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Qi W, Bai J, Wang R, Zeng X, Zhang L. SATB1, senescence and senescence-related diseases. J Cell Physiol 2024. [PMID: 38801120 DOI: 10.1002/jcp.31327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Aging leads to an accumulation of cellular mutations and damage, increasing the risk of senescence, apoptosis, and malignant transformation. Cellular senescence, which is pivotal in aging, acts as both a guard against cellular transformation and as a check against cancer progression. It is marked by stable cell cycle arrest, widespread macromolecular changes, a pro-inflammatory profile, and altered gene expression. However, it remains to be determined whether these differing subsets of senescent cells result from unique intrinsic programs or are influenced by their environmental contexts. Multiple transcription regulators and chromatin modifiers contribute to these alterations. Special AT-rich sequence-binding protein 1 (SATB1) stands out as a crucial regulator in this process, orchestrating gene expression by structuring chromatin into loop domains and anchoring DNA elements. This review provides an overview of cellular senescence and delves into the role of SATB1 in senescence-related diseases. It highlights SATB1's potential in developing antiaging and anticancer strategies, potentially contributing to improved quality of life and addressing aging-related diseases.
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Affiliation(s)
- Wenjing Qi
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Jinping Bai
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
| | - Ruoxi Wang
- Center for Cell Structure and Function, College of Life Sciences, Key Laboratory of Animal Resistance Biology of Shandong Province, Shandong Normal University, Jinan, Shandong, China
| | - Xianlu Zeng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun, Jilin, China
| | - Lihui Zhang
- Department of Bioscience, Changchun Normal University, Changchun, Jilin, China
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2
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Gu W, Huang X, Singh PNP, Li S, Lan Y, Deng M, Lacko LA, Gomez-Salinero JM, Rafii S, Verzi MP, Shivdasani RA, Zhou Q. A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin. Nat Commun 2024; 15:3595. [PMID: 38678016 PMCID: PMC11055869 DOI: 10.1038/s41467-024-47738-y] [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: 12/05/2022] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Plasticity among cell lineages is a fundamental, but poorly understood, property of regenerative tissues. In the gut tube, the small intestine absorbs nutrients, whereas the colon absorbs electrolytes. In a striking display of inherent plasticity, adult colonic mucosa lacking the chromatin factor SATB2 is converted to small intestine. Using proteomics and CRISPR-Cas9 screening, we identify MTA2 as a crucial component of the molecular machinery that, together with SATB2, restrains colonic plasticity. MTA2 loss in the adult mouse colon activated lipid absorptive genes and functional lipid uptake. Mechanistically, MTA2 co-occupies DNA with HNF4A, an activating pan-intestinal transcription factor (TF), on colonic chromatin. MTA2 loss leads to HNF4A release from colonic chromatin, and accumulation on small intestinal chromatin. SATB2 similarly restrains colonic plasticity through an HNF4A-dependent mechanism. Our study provides a generalizable model of lineage plasticity in which broadly-expressed TFs are retained on tissue-specific enhancers to maintain cell identity and prevent activation of alternative lineages, and their release unleashes plasticity.
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Affiliation(s)
- Wei Gu
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
- BeiGene Institute, BeiGene (Shanghai) Research & Development Co., Ltd, Shanghai, 200131, China.
| | - Xiaofeng Huang
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Pratik N P Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Sanlan Li
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Ying Lan
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Min Deng
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Lauretta A Lacko
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
- Human Therapeutic Organoid Core Facility, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jesus M Gomez-Salinero
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael P Verzi
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Qiao Zhou
- Division of Regenerative Medicine & Hartman Institute for Organ Regeneration, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
- Human Therapeutic Organoid Core Facility, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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Yu KQ, Li CF, Ye L, Song Y, Wang YH, Lin YR, Liao ST, Mei ZC, Lv L. Long Non-Coding RNA ANRIL Regulates Inflammatory Factor Expression in Ulcerative Colitis Via the miR-191-5p/SATB1 Axis. Inflammation 2024; 47:513-529. [PMID: 37985573 DOI: 10.1007/s10753-023-01925-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023]
Abstract
Ulcerative colitis, an inflammatory bowel disease, manifests with symptoms such as abdominal pain, diarrhea, and mucopurulent feces. The long non-coding RNA (lncRNA) ANRIL exhibits significantly reduced expression in UC, yet its specific mechanism is unknown. This study revealed that ANRIL is involved in the progression of UC by inhibiting IL-6 and TNF-α via miR-191-5P/SATB1 axis. We found that in patients with UC, interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were significantly overexpressed in inflamed colon sites, whereas ANRIL was significantly under-expressed and associated with disease severity. The downregulation of ANRIL resulted in the increased expression of IL-6 and TNF-α in LPS-treated FHCs. ANRIL directly targeted miR-191-5p, thereby inhibiting its expression and augmenting SATB1 expression. Moreover, overexpression of miR-191-5p abolished ANRIL-mediated inhibition of IL-6 and TNF-α production. Dual luciferase reporter assays revealed the specific binding of miR-191-5p to ANRIL and SATB1. Furthermore, the downregulation of ANRIL promoted DSS-induced colitis in mice. Together, we provide evidence that ANRIL plays a critical role in regulating IL-6 and TNF-α expression in UC by modulating the miR-191-5p/SATB1 axis. Our study provides novel insights into progression and molecular therapeutic strategies in UC.
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Affiliation(s)
- Ke-Qi Yu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Chuan-Fei Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Lu Ye
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Ya Song
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Yan-Hui Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Yu-Ru Lin
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China
| | - Sheng-Tao Liao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China.
| | - Zhe-Chuan Mei
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China.
| | - Lin Lv
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, Chongqing, 400010, China.
