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Zou K, Wang C, Zhou C, Yang Y, Zeng Z. Early growth response 1/Krüppel-like factor 5 pathway inhibitor alleviates lipopolysaccharide-induced lung injury by promoting autophagy. Eur J Pharmacol 2024; 964:176294. [PMID: 38158112 DOI: 10.1016/j.ejphar.2023.176294] [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: 10/18/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Early transcription factors play critical roles in the development of acute lung injury/acute respiratory distress syndrome (ALI/ARDS). Early growth response 1 (EGR1) is a transcription factor essential for various biological processes, including regulation of metabolism, differentiation, and inflammation. However, its role in ALI has been poorly reported. In this study, we aimed to determine the effect of EGR1 on ALI to gain insights into the theoretical basis for further treatment of ALI. By employing concerted molecular biology techniques, we showed that EGR1 protein was upregulated in mice. EGR1 protein was upregulated in mice and human lung epithelial cells in response to lipopolysaccharide (LPS) stimulation. EGR1 knockdown promoted autophagy and reduced LPS-induced pro-inflammatory mediator production. EGR1 was preferentially bound to the GCGTGGGCG motif region and EGR1-binding peak-related genes were mainly enriched in autophagy and injury stress-related pathways. Additionally, EGR1 promoted Krüppel-like factor 5 (KLF5) transcription by binding to the KLF5 promoter region, and KLF5 knockdown significantly decreased inflammatory damage, suggesting that EGR1 promotes ALI progression by regulating KLF5 expression. Furthermore, ML264, an inhibitor of the EGR1/KLF5 pathway axis, displayed a protective role in ALI to reduce inflammation. In conclusion, our findings demonstrate the potential of EGR1 knockdown to inhibit KLF5 and promote autophagy, further reducing the inflammatory response to mitigate ALI/ARDS. The EGR1/KLF5 pathway axis may be a valuable therapeutic target for the treatment of ALI/ARDS.
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Affiliation(s)
- Kang Zou
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China; Jiangxi Institute of Respiratory Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China; Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou City, 341000, Jiangxi Province, China
| | - Cheng Wang
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China; Jiangxi Institute of Respiratory Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China
| | - Chaoqi Zhou
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China
| | - Yuting Yang
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China
| | - Zhenguo Zeng
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang City, 330006, Jiangxi Province, China.
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Jiménez-Meléndez A, Shakya R, Markussen T, Robertson LJ, Myrmel M, Makvandi-Nejad S. Gene expression profile of HCT-8 cells following single or co-infections with Cryptosporidium parvum and bovine coronavirus. Sci Rep 2023; 13:22106. [PMID: 38092824 PMCID: PMC10719361 DOI: 10.1038/s41598-023-49488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Among the causative agents of neonatal diarrhoea in calves, two of the most prevalent are bovine coronavirus (BCoV) and the intracellular parasite Cryptosporidium parvum. Although several studies indicate that co-infections are associated with greater symptom severity, the host-pathogen interplay remains unresolved. Here, our main objective was to investigate the modulation of the transcriptome of HCT-8 cells during single and co-infections with BCoV and C. parvum. For this, HCT-8 cells were inoculated with (1) BCoV alone, (2) C. parvum alone, (3) BCoV and C. parvum simultaneously. After 24 and 72 h, cells were harvested and analyzed using high-throughput RNA sequencing. Following differential expression analysis, over 6000 differentially expressed genes (DEGs) were identified in virus-infected and co-exposed cells at 72 hpi, whereas only 52 DEGs were found in C. parvum-infected cells at the same time point. Pathway (KEGG) and gene ontology (GO) analysis showed that DEGs in the virus-infected and co-exposed cells were mostly associated with immune pathways (such as NF-κB, TNF-α or, IL-17), apoptosis and regulation of transcription, with a more limited effect exerted by C. parvum. Although the modulation observed in the co-infection was apparently dominated by the virus, over 800 DEGs were uniquely expressed in co-exposed cells at 72 hpi. Our findings provide insights on possible biomarkers associated with co-infection, which could be further explored using in vivo models.
