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Liu S, Peng Q, Fan B, Zhang G, He W, Wang C, Xie J, Song X, Yuan B, Guo R, Li J, Li B. Comparative transcriptome reveals EphA2 and c-Fos as key factors driving enhanced replication in high-passage porcine deltacoronavirus strain. Vet Microbiol 2024; 297:110211. [PMID: 39096790 DOI: 10.1016/j.vetmic.2024.110211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/05/2024]
Abstract
Porcine deltacoronavirus (PDCoV), a cross-species transmissible enterovirus, frequently induces severe diarrhea and vomiting symptoms in piglets, which not only pose a significant menace to the global pig industry but also a potential public safety risk. In a previous study, we isolated a vaccine candidate, PDCoV CZ2020-P100, by passaging a parental PDCoV strain in vitro, exhibiting attenuated virulence and enhanced replication. However, the factors underlying these differences between primary and passaged strains remain unknown. In this study, we present the transcriptional landscapes of porcine kidney epithelial cells (LLC-PK1) cells infected with PDCoV CZ2020-P1 strain and P100 strain using the RNA-sequencing. We identified 105 differentially expressed genes (DEGs) in P1-infected cells and 295 DEGs in P100-infected cells. Enrichment analyses indicated that many DEGs showed enrichment in immune and inflammatory responses, with a more and higher upregulation of DEGs enriched in the P100-infected group. Notably, the DEGs were concentrated in the MAPK pathway within the P100-infected group, with significant upregulation in EphA2 and c-Fos. Knockdown of EphA2 and c-Fos reduced PDCoV infection and significantly impaired P100 replication compared to P1, suggesting a novel mechanism in which EphA2 and c-Fos are highly involved in passaged virus replication. Our findings illuminate the resemblances and distinctions in the gene expression patterns of host cells infected with P1 and P100, confirming that EphA2 and c-Fos play key roles in high-passage PDCoV replication. These results enhance our understanding of the changes in virulence and replication capacity during the process of passaging.
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Affiliation(s)
- Shiyu Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China; College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qi Peng
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang 330045, China
| | - Baochao Fan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Gege Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Wenlong He
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Chuanhong Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Jingyuan Xie
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Xu Song
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Boshui Yuan
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Rongli Guo
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Jizong Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China
| | - Bin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture; Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing 210014, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
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2
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Li F, Tian J, Zhang L, He H, Song D. A multi-omics approach to reveal critical mechanisms of activator protein 1 (AP-1). Biomed Pharmacother 2024; 178:117225. [PMID: 39084078 DOI: 10.1016/j.biopha.2024.117225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024] Open
Abstract
The Activator Protein 1 (AP-1) transcription factor complex plays a pivotal role in the regulation of cancer-related genes, influencing cancer cell proliferation, invasion, migration, angiogenesis, and apoptosis. Composed of multiple subunits, AP-1 has diverse roles across different cancer types and environmental contexts, but its specific mechanisms remain unclear. The advent of multi-omics approaches has shed light on a more comprehensive understanding of AP-1's role and mechanism in gene regulation. This review collates recent genome-wide data on AP-1 and provides an overview of its expression, structure, function, and interaction across different diseases. An examination of these findings can illuminate the intricate nature of AP-1 regulation and its significant involvement in the progression of different diseases. Moreover, we discuss the potential use of AP-1 as a target for individual therapy and explore the various challenges associated with such an approach. Ultimately, this review provides valuable insights into the biology of AP-1 and its potential as a therapeutic target for cancer and disease treatments.
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Affiliation(s)
- Fei Li
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China; School of Public Health, North China University of Science and Technology, Tangshan 063000, China
| | - Jiaqi Tian
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China
| | - Lin Zhang
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China
| | - Huan He
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun 130021, China
| | - Dandan Song
- Clinical Medical Research Center for Women and Children Diseases, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, China.
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3
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Lin YC, Ku CC, Wuputra K, Liu CJ, Wu DC, Satou M, Mitsui Y, Saito S, Yokoyama KK. Possible Strategies to Reduce the Tumorigenic Risk of Reprogrammed Normal and Cancer Cells. Int J Mol Sci 2024; 25:5177. [PMID: 38791215 PMCID: PMC11120835 DOI: 10.3390/ijms25105177] [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: 03/16/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The reprogramming of somatic cells to pluripotent stem cells has immense potential for use in regenerating or redeveloping tissues for transplantation, and the future application of this method is one of the most important research topics in regenerative medicine. These cells are generated from normal cells, adult stem cells, or neoplastic cancer cells. They express embryonic stem cell markers, such as OCT4, SOX2, and NANOG, and can differentiate into all tissue types in adults, both in vitro and in vivo. However, tumorigenicity, immunogenicity, and heterogeneity of cell populations may hamper the use of this method in medical therapeutics. The risk of cancer formation is dependent on mutations of these stemness genes during the transformation of pluripotent stem cells to cancer cells and on the alteration of the microenvironments of stem cell niches at genetic and epigenetic levels. Recent reports have shown that the generation of induced pluripotent stem cells (iPSCs) derived from human fibroblasts could be induced using chemicals, which is a safe, easy, and clinical-grade manufacturing strategy for modifying the cell fate of human cells required for regeneration therapies. This strategy is one of the future routes for the clinical application of reprogramming therapy. Therefore, this review highlights the recent progress in research focused on decreasing the tumorigenic risk of iPSCs or iPSC-derived organoids and increasing the safety of iPSC cell preparation and their application for therapeutic benefits.
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Affiliation(s)
- Ying-Chu Lin
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
| | - Cha-Chien Ku
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Kenly Wuputra
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Chung-Jung Liu
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Deng-Chyang Wu
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Maki Satou
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
| | - Yukio Mitsui
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
| | - Shigeo Saito
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Research Institute, Horus Co., Ltd., Iruma 358-0032, Saitama, Japan; (M.S.); (Y.M.)
- Saito Laboratory of Cell Technology, Yaita 329-1571, Tochigi, Japan
| | - Kazunari K. Yokoyama
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Graduate Institute of Medicine, Department of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-C.K.); (K.W.)
- Regenerative Medicine and Cell Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (C.-J.L.); (D.-C.W.)
- Cell Therapy and Research Center, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
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4
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Mazzeo L, Ghosh S, Di Cicco E, Isma J, Tavernari D, Samarkina A, Ostano P, Youssef MK, Simon C, Dotto GP. ANKRD1 is a mesenchymal-specific driver of cancer-associated fibroblast activation bridging androgen receptor loss to AP-1 activation. Nat Commun 2024; 15:1038. [PMID: 38310103 PMCID: PMC10838290 DOI: 10.1038/s41467-024-45308-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: 02/27/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
There are significant commonalities among several pathologies involving fibroblasts, ranging from auto-immune diseases to fibrosis and cancer. Early steps in cancer development and progression are closely linked to fibroblast senescence and transformation into tumor-promoting cancer-associated fibroblasts (CAFs), suppressed by the androgen receptor (AR). Here, we identify ANKRD1 as a mesenchymal-specific transcriptional coregulator under direct AR negative control in human dermal fibroblasts (HDFs) and a key driver of CAF conversion, independent of cellular senescence. ANKRD1 expression in CAFs is associated with poor survival in HNSCC, lung, and cervical SCC patients, and controls a specific gene expression program of myofibroblast CAFs (my-CAFs). ANKRD1 binds to the regulatory region of my-CAF effector genes in concert with AP-1 transcription factors, and promotes c-JUN and FOS association. Targeting ANKRD1 disrupts AP-1 complex formation, reverses CAF activation, and blocks the pro-tumorigenic properties of CAFs in an orthotopic skin cancer model. ANKRD1 thus represents a target for fibroblast-directed therapy in cancer and potentially beyond.
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Affiliation(s)
- Luigi Mazzeo
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Soumitra Ghosh
- ORL service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Emery Di Cicco
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Jovan Isma
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Paola Ostano
- Cancer Genomics Laboratory, Edo and Elvo Tempia Valenta Foundation, Biella, 13900, Italy
| | - Markus K Youssef
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Christian Simon
- ORL service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- International Cancer Prevention Institute, Epalinges, Switzerland
| | - G Paolo Dotto
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
- Cutaneous Biology Research Center, Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
- ORL service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
- International Cancer Prevention Institute, Epalinges, Switzerland.