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4
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Yang F, Akhtar MN, Zhang D, El-Mayta R, Shin J, Dorsey JF, Zhang L, Xu X, Guo W, Bagley SJ, Fuchs SY, Koumenis C, Lathia JD, Mitchell MJ, Gong Y, Fan Y. An immunosuppressive vascular niche drives macrophage polarization and immunotherapy resistance in glioblastoma. SCIENCE ADVANCES 2024; 10:eadj4678. [PMID: 38416830 PMCID: PMC10901371 DOI: 10.1126/sciadv.adj4678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Cancer immunity is subjected to spatiotemporal regulation by leukocyte interaction with neoplastic and stromal cells, contributing to immune evasion and immunotherapy resistance. Here, we identify a distinct mesenchymal-like population of endothelial cells (ECs) that form an immunosuppressive vascular niche in glioblastoma (GBM). We reveal a spatially restricted, Twist1/SATB1-mediated sequential transcriptional activation mechanism, through which tumor ECs produce osteopontin to promote immunosuppressive macrophage (Mφ) phenotypes. Genetic or pharmacological ablation of Twist1 reverses Mφ-mediated immunosuppression and enhances T cell infiltration and activation, leading to reduced GBM growth and extended mouse survival, and sensitizing tumor to chimeric antigen receptor T immunotherapy. Thus, these findings uncover a spatially restricted mechanism controlling tumor immunity and suggest that targeting endothelial Twist1 may offer attractive opportunities for optimizing cancer immunotherapy.
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Affiliation(s)
- Fan Yang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Md Naushad Akhtar
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Duo Zhang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rakan El-Mayta
- Department of Bioengineering, University of Pennsylvania School of Engineering and Applied Science, Philadelphia, PA 19104, USA
| | - Junyoung Shin
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jay F. Dorsey
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen J. Bagley
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Serge Y Fuchs
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Justin D. Lathia
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael J. Mitchell
- Department of Bioengineering, University of Pennsylvania School of Engineering and Applied Science, Philadelphia, PA 19104, USA
| | - Yanqing Gong
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Xu L, Zheng S, Witzel K, Van De Slijke E, Baekelandt A, Mylle E, Van Damme D, Cheng J, De Jaeger G, Inzé D, Jiang H. Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana. Nat Commun 2024; 15:1286. [PMID: 38346986 PMCID: PMC10861482 DOI: 10.1038/s41467-024-45577-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
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Affiliation(s)
- Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Shiwei Zheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, 14979, Germany
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.
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6
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Gu M, Ren B, Fang Y, Ren J, Liu X, Wang X, Zhou F, Xiao R, Luo X, You L, Zhao Y. Epigenetic regulation in cancer. MedComm (Beijing) 2024; 5:e495. [PMID: 38374872 PMCID: PMC10876210 DOI: 10.1002/mco2.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as a prime target in the discovery of novel therapeutics. Our review delves into the complexities of epigenetic regulation, exploring its profound effects on tumor initiation, metastatic behavior, metabolic pathways, and the tumor microenvironment. We place a particular emphasis on the dysregulation at each level of epigenetic modulation, including but not limited to, the aberrations in enzymes responsible for DNA methylation and histone modification, subunit loss or fusions in chromatin remodeling complexes, and the disturbances in higher-order chromatin structure. Finally, we also evaluate therapeutic approaches that leverage the growing understanding of chromatin dysregulation, offering new avenues for cancer treatment.
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Affiliation(s)
- Minzhi Gu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Bo Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yuan Fang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Jie Ren
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiaohong Liu
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xing Wang
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Feihan Zhou
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Ruiling Xiao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Xiyuan Luo
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Lei You
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
| | - Yupei Zhao
- Department of General SurgeryPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijingP. R. China
- Key Laboratory of Research in Pancreatic TumorChinese Academy of Medical SciencesBeijingP. R. China
- National Science and Technology Key Infrastructure on Translational Medicine in Peking Union Medical College HospitalBeijingP. R. China
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7
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Miyano M, LaBarge MA. ELF5: A Molecular Clock for Breast Aging and Cancer Susceptibility. Cancers (Basel) 2024; 16:431. [PMID: 38275872 PMCID: PMC10813895 DOI: 10.3390/cancers16020431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Breast cancer is predominantly an age-related disease, with aging serving as the most significant risk factor, compounded by germline mutations in high-risk genes like BRCA1/2. Aging induces architectural changes in breast tissue, particularly affecting luminal epithelial cells by diminishing lineage-specific molecular profiles and adopting myoepithelial-like characteristics. ELF5 is an important transcription factor for both normal breast and breast cancer development. This review focuses on the role of ELF5 in normal breast development, its altered expression throughout aging, and its implications in cancer. It discusses the lineage-specific expression of ELF5, its regulatory mechanisms, and its potential as a biomarker for breast-specific biological age and cancer risk.
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Affiliation(s)
- Masaru Miyano
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Mark A. LaBarge
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer and Aging, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Biomarkers Research, University of Bergen, 5007 Bergen, Norway
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8
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Li F, Yan C, Yao Y, Yang Y, Liu Y, Fan D, Zhao J, Tang Z. Transcription Factor SATB2 Regulates Skeletal Muscle Cell Proliferation and Migration via HDAC4 in Pigs. Genes (Basel) 2024; 15:65. [PMID: 38254955 PMCID: PMC10815226 DOI: 10.3390/genes15010065] [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: 12/13/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Skeletal muscle development remarkably affects meat production and growth rate, regulated by complex regulatory mechanisms in pigs. Specific AT sequence-binding protein 2 (SATB2) is a classic transcription factor and chromatin organizer, which holds a profound effect in the regulation of chromatin remodeling. However, the regulation role of SATB2 concerning skeletal muscle cell fate through chromatin remodeling in pigs remains largely unknown. Here, we observed that SATB2 was expressed higher in the lean-type compared to the obese-type pigs, which also enriched the pathways of skeletal muscle development, chromatin organization, and histone modification. Functionally, knockdown SATB2 led to decreases in the proliferation and migration markers at the mRNA and protein expression levels, respectively, while overexpression SATB2 had the opposite effects. Further, we found histone deacetylase 4 (HDAC4) was a key downstream target gene of SATB2 related to chromatin remodeling. The binding relationship between SATB2 and HDAC4 was confirmed by a dual-luciferase reporter system and ChIP-qPCR analysis. Besides, we revealed that HDAC4 promoted the skeletal muscle cell proliferation and migration at the mRNA and protein expression levels, respectively. In conclusion, our study indicates that transcription factor SATB2 binding to HDAC4 positively contributes to skeletal muscle cell proliferation and migration, which might mediate the chromatin remodeling to influence myogenesis in pigs. This study develops a novel insight into understanding the molecular regulatory mechanism of myogenesis, and provides a promising gene for genetic breeding in pigs.