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Affiliation(s)
- Alejandro Jiménez-Meléndez
- Department of Paraclinical Sciences (PARAFAG), Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Ruchika Shakya
- Department of Paraclinical Sciences (PARAFAG), Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Turhan Markussen
- Department of Paraclinical Sciences (PARAFAG), Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Lucy J Robertson
- Department of Paraclinical Sciences (PARAFAG), Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Mette Myrmel
- Department of Paraclinical Sciences (PARAFAG), Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Shokouh Makvandi-Nejad
- Research Group Animal Health, Vaccinology, Norwegian Veterinary Institute, Ås, Norway
- Nykode Therapeutics ASA, Oslo Science Park, Oslo, Norway
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Yang R, Lu Y, Yin N, Faiola F. Transcriptomic Integration Analyses Uncover Common Bisphenol A Effects Across Species and Tissues Primarily Mediated by Disruption of JUN/FOS, EGFR, ER, PPARG, and P53 Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19156-19168. [PMID: 37978927 DOI: 10.1021/acs.est.3c02016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Bisphenol A (BPA) is a common endocrine disruptor widely used in the production of electronic, sports, and medical equipment, as well as consumer products like milk bottles, dental sealants, and thermal paper. Despite its widespread use, current assessments of BPA exposure risks remain limited due to the lack of comprehensive cross-species comparative analyses. To address this gap, we conducted a study aimed at identifying genes and fundamental molecular processes consistently affected by BPA in various species and tissues, employing an effective data integration method and bioinformatic analyses. Our findings revealed that exposure to BPA led to significant changes in processes like lipid metabolism, proliferation, and apoptosis in the tissues/cells of mammals, fish, and nematodes. These processes were found to be commonly affected in adipose, liver, mammary, uterus, testes, and ovary tissues. Additionally, through an in-depth analysis of signaling pathways influenced by BPA in different species and tissues, we observed that the JUN/FOS, EGFR, ER, PPARG, and P53 pathways, along with their downstream key transcription factors and kinases, were all impacted by BPA. Our study provides compelling evidence that BPA indeed induces similar toxic effects across different species and tissues. Furthermore, our investigation sheds light on the underlying molecular mechanisms responsible for these toxic effects. By uncovering these mechanisms, we gain valuable insights into the potential health implications associated with BPA exposure, highlighting the importance of comprehensive assessments and awareness of this widespread endocrine disruptor.
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Affiliation(s)
- Renjun Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanping Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nuoya Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Agarwal K, Choudhury B, Robinson LS, Morrill SR, Bouchibiti Y, Chilin-Fuentes D, Rosenthal SB, Fisch KM, Peipert JF, Lebrilla CB, Allsworth JE, Lewis AL, Lewis WG. Resident microbes shape the vaginal epithelial glycan landscape. Sci Transl Med 2023; 15:eabp9599. [PMID: 38019934 PMCID: PMC11419735 DOI: 10.1126/scitranslmed.abp9599] [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: 03/16/2022] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
Epithelial cells are covered in carbohydrates (glycans). This glycan coat or "glycocalyx" interfaces directly with microbes, providing a protective barrier against potential pathogens. Bacterial vaginosis (BV) is a condition associated with adverse health outcomes in which bacteria reside in direct proximity to the vaginal epithelium. Some of these bacteria, including Gardnerella, produce glycosyl hydrolase enzymes. However, glycans of the human vaginal epithelial surface have not been studied in detail. Here, we elucidate key characteristics of the "normal" vaginal epithelial glycan landscape and analyze the impact of resident microbes on the surface glycocalyx. In human BV, glycocalyx staining was visibly diminished in electron micrographs compared to controls. Biochemical and mass spectrometric analysis showed that, compared to normal vaginal epithelial cells, BV cells were depleted of sialylated N- and O-glycans, with underlying galactose residues exposed on the surface. Treatment of primary epithelial cells from BV-negative women with recombinant Gardnerella sialidases generated BV-like glycan phenotypes. Exposure of cultured VK2 vaginal epithelial cells to recombinant Gardnerella sialidase led to desialylation of glycans and induction of pathways regulating cell death, differentiation, and inflammatory responses. These data provide evidence that vaginal epithelial cells exhibit an altered glycan landscape in BV and suggest that BV-associated glycosidic enzymes may lead to changes in epithelial gene transcription that promote cell turnover and regulate responses toward the resident microbiome.