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5
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Liu D, Fu Y, Wang X, Wang X, Fang X, Zhou Y, Wang R, Zhang P, Jiang M, Jia D, Wang J, Chen H, Guo G, Han X. Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses. Stem Cell Reports 2023; 18:2464-2481. [PMID: 37995704 PMCID: PMC10724075 DOI: 10.1016/j.stemcr.2023.10.018] [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: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023] Open
Abstract
In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages, such as multilineage differentiation, angiogenesis, and close cell-cell interactions. To systematically investigate multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We identified 43 cell types, inferred 18 cell differentiation trajectories, and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. Additionally, we developed the developmental single-cell Basic Local Alignment Search Tool (dscBLAST), an R-based cell identification tool, to simplify the identification processes of developmental cells. Using dscBLAST, we aligned cells in multiple differentiation models to normally developing cells to further understand their differentiation states. Overall, our study offers new insights into stem cell differentiation and human embryonic development; dscBLAST shows favorable cell identification performance, providing a powerful identification tool for developmental cells.
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Affiliation(s)
- Daiyuan Liu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xueyi Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Danmei Jia
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jingjing Wang
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China; M20 Genomics, Hangzhou, China
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China; Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China.
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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. NATURE AGING 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Targeting IKKβ Activity to Limit Sterile Inflammation in Acetaminophen-Induced Hepatotoxicity in Mice. Pharmaceutics 2023; 15:pharmaceutics15020710. [PMID: 36840032 PMCID: PMC9959252 DOI: 10.3390/pharmaceutics15020710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The kinase activity of inhibitory κB kinase β (IKKβ) acts as a signal transducer in the activating pathway of nuclear factor-κB (NF-κB), a master regulator of inflammation and cell death in the development of numerous hepatocellular injuries. However, the importance of IKKβ activity on acetaminophen (APAP)-induced hepatotoxicity remains to be defined. Here, a derivative of caffeic acid benzylamide (CABA) inhibited the kinase activity of IKKβ, as did IMD-0354 and sulfasalazine which show therapeutic efficacy against inflammatory diseases through a common mechanism: inhibiting IKKβ activity. To understand the importance of IKKβ activity in sterile inflammation during hepatotoxicity, C57BL/6 mice were treated with CABA, IMD-0354, or sulfasalazine after APAP overdose. These small-molecule inhibitors of IKKβ activity protected the APAP-challenged mice from necrotic injury around the centrilobular zone in the liver, and rescued the mice from hepatic damage-associated lethality. From a molecular perspective, IKKβ inhibitors directly interrupted sterile inflammation in the Kupffer cells of APAP-challenged mice, such as damage-associated molecular pattern (DAMP)-induced activation of NF-κB activity via IKKβ, and NF-κB-regulated expression of cytokines and chemokines. However, CABA did not affect the upstream pathogenic events, including oxidative stress with glutathione depletion in hepatocytes after APAP overdose. N-acetyl cysteine (NAC), the only FDA-approved antidote against APAP overdose, replenishes cellular levels of glutathione, but its limited efficacy is concerning in late-presenting patients who have already undergone oxidative stress in the liver. Taken together, we propose a novel hypothesis that chemical inhibition of IKKβ activity in sterile inflammation could mitigate APAP-induced hepatotoxicity in mice, and have the potential to complement NAC treatment in APAP overdoses.
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8
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Pi Z, Qiu X, Liu J, Shi Y, Zeng Z, Xiao R. Activating Protein-1 (AP-1): A Promising Target for the Treatment of Fibrotic Diseases. Curr Med Chem 2023; 31:CMC-EPUB-129375. [PMID: 36757030 DOI: 10.2174/0929867330666230209100059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/04/2022] [Accepted: 12/29/2022] [Indexed: 02/10/2023]
Abstract
The fibrosis of tissues and organs occurs via an aberrant tissue remodeling process characterized by an excessive deposition of extracellular matrix, which can lead to organ dysfunction, organ failure, and death. Because the pathogenesis of fibrosis remains unclear and elusive, there is currently no medication to reverse it; hence, this process deserves further study. Activating protein-1 (AP-1)-comprising Jun (c-Jun, JunB, JunD), Fos (c-fos, FosB, Fra1, and Fra2), and activating transcription factor-is a versatile dimeric transcription factor. Numerous studies have demonstrated that AP-1 plays a crucial role in advancing tissue and organ fibrosis via induction of the expression of fibrotic molecules and activating fibroblasts. This review focuses on the role of AP-1 in a range of fibrotic disorders as well as on the antifibrotic effects of AP-1 inhibitors. It also discusses the potential of AP-1 as a new therapeutic target in conditions involving tissue and organ fibrosis.
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Affiliation(s)
- Zixin Pi
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Department of Medical Genetics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Xiangning Qiu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Jiani Liu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yaqian Shi
- Second Xiangya Hospital of Central South University Department of Dermatology Changsha China
| | - Zhuotong Zeng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Rong Xiao
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
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9
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Merhi M, Ahmad F, Taib N, Inchakalody V, Uddin S, Shablak A, Dermime S. The complex network of transcription factors, immune checkpoint inhibitors and stemness features in colorectal cancer: A recent update. Semin Cancer Biol 2023; 89:1-17. [PMID: 36621515 DOI: 10.1016/j.semcancer.2023.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Cancer immunity is regulated by several mechanisms that include co-stimulatory and/or co-inhibitory molecules known as immune checkpoints expressed by the immune cells. In colorectal cancer (CRC), CTLA-4, LAG3, TIM-3 and PD-1 are the major co-inhibitory checkpoints involved in tumor development and progression. On the other hand, the deregulation of transcription factors and cancer stem cells activity plays a major role in the development of drug resistance and in the spread of metastatic disease in CRC. In this review, we describe how the modulation of such transcription factors affects the response of CRC to therapies. We also focus on the role of cancer stem cells in tumor metastasis and chemoresistance and discuss both preclinical and clinical approaches for targeting stem cells to prevent their tumorigenic effect. Finally, we provide an update on the clinical applications of immune checkpoint inhibitors in CRC and discuss the regulatory effects of transcription factors on the expression of the immune inhibitory checkpoints with specific focus on the PD-1 and PD-L1 molecules.
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Affiliation(s)
- Maysaloun Merhi
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Fareed Ahmad
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Inchakalody
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Alaaeldin Shablak
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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10
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Wang R, Zhang P, Wang J, Ma L, E W, Suo S, Jiang M, Li J, Chen H, Sun H, Fei L, Zhou Z, Zhou Y, Chen Y, Zhang W, Wang X, Mei Y, Sun Z, Yu C, Shao J, Fu Y, Xiao Y, Ye F, Fang X, Wu H, Guo Q, Fang X, Li X, Gao X, Wang D, Xu PF, Zeng R, Xu G, Zhu L, Wang L, Qu J, Zhang D, Ouyang H, Huang H, Chen M, NG SC, Liu GH, Yuan GC, Guo G, Han X. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res 2023; 51:501-516. [PMID: 35929025 PMCID: PMC9881150 DOI: 10.1093/nar/gkac633] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal-Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging.
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Affiliation(s)
- Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | | | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Zhongyi Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Jikai Shao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Hanyu Wu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Qile Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
| | - Xiunan Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xianzhi Gao
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Dan Wang
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peng-Fei Xu
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Rui Zeng
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gang Xu
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lijun Zhu
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Hongwei Ouyang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - He Huang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shyh-Chang NG
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, NY, NY 10029, USA
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
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11
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Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
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Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
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12
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Hojo H, Saito T, He X, Guo Q, Onodera S, Azuma T, Koebis M, Nakao K, Aiba A, Seki M, Suzuki Y, Okada H, Tanaka S, Chung UI, McMahon AP, Ohba S. Runx2 regulates chromatin accessibility to direct the osteoblast program at neonatal stages. Cell Rep 2022; 40:111315. [PMID: 36070691 PMCID: PMC9510047 DOI: 10.1016/j.celrep.2022.111315] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts. Hojo et al. investigate the gene-regulatory landscape underlying specification of skeletal cell types in neonatal mice. Runx2, an osteoblast determinant, engages with cell-type-distinct chromatin-accessible regions and is essential for establishment of chromatin accessibility in osteoblasts. The study provides insights into enhancer networks in skeletal development.
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Affiliation(s)
- Hironori Hojo
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Taku Saito
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Xinjun He
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Qiuyu Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shoko Onodera
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Toshifumi Azuma
- Department of Biochemistry, Tokyo Dental College, Tokyo 101-0061, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kazuki Nakao
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Atsu Aiba
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sakae Tanaka
- Orthopedic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Ung-Il Chung
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8655, Japan
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Shinsuke Ohba
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, Nagasaki 852-8588, Japan; Department of Oral Anatomy and Developmental Biology, Graduate School of Dentistry, Osaka University, Osaka 565-0871, Japan.