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Affiliation(s)
- Fanqinyu Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
| | - Chao Yan
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yilong Yao
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yalan Yang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
| | - Yanwen Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Danyang Fan
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Junxing Zhao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
| | - Zhonglin Tang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China;
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (C.Y.); (Y.Y.); (Y.L.); (D.F.)
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China;
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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9
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Trujillo-Ochoa JL, Kazemian M, Afzali B. The role of transcription factors in shaping regulatory T cell identity. Nat Rev Immunol 2023; 23:842-856. [PMID: 37336954 PMCID: PMC10893967 DOI: 10.1038/s41577-023-00893-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 06/21/2023]
Abstract
Forkhead box protein 3-expressing (FOXP3+) regulatory T cells (Treg cells) suppress conventional T cells and are essential for immunological tolerance. FOXP3, the master transcription factor of Treg cells, controls the expression of multiples genes to guide Treg cell differentiation and function. However, only a small fraction (<10%) of Treg cell-associated genes are directly bound by FOXP3, and FOXP3 alone is insufficient to fully specify the Treg cell programme, indicating a role for other accessory transcription factors operating upstream, downstream and/or concurrently with FOXP3 to direct Treg cell specification and specialized functions. Indeed, the heterogeneity of Treg cells can be at least partially attributed to differential expression of transcription factors that fine-tune their trafficking, survival and functional properties, some of which are niche-specific. In this Review, we discuss the emerging roles of accessory transcription factors in controlling Treg cell identity. We specifically focus on members of the basic helix-loop-helix family (AHR), basic leucine zipper family (BACH2, NFIL3 and BATF), CUT homeobox family (SATB1), zinc-finger domain family (BLIMP1, Ikaros and BCL-11B) and interferon regulatory factor family (IRF4), as well as lineage-defining transcription factors (T-bet, GATA3, RORγt and BCL-6). Understanding the imprinting of Treg cell identity and specialized function will be key to unravelling basic mechanisms of autoimmunity and identifying novel targets for drug development.
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Affiliation(s)
- Jorge L Trujillo-Ochoa
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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10
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Cheng MW, Mitra M, Coller HA. Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Commun Biol 2023; 6:1138. [PMID: 37973839 PMCID: PMC10654613 DOI: 10.1038/s42003-023-05459-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: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.
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Affiliation(s)
- Michael W Cheng
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hilary A Coller
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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11
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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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12
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Sharma S, Tyagi W, Tamang R, Das S. HDAC5 modulates SATB1 transcriptional activity to promote lung adenocarcinoma. Br J Cancer 2023; 129:586-600. [PMID: 37400677 PMCID: PMC10421875 DOI: 10.1038/s41416-023-02341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/29/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Dysregulation of histone deacetylases has been linked to diverse cancers. HDAC5 is a histone deacetylase belonging to Class IIa family of histone deacetylases. Limited substrate repertoire restricts the understanding of molecular mechanisms underlying its role in tumorigenesis. METHODS We employed a biochemical screen to identify SATB1 as HDAC5-interacting protein. Coimmunoprecipitation and deacetylation assay were performed to validate SATB1 as a HDAC5 substrate. Proliferation, migration assay and xenograft studies were performed to determine the effect of HDAC5-SATB1 interaction on tumorigenesis. RESULTS Here we report that HDAC5 binds to and deacetylates SATB1 at the conserved lysine 411 residue. Furthermore, dynamic regulation of acetylation at this site is determined by TIP60 acetyltransferase. We also established that HDAC5-mediated deacetylation is critical for SATB1-dependent downregulation of key tumor suppressor genes. Deacetylated SATB1 also represses SDHA-induced epigenetic remodeling and anti-proliferative transcriptional program. Thus, SATB1 spurs malignant phenotype in a HDAC5-dependent manner. CONCLUSIONS Our study highlights the pivotal role of HDAC5 in tumorigenesis. Our findings provide key insights into molecular mechanisms underlying SATB1 promoted tumor growth and metastasis.
