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Li X, Zeng S, Chen L, Zhang Y, Li X, Zhang B, Su D, Du Q, Zhang J, Wang H, Zhong Z, Zhang J, Li P, Jiang A, Long K, Li M, Ge L. An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation. Cell Prolif 2024; 57:e13552. [PMID: 37905345 PMCID: PMC10905358 DOI: 10.1111/cpr.13552] [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: 04/24/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 11/02/2023] Open
Abstract
Cebpa is a master transcription factor gene for adipogenesis. However, the mechanisms of enhancer-promoter chromatin interactions controlling Cebpa transcriptional regulation during adipogenic differentiation remain largely unknown. To reveal how the three-dimensional structure of Cebpa changes during adipogenesis, we generated high-resolution chromatin interactions of Cebpa in 3T3-L1 preadipocytes and 3T3-L1 adipocytes using circularized chromosome conformation capture sequencing (4C-seq). We revealed dramatic changes in chromatin interactions and chromatin status at interaction sites during adipogenic differentiation. Based on this, we identified five active enhancers of Cebpa in 3T3-L1 adipocytes through epigenomic data and luciferase reporter assays. Next, epigenetic repression of Cebpa-L1-AD-En2 or -En3 by the dCas9-KRAB system significantly down-regulated Cebpa expression and inhibited adipocyte differentiation. Furthermore, experimental depletion of cohesin decreased the interaction intensity between Cebpa-L1-AD-En2 and the Cebpa promoter and down-regulated Cebpa expression, indicating that long-range chromatin loop formation was mediated by cohesin. Two transcription factors, RXRA and PPARG, synergistically regulate the activity of Cebpa-L1-AD-En2. To test whether Cebpa-L1-AD-En2 plays a role in adipose tissue development, we injected dCas9-KRAB-En2 lentivirus into the inguinal white adipose tissue (iWAT) of mice to suppress the activity of Cebpa-L1-AD-En2. Repression of Cebpa-L1-AD-En2 significantly decreased Cebpa expression and adipocyte size, altered iWAT transcriptome, and affected iWAT development. We identified functional enhancers regulating Cebpa expression and clarified the crucial roles of Cebpa-L1-AD-En2 and Cebpa promoter interaction in adipocyte differentiation and adipose tissue development.
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Affiliation(s)
- Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sha Zeng
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Li Chen
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Xuemin Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Biwei Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Duo Su
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qinjiao Du
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haoming Wang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Zhining Zhong
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jinwei Zhang
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and GeneticsSichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Anan Jiang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Chongqing Academy of Animal SciencesChongqingChina
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Liangpeng Ge
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
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Akhtar F, Ruiz JH, Liu YG, Resendez RG, Feliers D, Morales LD, Diaz-Badillo A, Lehman DM, Arya R, Lopez-Alvarenga JC, Blangero J, Duggirala R, Mummidi S. Functional characterization of the disease-associated CCL2 rs1024611G-rs13900T haplotype: The role of the RNA-binding protein HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564937. [PMID: 37961304 PMCID: PMC10635030 DOI: 10.1101/2023.10.31.564937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles:A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles:_C>T) in the CCL2 3' untranslated region (3' UTR) that is in perfect LD with rs1024611 to demonstrate allelic expression imbalance (AEI) of CCL2 in heterozygous individuals. Here we tested the hypothesis that the rs13900 could modulate CCL2 expression by altering mRNA turnover and/or translatability. The rs13900 T allele conferred greater stability to the CCL2 transcript when compared to the rs13900 C allele. The rs13900 T allele also had increased binding to Human Antigen R (HuR), an RNA-binding protein, in vitro and ex vivo. The rs13900 alleles imparted differential activity to reporter vectors and influenced the translatability of the reporter transcript. We further demonstrated a role for HuR in mediating allele-specific effects on CCL2 expression in overexpression and silencing studies. The presence of the rs1024611G-rs13900T conferred a distinct transcriptomic signature related to inflammation and immunity. Our studies suggest that the differential interactions of HuR with rs13900 could modulate CCL2 expression and explain the interindividual differences in CCL2-mediated disease susceptibility.