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13
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Comandante-Lou N, Baumann DG, Fallahi-Sichani M. AP-1 transcription factor network explains diverse patterns of cellular plasticity in melanoma cells. Cell Rep 2022; 40:111147. [PMID: 35926467 DOI: 10.1016/j.celrep.2022.111147] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/04/2022] [Accepted: 07/07/2022] [Indexed: 12/28/2022] Open
Abstract
Cellular plasticity associated with fluctuations in transcriptional programs allows individual cells in a tumor to adopt heterogeneous differentiation states and switch phenotype during their adaptive responses to therapies. Despite increasing knowledge of such transcriptional programs, the molecular basis of cellular plasticity remains poorly understood. Here, we combine multiplexed transcriptional and protein measurements at population and single-cell levels with multivariate statistical modeling to show that the state of AP-1 transcription factor network plays a unifying role in explaining diverse patterns of plasticity in melanoma. We find that a regulated balance among AP-1 factors cJUN, JUND, FRA2, FRA1, and cFOS determines the intrinsic diversity of differentiation states and adaptive responses to MAPK inhibitors in melanoma cells. Perturbing this balance through genetic depletion of specific AP-1 proteins, or by MAPK inhibitors, shifts cellular heterogeneity in a predictable fashion. Thus, AP-1 may serve as a critical node for manipulating cellular plasticity with potential therapeutic implications.
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Affiliation(s)
- Natacha Comandante-Lou
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Douglas G Baumann
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Fallahi-Sichani
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.
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14
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Lv X, Li Q, Liu H, Gong M, Zhao Y, Hu J, Wu F, Wu X. JUN
activation modulates chromatin accessibility to drive
TNFα
‐induced mesenchymal transition in glioblastoma. J Cell Mol Med 2022; 26:4602-4612. [PMID: 35851726 PMCID: PMC9357637 DOI: 10.1111/jcmm.17490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/13/2022] [Accepted: 07/05/2022] [Indexed: 11/27/2022] Open
Abstract
Chromatin dynamics as well as genetic evolution underlies the adaptability of tumour cells to environmental cues. Three subtypes of tumour cells have been identified in glioblastoma, one of the commonest malignant brain tumours in adults. During tumour progression or under therapeutic pressure, the non‐mesenchymal subtypes may progress to the mesenchymal subtype, leading to unfavourable prognosis. However, the molecular mechanisms for this transition remain poorly understood. Here taking a TNFα‐induced cellular model, we profile the chromatin accessibility dynamics during mesenchymal transition. Moreover, we identify the JUN family as one of the key driving transcription factors for the gained chromatin accessibility. Accordingly, inhibition of JUN phosphorylation and therefore its transcription activity successfully impedes TNFα‐induced chromatin remodelling and mesenchymal transition. In line with these findings based on experimental models, JUN activity is positively correlated with mesenchymal features in clinical glioblastoma specimens. Together, this study unveils a deregulated transcription regulatory network in glioblastoma progression and hopefully provides a rationale for anti‐glioblastoma therapy.
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Affiliation(s)
- Xuejiao Lv
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
| | - Qian Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
| | - Hang Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
| | - Meihan Gong
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
| | - Yingying Zhao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
| | - Jinyang Hu
- Department of Neurosurgery Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan China
| | - Fan Wu
- Department of Molecular Neuropathology Beijing Neurosurgical Institute, Capital Medical University Beijing China
| | - Xudong Wu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Cell Biology Tianjin Medical University Tianjin China
- Department of Neurosurgery Tianjin Medical University General Hospital Tianjin China
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15
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Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development. Nat Genet 2022; 54:1051-1061. [PMID: 35817981 DOI: 10.1038/s41588-022-01118-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/01/2022] [Indexed: 12/21/2022]
Abstract
Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell differentiation. Recent advances in single-cell genomics are altering our understanding of the Waddington landscape, yet the molecular mechanisms of cell-fate decisions remain poorly understood. We constructed a cell landscape of mouse lineage differentiation during development at the single-cell level and described both lineage-common and lineage-specific regulatory programs during cell-type maturation. We also found lineage-common regulatory programs that are broadly active during the development of invertebrates and vertebrates. In particular, we identified Xbp1 as an evolutionarily conserved regulator of cell-fate determinations across different species. We demonstrated that Xbp1 transcriptional regulation is important for the stabilization of the gene-regulatory networks for a wide range of mouse cell types. Our results offer genetic and molecular insights into cellular gene-regulatory programs and will serve as a basis for further advancing the understanding of cell-fate decisions.
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16
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Zhang H, Pei L, Ouyang Z, Wang H, Chen X, Jiang K, Huang S, Jiang R, Xiang Y, Wei K. AP-1 activation mediates postnatal cardiomyocyte maturation. Cardiovasc Res 2022; 119:536-550. [PMID: 35640820 DOI: 10.1093/cvr/cvac088] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS Postnatal maturation of mammalian cardiomyocytes proceeds rapidly after birth, with most of the myocytes exiting cell cycle, becoming binucleated, and adopting oxidative phosphorylation as the primary metabolic route. The triggers and transcriptional programs regulating cardiomyocyte maturation have not been fully understood yet. We performed single cell RNA-Seq in postnatal rat hearts in order to identify the important factors for this process. METHODS AND RESULTS Single cell RNA-Seq profiling was performed of postnatal day 1 and day 7 rat hearts, and we found that members of the AP-1 transcription factors showed a transient upregulation in the maturing cardiomyocytes, suggesting their functional involvement in the process. Activating members of the AP-1 family by palmitate or adrenergic stimulation inhibited cardiomyocyte cytokinesis and promoted cardiomyocyte maturation. In contrast, knocking down AP-1 members Atf3 and Jun promoted cardiomyocyte cytokinesis, reduced polyploidy and inhibited maturation. Mechanistically, RNA-Seq results and rescue experiments indicated that AP-1 members activate the expression of fatty acid metabolic genes to promote cardiomyocyte maturation. Finally, intraperitoneal injection of AP-1 inhibitor T-5224 in neonatal mice inhibits cardiomyocyte maturation in vivo. CONCLUSION Our results are the first evidence implicating AP-1 transcription factors in postnatal cardiomyocyte maturation both in vitro and in vivo, which expand our understanding of the molecular mechanism of cardiomyocyte maturation, and may lead to novel therapies to treat congenital heart diseases. TRANSLATIONAL PERSPECTIVE Postnatal cardiomyocyte maturation is a crucial process of cardiac development that determines fitness of the adult heart, and can be affected by multiple congenital heart diseases which lead to adult heart conditions. Our finding that AP-1 transcription factors transiently activated by multiple cues such as fatty acid and adrenergic signal promote cardiomyocyte maturation provided novel targets for therapeutic intervention, which may be applied during the narrow time window of postnatal cardiomyocyte maturation to treat congenital heart diseases and limit their impact on the adult heart.
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Affiliation(s)
- Hongjie Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Lijuan Pei
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Zhaohui Ouyang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Haocun Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Xin Chen
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Kai Jiang
- Shanghai East Hospital, Key Laboratory of Arrhythmias of the Ministry of Education of China, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shiqi Huang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Rui Jiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
| | - Yaozu Xiang
- Shanghai East Hospital, Key Laboratory of Arrhythmias of the Ministry of Education of China, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ke Wei
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, P.R. China
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17
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Yu F, Li W, Wang L, Que S, Lu L. Characterization of grass carp FosB, Fosl2, JunD transcription factors in response to GCRV infection. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Shah K, Maradana MR, Joaquina Delàs M, Metidji A, Graelmann F, Llorian M, Chakravarty P, Li Y, Tolaini M, Shapiro M, Kelly G, Cheshire C, Bhurta D, Bharate SB, Stockinger B. Cell-intrinsic Aryl Hydrocarbon Receptor signalling is required for the resolution of injury-induced colonic stem cells. Nat Commun 2022; 13:1827. [PMID: 35383166 PMCID: PMC8983642 DOI: 10.1038/s41467-022-29098-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/23/2022] [Indexed: 12/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is an environmental sensor that integrates microbial and dietary cues to influence physiological processes within the intestinal microenvironment, protecting against colitis and colitis-associated colorectal cancer development. Rapid tissue regeneration upon injury is important for the reinstatement of barrier integrity and its dysregulation promotes malignant transformation. Here we show that AHR is important for the termination of the regenerative response and the reacquisition of mature epithelial cell identity post injury in vivo and in organoid cultures in vitro. Using an integrative multi-omics approach in colon organoids, we show that AHR is required for timely termination of the regenerative response through direct regulation of transcription factors involved in epithelial cell differentiation as well as restriction of chromatin accessibility to regeneration-associated Yap/Tead transcriptional targets. Safeguarding a regulated regenerative response places AHR at a pivotal position in the delicate balance between controlled regeneration and malignant transformation. Rapid intestinal regeneration after injury is critical to maintain barrier integrity and homeostasis, but must be tightly controlled to prevent tumorigenesis. Here they show that the aryl hydrocarbon receptor is required to terminate the regenerative response after wound healing.