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Affiliation(s)
- Shalakha Sharma
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Witty Tyagi
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rohini Tamang
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeev Das
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Zelenka T, Papamatheakis DA, Tzerpos P, Panagopoulos G, Tsolis KC, Papadakis VM, Mariatos Metaxas D, Papadogkonas G, Mores E, Kapsetaki M, Papamatheakis J, Stanek D, Spilianakis C. A novel SATB1 protein isoform with different biophysical properties. Front Cell Dev Biol 2023; 11:1242481. [PMID: 37635874 PMCID: PMC10457122 DOI: 10.3389/fcell.2023.1242481] [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: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1's mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | | | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Vassilis M. Papadakis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Eleftherios Mores
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Joseph Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - David Stanek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
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14
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Nomura A, Kobayashi T, Seo W, Ohno-Oishi M, Kakugawa K, Muroi S, Yoshida H, Endo TA, Moro K, Taniuchi I. Identification of a novel enhancer essential for Satb1 expression in T H2 cells and activated ILC2s. Life Sci Alliance 2023; 6:e202301897. [PMID: 37193606 PMCID: PMC10189277 DOI: 10.26508/lsa.202301897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/18/2023] Open
Abstract
The genome organizer, special AT-rich binding protein-1 (SATB1), functions to globally regulate gene networks during primary T cell development and plays a pivotal role in lineage specification in CD4+ helper-, CD8+ cytotoxic-, and FOXP3+ regulatory-T cell subsets. However, it remains unclear how Satb1 gene expression is controlled, particularly in effector T cell function. Here, by using a novel reporter mouse strain expressing SATB1-Venus and genome editing, we have identified a cis-regulatory enhancer, essential for maintaining Satb1 expression specifically in TH2 cells. This enhancer is occupied by STAT6 and interacts with Satb1 promoters through chromatin looping in TH2 cells. Reduction of Satb1 expression, by the lack of this enhancer, resulted in elevated IL-5 expression in TH2 cells. In addition, we found that Satb1 is induced in activated group 2 innate lymphoid cells (ILC2s) through this enhancer. Collectively, these results provide novel insights into how Satb1 expression is regulated in TH2 cells and ILC2s during type 2 immune responses.
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Affiliation(s)
- Aneela Nomura
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Tetsuro Kobayashi
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Wooseok Seo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Michiko Ohno-Oishi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Kiyokazu Kakugawa
- Laboratory for Immune Crosstalk, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Sawako Muroi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Hideyuki Yoshida
- Laboratory for YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
| | - Kazuyo Moro
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
- Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School for Medicine, Osaka University, Osaka, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences(IMS), Yokohama, Japan
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15
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Chen Y, Huang Z, Chen S, Tan L, He L, Yuan D, Zheng L, Zhong JH, Li A, Zhang H, Tan H, Xu L. Immediate early response 3 gene promotes aggressive progression and autophagy of AML by negatively regulating AKT/mTOR. Transl Oncol 2023; 35:101711. [PMID: 37327583 DOI: 10.1016/j.tranon.2023.101711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/28/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Immediate early response 3 (IER3) plays a vital role in many tumors. This study aims to explore the function and mechanism of IER3 in Acute myeloid leukemia (AML). METHODS The expression of IER3 in AML was performed by bioinformatics analysis. CCK-8 proliferation assay, flow cytometry cycle assay, clone formation assay, and tumorigenic ability were used to investigate the effect of IER3 on AML cells. Unbiased label-free quantitative proteomics and label-free quantitative phosphoproteomics analysis were performed. The regulatory relationship between SATB1(Special AT-rich sequence binding protein 1) and IER3 was investigated by Real time-PCR, Western blot, Chromatin immunoprecipitation (CHIP), and PCR. RESULTS The result indicated that the prognosis of the high IER3 expression group was significantly worse than that of the low expression group. CCK-8 assay showed that IER3 enhanced the proliferation ability. Cell cycle analysis showed IER3 could promote HL60 cells to enter the S phase of DNA synthesis from the quiescent phase. IER3 could stimulate HEL cells to enter mitosis. Clone-formation experiments suggested that IER3 enhanced clonogenic ability.IER3 promoted the tumorigenesis of AML. Further experimental investigation revealed that IER3 promoted autophagy and induced the occurrence and development of AML by negatively regulating the phosphorylation activation of AKT/mTOR pathway. SATB1 was found to bind to the promoter region of IER3 gene and negatively regulate its transcription. CONCLUSION IER3 could promote the development of AML and induce autophagy of AML cells by negatively regulating the phosphorylation and activation of AKT/mTOR. By the way, SATB1 may negatively target regulates IER3 transcription.
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Affiliation(s)
- Yimin Chen
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Zhenqian Huang
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Shuyi Chen
- Department of Hematology, First People's Hospital of Foshan, 81 Linnan North Road, Chancheng, Foshan, Guangdong 528000, China
| | - Li Tan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Lang He
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Danyun Yuan
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Lixia Zheng
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Jing Hua Zhong
- The First Clinical Academy, Guangzhou Medical University, Guangzhou, 510230, China; Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical, University, Guangzhou, 510230, China
| | - Anqiao Li
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Heng Zhang
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Huo Tan
- Department of Hematology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China
| | - Lihua Xu
- Department of Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China; Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical, University, Guangzhou, 510230, China
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16
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Guo R, Li J, Hu J, Fu Q, Yan Y, Xu S, Wang X, Jiao F. Combination of epidrugs with immune checkpoint inhibitors in cancer immunotherapy: From theory to therapy. Int Immunopharmacol 2023; 120:110417. [PMID: 37276826 DOI: 10.1016/j.intimp.2023.110417] [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: 04/19/2023] [Revised: 05/28/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023]
Abstract
Immunotherapy based on immune checkpoint inhibitors (ICIs) has revolutionized treatment strategies in multiple types of cancer. However, the resistance and relapse as associated with the extreme complexity of cancer-immunity interactions remain a major challenge to be resolved. Owing to the epigenome plasticity of cancer and immune cells, a growing body of evidence has been presented indicating that epigenetic treatments have the potential to overcome current limitations of immunotherapy, thus providing a rationalefor the combination of ICIs with epigenetic agents (epidrugs). In this review, we first make an overview about the epigenetic regulations in tumor biology and immunodevelopment. Subsequently, a diverse array of inhibitory agents under investigations targeted epigenetic modulators (Azacitidine, Decitabine, Vorinostat, Romidepsin, Belinostat, Panobinostat, Tazemetostat, Enasidenib and Ivosidenib, etc.) and immune checkpoints (Atezolizmab, Avelumab, Cemiplimab, Durvalumb, Ipilimumab, Nivolumab and Pembrolizmab, etc.) to increase anticancer responses were described and the potential mechanisms were further discussed. Finally, we summarize the findings of clinical trials and provide a perspective for future clinical studies directed at investigating the combination of epidrugs with ICIs as a treatment for cancer.