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Affiliation(s)
- Feroz Akhtar
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Joselin Hernandez Ruiz
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Ya-Guang Liu
- Department of Pathology, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Roy G. Resendez
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Denis Feliers
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Liza D. Morales
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Alvaro Diaz-Badillo
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Donna M. Lehman
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Rector Arya
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Juan Carlos Lopez-Alvarenga
- Department of Population Health and Biostatistics, School of Medicine, University of Texas Rio Grande Valley, Harlingen, Texas, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, Department of Genetics, School of Medicine, University of Texas Rio Grane Valley, Brownsville, USA
| | - Ravindranath Duggirala
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
| | - Srinivas Mummidi
- Department of Health and Behavioral Sciences, Texas A&M University- San Antonio, Texas, USA
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Filipescu D, Carcamo S, Agarwal A, Tung N, Humblin É, Goldberg MS, Vyas NS, Beaumont KG, Demircioglu D, Sridhar S, Ghiraldini FG, Capparelli C, Aplin AE, Salmon H, Sebra R, Kamphorst AO, Merad M, Hasson D, Bernstein E. MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping. Nat Cell Biol 2023; 25:1332-1345. [PMID: 37605008 PMCID: PMC10495263 DOI: 10.1038/s41556-023-01208-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/20/2023] [Indexed: 08/23/2023]
Abstract
MacroH2A has established tumour suppressive functions in melanoma and other cancers, but an unappreciated role in the tumour microenvironment. Using an autochthonous, immunocompetent mouse model of melanoma, we demonstrate that mice devoid of macroH2A variants exhibit increased tumour burden compared with wild-type counterparts. MacroH2A-deficient tumours accumulate immunosuppressive monocytes and are depleted of functional cytotoxic T cells, characteristics consistent with a compromised anti-tumour response. Single cell and spatial transcriptomics identify increased dedifferentiation along the neural crest lineage of the tumour compartment and increased frequency and activation of cancer-associated fibroblasts following macroH2A loss. Mechanistically, macroH2A-deficient cancer-associated fibroblasts display increased myeloid chemoattractant activity as a consequence of hyperinducible expression of inflammatory genes, which is enforced by increased chromatin looping of their promoters to enhancers that gain H3K27ac. In summary, we reveal a tumour suppressive role for macroH2A variants through the regulation of chromatin architecture in the tumour stroma with potential implications for human melanoma.
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Affiliation(s)
- Dan Filipescu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Saul Carcamo
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aman Agarwal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Navpreet Tung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Étienne Humblin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew S Goldberg
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nikki S Vyas
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deniz Demircioglu
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Subhasree Sridhar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Flavia G Ghiraldini
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Claudia Capparelli
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Andrew E Aplin
- Department of Pharmacology, Physiology and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hélène Salmon
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institut Curie, INSERM, U932, and PSL Research University, Paris, France
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice O Kamphorst
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bioinformatics for Next Generation Sequencing Facility, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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4
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Exploring high-resolution chromatin interaction changes and functional enhancers of myogenic marker genes during myogenic differentiation. J Biol Chem 2022; 298:102149. [PMID: 35787372 PMCID: PMC9352921 DOI: 10.1016/j.jbc.2022.102149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Skeletal muscle differentiation (myogenesis) is a complex and highly coordinated biological process regulated by a series of myogenic marker genes. Chromatin interactions between gene’s promoters and their enhancers have an important role in transcriptional control. However, the high-resolution chromatin interactions of myogenic genes and their functional enhancers during myogenesis remain largely unclear. Here, we used circularized chromosome conformation capture coupled with next generation sequencing (4C-seq) to investigate eight myogenic marker genes in C2C12 myoblasts (C2C12-MBs) and C2C12 myotubes (C2C12-MTs). We revealed dynamic chromatin interactions of these marker genes during differentiation and identified 163 and 314 significant interaction sites (SISs) in C2C12-MBs and C2C12-MTs, respectively. The interacting genes of SISs in C2C12-MTs were mainly involved in muscle development, and histone modifications of the SISs changed during differentiation. Through functional genomic screening, we also identified 25 and 41 putative active enhancers in C2C12-MBs and C2C12-MTs, respectively. Using luciferase reporter assays for putative enhancers of Myog and Myh3, we identified eight activating enhancers. Furthermore, dCas9-KRAB epigenome editing and RNA-Seq revealed a role for Myog enhancers in the regulation of Myog expression and myogenic differentiation in the native genomic context. Taken together, this study lays the groundwork for understanding 3D chromatin interaction changes of myogenic genes during myogenesis and provides insights that contribute to our understanding of the role of enhancers in regulating myogenesis.