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Affiliation(s)
| | | | | | - Amina Metidji
- Department of Oncology, St Jude Children's Hospital, Memphis, TN, USA
| | - Frederike Graelmann
- Immunology and Environment, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | | | | | - Ying Li
- The Francis Crick Institute, London, UK
| | | | | | | | | | - Deendyal Bhurta
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Sandip B Bharate
- Natural Products & Medicinal Chemistry Division, CSIR - Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
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19
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Bhattacharya A, Fushimi A, Yamashita N, Hagiwara M, Morimoto Y, Rajabi H, Long MD, Abdulla M, Ahmad R, Street K, Liu S, Liu T, Kufe D. MUC1-C Dictates JUN and BAF-Mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells. Mol Cancer Res 2022; 20:556-567. [PMID: 35022313 PMCID: PMC8983489 DOI: 10.1158/1541-7786.mcr-21-0672] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/15/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022]
Abstract
The oncogenic MUC1-C protein promotes dedifferentiation of castrate-resistant prostate cancer (CRPC) and triple-negative breast cancer (TNBC) cells. Chromatin remodeling is critical for the cancer stem cell (CSC) state; however, there is no definitive evidence that MUC1-C regulates chromatin accessibility and thereby expression of stemness-associated genes. We demonstrate that MUC1-C drives global changes in chromatin architecture in the dedifferentiation of CRPC and TNBC cells. Our results show that MUC1-C induces differentially accessible regions (DAR) across their genomes, which are significantly associated with differentially expressed genes (DEG). Motif and cistrome analysis further demonstrated MUC1-C-induced DARs align with genes regulated by the JUN/AP-1 family of transcription factors. MUC1-C activates the BAF chromatin remodeling complex, which is recruited by JUN in enhancer selection. In studies of the NOTCH1 gene, which is required for CRPC and TNBC cell self-renewal, we demonstrate that MUC1-C is necessary for (i) occupancy of JUN and ARID1A/BAF, (ii) increases in H3K27ac and H3K4me3 signals, and (iii) opening of chromatin accessibility on a proximal enhancer-like signature. Studies of the EGR1 and LY6E stemness-associated genes further demonstrate that MUC1-C-induced JUN/ARID1A complexes regulate chromatin accessibility on proximal and distal enhancer-like signatures. These findings uncover a role for MUC1-C in chromatin remodeling that is mediated at least in part by JUN/AP-1 and ARID1A/BAF in association with driving the CSC state. IMPLICATIONS These findings show that MUC1-C, which is necessary for the CRPC and TNBC CSC state, activates a novel pathway involving JUN/AP-1 and ARID1A/BAF that regulates chromatin accessibility of stemness-associated gene enhancers.
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Affiliation(s)
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Masayuki Hagiwara
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Yoshihiro Morimoto
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Hasan Rajabi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Maha Abdulla
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rehan Ahmad
- Colorectal Research Chair, Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Kelly Street
- Department of Data Science, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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20
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Environmental adaptation in fish induced changes in the regulatory region of fatty acid elongase gene, elovl5, involved in long-chain polyunsaturated fatty acid biosynthesis. Int J Biol Macromol 2022; 204:144-153. [PMID: 35120941 DOI: 10.1016/j.ijbiomac.2022.01.184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
Fish are the main source of long-chain polyunsaturated fatty acids (LC-PUFA) for human consumption. In the process of evolution via natural selection, adaptation to distinct environments has likely driven changes in the endogenous capacity for LC-PUFA biosynthesis between marine and freshwater fishes. However, the molecular mechanisms underlying adaptive changes in this metabolic pathway are poorly understood. Here, we compared the transcriptional regulation of elongation of very long chain fatty acids protein 5 (Elovl5), which is one of the critical enzymes in LC-PUFA biosynthesis pathway, in marine large yellow croaker (Larimichthys crocea) and freshwater rainbow trout (Oncorhynchus mykiss). Comparative transcriptomic and absolute mRNA quantification analyses revealed that the expression of elovl5 in rainbow trout was markedly higher than that in large yellow croaker. Correspondingly, the number of chromatin accessible areas in the regulatory region of elovl5 in rainbow trout was higher than in large yellow croaker, which revealed that chromatin accessibility in the regulatory region of elovl5 in rainbow trout was higher. Furthermore, the differences in sequence and activity of the elovl5 promoter were observed between rainbow trout and large yellow croaker, and transcription factors including CCAAT/enhancer-binding protein β (CEBPβ), GATA binding protein 3 (GATA3) and upstream stimulatory factor 2 (USF2) displayed different regulatory roles on elovl5 expression between the two species. We propose that changes in the gene regulatory region driven by natural selection likely play a key role in differences in elovl5 expression and the activity of Elovl5, which may influence the LC-PUFA biosynthesis capacities of rainbow trout and large yellow croaker. These findings may also provide opportunities to improve the quality of aquatic products and, consequently, human health.
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21
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Wang H, Yang Y, Qian Y, Liu J, Qian L. Delineating chromatin accessibility re-patterning at single cell level during early stage of direct cardiac reprogramming. J Mol Cell Cardiol 2022; 162:62-71. [PMID: 34509499 PMCID: PMC8766888 DOI: 10.1016/j.yjmcc.2021.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 01/03/2023]
Abstract
Direct conversion of cardiac fibroblast into induced cardiomyocytes (iCMs) by forced expression of cardiac transcription factors, such as Mef2c, Gata4, and Tbx5 (MGT), holds great promise for regenerative medicine. The process of cardiac reprogramming consists of waves of transcriptome remodelling events. However, how this transcriptome remodelling is driven by the upstream chromatin landscape alteration is still unclear. In this study, we performed single-cell ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) on early reprogramming iCMs given the known epigenetic changes as early as day 3. This approach unveiled networks of transcription factors (TFs) involved in the early shift of chromatin accessibility during cardiac reprogramming. Combining our analysis with functional assays, we identified Smad3 to be a bimodal TF in cardiac reprogramming, a barrier in the initiation of reprogramming and a facilitator during the intermediate stage of reprogramming. Moreover, integrative analysis of scATAC-seq with scRNA-seq data led to the identification of active TFs important for iCM conversion. Finally, we discovered a global rewiring of cis-regulatory interactions of cardiac genes along the reprogramming trajectory. Collectively, our scATAC-seq study and the integrative analysis with scRNA-seq data provided valuable resources to understand the epigenomic heterogeneity and its alteration in relation to transcription changes during early stage of cardiac reprogramming.
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Affiliation(s)
- Haofei Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, United States of America,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, United States of America,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Yunzhe Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, United States of America,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, United States of America,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, United States of America,McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, United States of America,Corresponding author Dr. Li Qian, 111 Mason Farm Rd, University of North Carolina, Chapel Hill Chapel Hill, NC 27599, Phone: 919-962-0340, Fax: 919-966-6012,
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22
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He K, Feng Y, An S, Liu F, Xiang G. Integrative epigenomic profiling reveal AP-1 is a key regulator in intrahepatich cholangiocarcinoma. Genomics 2021; 114:241-252. [PMID: 34942351 DOI: 10.1016/j.ygeno.2021.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 04/19/2021] [Accepted: 12/14/2021] [Indexed: 01/14/2023]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor with poor prognosis while its mechanisms of pathogenesis remain elusive. In this study, we performed systemic epigenomic and transcriptomic profiling via MNase-seq, ChIP-seq and RNA-seq in normal cholangiocyte and ICC cell lines. We showed that active histone modifications (H3K4me3, H3K4me1 and H3K27ac) were less enriched on cancer-related genes in ICC cell lines compared to control. The region of different histone modification patterns is enrichment in sites of AP-1 motif. Subsequent analysis showed that ICC had different nucleosome occupancy in differentially expressed genes compared to a normal cell line. Furthermore, we found that AP-1 plays a key role in ICC and regulates ICC-related genes through its AP-1 binding site. This study is the first report showing the global features of histone modification, transcript, and nucleosome profiles in ICC; we also show that the transcription factor AP-1 might be a key target gene in ICC.