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Affiliation(s)
- Kavita Agarwal
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Biswa Choudhury
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Lloyd S. Robinson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Sydney R. Morrill
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Yasmine Bouchibiti
- Department of Chemistry, University of California, Davis, Davis, CA 95616, United States of America
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616, United States of America
| | - Daisy Chilin-Fuentes
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Sara B. Rosenthal
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Kathleen M. Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Center for Computational Biology & Bioinformatics, UCSD, La Jolla, CA 92093, United States of America
| | - Jeffrey F. Peipert
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, United States of America
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA 95616, United States of America
- Department of Food Science and Technology, University of California, Davis, Davis, CA 95616, United States of America
| | - Jenifer E. Allsworth
- Department of Biomedical and Health Informatics, University of Missouri, Kansas City School of Medicine, Kansas City, MO 64110, United States of America
| | - Amanda L. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
| | - Warren G. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego (UCSD), La Jolla, CA 92093, United States of America
- Glycobiology Research and Training Center, UCSD, La Jolla, CA 92093, United States of America
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Zhang M, Lv L, Luo H, Cai H, Yu L, Jiang Y, Gao F, Tong W, Li L, Li G, Zhou Y, Tong G, Liu C. The CD2v protein of African swine fever virus inhibits macrophage migration and inflammatory cytokines expression by downregulating EGR1 expression through dampening ERK1/2 activity. Vet Res 2023; 54:106. [PMID: 37968713 PMCID: PMC10648359 DOI: 10.1186/s13567-023-01239-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: 07/11/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
African swine fever virus (ASFV) is a highly contagious and deadly virus that leads to high mortality rates in domestic swine populations. Although the envelope protein CD2v of ASFV has been implicated in immunomodulation, the molecular mechanisms underlying CD2v-mediated immunoregulation remain unclear. In this study, we generated a stable CD2v-expressing porcine macrophage (PAM-CD2v) line and investigated the CD2v-dependent transcriptomic landscape using RNA-seq. GO terms enrichment analysis and gene set enrichment analysis revealed that CD2v predominantly affected the organization and assembly process of the extracellular matrix. Wound healing and Transwell assays showed that CD2v inhibited swine macrophage migration. Further investigation revealed a significant decrease in the expression of transcription factor early growth response 1 (EGR1) through inhibiting the activity of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Notably, EGR1 knockout in swine macrophages restricted cell migration, whereas EGR1 overexpression in PAM-CD2v restored the ability of macrophage migration, suggesting that CD2v inhibits swine macrophage motility by downregulating EGR1 expression. Furthermore, we performed chromatin immunoprecipitation and sequencing for EGR1 and the histone mark H3K27 acetylation (H3K27ac), and we found that EGR1 co-localized with the activated histone modification H3K27ac neighboring the transcriptional start sites. Further analysis indicated that EGR1 and H3K27ac co-occupy the promoter regions of cell locomotion-related genes. Finally, by treating various derivatives of swine macrophages with lipopolysaccharides, we showed that depletion of EGR1 decreased the expression of inflammatory cytokines including TNFα, IL1α, IL1β, IL6, and IL8, which play essential roles in inflammation and host immune response. Collectively, our results provide new insights into the immunomodulatory mechanism of ASFV CD2v.
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Affiliation(s)
- Min Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lilei Lv
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Huaye Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Hongming Cai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China.
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China.
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6
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Summers JA, Jones KL. Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth. FRONTIERS IN OPHTHALMOLOGY 2023; 3:1245891. [PMID: 38390290 PMCID: PMC10883300 DOI: 10.3389/fopht.2023.1245891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/06/2023] [Indexed: 02/24/2024]
Abstract
Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.
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Affiliation(s)
- Jody A Summers
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States
| | - Kenneth L Jones
- Bioinformatic Solutions LLC, Sheridan, Wyoming, 82801, United States
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Zou K, Zeng Z. Role of early growth response 1 in inflammation-associated lung diseases. Am J Physiol Lung Cell Mol Physiol 2023; 325:L143-L154. [PMID: 37401387 PMCID: PMC10511164 DOI: 10.1152/ajplung.00413.2022] [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: 01/04/2023] [Revised: 05/03/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
Early growth response 1 (EGR1), which is involved in cell proliferation, differentiation, apoptosis, adhesion, migration, and immune and inflammatory responses, is a zinc finger transcription factor. EGR1 is a member of the EGR family of early response genes and can be activated by external stimuli such as neurotransmitters, cytokines, hormones, endotoxins, hypoxia, and oxidative stress. EGR1 expression is upregulated during several common respiratory diseases, such as acute lung injury/acute respiratory distress syndrome, chronic obstructive pulmonary disease, asthma, pneumonia, and novel coronavirus disease 2019. Inflammatory response is the common pathophysiological basis of these common respiratory diseases. EGR1 is highly expressed early in the disease, amplifying pathological signals from the extracellular environment and driving disease progression. Thus, EGR1 may be a target for early and effective intervention in these inflammation-associated lung diseases.