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The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages. Mol Cell 2021; 81:953-968.e9. [PMID: 33503407 DOI: 10.1016/j.molcel.2020.12.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/20/2020] [Accepted: 12/24/2020] [Indexed: 01/08/2023]
Abstract
While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the involvement of corepressors is not. Using inflammatory macrophage activation as a model, we investigate here a corepressor complex containing GPS2 and SMRT both genome-wide and at the Ccl2 locus, encoding the chemokine CCL2 (MCP-1). We report that corepressors co-occupy candidate enhancers along with the coactivators CBP (H3K27 acetylase) and MED1 (mediator) but act antagonistically by repressing eRNA transcription-coupled H3K27 acetylation. Genome editing, transcriptional interference, and cistrome analysis reveals that apparently related enhancer and silencer elements control Ccl2 transcription in opposite ways. 4C-seq indicates that corepressor depletion or inflammatory signaling functions mechanistically similarly to trigger enhancer activation. In ob/ob mice, adipose tissue macrophage-selective depletion of the Ccl2 enhancer-transcribed eRNA reduces metaflammation. Thus, the identified corepressor-eRNA-chemokine pathway operates in vivo and suggests therapeutic opportunities by targeting eRNAs in immuno-metabolic diseases.
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6
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Ho EYK, Cao Q, Gu M, Chan RWL, Wu Q, Gerstein M, Yip KY. Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Brief Bioinform 2019; 21:836-850. [PMID: 30895290 DOI: 10.1093/bib/bbz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 01/22/2023] Open
Abstract
Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profiling of enhancer activities genome-wide, it has become increasingly evidenced that this classical definition has left substantial gray areas in different aspects. Here we survey a representative set of recent research articles and report the definitions of enhancers they have adopted. The results reveal that a wide spectrum of definitions is used usually without the definition stated explicitly, which could lead to difficulties in data interpretation and downstream analyses. Based on these findings, we discuss the practical implications and suggestions for future studies.
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Affiliation(s)
| | - Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Mengting Gu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ricky Wai-Lun Chan
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Qiong Wu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Program in Computational Biology and Bioinformatics.,Department of Computer Science, Yale University, New Haven, Connecticut, USA
| | - Kevin Y Yip
- Department of Biomedical Engineering.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre.,CUHK-BGI Innovation Institute of Trans-omics.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong
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7
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Tam KT, Chan PK, Zhang W, Law PP, Tian Z, Fung Chan GC, Philipsen S, Festenstein R, Tan-Un KC. Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach. Nucleic Acids Res 2017; 45:115-126. [PMID: 27651453 PMCID: PMC5224503 DOI: 10.1093/nar/gkw820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 12/24/2022] Open
Abstract
Neuroglobin (NGB) is predominantly expressed in the brain and retina. Studies suggest that NGB exerts protective effects to neuronal cells and is implicated in reducing the severity of stroke and Alzheimer's disease. However, little is known about the mechanisms which regulate the cell type-specific expression of the gene. In this study, we hypothesized that distal regulatory elements (DREs) are involved in optimal expression of the NGB gene. By chromosome conformation capture we identified two novel DREs located -70 kb upstream and +100 kb downstream from the NGB gene. ENCODE database showed the presence of DNaseI hypersensitive and transcription factors binding sites in these regions. Further analyses using luciferase reporters and chromatin immunoprecipitation suggested that the -70 kb region upstream of the NGB gene contained a neuronal-specific enhancer and GATA transcription factor binding sites. Knockdown of GATA-2 caused NGB expression to drop dramatically, indicating GATA-2 as an essential transcription factor for the activation of NGB expression. The crucial role of the DRE in NGB expression activation was further confirmed by the drop in NGB level after CRISPR-mediated deletion of the DRE. Taken together, we show that the NGB gene is regulated by a cell type-specific loop formed between its promoter and the novel DRE.