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Affiliation(s)
- Ke He
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou 510317, China; Department of Biochemistry, Zhongshan School of Medicine; Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, OX37LD, United Kingdom
| | - Sanqi An
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou 510317, China; Department of Biochemistry, Zhongshan School of Medicine; Center for Stem Cell Biology and Tissue Engineering, Key laboratory of ministry of education, Sun Yat-sen University, Guangzhou 510080, China
| | - Fei Liu
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Guoan Xiang
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou 510317, China.
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23
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Aman S, Li Y, Cheng Y, Yang Y, Lv L, Li B, Xia K, Li S, Wu H. DACH1 inhibits breast cancer cell invasion and metastasis by down-regulating the transcription of matrix metalloproteinase 9. Cell Death Discov 2021; 7:351. [PMID: 34772908 PMCID: PMC8590022 DOI: 10.1038/s41420-021-00733-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022] Open
Abstract
Human Dachshund homolog 1 (DACH1) is usually defined as a tumor suppressor, which plays an influential role in tumor growth and metastasis in a variety of cancer cells. However, the underlying mechanisms in these process are not yet fully clarified. In this study, DACH1 inhibited the invasion and metastasis of breast cancer cells by decreasing MMP9 expression. Mechanistically, DACH1 represses the transcriptional level of MMP9 by interacting with p65 and c-Jun at the NF-κB and AP-1 binding sites in MMP9 promoter respectively, and the association of DACH1 and p65 promote the recruitment of HDAC1 to the NF-κB binding site in MMP9 promoter, resulting in the reduction of the acetylation level and the transcriptional activity of p65. Accordingly, the level of MMP9 was decreased. In conclusion, we found a new mechanism that DACH1 could inhibit the metastasis of breast cancer cells by inhibiting the expression of MMP9.
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Affiliation(s)
- Sattout Aman
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Yanan Li
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Yunmeng Cheng
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Yuxi Yang
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Linlin Lv
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Bowen Li
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Kangkai Xia
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China
| | - Shujing Li
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China.
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China.
| | - Huijian Wu
- School of Bioengineering & Key Laboratory of Protein Modification and Disease, Liaoning Province, Dalian University of Technology, Dalian, China.
- 2 Ling Gong Road, Dalian, 116024, Liaoning, China.
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24
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Kuonen F, Li NY, Haensel D, Patel T, Gaddam S, Yerly L, Rieger K, Aasi S, Oro AE. c-FOS drives reversible basal to squamous cell carcinoma transition. Cell Rep 2021; 37:109774. [PMID: 34610301 PMCID: PMC8515919 DOI: 10.1016/j.celrep.2021.109774] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/28/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
While squamous transdifferentiation within subpopulations of adenocarcinomas represents an important drug resistance problem, its underlying mechanism remains poorly understood. Here, using surface markers of resistant basal cell carcinomas (BCCs) and patient single-cell and bulk transcriptomic data, we uncover the dynamic roadmap of basal to squamous cell carcinoma transition (BST). Experimentally induced BST identifies activator protein 1 (AP-1) family members in regulating tumor plasticity, and we show that c-FOS plays a central role in BST by regulating the accessibility of distinct AP-1 regulatory elements. Remarkably, despite prominent changes in cell morphology and BST marker expression, we show using inducible model systems that c-FOS-mediated BST demonstrates reversibility. Blocking EGFR pathway activation after c-FOS induction partially reverts BST in vitro and prevents BST features in both mouse models and human tumors. Thus, by identifying the molecular basis of BST, our work reveals a therapeutic opportunity targeting plasticity as a mechanism of tumor resistance.
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MESH Headings
- Animals
- Carcinoma, Basal Cell/metabolism
- Carcinoma, Basal Cell/pathology
- Carcinoma, Basal Cell/veterinary
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/veterinary
- Cell Transdifferentiation/drug effects
- Chromatin Assembly and Disassembly
- Drug Resistance, Neoplasm/genetics
- Humans
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Mucin-1/metabolism
- Protein Kinase Inhibitors/pharmacology
- Proto-Oncogene Proteins c-fos/antagonists & inhibitors
- Proto-Oncogene Proteins c-fos/genetics
- Proto-Oncogene Proteins c-fos/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Signal Transduction/drug effects
- Transcription Factor AP-1/metabolism
- Transforming Growth Factor beta/antagonists & inhibitors
- Transforming Growth Factor beta/genetics
- Transforming Growth Factor beta/metabolism
- ras Proteins/genetics
- ras Proteins/metabolism
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Affiliation(s)
- François Kuonen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Dermatology and Venereology, Hôpital de Beaumont, Lausanne University Hospital Center, 1011 Lausanne, Switzerland.
| | - Nancy Yanzhe Li
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Haensel
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tiffany Patel
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Yerly
- Department of Dermatology and Venereology, Hôpital de Beaumont, Lausanne University Hospital Center, 1011 Lausanne, Switzerland
| | - Kerri Rieger
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sumaira Aasi
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony E Oro
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
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25
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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Small molecule ERK5 kinase inhibitors paradoxically activate ERK5 signalling: be careful what you wish for…. Biochem Soc Trans 2021; 48:1859-1875. [PMID: 32915196 PMCID: PMC7609025 DOI: 10.1042/bst20190338] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
ERK5 is a protein kinase that also contains a nuclear localisation signal and a transcriptional transactivation domain. Inhibition of ERK5 has therapeutic potential in cancer and inflammation and this has prompted the development of ERK5 kinase inhibitors (ERK5i). However, few ERK5i programmes have taken account of the ERK5 transactivation domain. We have recently shown that the binding of small molecule ERK5i to the ERK5 kinase domain stimulates nuclear localisation and paradoxical activation of its transactivation domain. Other kinase inhibitors paradoxically activate their intended kinase target, in some cases leading to severe physiological consequences highlighting the importance of mitigating these effects. Here, we review the assays used to monitor ERK5 activities (kinase and transcriptional) in cells, the challenges faced in development of small molecule inhibitors to the ERK5 pathway, and classify the molecular mechanisms of paradoxical activation of protein kinases by kinase inhibitors.
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Sahm A, Koch P, Horvath S, Hoffmann S. An analysis of methylome evolution in primates. Mol Biol Evol 2021; 38:4700-4714. [PMID: 34175932 PMCID: PMC8557466 DOI: 10.1093/molbev/msab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.
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Affiliation(s)
- Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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Wang Z, Qiao Y, Chen Z, Liang Y, Cui L, Zhang Y, Li X, Xu L, Wei P, Liu S, Li H. Fos Facilitates Gallid Alpha-Herpesvirus 1 Infection by Transcriptional Control of Host Metabolic Genes and Viral Immediate Early Gene. Viruses 2021; 13:v13061110. [PMID: 34207926 PMCID: PMC8229045 DOI: 10.3390/v13061110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Gallid alpha-herpesvirus 1, also known as avian infectious laryngotracheitis virus (ILTV), continues to cause huge economic losses to the poultry industry worldwide. Similar to that of other herpesvirus-encoded proteins, the expression of viral genes encoded by ILTV is regulated by a cascade, and the underlying regulatory mechanism remains largely unclear. The viral immediate-early (IE) gene ICP4 plays a prominent role in the initiation of the transcription of early and late genes during ILTV replication. In this study, we identified AP-1 as the key regulator of the transcription of ILTV genes by bioinformatics analysis of genome-wide transcriptome data. Subsequent functional studies of the key members of the AP-1 family revealed that Fos, but not Jun, regulates ILTV infection through AP-1 since knockdown of Fos, but not Jun, by gene silencing significantly reduced ICP4 transcription and subsequent viral genome replication and virion production. Using several approaches, we identified ICP4 as a bona fide target gene of Fos that regulated Fos and has Fos response elements within its promoter. Neither the physical binding of Jun to the promoter of ICP4 nor the transcriptional activity of Jun was observed. In addition, knockdown of Fos reduced the transcription of MDH1 and ATP5A1, genes encoding two host rate-limiting enzymes essential for the production of the TCA intermediates OAA and ATP. The biological significance of the transcriptional regulation of MDH1 and ATP5A1 by Fos in ILTV infection was supported by the fact that anaplerosis of OAA and ATP rescued both ICP4 transcription and virion production in infected cells under when Fos was silenced. Our study identified the transcription factor Fos as a key regulator of ILTV infection through its transcription factor function on both the virus and host sides, improving the current understanding of both avian herpesvirus–host interactions and the roles of AP-1 in viral infection.