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Affiliation(s)
- Kang Zou
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical College, Ganzhou, People's Republic of China
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Zhenguo Zeng
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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8
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Banerji R, Joshi R, Saroj SD. Acyl Homoserine Lactone Sensitised Streptococcus Pyogenes Differentially Regulates the Transcriptional Expression of Early Growth Response 1 (EGR1) in Epithelial and Macrophage Cells. Curr Microbiol 2023; 80:268. [PMID: 37402084 DOI: 10.1007/s00284-023-03375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/14/2023] [Indexed: 07/05/2023]
Abstract
The host transcriptional activator Early growth response 1 (EGR1) plays a vital role in cell cycle and differentiation, cell proliferation, and regulation of cytokines and several growth factors. It is an immediate-early gene that is expressed as an initial response to various environmental stimuli. Bacterial infection is one such factor that can trigger the expression of EGR1 in host. Therefore, it is imperative to understand expression of EGR1 during early stages of host-pathogen interaction. Streptococcus pyogenes is an opportunistic bacteria causing skin and respiratory tract infections in humans. The quorum-sensing molecule, N-(3-oxododecanoyl)-l-homoserine lactone (Oxo-C12), not synthesised by S. pyogenes, can be sensed by S. pyogenes leading to molecular changes in the pathogen. In this study, we investigated the role of Oxo-C12 on EGR1 regulation in lung epithelial and murine macrophage cell line upon S. pyogenes infection. We report that Oxo-C12 sensitised S. pyogenes upregulates the transcriptional expression of EGR1 through ERK1/2 pathway. It was observed that EGR1 was not involved in the intial attachment of S. pyogenes to A549 cells. However, inhibition of EGR1 in macrophage cell line, J774A.1, through the ERK1/2 pathway resulted in decreased adhesion of S. pyogenes. The EGR1 upregulation by Oxo-C12 sensitised S. pyogenes plays a vital role in enhancing the survival of S. pyogenes in murine macrophages, leading to persistent infection. Thus, understanding the molecular modulation in the host during bacterial infection will further help develop therapeutics to target specific sites.
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Affiliation(s)
- Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India
| | - Riya Joshi
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India
| | - Sunil D Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, Lavale, Maharashtra, 412115, Pune, India.
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9
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Guo Y, Miao X, Sun X, Li L, Zhou A, Zhu X, Xu Y, Wang Q, Li Z, Fan Z. Zinc finger transcription factor Egf1 promotes non-alcoholic fatty liver disease. JHEP Rep 2023; 5:100724. [PMID: 37234276 PMCID: PMC10206499 DOI: 10.1016/j.jhepr.2023.100724] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 02/22/2023] [Indexed: 05/27/2023] Open
Abstract
Background & Aims Non-alcoholic fatty liver disease (NAFLD) contributes to the global epidemic of metabolic syndrome and is considered a prelude to end-stage liver diseases such as cirrhosis and hepatocellular carcinoma. During NAFLD pathogenesis, hepatic parenchymal cells (hepatocytes) undergo both morphological and functional changes owing to a rewired transcriptome. The underlying mechanism is not entirely clear. In the present study, we investigated the involvement of early growth response 1 (Egr1) in NAFLD. Methods Quantitative PCR, Western blotting, and histochemical staining were used to assess gene expression levels. Chromatin immunoprecipitation was used to evaluate protein binding to DNA. NAFLD was evaluated in leptin receptor-deficient (db/db) mice. Results We report here that Egr1 was upregulated by pro-NAFLD stimuli in vitro and in vivo. Further analysis revealed that serum response factor (SRF) was recruited to the Egr1 promoter and mediated Egr1 transactivation. Importantly, Egr1 depletion markedly mitigated NAFLD in db/db mice. RNA sequencing revealed that Egr1 knockdown in hepatocytes, on the one hand, boosted fatty acid oxidation (FAO) and, on the other hand, suppressed the synthesis of chemoattractants. Mechanistically, Egr1 interacted with peroxisome proliferator-activated receptor α (PPARα) to repress PPARα-dependent transcription of FAO genes by recruiting its co-repressor NGFI-A binding protein 1 (Nab1), which potentially led to promoter deacetylation of FAO genes. Conclusions Our data identify Egr1 as a novel modulator of NAFLD and a potential target for NAFLD intervention. Impact and Implications Non-alcoholic fatty liver disease (NAFLD) precedes cirrhosis and hepatocellular carcinoma. In this paper, we describe a novel mechanism whereby early growth response 1 (Egr1), a transcription factor, contributes to NAFLD pathogenesis by regulating fatty acid oxidation. Our data provide novel insights and translational potential for NAFLD intervention.