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Affiliation(s)
- Ruoyu Guo
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Jixia Li
- Department of Clinical Laboratory Medicine, Yantaishan Hospital, Yantai 264003, PR China
| | - Jinxia Hu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Qiang Fu
- School of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai 264003, PR China
| | - Yunfei Yan
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Sen Xu
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China
| | - Xin Wang
- Department of Clinical Laboratory & Health Service Training, 970 Hospital of the PLA Joint Logistic Support Force, Yantai 264002, PR China.
| | - Fei Jiao
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai 264003, PR China.
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17
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Londoño AF, Scorpio DG, Dumler JS. Innate immunity in rickettsial infections. Front Cell Infect Microbiol 2023; 13:1187267. [PMID: 37228668 PMCID: PMC10203653 DOI: 10.3389/fcimb.2023.1187267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Rickettsial agents are a diverse group of alpha-proteobacteria within the order Rickettsiales, which possesses two families with human pathogens, Rickettsiaceae and Anaplasmataceae. These obligate intracellular bacteria are most frequently transmitted by arthropod vectors, a first step in the pathogens' avoidance of host cell defenses. Considerable study of the immune responses to infection and those that result in protective immunity have been conducted. Less study has focused on the initial events and mechanism by which these bacteria avoid the innate immune responses of the hosts to survive within and propagate from host cells. By evaluating the major mechanisms of evading innate immunity, a range of similarities among these bacteria become apparent, including mechanisms to escape initial destruction in phagolysosomes of professional phagocytes, those that dampen the responses of innate immune cells or subvert signaling and recognition pathways related to apoptosis, autophagy, proinflammatory responses, and mechanisms by which these microbes attach to and enter cells or those molecules that trigger the host responses. To illustrate these principles, this review will focus on two common rickettsial agents that occur globally, Rickettsia species and Anaplasma phagocytophilum.
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Affiliation(s)
- Andrés F. Londoño
- The Henry M. Jackson Foundation for Advancement in Military Medicine, Bethesda, MD, United States
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Diana G. Scorpio
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - J. Stephen Dumler
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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18
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Wang B, Ji L, Bian Q. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites. Cell Rep 2023; 42:112323. [PMID: 37000624 DOI: 10.1016/j.celrep.2023.112323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.
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Affiliation(s)
- Bao Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Luzhang Ji
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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19
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Lozano D, López JM, Jiménez S, Morona R, Ruíz V, Martínez A, Moreno N. Expression of SATB1 and SATB2 in the brain of bony fishes: what fish reveal about evolution. Brain Struct Funct 2023; 228:921-945. [PMID: 37002478 PMCID: PMC10147777 DOI: 10.1007/s00429-023-02632-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/15/2023] [Indexed: 04/03/2023]
Abstract
AbstractSatb1 and Satb2 belong to a family of homeodomain proteins with highly conserved functional and regulatory mechanisms and posttranslational modifications in evolution. However, although their distribution in the mouse brain has been analyzed, few data exist in other non-mammalian vertebrates. In the present study, we have analyzed in detail the sequence of SATB1 and SATB2 proteins and the immunolocalization of both, in combination with additional neuronal markers of highly conserved populations, in the brain of adult specimens of different bony fish models at key evolutionary points of vertebrate diversification, in particular including representative species of sarcopterygian and actinopterygian fishes. We observed a striking absence of both proteins in the pallial region of actinopterygians, only detected in lungfish, the only sarcopterygian fish. In the subpallium, including the amygdaloid complex, or comparable structures, we identified that the detected expressions of SATB1 and SATB2 have similar topologies in the studied models. In the caudal telencephalon, all models showed significant expression of SATB1 and SATB2 in the preoptic area, including the acroterminal domain of this region, where the cells were also dopaminergic. In the alar hypothalamus, all models showed SATB2 but not SATB1 in the subparaventricular area, whereas in the basal hypothalamus the cladistian species and the lungfish presented a SATB1 immunoreactive population in the tuberal hypothalamus, also labeled with SATB2 in the latter and colocalizing with the gen Orthopedia. In the diencephalon, all models, except the teleost fish, showed SATB1 in the prethalamus, thalamus and pretectum, whereas only lungfish showed also SATB2 in prethalamus and thalamus. At the midbrain level of actinopterygian fish, the optic tectum, the torus semicircularis and the tegmentum harbored populations of SATB1 cells, whereas lungfish housed SATB2 only in the torus and tegmentum. Similarly, the SATB1 expression in the rhombencephalic central gray and reticular formation was a common feature. The presence of SATB1 in the solitary tract nucleus is a peculiar feature only observed in non-teleost actinopterygian fishes. At these levels, none of the detected populations were catecholaminergic or serotonergic. In conclusion, the protein sequence analysis revealed a high degree of conservation of both proteins, especially in the functional domains, whereas the neuroanatomical pattern of SATB1 and SATB2 revealed significant differences between sarcopterygians and actinopterygians, and these divergences may be related to the different functional involvement of both in the acquisition of various neural phenotypes.
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Affiliation(s)
- Daniel Lozano
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Jesús M López
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Sara Jiménez
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Ruth Morona
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Víctor Ruíz
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Ana Martínez
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain
| | - Nerea Moreno
- Department of Cell Biology, Faculty of Biology, University Complutense, 28040, Madrid, Spain.