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MESH Headings
- Binding Sites
- CRISPR-Cas Systems
- Cell Line, Tumor
- Chromosomes, Human, Pair 14/chemistry
- Deoxyribonuclease I/genetics
- Deoxyribonuclease I/metabolism
- GATA2 Transcription Factor/genetics
- GATA2 Transcription Factor/metabolism
- Gene Editing
- Gene Expression Regulation
- Genes, Reporter
- Globins/antagonists & inhibitors
- Globins/genetics
- Globins/metabolism
- HeLa Cells
- Humans
- K562 Cells
- Luciferases/genetics
- Luciferases/metabolism
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neuroglobin
- Neurons/cytology
- Neurons/metabolism
- Organ Specificity
- Protein Binding
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Regulatory Elements, Transcriptional
- Signal Transduction
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Affiliation(s)
- Kin Tung Tam
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
| | - Ping Kei Chan
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College School of Medicine, London W12 0NN, United Kingdom
| | - Wei Zhang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
| | - Pui Pik Law
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College School of Medicine, London W12 0NN, United Kingdom
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
| | - Zhipeng Tian
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
- School of Professional and Continuing Education (HKU SPACE), The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
| | - Godfrey Chi Fung Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Richard Festenstein
- Gene Control Mechanisms and Disease Group, Department of Medicine, Division of Brain Sciences and MRC Clinical Sciences Centre, Imperial College School of Medicine, London W12 0NN, United Kingdom
| | - Kian Cheng Tan-Un
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
- School of Professional and Continuing Education (HKU SPACE), The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., China
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8
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Uyangaa E, Kim JH, Patil AM, Choi JY, Kim SB, Eo SK. Distinct Upstream Role of Type I IFN Signaling in Hematopoietic Stem Cell-Derived and Epithelial Resident Cells for Concerted Recruitment of Ly-6Chi Monocytes and NK Cells via CCL2-CCL3 Cascade. PLoS Pathog 2015; 11:e1005256. [PMID: 26618488 PMCID: PMC4664252 DOI: 10.1371/journal.ppat.1005256] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/09/2015] [Indexed: 12/24/2022] Open
Abstract
Type I interferon (IFN-I)-dependent orchestrated mobilization of innate cells in inflamed tissues is believed to play a critical role in controlling replication and CNS-invasion of herpes simplex virus (HSV). However, the crucial regulators and cell populations that are affected by IFN-I to establish the early environment of innate cells in HSV-infected mucosal tissues are largely unknown. Here, we found that IFN-I signaling promoted the differentiation of CCL2-producing Ly-6Chi monocytes and IFN-γ/granzyme B-producing NK cells, whereas deficiency of IFN-I signaling induced Ly-6Clo monocytes producing CXCL1 and CXCL2. More interestingly, recruitment of Ly-6Chi monocytes preceded that of NK cells with the levels peaked at 24 h post-infection in IFN-I–dependent manner, which was kinetically associated with the CCL2-CCL3 cascade response. Early Ly-6Chi monocyte recruitment was governed by CCL2 produced from hematopoietic stem cell (HSC)-derived leukocytes, whereas NK cell recruitment predominantly depended on CC chemokines produced by resident epithelial cells. Also, IFN-I signaling in HSC-derived leukocytes appeared to suppress Ly-6Ghi neutrophil recruitment to ameliorate immunopathology. Finally, tissue resident CD11bhiF4/80hi macrophages and CD11chiEpCAM+ dendritic cells appeared to produce initial CCL2 for migration-based self-amplification of early infiltrated Ly-6Chi monocytes upon stimulation by IFN-I produced from infected epithelial cells. Ultimately, these results decipher a detailed IFN-I–dependent pathway that establishes orchestrated mobilization of Ly-6Chi monocytes and NK cells through CCL2-CCL3 cascade response of HSC-derived leukocytes and epithelium-resident cells. Therefore, this cascade response of