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Affiliation(s)
- Yan Guo
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xiulian Miao
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xinyue Sun
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Luyang Li
- Department of Oral Medicine, Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Anqi Zhou
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xi Zhu
- Department of Infectious Diseases, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Yong Xu
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Qinghua Wang
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Zilong Li
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Zhiwen Fan
- Department of Pathology, Affiliated Nanjing Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
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10
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Summers JA, Jones KL. Single Cell Transcriptomics Identifies Distinct Choroid Cell Populations Involved in Visually Guided Eye Growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542876. [PMID: 37398381 PMCID: PMC10312561 DOI: 10.1101/2023.05.30.542876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Postnatal ocular growth is regulated by a vision-dependent mechanism, termed emmetropization, which acts to minimize refractive error through coordinated growth of the ocular tissues. Many studies suggest that the ocular choroid participates in the emmetropization process via the production of scleral growth regulators that control ocular elongation and refractive development. To elucidate the role of the choroid in emmetropization, we used single-cell RNA sequencing (scRNA-seq) to characterize the cell populations in the chick choroid and compare gene expression changes in these cell populations during conditions in which the eye is undergoing emmetropization. UMAP clustering analysis identified 24 distinct cell clusters in all chick choroids. 7 clusters were identified as fibroblast subpopulations; 5 clusters represented different populations of endothelial cells; 4 clusters were CD45+ macrophages, T cells and B cells; 3 clusters were Schwann cell subpopulations; and 2 clusters were identified as melanocytes. Additionally, single populations of RBCs, plasma cells and neuronal cells were identified. Significant changes in gene expression between control and treated choroids were identified in 17 cell clusters, representing 95% of total choroidal cells. The majority of significant gene expression changes were relatively small (< 2 fold). The highest changes in gene expression were identified in a rare cell population (0.11% - 0.49% of total choroidal cells). This cell population expressed high levels of neuron-specific genes as well as several opsin genes suggestive of a rare neuronal cell population that is potentially light sensitive. Our results, for the first time, provide a comprehensive profile of the major choroidal cell types and their gene expression changes during the process of emmetropization as well as insights into the canonical pathways and upstream regulators that coordinate postnatal ocular growth.
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Affiliation(s)
- Jody A Summers
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States
| | - Kenneth L Jones
- Bioinformatic Solutions LLC, Sheridan, Wyoming, 82801, United States
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11
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Dickenson RE, Pellon A, Ponde NO, Hepworth O, Daniels Gatward LF, Naglik JR, Moyes DL. EGR1 regulates oral epithelial cell responses to Candida albicans via the EGFR- ERK1/2 pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535186. [PMID: 37066428 PMCID: PMC10103955 DOI: 10.1101/2023.03.31.535186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Candida albicans is a fungal pathobiont colonising mucosal surfaces of the human body, including the oral cavity. Under certain predisposing conditions, C. albicans invades mucosal tissues activating EGFR-MAPK signalling pathways in epithelial cells via the action of its peptide toxin candidalysin. However, our knowledge of the epithelial mechanisms involved during C. albicans colonisation is rudimentary. Here, we describe the role of the transcription factor early growth response protein 1 (EGR1) in human oral epithelial cells (OECs) in response to C. albicans. EGR1 expression increases in OECs when exposed to C. albicans independently of fungal viability, morphology, or candidalysin release, suggesting EGR1 is involved in the fundamental recognition of C. albicans, rather than in response to invasion or 'pathogenesis'. Upregulation of EGR1 is mediated by EGFR via Raf1, ERK1/2 and NF-κB signalling but not PI3K/mTOR signalling. Notably, EGR1 mRNA silencing impacts on anti-C. albicans immunity, reducing GM-CSF, IL-1α and IL-1β release, and increasing IL-6 and IL-8 production. These findings identify an important role for EGR1 in priming epithelial cells to respond to subsequent invasive infection by C. albicans and elucidate the regulation circuit of this transcription factor after contact.