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20
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Luo J, Yuan J, Yang Y, Jiang Y, Yan J, Tong Q. Special AT-rich sequence binding protein 1 promotes multidrug resistance in gastric cancer by regulation of Ezrin to alter subcellular localization of ATP-binding cassette transporters. Cancer Sci 2022; 114:1353-1364. [PMID: 36522839 PMCID: PMC10067392 DOI: 10.1111/cas.15693] [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: 03/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Multidrug resistance is a primary factor in the poor response to chemotherapy and subsequent death in gastric cancer patients. However, the molecular mechanisms involved remain unclear. In this study, the high expression of special AT-rich sequence binding protein 1 (SATB1) in gastric cancer was found to be associated with reduced sensitivity to various chemotherapy drugs. Our results demonstrate that SATB1 can promote chemotherapy resistance in gastric cancer in vitro and in vivo. SATB1 exerts its effect by enhancing the activity of multiple ATP-binding cassette (ABC) transporters (P-glycoprotein, multidrug resistance-associated protein, and breast cancer resistance protein) in gastric cancer cell lines. We also found that SATB1 affects ABC transporters by altering the subcellular localization of the ABC transporter rather than its expression. Subsequently, we confirmed that Ezrin binds to various ABC transporters and affects their subcellular localization. In addition, we found that SATB1 can also bind to the Ezrin promoter and regulate its expression. In the present study, we elucidate the mechanism of SATB1-mediated multidrug resistance in gastric cancer, providing a basis for SATB1 as a potential target for reversal of resistance.
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Affiliation(s)
- Jiajun Luo
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingwen Yuan
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Yang
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yue Jiang
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
| | - Junfeng Yan
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiang Tong
- Department of Gastrointestinal Surgery I Section, Renmin Hospital of Wuhan University, Wuhan, China
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21
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Yu W, Chakravarthi VP, Borosha S, Dilower I, Lee EB, Ratri A, Starks RR, Fields PE, Wolfe MW, Faruque MO, Tuteja G, Rumi MAK. Transcriptional regulation of Satb1 in mouse trophoblast stem cells. Front Cell Dev Biol 2022; 10:918235. [PMID: 36589740 PMCID: PMC9795202 DOI: 10.3389/fcell.2022.918235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
SATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages that emerge during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 act to maintain the trophoblast stem-state. However, the molecular mechanisms that regulate TS-specific Satb expression are not yet known. We identified Satb1 variant 2 as the predominant transcript in trophoblasts. Histone marks, and RNA polymerase II occupancy in TS cells indicated an active state of the promoter. A novel cis-regulatory region with active histone marks was identified ∼21 kbp upstream of the variant 2 promoter. CRISPR/Cas9 mediated disruption of this sequence decreased Satb1 expression in TS cells and chromosome conformation capture analysis confirmed looping of this distant regulatory region into the proximal promoter. Scanning position weight matrices across the enhancer predicted two ELF5 binding sites in close proximity to SATB1 sites, which were confirmed by chromatin immunoprecipitation. Knockdown of ELF5 downregulated Satb1 expression in TS cells and overexpression of ELF5 increased the enhancer-reporter activity. Interestingly, ELF5 interacts with SATB1 in TS cells, and the enhancer activity was upregulated following SATB overexpression. Our findings indicate that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping of an enhancer that interacts with ELF5 and SATB proteins.
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Affiliation(s)
- Wei Yu
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - V. Praveen Chakravarthi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Shaon Borosha
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Iman Dilower
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Eun Bee Lee
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Anamika Ratri
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Rebekah R. Starks
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Patrick E. Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Michael W. Wolfe
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, United States
| | - M. Omar Faruque
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - M. A. Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States,*Correspondence: M. A. Karim Rumi,
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22
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Zelenka T, Klonizakis A, Tsoukatou D, Papamatheakis DA, Franzenburg S, Tzerpos P, Tzonevrakis IR, Papadogkonas G, Kapsetaki M, Nikolaou C, Plewczynski D, Spilianakis C. The 3D enhancer network of the developing T cell genome is shaped by SATB1. Nat Commun 2022; 13:6954. [PMID: 36376298 PMCID: PMC9663569 DOI: 10.1038/s41467-022-34345-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Despina Tsoukatou
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, HU-4032, Hungary
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Christoforos Nikolaou
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Institute for Bioinnovation, Biomedical Sciences Research Centre "Alexander Fleming", 16672, Vari, Greece
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece.
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23
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Gupta PK, Allocco JB, Fraipont JM, McKeague ML, Wang P, Andrade MS, McIntosh C, Chen L, Wang Y, Li Y, Andrade J, Conejo-Garcia JR, Chong AS, Alegre ML. Reduced Satb1 expression predisposes CD4 + T conventional cells to Treg suppression and promotes transplant survival. Proc Natl Acad Sci U S A 2022; 119:e2205062119. [PMID: 36161903 PMCID: PMC9546564 DOI: 10.1073/pnas.2205062119] [Citation(s) in RCA: 1] [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: 03/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Limiting CD4+ T cell responses is important to prevent solid organ transplant rejection. In a mouse model of costimulation blockade-dependent cardiac allograft tolerance, we previously reported that alloreactive CD4+ conventional T cells (Tconvs) develop dysfunction, losing proliferative capacity. In parallel, induction of transplantation tolerance is dependent on the presence of regulatory T cells (Tregs). Whether susceptibility of CD4+ Tconvs to Treg suppression is modulated during tolerance induction is unknown. We found that alloreactive Tconvs from transplant tolerant mice had augmented sensitivity to Treg suppression when compared with memory T cells from rejector mice and expressed a transcriptional profile distinct from these memory T cells, including down-regulated expression of the transcription factor Special AT-rich sequence-binding protein 1 (Satb1). Mechanistically, Satb1 deficiency in CD4+ T cells limited their expression of CD25 and IL-2, and addition of Tregs, which express higher levels of CD25 than Satb1-deficient Tconvs and successfully competed for IL-2, resulted in greater suppression of Satb1-deficient than wild-type Tconvs in vitro. In vivo, Satb1-deficient Tconvs were more susceptible to Treg suppression, resulting in significantly prolonged skin allograft survival. Overall, our study reveals that transplantation tolerance is associated with Tconvs' susceptibility to Treg suppression, via modulated expression of Tconv-intrinsic Satb1. Targeting Satb1 in the context of Treg-sparing immunosuppressive therapies might be exploited to improve transplant outcomes.