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Affiliation(s)
- Zhitao Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yangyang Qiao
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Zhijie Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yumeng Liang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Lu Cui
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Yanhui Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Xuefeng Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Li Xu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
| | - Ping Wei
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (P.W.); (S.L.); (H.L.); Tel.: +86-451-51051700 (H.L.)
| | - Shengwang Liu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
- Correspondence: (P.W.); (S.L.); (H.L.); Tel.: +86-451-51051700 (H.L.)
| | - Hai Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Z.W.); (Y.Q.); (Z.C.); (Y.L.); (L.C.); (Y.Z.); (X.L.); (L.X.)
- Correspondence: (P.W.); (S.L.); (H.L.); Tel.: +86-451-51051700 (H.L.)
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Gammacoronavirus Avian Infectious Bronchitis Virus and Alphacoronavirus Porcine Epidemic Diarrhea Virus Exploit a Cell-Survival Strategy via Upregulation of cFOS to Promote Viral Replication. J Virol 2021; 95:JVI.02107-20. [PMID: 33239458 PMCID: PMC7851560 DOI: 10.1128/jvi.02107-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Coronaviruses have evolved a variety of strategies to optimize cellular microenvironment for efficient replication. In this study, we report the induction of AP-1 transcription factors by coronavirus infection based on genome-wide analyses of differentially expressed genes in cells infected with avian coronavirus infectious bronchitis virus (IBV). Most members of the AP-1 transcription factors were subsequently found to be upregulated during the course of IBV and porcine epidemic diarrhea virus (PEDV) infection of cultured cells as well as in IBV-infected chicken embryos. Further characterization of the induction kinetics and functional roles of cFOS in IBV replication demonstrated that upregulation of cFOS at early to intermediate phases of IBV replication cycles suppresses IBV-induced apoptosis and promotes viral replication. Blockage of nuclear translocation of cFOS by peptide inhibitor NLSP suppressed IBV replication and apoptosis, ruling out the involvement of the cytoplasmic functions of cFOS in the replication of IBV. Furthermore, knockdown of ERK1/2 and inhibition of JNK and p38 kinase activities reduced cFOS upregulation and IBV replication. This study reveals an important function of cFOS in the regulation of coronavirus-induced apoptosis, facilitating viral replication.IMPORTANCE The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by a newly emerged zoonotic coronavirus (SARS-CoV-2), highlights the importance of coronaviruses as human and animal pathogens and our knowledge gaps in understanding the cellular mechanisms, especially mechanisms shared among human and animal coronaviruses, exploited by coronaviruses for optimal replication and enhanced pathogenicity. This study reveals that upregulation of cFOS, along with other AP-1 transcription factors, as a cell-survival strategy is such a mechanism utilized by coronaviruses during their replication cycles. Through induction and regulation of apoptosis of the infected cells at early to intermediate phases of the replication cycles, subtle but appreciable differences in coronavirus replication efficiency were observed when the expression levels of cFOS were manipulated in the infected cells. As the AP-1 transcription factors are multi-functional, further studies of their regulatory roles in proinflammatory responses may provide new insights into the pathogenesis and virus-host interactions during coronavirus infection.
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Transcription factors in colorectal cancer: molecular mechanism and therapeutic implications. Oncogene 2020; 40:1555-1569. [PMID: 33323976 DOI: 10.1038/s41388-020-01587-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) is a major cause of cancer mortality worldwide, however, the molecular mechanisms underlying the pathogenesis of CRC remain largely unclear. Recent studies have revealed crucial roles of transcription factors in CRC development. Transcription factors essential for the regulation of gene expression by interacting with transcription corepressor/enhancer complexes and they orchestrate downstream signal transduction. Deregulation of transcription factors is a frequent occurrence in CRC, and the accompanying drastic changes in gene expression profiles play fundamental roles in multistep process of tumorigenesis, from cellular transformation, disease progression to metastatic disease. Herein, we summarized current and emerging key transcription factors that participate in CRC tumorigenesis, and highlighted their oncogenic or tumor suppressive functions. Moreover, we presented critical transcription factors of CRC, emphasized the major molecular mechanisms underlying their effect on signal cascades associated with tumorigenesis, and summarized of their potential as molecular biomarkers for CRC prognosis therapeutic response, as well as drug targets for CRC treatment. A better understanding of transcription factors involved in the development of CRC will provide new insights into the pathological mechanisms and reveal novel prognostic biomarkers and therapeutic strategies for CRC.
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Guerrero-Martínez JA, Ceballos-Chávez M, Koehler F, Peiró S, Reyes JC. TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains. Nat Commun 2020; 11:6196. [PMID: 33273453 PMCID: PMC7713251 DOI: 10.1038/s41467-020-19877-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
The Transforming Growth Factor-β (TGFβ) signaling pathway controls transcription by regulating enhancer activity. How TGFβ-regulated enhancers are selected and what chromatin changes are associated with TGFβ-dependent enhancers regulation are still unclear. Here we report that TGFβ treatment triggers fast and widespread increase in chromatin accessibility in about 80% of the enhancers of normal mouse mammary epithelial-gland cells, irrespective of whether they are activated, repressed or not regulated by TGFβ. This enhancer opening depends on both the canonical and non-canonical TGFβ pathways. Most TGFβ-regulated genes are located around enhancers regulated in the same way, often creating domains of several co-regulated genes that we term TGFβ regulatory domains (TRD). CRISPR-mediated inactivation of enhancers within TRDs impairs TGFβ-dependent regulation of all co-regulated genes, demonstrating that enhancer targeting is more promiscuous than previously anticipated. The area of TRD influence is restricted by topologically associating domains (TADs) borders, causing a bias towards co-regulation within TADs.
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Affiliation(s)
- Jose A Guerrero-Martínez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain
| | - María Ceballos-Chávez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain
| | - Florian Koehler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Jose C Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Avenida Americo Vespucio 24, 41092, Seville, Spain.
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32
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Schwartz M, Portugez AS, Attia BZ, Tannenbaum M, Cohen L, Loza O, Chase E, Turman Y, Kaplan T, Salah Z, Hakim O. Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation. Commun Biol 2020; 3:696. [PMID: 33239721 PMCID: PMC7809021 DOI: 10.1038/s42003-020-01398-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 10/16/2020] [Indexed: 12/15/2022] Open
Abstract
Gene transcription is regulated by distant regulatory elements via combinatorial binding of transcription factors. It is increasingly recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene-induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional changes associated with this process. Using Hi-C data, we observe spatial coupling between differentially expressed genes and their differentially accessible regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as determinants of transcriptional alterations at the early stages of oncogenic HRas-induced transformation in human mammary epithelial cells. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.
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Affiliation(s)
- Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Sarusi Portugez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Bracha Zukerman Attia
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Leslie Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Emily Chase
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yousef Turman
- Al-Quds-Bard College for Arts and Sciences, Al-Quds University, Abu Dis, Palestinian Terretories, Palestine
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zaidoun Salah
- Al-Quds-Bard College for Arts and Sciences, Al-Quds University, Abu Dis, Palestinian Terretories, Palestine
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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Cui L, Chen SY, Lerbs T, Lee JW, Domizi P, Gordon S, Kim YH, Nolan G, Betancur P, Wernig G. Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity. Nat Commun 2020; 11:2795. [PMID: 32493933 PMCID: PMC7270081 DOI: 10.1038/s41467-020-16466-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 04/27/2020] [Indexed: 02/04/2023] Open
Abstract
The transcription factor JUN is highly expressed in pulmonary fibrosis. Its induction in mice drives lung fibrosis, which is abrogated by administration of anti-CD47. Here, we use high-dimensional mass cytometry to profile protein expression and secretome of cells from patients with pulmonary fibrosis. We show that JUN is activated in fibrotic fibroblasts that expressed increased CD47 and PD-L1. Using ATAC-seq and ChIP-seq, we found that activation of JUN rendered promoters and enhancers of CD47 and PD-L1 accessible. We further detect increased IL-6 that amplified JUN-mediated CD47 enhancer activity and protein expression. Using an in vivo mouse model of fibrosis, we found two distinct mechanisms by which blocking IL-6, CD47 and PD-L1 reversed fibrosis, by increasing phagocytosis of profibrotic fibroblasts and by eliminating suppressive effects on adaptive immunity. Our results identify specific immune mechanisms that promote fibrosis and suggest a therapeutic approach that could be used alongside conventional anti-fibrotics for pulmonary fibrosis. Fibroblast contributions to lung fibrosis and in particular their crosstalk with immune cells in the lung are incompletely understood. Here, the authors show an overall immune suppressive environment transcriptionally controlled and maintained by fibroblasts in lung fibrosis with possible therapeutic implications.