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Affiliation(s)
- Ruth E Dickenson
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
- Department of Infectious Diseases, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aize Pellon
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Nicole O Ponde
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
- Now at Department of Medicine, University of Pittsburgh, USA
| | - Olivia Hepworth
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Lydia F Daniels Gatward
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Cardiovascular and Metabolic Medicine & Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Julian R Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - David L Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
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12
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Woodson CM, Kehn-Hall K. Examining the role of EGR1 during viral infections. Front Microbiol 2022; 13:1020220. [PMID: 36338037 PMCID: PMC9634628 DOI: 10.3389/fmicb.2022.1020220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 09/06/2023] Open
Abstract
Early growth response 1 (EGR1) is a multifunctional mammalian transcription factor capable of both enhancing and/or inhibiting gene expression. EGR1 can be activated by a wide array of stimuli such as exposure to growth factors, cytokines, apoptosis, and various cellular stress states including viral infections by both DNA and RNA viruses. Following induction, EGR1 functions as a convergence point for numerous specialized signaling cascades and couples short-term extracellular signals to influence transcriptional regulation of genes required to initiate the appropriate biological response. The role of EGR1 has been extensively studied in both physiological and pathological conditions of the adult nervous system where it is readily expressed in various regions of the brain and is critical for neuronal plasticity and the formation of memories. In addition to its involvement in neuropsychiatric disorders, EGR1 has also been widely examined in the field of cancer where it plays paradoxical roles as a tumor suppressor gene or oncogene. EGR1 is also associated with multiple viral infections such as Venezuelan equine encephalitis virus (VEEV), Kaposi's sarcoma-associated herpesvirus (KSHV), herpes simplex virus 1 (HSV-1), human polyomavirus JC virus (JCV), human immunodeficiency virus (HIV), and Epstein-Barr virus (EBV). In this review, we examine EGR1 and its role(s) during viral infections. First, we provide an overview of EGR1 in terms of its structure, other family members, and a brief overview of its roles in non-viral disease states. We also review upstream regulators of EGR1 and downstream factors impacted by EGR1. Then, we extensively examine EGR1 and its roles, both direct and indirect, in regulating replication of DNA and RNA viruses.
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Affiliation(s)
- Caitlin M. Woodson
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylene Kehn-Hall
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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13
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Yuan L, Fung TS, He J, Chen RA, Liu DX. Modulation of Viral Replication, Apoptosis and Antiviral Response by Induction and Mutual Regulation of EGR and AP-1 Family Genes During Coronavirus Infection. Emerg Microbes Infect 2022; 11:1717-1729. [PMID: 35727266 PMCID: PMC9262369 DOI: 10.1080/22221751.2022.2093133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Coronaviruses have evolved a variety of strategies to exploit normal cellular processes and signalling pathways for their efficient reproduction in a generally hostile cellular environment. One immediate-early response gene (IEG) family, the AP-1 gene family, was previously shown to be activated by coronavirus infection. In this study, we report that another IEG family, the EGR family, is also activated in cells infected with four different coronaviruses in three genera, i.e. gammacoronavirus infectious bronchitis virus (IBV), alphacoronaviruses porcine epidemic diarrhoea virus (PEDV) and human coronavirus-229E (HCoV-229E), and betacoronavirus HCoV-OC43. Knockdown of EGR1 reduced the expression of cJUN and cFOS, and knockdown of cJUN and/or cFOS reduced the expression of EGR1, demonstrating that these two IEG families may be cross-activated and mutual regulated. Furthermore, ERK1/2 was identified as an upstream kinase, and JNK and p38 as inhibitors of EGR1 activation in coronavirus-infected cells. However, upregulation of EGR family genes, in particular EGR1, appears to play a differential role in regulating viral replication, apoptosis and antiviral response. EGR1 was shown to play a limited role in regulation of coronavirus replication, and an anti-apoptotic role in cells infected with IBV or PEDV, but not in cells infected with HCoV-229E. Upregulation of EGR1 may also play a differential role in the regulation of antiviral response against different coronaviruses. This study reveals a novel regulatory network shared by different coronaviruses in the immediate-early response of host cells to infection.