resident–to-hematopoietic–to-resident cells that drives cytokine–to-chemokine–to-cytokine production to recruit orchestrated innate cells is critical for attenuation of HSV replication in inflamed tissues. Herpes simplex virus type 1 and 2 (HSV-1 and HSV-2) are the most common cause of genital ulceration in humans worldwide with lifelong latent infection after peripheral replication in mucosal tissues. Furthermore, acquisition of human immunodeficiency virus (HIV) is increased in HSV-infected individuals, underscoring the contribution of this virus in facilitating increased susceptibility to other microbial pathogens. Therefore, it is imperative to characterize the host defense to HSV infection and identify key components that regulate virus resistance, in order to devise therapeutic strategy. Although type I interferon (IFN-I)-dependent orchestrated mobilization of innate cells in inflamed tissues is considered a key player to control replication and CNS-invasion of HSV, the regulators and cell population that are affected by IFN-I to establish the orchestrated environment of innate cells in HSV-infected tissues are largely unknown. In the present study, we demonstrate that IFN-I signal governs the sequential recruitment of Ly-6Chi monocytes and then NK cells into mucosal tissues, depending on CCL2-CCL3 cascade mediated by HSC-derived leukocytes and epithelial resident cells, respectively. Also, tissue resident CD11bhiF4/80hi macrophages and CD11chiEpCAM+ dendritic cells were involved in producing the initial CCL2 for migration-based self-amplification of rapidly infiltrated Ly-6Chi monocytes through stimulation by IFN-I produced from infected epithelial cells. This study deciphers detailed IFN-I-dependent pathway that establishes orchestrated mobilization of Ly-6Chi monocytes and NK cells through CCL2-CCL3 cascade.
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Affiliation(s)
- Erdenebileg Uyangaa
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Jin Hyoung Kim
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Ajit Mahadev Patil
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Jin Young Choi
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Seong Bum Kim
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Seong Kug Eo
- College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Iksan, Republic of Korea
- Department of Bioactive Material Sciences, Graduate School, Chonbuk National University, Jeonju, Republic of Korea
- * E-mail:
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Brambilla R, Morton PD, Ashbaugh JJ, Karmally S, Lambertsen KL, Bethea JR. Astrocytes play a key role in EAE pathophysiology by orchestrating in the CNS the inflammatory response of resident and peripheral immune cells and by suppressing remyelination. Glia 2013; 62:452-67. [DOI: 10.1002/glia.22616] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/21/2013] [Accepted: 11/21/2013] [Indexed: 12/19/2022]
Affiliation(s)
- Roberta Brambilla
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine; University of Miami; Miami Florida
- The Neuroscience Program, Miller School of Medicine; University of Miami; Miami Florida
| | - Paul D. Morton
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine; University of Miami; Miami Florida
- The Neuroscience Program, Miller School of Medicine; University of Miami; Miami Florida
| | - Jessica Jopek Ashbaugh
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine; University of Miami; Miami Florida
- Department of Microbiology and Immunology, Miller School of Medicine; University of Miami; Miami Florida
| | - Shaffiat Karmally
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine; University of Miami; Miami Florida
| | - Kate Lykke Lambertsen
- Department of Neurobiology Research, Institute of Molecular Medicine; University of Southern Denmark; Odense Denmark
| | - John R. Bethea
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine; University of Miami; Miami Florida
- The Neuroscience Program, Miller School of Medicine; University of Miami; Miami Florida
- Department of Microbiology and Immunology, Miller School of Medicine; University of Miami; Miami Florida
