal
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Immunology and Allergology IA, 12203 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Institute of Allergology, Hindenburgdamm 30, 12203 Berlin, Germany
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21
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Kee MZ, Teh AL, Clappison A, Pokhvisneva I, MacIssac JL, Lin DT, Ramadori KE, Broekman BF, Chen H, Daniel ML, Karnani N, Kobor MS, Gluckman PD, Chong YS, Huang JY, Meaney MJ. Fetal sex-specific epigenetic associations with prenatal maternal depressive symptoms. iScience 2022; 25:104860. [PMID: 36046194 PMCID: PMC9421382 DOI: 10.1016/j.isci.2022.104860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/14/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Prenatal maternal mental health is a global health challenge with poorly defined biological mechanisms. We used maternal blood samples collected during the second trimester from a Singaporean longitudinal birth cohort study to examine the association between inter-individual genome-wide DNA methylation and prenatal maternal depressive symptoms. We found that (1) the maternal methylome was significantly associated with prenatal maternal depressive symptoms only in mothers with a female fetus; and (2) this sex-dependent association was observed in a comparable, UK-based birth cohort study. Qualitative analyses showed fetal sex-specific differences in genomic features of depression-related CpGs and genes mapped from these CpGs in mothers with female fetuses implicated in a depression-associated WNT/β-catenin signaling pathway. These same genes also showed enriched expression in brain regions linked to major depressive disorder. We also found similar female-specific associations with fetal-facing placenta methylome. Our fetal sex-specific findings provide evidence for maternal-fetal interactions as a mechanism for intergenerational transmission.
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Affiliation(s)
- Michelle Z.L. Kee
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
| | - Ai Ling Teh
- Bioinformatics, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
| | - Andrew Clappison
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Irina Pokhvisneva
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Julie L. MacIssac
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - David T.S. Lin
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Katia E. Ramadori
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Birit F.P. Broekman
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
- Department of Psychiatry, Amsterdam UMC and OLVG, VU University, 1007 Amsterdam, the Netherlands
| | - Helen Chen
- Department of Psychological Medicine (Mental Wellness Service), KK Women’s and Children’s Hospital, Singapore 229899, Singapore
| | - Mary Lourdes Daniel
- Department of Child Development, KK Women’s and Children’s Hospital, Singapore 229899, Singapore
| | - Neerja Karnani
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Peter D. Gluckman
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
- Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Yap Seng Chong
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Jonathan Y. Huang
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
- Centre for Quantitative Medicine, Health Services and System Research Signature Research Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Michael J. Meaney
- Translation Neuroscience, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
- Bioinformatics, Singapore Institute for Clinical Sciences, ASTAR, Singapore 117609, Singapore
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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22
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Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma. Cell Discov 2022; 8:68. [PMID: 35853872 PMCID: PMC9296597 DOI: 10.1038/s41421-022-00415-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
The clear cell renal cell carcinoma (ccRCC) microenvironment consists of many different cell types and structural components that play critical roles in cancer progression and drug resistance, but the cellular architecture and underlying gene regulatory features of ccRCC have not been fully characterized. Here, we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to generate transcriptional and epigenomic landscapes of ccRCC. We identified tumor cell-specific regulatory programs mediated by four key transcription factors (TFs) (HOXC5, VENTX, ISL1, and OTP), and these TFs have prognostic significance in The Cancer Genome Atlas (TCGA) database. Targeting these TFs via short hairpin RNAs (shRNAs) or small molecule inhibitors decreased tumor cell proliferation. We next performed an integrative analysis of chromatin accessibility and gene expression for CD8+ T cells and macrophages to reveal the different regulatory elements in their subgroups. Furthermore, we delineated the intercellular communications mediated by ligand–receptor interactions within the tumor microenvironment. Taken together, our multiomics approach further clarifies the cellular heterogeneity of ccRCC and identifies potential therapeutic targets.
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IL-3 Expands Pre-Basophil and Mast Cell Progenitors by Upregulating the IL-3 Receptor Expression. Cell Immunol 2022; 374:104498. [PMID: 35334276 PMCID: PMC9161734 DOI: 10.1016/j.cellimm.2022.104498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/20/2022]
Abstract
Basophils and mast cells play a critical role in allergic inflammation and provide protective immunity against certain types of parasitic infections. Expansion of basophils and mast cells to the critical numbers is believed to be an essential step in enabling basophils and mast cells to carry out their protective functions. However, factors that drive basophil and mast cell expansion are still incompletely understood. We tested the roles of cytokines and growth factors IL-3, TSLP, GM-CSF, IL-5, SCF, IL-7, IL-25, and IL-33 in promoting the differentiation of pre-basophil and mast cell progenitors (pre-BMPs)in vitro.We found that while GM-CSF only expanded basophils, IL-3 promoted the differentiation of pre-BMPs into both basophils and mast cells. We found that IL-3 expanded the number of pre-BMPsin vivo. We showed that IL-3 upregulatedIl3ramRNA and protein expression on pre-BMPs, supporting that IL-3 expands pre-BMPs in part by upregulating the IL-3 receptor expression. Although Gata2 mRNA expression was upregulated by IL-3 treatment in pre-BMPs, it is dispensable for IL-3-mediated upregulation of IL-3 receptor expression. Our study reveals a novel mechanism through which IL-3 expands basophil and mast cells.