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Affiliation(s)
- Pawan K. Gupta
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Jennifer B. Allocco
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Jane M. Fraipont
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Michelle L. McKeague
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Peter Wang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Michael S. Andrade
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637
| | - Christine McIntosh
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Luqiu Chen
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Ying Wang
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Yan Li
- Center for Research Informatics, University of Chicago, Chicago, IL 60637
| | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, IL 60637
| | - José R. Conejo-Garcia
- Department of Immunology, Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, FL 33612
| | - Anita S. Chong
- Section of Transplantation, Department of Surgery, University of Chicago, Chicago, IL 60637
| | - Maria-Luisa Alegre
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL 60637
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24
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Chromatin organizer SATB1 controls the cell identity of CD4 + CD8 + double-positive thymocytes by regulating the activity of super-enhancers. Nat Commun 2022; 13:5554. [PMID: 36138028 PMCID: PMC9500044 DOI: 10.1038/s41467-022-33333-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/14/2022] [Indexed: 11/19/2022] Open
Abstract
CD4+ and CD8+ double-positive (DP) thymocytes play a crucial role in T cell development in the thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCRβ. DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, regulatory T cells, or invariant nature kill T cells (iNKT) in response to TCR signaling. Chromatin organizer SATB1 is highly expressed in DP cells and is essential in regulating Tcra rearrangement and differentiation of DP cells. Here we explored the mechanism of SATB1 orchestrating gene expression in DP cells. Single-cell RNA sequencing shows that Satb1 deletion changes the cell identity of DP thymocytes and down-regulates genes specifically and highly expressed in DP cells. Super-enhancers regulate the expressions of DP-specific genes, and our Hi-C data show that SATB1 deficiency in thymocytes reduces super-enhancer activity by specifically decreasing interactions among super-enhancers and between super-enhancers and promoters. Our results reveal that SATB1 plays a critical role in thymocyte development to promote the establishment of DP cell identity by globally regulating super-enhancers of DP cells at the chromatin architectural level.
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25
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Lin GW, Liang YC, Wu P, Chen CK, Lai YC, Jiang TX, Haung YH, Chuong CM. Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken. Dev Dyn 2022; 251:1490-1508. [PMID: 34240503 PMCID: PMC8742846 DOI: 10.1002/dvdy.396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. RESULTS Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins (1) are often tuned up or down collectively as a sub-cluster, and (2) these changes occur in a temporo-spatial specific manner. CONCLUSIONS These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.
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Affiliation(s)
- Gee-Way Lin
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Integrative Stem Cell Center, China Medical University and Hospital, China Medical University, Taichung 40447, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402204, Taiwan
| | - Yung-Chih Lai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Integrative Stem Cell Center, China Medical University and Hospital, China Medical University, Taichung 40447, Taiwan
- Institute of New Drug Development, China Medical University, Taichung 40402, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yen-Hua Haung
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- TMU Research Center of Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, 11031, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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26
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Nüssing S, Miosge LA, Lee K, Olshansky M, Barugahare A, Roots CM, Sontani Y, Day EB, Koutsakos M, Kedzierska K, Goodnow CC, Russ BE, Daley SR, Turner SJ. SATB1 ensures appropriate transcriptional programs within naïve CD8
+
T cells. Immunol Cell Biol 2022; 100:636-652. [PMID: 35713361 PMCID: PMC9542893 DOI: 10.1111/imcb.12566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Simone Nüssing
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Lisa A Miosge
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - Kah Lee
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | | | - Carla M Roots
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - Yovina Sontani
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
| | - E Bridie Day
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity University of Melbourne Parkville VIC Australia
| | - Christopher C Goodnow
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
- Garvan Institute of Medical Research & Cellular Genomics Futures Institute University of New South Wales Darlinghurst NSW Australia
| | - Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
| | - Stephen R Daley
- John Curtin School of Medical Research Australian National University Canberra ACT Australia
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health Queensland University of Technology Brisbane QLD Australia
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedicine Discovery Institute Monash University Clayton VIC Australia
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27
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Patasova K, Khawaja AP, Wojciechowski R, Mahroo OA, Falchi M, Rahi JS, Hammond CJ, Hysi PG. A genome-wide analysis of 340 318 participants identifies four novel loci associated with the age of first spectacle wear. Hum Mol Genet 2022; 31:3012-3019. [PMID: 35220419 PMCID: PMC9433727 DOI: 10.1093/hmg/ddac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 02/14/2022] [Accepted: 02/24/2022] [Indexed: 11/24/2022] Open
Abstract
Refractive errors, particularly myopia, are the most common eye conditions, often leading to serious visual impairment. The age of onset is correlated with the severity of refractive error in adulthood observed in epidemiological and genetic studies and can be used as a proxy in refractive error genetic studies. To further elucidate genetic factors that influence refractive error, we analysed self-reported age of refractive error correction data from the UK Biobank European and perform genome-wide time-to-event analyses on the age of first spectacle wear (AFSW). Genome-wide proportional hazards ratio analyses were conducted in 340 318 European subjects. We subsequently assessed the similarities and differences in the genetic architectures of refractive error correction from different causes. All-cause AFSW was genetically strongly correlated (rg = -0.68) with spherical equivalent (the measured strength of spectacle lens required to correct the refractive error) and was used as a proxy for refractive error. Time-to-event analyses found genome-wide significant associations at 44 independent genomic loci, many of which (GJD2, LAMA2, etc.) were previously associated with refractive error. We also identified six novel regions associated with AFSW, the most significant of which was on chromosome 17q (P = 3.06 × 10-09 for rs55882072), replicating in an independent dataset. We found that genes associated with AFSW were significantly enriched for expression in central nervous system tissues and were involved in neurogenesis. This work demonstrates the merits of time-to-event study design in the genetic investigation of refractive error and contributes additional knowledge on its genetic risk factors in the general population.