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Affiliation(s)
- Lu Cui
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Tristan Lerbs
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Pablo Domizi
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Sydney Gordon
- Orca Biosystems, 3475 Edison Way, Suite B, Menlo Park, 94025, CA, USA
| | - Yong-Hun Kim
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Garry Nolan
- Baxter Laboratories Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305, CA, USA
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco, 94143, CA, USA
| | - Gerlinde Wernig
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, 94305, CA, USA.
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TGFβ and EGF signaling orchestrates the AP-1- and p63 transcriptional regulation of breast cancer invasiveness. Oncogene 2020; 39:4436-4449. [PMID: 32350443 PMCID: PMC7253358 DOI: 10.1038/s41388-020-1299-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 01/16/2023]
Abstract
Activator protein (AP)-1 transcription factors are essential elements of the pro-oncogenic functions of transforming growth factor-β (TGFβ)-SMAD signaling. Here we show that in multiple HER2+ and/or EGFR+ breast cancer cell lines these AP-1-dependent tumorigenic properties of TGFβ critically rely on epidermal growth factor receptor (EGFR) activation and expression of the ΔN isoform of transcriptional regulator p63. EGFR and ΔNp63 enabled and/or potentiated the activation of a subset of TGFβ-inducible invasion/migration-associated genes, e.g., ITGA2, LAMB3, and WNT7A/B, and enhanced the recruitment of SMAD2/3 to these genes. The TGFβ- and EGF-induced binding of SMAD2/3 and JUNB to these gene loci was accompanied by p63-SMAD2/3 and p63-JUNB complex formation. p63 and EGFR were also found to strongly potentiate TGFβ induction of AP-1 proteins and, in particular, FOS family members. Ectopic overexpression of FOS could counteract the decrease in TGFβ-induced gene activation after p63 depletion. p63 is also involved in the transcriptional regulation of heparin binding (HB)-EGF and EGFR genes, thereby establishing a self-amplification loop that facilitates and empowers the pro-invasive functions of TGFβ. These cooperative pro-oncogenic functions of EGFR, AP-1, p63, and TGFβ were efficiently inhibited by clinically relevant chemical inhibitors. Our findings may, therefore, be of importance for therapy of patients with breast cancers with an activated EGFR-RAS-RAF pathway.
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35
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Shan Y, Zhang Y, Zhao Y, Wang T, Zhang J, Yao J, Ma N, Liang Z, Huang W, Huang K, Zhang T, Su Z, Chen Q, Zhu Y, Wu C, Zhou T, Sun W, Wei Y, Zhang C, Li C, Su S, Liao B, Zhong M, Zhong X, Nie J, Pei D, Pan G. JMJD3 and UTX determine fidelity and lineage specification of human neural progenitor cells. Nat Commun 2020; 11:382. [PMID: 31959746 PMCID: PMC6971254 DOI: 10.1038/s41467-019-14028-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/13/2019] [Indexed: 02/08/2023] Open
Abstract
Neurogenesis, a highly orchestrated process, entails the transition from a pluripotent to neural state and involves neural progenitor cells (NPCs) and neuronal/glial subtypes. However, the precise epigenetic mechanisms underlying fate decision remain poorly understood. Here, we delete KDM6s (JMJD3 and/or UTX), the H3K27me3 demethylases, in human embryonic stem cells (hESCs) and show that their deletion does not impede NPC generation from hESCs. However, KDM6-deficient NPCs exhibit poor proliferation and a failure to differentiate into neurons and glia. Mechanistically, both JMJD3 and UTX are found to be enriched in gene loci essential for neural development in hNPCs, and KDM6 impairment leads to H3K27me3 accumulation and blockade of DNA accessibility at these genes. Interestingly, forced expression of neuron-specific chromatin remodelling BAF (nBAF) rescues the neuron/glia defect in KDM6-deficient NPCs despite H3K27me3 accumulation. Our findings uncover the differential requirement of KDM6s in specifying NPCs and neurons/glia and highlight the contribution of individual epigenetic regulators in fate decisions in a human development model. Neurogenesis is an ordered transition from pluriptotent cells to neural precursor cells (NPCs) to neurons. Here the authors show that loss of the lysine demethylases JMJD3 and UTX leads reduced DNA accessibility at neurogenesis loci in human NPCs, and that the chromatin remodeller BAF can rescue differentiation defects.
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Affiliation(s)
- Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jiao Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ning Ma
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Zechuan Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wenhao Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Ke Huang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tian Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Zhenghui Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Qianyu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanling Zhu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chuman Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Wei Sun
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Yanxing Wei
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Chenxu Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Shuquan Su
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Baojian Liao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Mei Zhong
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaofen Zhong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Jinfu Nie
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China. .,Shandong Medicinal Biotechnology Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250012, China. .,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong, China.
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36
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Weiterer S, Meier‐Soelch J, Georgomanolis T, Mizi A, Beyerlein A, Weiser H, Brant L, Mayr‐Buro C, Jurida L, Beuerlein K, Müller H, Weber A, Tenekeci U, Dittrich‐Breiholz O, Bartkuhn M, Nist A, Stiewe T, van IJcken WFJ, Riedlinger T, Schmitz ML, Papantonis A, Kracht M. Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner. EMBO J 2020; 39:e101533. [PMID: 31701553 PMCID: PMC6939198 DOI: 10.15252/embj.2019101533] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
How cytokine-driven changes in chromatin topology are converted into gene regulatory circuits during inflammation still remains unclear. Here, we show that interleukin (IL)-1α induces acute and widespread changes in chromatin accessibility via the TAK1 kinase and NF-κB at regions that are highly enriched for inflammatory disease-relevant SNPs. Two enhancers in the extended chemokine locus on human chromosome 4 regulate the IL-1α-inducible IL8 and CXCL1-3 genes. Both enhancers engage in dynamic spatial interactions with gene promoters in an IL-1α/TAK1-inducible manner. Microdeletions of p65-binding sites in either of the two enhancers impair NF-κB recruitment, suppress activation and biallelic transcription of the IL8/CXCL2 genes, and reshuffle higher-order chromatin interactions as judged by i4C interactome profiles. Notably, these findings support a dominant role of the IL8 "master" enhancer in the regulation of sustained IL-1α signaling, as well as for IL-8 and IL-6 secretion. CRISPR-guided transactivation of the IL8 locus or cross-TAD regulation by TNFα-responsive enhancers in a different model locus supports the existence of complex enhancer hierarchies in response to cytokine stimulation that prime and orchestrate proinflammatory chromatin responses downstream of NF-κB.
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Affiliation(s)
- Sinah‐Sophia Weiterer
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Johanna Meier‐Soelch
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | | | - Athanasia Mizi
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Anna Beyerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Hendrik Weiser
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Lilija Brant
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Christin Mayr‐Buro
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Liane Jurida
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Knut Beuerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Helmut Müller
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Axel Weber
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Ulas Tenekeci
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Oliver Dittrich‐Breiholz
- Research Core Unit GenomicsInstitute of Physiological ChemistryMedical School HannoverHannoverGermany
| | - Marek Bartkuhn
- Institute for GeneticsJustus Liebig University GiessenGiessenGermany
| | - Andrea Nist
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
| | - Thorsten Stiewe
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
| | | | - Tabea Riedlinger
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - M Lienhard Schmitz
- Member of the German Center for Lung Research (DZL)GiessenGermany
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - Argyris Papantonis
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Michael Kracht
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
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37
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Sundqvist A, Voytyuk O, Hamdi M, Popeijus HE, Bijlsma-van der Burgt C, Janssen J, Martens JW, Moustakas A, Heldin CH, ten Dijke P, van Dam H. JNK-Dependent cJun Phosphorylation Mitigates TGFβ- and EGF-Induced Pre-Malignant Breast Cancer Cell Invasion by Suppressing AP-1-Mediated Transcriptional Responses. Cells 2019; 8:E1481. [PMID: 31766464 PMCID: PMC6952832 DOI: 10.3390/cells8121481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/12/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Transforming growth factor-β (TGFβ) has both tumor-suppressive and tumor-promoting effects in breast cancer. These functions are partly mediated through Smads, intracellular transcriptional effectors of TGFβ. Smads form complexes with other DNA-binding transcription factors to elicit cell-type-dependent responses. Previously, we found that the collagen invasion and migration of pre-malignant breast cancer cells in response to TGFβ and epidermal growth factor (EGF) critically depend on multiple Jun and Fos components of the activator protein (AP)-1 transcription factor complex. Here we report that the same process is negatively regulated by Jun N-terminal kinase (JNK)-dependent cJun phosphorylation. This was demonstrated by analysis of phospho-deficient, phospho-mimicking, and dimer-specific cJun mutants, and experiments employing a mutant version of the phosphatase MKP1 that specifically inhibits JNK. Hyper-phosphorylation of cJun by JNK strongly inhibited its ability to induce several Jun/Fos-regulated genes and to promote migration and invasion. These results show that MEK-AP-1 and JNK-phospho-cJun exhibit distinct pro- and anti-invasive functions, respectively, through differential regulation of Smad- and AP-1-dependent TGFβ target genes. Our findings are of importance for personalized cancer therapy, such as for patients suffering from specific types of breast tumors with activated EGF receptor-Ras or inactivated JNK pathways.