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Affiliation(s)
- Lixia Yuan
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - To Sing Fung
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China
| | - Jiawen He
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - Rui Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
| | - Ding Xiang Liu
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, Guangdong, People's Republic of China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526000, Guangdong, China
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14
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Yang JCS, Huang LH, Wu SC, Wu YC, Wu CJ, Lin CW, Tsai PY, Chien PC, Hsieh CH. Recovery of Dysregulated Genes in Cancer-Related Lower Limb Lymphedema After Supermicrosurgical Lymphaticovenous Anastomosis – A Prospective Longitudinal Cohort Study. J Inflamm Res 2022; 15:761-773. [PMID: 35153500 PMCID: PMC8824698 DOI: 10.2147/jir.s350421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/15/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Johnson Chia-Shen Yang
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Lien-Hung Huang
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shao-Chun Wu
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Chan Wu
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chia-Jung Wu
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chia-Wei Lin
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Pei-Yu Tsai
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Peng-Chen Chien
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ching-Hua Hsieh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Correspondence: Ching-Hua Hsieh, Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, 123 Dapi Road, Niaosong District, Kaohsiung City, 833, Taiwan, Tel +886-7-7317123, ext.8002, Fax +886-7-7354309, Email
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15
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Chu YB, Li J, Jia P, Cui J, Zhang R, Kang X, Lv M, Zhang S. Irf1- and Egr1-activated transcription plays a key role in macrophage polarization: A multiomics sequencing study with partial validation. Int Immunopharmacol 2021; 99:108072. [PMID: 34426111 DOI: 10.1016/j.intimp.2021.108072] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Macrophage polarization has a causal role in the pathogenesis and resolution of various clinical diseases. DNA-binding transcription factors (TFs) have been identified as essential factors during gene transcription. Better insight into the TFs that regulate macrophage polarization could provide novel therapeutic targets. METHODS IFN-γ (50 ng/mL) or IL4 (20 ng/mL) was utilized to stimulate bone marrow-derived macrophages from mice for 24 h for M1- and M2-polarized macrophage model construction, respectively. First, ATAC-seq (Assay for Targeting Accessible-Chromatin with high throughout sequencing) and motif analysis were conducted to identify potential transcription factors (TFs) involved in M1 and M2 macrophage polarization. Second, essential TFs were identified through RNA-seq, after which, their expression was compared between M0-polarized and M1/M2-polarized macrophages. Furthermore, a multiomic analysis of RNA-seq (siRNA knock down of the identified TFs), ChIP-seq and ATAC-seq was utilized to explore the TF-regulated molecular network. GO and KEGG analyses were used to expound the main functions of the TF-regulated molecular network. Finally, the top 5 TF-regulated genes were validated through flow cytometry, ELISA and qPCR. The cut-off values for high-throughput sequencing and qPCR were FDR < 0.05 and P < 0.05, respectively. RESULTS Compared with M0 macrophages, 10,771 and 4,848 peaks were identified by ATAC-seq during M1 and M2 macrophage polarization, respectively (FDR < 0.05). Fifty and 62 TF binding motifs were identified for the TFs that participate in M1 and M2 macrophage polarization, respectively. The most significantly highly expressed TFs in M1 and M2 macrophages were identified by RNA-seq as Irf1 and Egr1, with LogFC values of 3.2 and 2.8, respectively. Multiomic analyses further found that Irf1 regulated the transcription of 90 genes and that Egr1 regulated the transcription of 116 genes. The Irf1-regulated molecular network played a key role in the inflammatory response and viral defence of M1 macrophages, and 116 Egr1-regulated genes included anti-inflammatory and cell proliferation genes. Validation experiments indicated that IFN-γ-induced Gbp5, Nos2, CD86, Cxcl10 and Cxcl5 expression was significantly downregulated in siIrf1-BMDMs, and IL4-induced Itgax, Nipal1, Bhlhe40, CD206 and Ffar4 expression was significantly downregulated in siEgr1-BMDMs (P < 0.05). CONCLUSIONS Through multiomic analyses of epigenetic sequencing and RNA-seq with partial validation, the current study found that Irf1- and Egr1-induced transcription plays key roles in M1 and M2 macrophage polarization, respectively.
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Affiliation(s)
- Yan-Biao Chu
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Pingdong Jia
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Jiyun Cui
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Ronghua Zhang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Xueli Kang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Meng Lv
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Shi Zhang
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China; Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China; Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
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