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24
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Takai J, Shimada T, Nakamura T, Engel JD, Moriguchi T. Gata2 heterozygous mutant mice exhibit reduced inflammatory responses and impaired bacterial clearance. iScience 2021; 24:102836. [PMID: 34471858 PMCID: PMC8390858 DOI: 10.1016/j.isci.2021.102836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/17/2021] [Accepted: 07/08/2021] [Indexed: 01/18/2023] Open
Abstract
Infectious diseases continually pose global medical challenges. The transcription factor GATA2 establishes gene networks and defines cellular identity in hematopoietic stem/progenitor cells and in progeny committed to specific lineages. GATA2-haploinsufficient patients exhibit a spectrum of immunodeficiencies associated with bacterial, viral, and fungal infections. Despite accumulating clinical knowledge of the consequences of GATA2 haploinsufficiency in humans, it is unclear how GATA2 haploinsufficiency compromises host anti-infectious defenses. To address this issue, we examined Gata2-heterozygous mutant (G2 Het) mice as a model for human GATA2 haploinsufficiency. In vivo inflammation imaging and cytokine multiplex analysis demonstrated that G2 Het mice had attenuated inflammatory responses with reduced levels of inflammatory cytokines, particularly IFN-γ, IL-12p40, and IL-17A, during lipopolysaccharide-induced acute inflammation. Consequently, bacterial clearance was significantly impaired in G2 Het mice after cecal ligation and puncture-induced polymicrobial peritonitis. These results provide direct molecular insights into GATA2-directed host defenses and the pathogenic mechanisms underlying observed immunodeficiencies in GATA2-haploinsufficient patients.
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Affiliation(s)
- Jun Takai
- Division of Medical Biochemistry, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan
| | - Takashi Shimada
- Division of Medical Biochemistry, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan
| | - Tadaho Nakamura
- Division of Pharmacology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan
| | - James Douglas Engel
- Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Takashi Moriguchi
- Division of Medical Biochemistry, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan
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25
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Higashijima Y, Kanki Y. Potential roles of super enhancers in inflammatory gene transcription. FEBS J 2021; 289:5762-5775. [PMID: 34173323 DOI: 10.1111/febs.16089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/26/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022]
Abstract
Acute and chronic inflammation is a basic pathological event that contributes to atherosclerosis, cancer, infectious diseases, and immune disorders. Inflammation is an adaptive process to both external and internal stimuli experienced by the human body. Although the mechanism of gene transcription is highly complicated and orchestrated in a timely and spatial manner, recent developments in next-generation sequencing, genome-editing, cryo-electron microscopy, and single cell-based technologies could provide us with insights into the roles of super enhancers (SEs). Initially, SEs were implicated in determining cell fate; subsequent studies have clarified that SEs are associated with various pathological conditions, including cancer and inflammatory diseases. Recent technological advances have unveiled the molecular mechanisms of SEs, which involve epigenetic histone modifications, chromatin three-dimensional structures, and phase-separated condensates. In this review, we discuss the relationship between inflammation and SEs and the therapeutic potential of SEs for inflammatory diseases.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Japan.,Laboratory of Laboratory/Sports Medicine, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Japan
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26
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Wang HN, Ji K, Zhang LN, Xie CC, Li WY, Zhao ZF, Chen JJ. Inhibition of c-Fos expression attenuates IgE-mediated mast cell activation and allergic inflammation by counteracting an inhibitory AP1/Egr1/IL-4 axis. J Transl Med 2021; 19:261. [PMID: 34130714 PMCID: PMC8207675 DOI: 10.1186/s12967-021-02932-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Background Activator protein-1 (AP1), a c-Fos–JUN transcription factor complex, mediates many cytobiological processes. c-Fos has been implicated in immunoglobulin (Ig)E activation of mast cells (MCs) via high-affinity IgE Fc receptor (FcεRI) binding. This study examined c-Fos involvement in MC activation and tested the effects of the c-Fos/AP1 inhibitor T-5224 on MCs activation and allergic responses. Methods In vitro studies were conducted with two MC model systems: rat basophilic leukemia cells (RBLs) and mouse bone marrow derived mast cells (BMMCs). MC degranulation and effector functions were examined with β-hexosaminidase release and cytokine secretion assays. c-Fos/AP1 was inhibited with T-5224. c-Fos activity was suppressed with short hairpin RNA targeting c-Fos (shFos). In vivo immune responses were evaluated in passive cutaneous anaphylaxis (PCA) and