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Affiliation(s)
- Anders Sundqvist
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; (A.M.); (C.-H.H.); (P.t.D.)
| | - Oleksandr Voytyuk
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; (A.M.); (C.-H.H.); (P.t.D.)
| | - Mohamed Hamdi
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
| | - Herman E. Popeijus
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
| | - Corina Bijlsma-van der Burgt
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
| | - Josephine Janssen
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands;
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; (A.M.); (C.-H.H.); (P.t.D.)
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; (A.M.); (C.-H.H.); (P.t.D.)
| | - Peter ten Dijke
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden; (A.M.); (C.-H.H.); (P.t.D.)
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
| | - Hans van Dam
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; (M.H.); (H.E.P.); (C.B.-v.d.B.); (J.J.)
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38
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Zhou X, Zhang K, Qi W, Zhou Y, Hong T, Xiong T, Xie M, Nie S. Exopolysaccharides from Lactobacillus plantarum NCU116 Enhances Colonic Mucosal Homeostasis by Controlling Epithelial Cell Differentiation and c-Jun/Muc2 Signaling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9831-9839. [PMID: 31407897 DOI: 10.1021/acs.jafc.9b03939] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Probiotic lactobacilli and their exopolysaccharides (EPS) are thought to modulate mucosal homeostasis; however, their mechanisms remain elusive. Thus, we tried to clarify the role of exopolysaccharides from Lactobacillus plantarum NCU116 (EPS116) in the intestinal mucosal homeostasis. Our results indicated that EPS116 regulated the colon mucosal healing and homeostasis, enhanced the goblet cell differentiation, and promoted the expression of Muc2 gene in vivo and in vitro. Further experiments showed that EPS116 promoted the expression and phosphorylation of transcription factor c-Jun and facilitated its binding to the promoter of Muc2. Moreover, knocking down c-Jun or inhibiting its function in LS 174T cells treated with EPS116 led to decreased expression of Muc2, implying that EPS116 promoted the colonic mucosal homeostasis and Muc2 expression via c-Jun. Therefore, our study uncovered a novel model where EPS116 enhanced colon mucosal homeostasis by controlling the epithelial cell differentiation and c-Jun/Muc2 signaling.
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Affiliation(s)
- Xingtao Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Ke Zhang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Wucheng Qi
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - YuJia Zhou
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Tao Hong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Tao Xiong
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang) , Nanchang University , 235 Nanjing East Road , Nanchang , Jiangxi 330047 , China
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39
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Bianco S, Bellefleur AM, Beaulieu É, Beauparlant CJ, Bertolin K, Droit A, Schoonjans K, Murphy BD, Gévry N. The Ovulatory Signal Precipitates LRH-1 Transcriptional Switching Mediated by Differential Chromatin Accessibility. Cell Rep 2019; 28:2443-2454.e4. [DOI: 10.1016/j.celrep.2019.07.088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/01/2019] [Accepted: 07/24/2019] [Indexed: 12/23/2022] Open
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40
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Bejjani F, Evanno E, Zibara K, Piechaczyk M, Jariel-Encontre I. The AP-1 transcriptional complex: Local switch or remote command? Biochim Biophys Acta Rev Cancer 2019; 1872:11-23. [PMID: 31034924 DOI: 10.1016/j.bbcan.2019.04.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
Abstract
The ubiquitous family of AP-1 dimeric transcription complexes is involved in virtually all cellular and physiological functions. It is paramount for cells to reprogram gene expression in response to cues of many sorts and is involved in many tumorigenic processes. How AP-1 controls gene transcription has largely remained elusive till recently. The advent of the "omics" technologies permitting genome-wide studies of transcription factors has however changed and improved our view of AP-1 mechanistical actions. If these studies confirm that AP-1 can sometimes act as a local transcriptional switch operating in the vicinity of transcription start sites (TSS), they strikingly indicate that AP-1 principally operates as a remote command binding to distal enhancers, placing chromatin architecture dynamics at the heart of its transcriptional actions. They also unveil novel constraints operating on AP-1, as well as novel mechanisms used to regulate gene expression via transcription-pioneering-, chromatin-remodeling- and chromatin accessibility maintenance effects.
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Affiliation(s)
- Fabienne Bejjani
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France; PRASE and Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon
| | - Emilie Evanno
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Kazem Zibara
- PRASE and Biology Department, Faculty of Sciences - I, Lebanese University, Beirut, Lebanon
| | - Marc Piechaczyk
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
| | - Isabelle Jariel-Encontre
- Equipe Labellisée Ligue Nationale contre le Cancer, Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France.
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41
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Chakravarthi VP, Khristi V, Ghosh S, Yerrathota S, Dai E, Roby KF, Wolfe MW, Rumi MAK. ESR2 Is Essential for Gonadotropin-Induced Kiss1 Expression in Granulosa Cells. Endocrinology 2018; 159:3860-3873. [PMID: 30277501 PMCID: PMC6260246 DOI: 10.1210/en.2018-00608] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
Hypothalamic expression of Kiss1 plays an essential role in the onset of puberty, gonadal development, and ovulation. Estrogens regulate the expression of Kiss1 in the hypothalamus through estrogen receptor-α. Kiss1 is also expressed in the ovary, where its expression correlates with the onset of puberty and progression of the estrous cycle. To date, estrogen regulation of Kiss1 expression in the ovary has not been investigated. We recently observed that gonadotropin-induced Kiss1 expression was absent in Esr2-null rat ovaries even though Esr1 was present. Wild-type granulosa cells abundantly expressed Kiss1 and oocytes expressed the Kiss1 receptor. We characterized estrogen receptor-β (ESR2) regulation of Kiss1 expression in granulosa cells by identifying granulosa cell-specific transcript variants and potential regulatory regions. The Kiss1 promoter, an upstream enhancer, and a downstream enhancer all possessed conserved estrogen response elements (EREs) and showed active histone marks in gonadotropin-stimulated granulosa cells. The transcriptionally active Kiss1 promoter, as well as the enhancers, also revealed enrichment for ESR2 binding. Furthermore, activity of a Kiss1 promoter construct was induced after overexpression of ESR2 and was blocked upon mutation of an ERE within the promoter. Finally, pregnant mare serum gonadotropin and human chorionic gonadotropin administration induced phosphorylation of ESR2 and upregulated the AP-1 proteins FOSL2 and JUNB in granulosa cells. Activated MAPK ERK2 was associated with the ESR2 phosphorylation in granulosa cells, and AP-1 factors could synergistically activate the Kiss1 promoter activity. These gonadotropin-induced changes paralleled Kiss1 expression in granulosa cells. We conclude that gonadotropin-stimulated Kiss1 expression in granulosa cells is dependent on both the activation of ESR2 and the upregulation of AP-1.
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Affiliation(s)
- V Praveen Chakravarthi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Vincentaben Khristi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Subhra Ghosh
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Sireesha Yerrathota
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Eddie Dai
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Katherine F Roby
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
- Institute for Reproduction and Perinatal Health, University of Kansas Medical Center, Kansas City, Kansas
| | - Michael W Wolfe
- Institute for Reproduction and Perinatal Health, University of Kansas Medical Center, Kansas City, Kansas
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas
| | - M A Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Institute for Reproduction and Perinatal Health, University of Kansas Medical Center, Kansas City, Kansas
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