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Conrady CD, Zheng M, Mandal NA, van Rooijen N, Carr DJ. IFN-α-driven CCL2 production recruits inflammatory monocytes to infection site in mice. Mucosal Immunol 2013; 6:45-55. [PMID: 22692455 PMCID: PMC3449026 DOI: 10.1038/mi.2012.46] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) is the leading cause of corneal blindness in the developed world due to reactivation of infectious virus and the subsequent immune response. The innate response that facilitates viral control in the cornea is currently unknown. In the present study using a mouse chimera model, we found that a bone marrow component is crucial in inhibiting viral replication and identified inflammatory monocytes (F4/80(+) Gr1(+)) as the responsible cell. CCL2 was critical for recruiting inflammatory monocytes, and a loss of this chemokine in CCL2(-/-) mice resulted in a loss of viral containment and inflammatory monocyte recruitment. To confirm these results, clodronate depletion of inflammatory monocytes resulted in elevated viral titers. Furthermore, siRNA targeting the innate sensor p204/IFI-16 resulted in a loss of CCL2 production. In conclusion, CCL2 expression driven by IFI-16 recognition of HSV-1 facilitates the recruitment of inflammatory monocytes into the cornea proper to control viral replication.
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Affiliation(s)
- Christopher D. Conrady
- Department of Microbiology, Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Min Zheng
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Nawajes A. Mandal
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niko van Rooijen
- Department of Molecular Cell Biology and Immunology, VU Medical Center, Amsterdam, The Netherlands
| | - Daniel J.J. Carr
- Department of Microbiology, Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Corresponding author: Daniel J.J. Carr, Ph.D., Department of Ophthalmology, DMEI #415, OUHSC, 608 Stanton L. Young Blvd., Oklahoma City, OK. 73104 USA; telephone: 405-271-8784;
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The rs1024611 regulatory region polymorphism is associated with CCL2 allelic expression imbalance. PLoS One 2012; 7:e49498. [PMID: 23166687 PMCID: PMC3500309 DOI: 10.1371/journal.pone.0049498] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/09/2012] [Indexed: 01/16/2023] Open
Abstract
CC chemokine ligand 2 (CCL2) is the most potent monocyte chemoattractant and inter-individual differences in its expression level have been associated with genetic variants mapping to the cis-regulatory regions of the gene. An A to G polymorphism in the CCL2 enhancer region at position -2578 (rs1024611; A>G), was found in most studies to be associated with higher serum CCL2 levels and increased susceptibility to a variety of diseases such as HIV-1 associated neurological disorders, tuberculosis, and atherosclerosis. However, the precise mechanism by which rs1024611influences CCL2 expression is not known. To address this knowledge gap, we tested the hypothesis that rs1024611G polymorphism is associated with allelic expression imbalance (AEI) of CCL2. We used haplotype analysis and identified a transcribed SNP in the 3'UTR (rs13900; C>T) can serve as a proxy for the rs1024611 and demonstrated that the rs1024611G allele displayed a perfect linkage disequilibrium with rs13900T allele. Allele-specific transcript quantification in lipopolysaccharide treated PBMCs obtained from heterozygous donors showed that rs13900T allele were expressed at higher levels when compared to rs13900C allele in all the donors examined suggesting that CCL2 is subjected to AEI and that that the allele containing rs1024611G is preferentially transcribed. We also found that AEI of CCL2 is a stable trait and could be detected in newly synthesized RNA. In contrast to these in vivo findings, in vitro assays with haplotype-specific reporter constructs indicated that the haplotype bearing rs1024611G had a lower or similar transcriptional activity when compared to the haplotype containing rs1024611A. This discordance between the in vivo and in vitro expression studies suggests that the CCL2 regulatory region polymorphisms may be functioning in a complex and context-dependent manner. In summary, our studies provide strong functional evidence and a rational explanation for the phenotypic effects of the CCL2 rs1024611G allele.