ovalbumin-induced active systemic anaphylaxis (ASA) models, as well as in an oxazolone (OXA)-induced model of atopic dermatitis, a common allergic disease. Results c-Fos expression was elevated transcriptionally and translationally in IgE-stimulated MCs. c-Fos binding of the Egr1 (early growth response 1) promoter upregulated Egr1 transcription, leading to production of interleukin (IL)4. T-5224 reduced FcεRI-mediated MC degranulation (evidenced by β-hexosaminidase activity and histamine levels) and diminished EGR1 and IL4 expression. T-5224 attenuated IgE-mediated allergic responses in PCA and ASA models, and it suppressed MC-mediated atopic dermatitis in mice. Conclusion IgE binding can activate MCs via a c-Fos/Egr1/IL-4 axis. T-5224 suppresses MC activation in vitro and in vivo and thus represents a promising potential strategy for targeting MC activation to treat allergic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02932-0.
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Affiliation(s)
- Hui-Na Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Kunmei Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Li-Na Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Chu-Chu Xie
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Wei-Yong Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Zhen-Fu Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China
| | - Jia-Jie Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Laboratory Department of South China Hospital, Health Science Center, Shenzhen University, No. 1066 Xueyuan Road, Nanshan District, Shenzhen, 518060, People's Republic of China.
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Srivastava M, Kaplan MH. Transcription Factors in the Development and Pro-Allergic Function of Mast Cells. FRONTIERS IN ALLERGY 2021; 2:679121. [PMID: 35387064 PMCID: PMC8974754 DOI: 10.3389/falgy.2021.679121] [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: 03/11/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Mast cells (MCs) are innate immune cells of hematopoietic origin localized in the mucosal tissues of the body and are broadly implicated in the pathogenesis of allergic inflammation. Transcription factors have a pivotal role in the development and differentiation of mast cells in response to various microenvironmental signals encountered in the resident tissues. Understanding the regulation of mast cells by transcription factors is therefore vital for mechanistic insights into allergic diseases. In this review we summarize advances in defining the transcription factors that impact the development of mast cells throughout the body and in specific tissues, and factors that are involved in responding to the extracellular milieu. We will further describe the complex networks of transcription factors that impact mast cell physiology and expansion during allergic inflammation and functions from degranulation to cytokine secretion. As our understanding of the heterogeneity of mast cells becomes more detailed, the contribution of specific transcription factors in mast cell-dependent functions will potentially offer new pathways for therapeutic targeting.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University, Indianapolis, IN, United States
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Mark H. Kaplan
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Blank U, Huang H, Kawakami T. The high affinity IgE receptor: a signaling update. Curr Opin Immunol 2021; 72:51-58. [PMID: 33838574 DOI: 10.1016/j.coi.2021.03.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023]
Abstract
Here we update receptor proximal and distant signaling events of the mast cell high affinity IgE receptor (FcεRI) launching immediate type I hypersensitivity and an inflammatory cytokine-chemokine cascade. Different physiologic antigen concentrations, their affinity, and valency for the IgE ligand produce distinct intracellular signaling events with different outcomes. Investigating mast cell degranulation has revealed a complex molecular machinery that relays proximal signaling to cytoskeletal reorganization, granule transport and membrane fusion. Several new phosphorylation- and calcium-responsive effectors have been described. FcεRI signaling also promotes de novo gene transcription. Recent progress has identified enhancers at genes that are upregulated in mast cells after stimulation through FcεRI using next generation sequencing methods. Enhancers at genes that respond to antigenic stimulation in human mast cells revealed Ca2+-dependency. Stimulation-responsive super enhancers in mouse mast cells have also been identified. Mast cell lineage-determining transcription factor GATA2 primes these enhancers to respond to antigenic stimulation.
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Affiliation(s)
- Ulrich Blank
- Université de Paris, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS ERL8252, Faculté de Médecine site Bichat, Paris, France; Laboratoire d'Excellence Inflamex, Paris, France.
| | - Hua Huang
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Toshiaki Kawakami
- Laboratory of Allergic Diseases, Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Dermatology, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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