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Inflammatory monocyte recruitment is regulated by interleukin-23 during systemic bacterial infection. Infect Immun 2012; 80:4099-105. [PMID: 22966045 DOI: 10.1128/iai.00589-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Listeria monocytogenes is a gram-positive intracellular pathogen that causes meningitis and septicemia in immunocompromised individuals and spontaneous abortion in pregnant women. The innate immune response against L. monocytogenes is primarily mediated by neutrophils and monocytes. Interleukin-23 (IL-23) is an important proinflammatory cytokine well known for its role in neutrophil recruitment in various infectious and autoimmune diseases. We have previously shown that IL-23 is required for host resistance against L. monocytogenes and for neutrophil recruitment to the liver, but not the spleen, during infection. Despite efficient neutrophil recruitment to the spleen, IL-23p19 knockout (KO) mice have an increased bacterial burden in this organ, suggesting that IL-23 may regulate the recruitment/function of another cell type to the spleen. In this study, we show that specific depletion of neutrophils abrogated the differences in bacterial burdens in the livers but not the spleens of C57BL/6 (B6) and IL-23p19 KO mice. Interestingly, L. monocytogenes-infected IL-23p19 KO mice had fewer monocytes in the spleen than B6 mice, as well as a reduction in the monocyte-recruiting chemokines CCL2 and CCL7. Additionally, the overall concentrations of tumor necrosis factor alpha (TNF-α) and nitric oxide (NO(•)), as well as the percentages and total numbers of monocytes producing TNF-α and NO(•), were reduced in IL-23p19 KO mice compared to levels in B6 mice, leading to increased bacterial burdens in the spleens of L. monocytogenes-infected IL-23p19 KO mice. Collectively, our data establish that IL-23 is required for the optimal recruitment of TNF-α- and NO(•)-producing inflammatory monocytes, thus revealing a novel mechanism by which this proinflammatory cytokine provides protection against bacterial infection.
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Patel JK, Clifford RL, Deacon K, Knox AJ. Ciclesonide inhibits TNFα- and IL-1β-induced monocyte chemotactic protein-1 (MCP-1/CCL2) secretion from human airway smooth muscle cells. Am J Physiol Lung Cell Mol Physiol 2012; 302:L785-92. [PMID: 22246000 PMCID: PMC3331580 DOI: 10.1152/ajplung.00257.2011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Monocyte chemotactic protein-1 (MCP-1) is a member of the CC family of cytokines. It has monocyte and lymphocyte chemotactic activity and stimulates histamine release from basophils. MCP-1 is implicated in the pathogenesis of inflammatory diseases, including asthma. The airway smooth muscle (ASM) layer is thickened in asthma, and the growth factors and cytokines secreted by ASM cells play a role in the inflammatory response of the bronchial wall. Glucocorticoids and β2-agonists are first-line drug treatments for asthma. Little is known about the effect of asthma treatments on MCP-1 production from human ASM cells. Here, we determined the effect of ciclesonide (a glucocorticoid) and formoterol (a β2-agonist) on MCP-1 production from human ASM cells. TNFα and IL-1β induced MCP-1 secretion from human ASM cells. Formoterol had no effect on MCP-1 expression, while ciclesonide significantly inhibited IL-1β- and TNFα-induced MCP-1. Furthermore, ciclesonide inhibited IL-1β- and TNFα-induced MCP-1 mRNA and IL-1β- and TNFα-induced MCP-1 promoter and enhancer luciferase reporters. Western blots showed that ciclesonide had no effect on IκB degradation. Finally, ciclesonide inhibited an NF-κB luciferase reporter. Our data show that ciclesonide inhibits IL-1β- and TNFα-induced MCP-1 production from human ASM cells via a transcriptional mechanism involving inhibition of NF-κB binding.
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Affiliation(s)
- Jamie K Patel
- Division of Respiratory Medicine, Nottingham Respiratory Biomedical Research Unit, University of Nottingham, United Kingdom
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