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Affiliation(s)
- Karina Patasova
- Section of Ophthalmology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and the UCL Institute of Ophthalmology, London WC1E 6BT, UK
| | | | - Omar A Mahroo
- Section of Ophthalmology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
- NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and the UCL Institute of Ophthalmology, London WC1E 6BT, UK
- Department of Ophthalmology, St Thomas’ Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
| | - Jugnoo S Rahi
- Institute of Ophthalmology, University College London, London WC1E 6BT, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1EH, UK
- Ulverscroft Vision Research Group, University College London, London WC1N 1EH, UK
| | - Chris J Hammond
- Section of Ophthalmology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, London SE1 7EH, UK
| | - Pirro G Hysi
- To whom correspondence should be addressed at: St Thomas’ Hospital, Westminster Bridge Road, London SE1 7EH, UK. Tel: +44 (0)2071888545; Fax: +44 (0)2071886761;
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28
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Vickridge E, Faraco CCF, Nepveu A. Base excision repair accessory factors in senescence avoidance and resistance to treatments. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:703-720. [PMID: 36176767 PMCID: PMC9511810 DOI: 10.20517/cdr.2022.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023]
Abstract
Cancer cells, in which the RAS and PI3K pathways are activated, produce high levels of reactive oxygen species (ROS), which cause oxidative DNA damage and ultimately cellular senescence. This process has been documented in tissue culture, mouse models, and human pre-cancerous lesions. In this context, cellular senescence functions as a tumour suppressor mechanism. Some rare cancer cells, however, manage to adapt to avoid senescence and continue to proliferate. One well-documented mode of adaptation involves increased production of antioxidants often associated with inactivation of the KEAP1 tumour suppressor gene and the resulting upregulation of the NRF2 transcription factor. In this review, we detail an alternative mode of adaptation to oxidative DNA damage induced by ROS: the increased activity of the base excision repair (BER) pathway, achieved through the enhanced expression of BER enzymes and DNA repair accessory factors. These proteins, exemplified here by the CUT domain proteins CUX1, CUX2, and SATB1, stimulate the activity of BER enzymes. The ensued accelerated repair of oxidative DNA damage enables cancer cells to avoid senescence despite high ROS levels. As a by-product of this adaptation, these cancer cells exhibit increased resistance to genotoxic treatments including ionizing radiation, temozolomide, and cisplatin. Moreover, considering the intrinsic error rate associated with DNA repair and translesion synthesis, the elevated number of oxidative DNA lesions caused by high ROS leads to the accumulation of mutations in the cancer cell population, thereby contributing to tumour heterogeneity and eventually to the acquisition of resistance, a major obstacle to clinical treatment.
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Affiliation(s)
- Elise Vickridge
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Camila C. F. Faraco
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- These authors contributed equally to this work
| | - Alain Nepveu
- Goodman Cancer Institute, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Departments of Biochemistry, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Medicine, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
- Oncology, McGill University, 1160 Pine avenue West, Montreal, Québec H3A 1A3, Canada
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29
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Papadogkonas G, Papamatheakis DA, Spilianakis C. 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. Front Immunol 2022; 13:921375. [PMID: 35812421 PMCID: PMC9257000 DOI: 10.3389/fimmu.2022.921375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/26/2022] [Indexed: 12/12/2022] Open
Abstract
In the heart of innate and adaptive immunity lies the proper spatiotemporal development of several immune cell lineages. Multiple studies have highlighted the necessity of epigenetic and transcriptional regulation in cell lineage specification. This mode of regulation is mediated by transcription factors and chromatin remodelers, controlling developmentally essential gene sets. The core of transcription and epigenetic regulation is formulated by different epigenetic modifications determining gene expression. Apart from “classic” epigenetic modifications, 3D chromatin architecture is also purported to exert fundamental roles in gene regulation. Chromatin conformation both facilitates cell-specific factor binding at specified regions and is in turn modified as such, acting synergistically. The interplay between global and tissue-specific protein factors dictates the epigenetic landscape of T and innate lymphoid cell (ILC) lineages. The expression of global genome organizers such as CTCF, YY1, and the cohesin complexes, closely cooperate with tissue-specific factors to exert cell type-specific gene regulation. Special AT-rich binding protein 1 (SATB1) is an important tissue-specific genome organizer and regulator controlling both long- and short-range chromatin interactions. Recent indications point to SATB1’s cooperation with the aforementioned factors, linking global to tissue-specific gene regulation. Changes in 3D genome organization are of vital importance for proper cell development and function, while disruption of this mechanism can lead to severe immuno-developmental defects. Newly emerging data have inextricably linked chromatin architecture deregulation to tissue-specific pathophysiological phenotypes. The combination of these findings may shed light on the mechanisms behind pathological conditions.
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Affiliation(s)
- George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
- *Correspondence: Charalampos Spilianakis,
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30
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Multi- and Transgenerational Effects of Developmental Exposure to Environmental Levels of PFAS and PFAS Mixture in Zebrafish ( Danio rerio). TOXICS 2022; 10:toxics10060334. [PMID: 35736942 PMCID: PMC9228135 DOI: 10.3390/toxics10060334] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are ubiquitous in the environment and are tied to myriad health effects. Despite the phasing out of the manufacturing of two types of PFASs (perfluorosulfonic acid (PFOS) and perfluorooctanoic acid (PFOA)), chemical composition renders them effectively indestructible by ambient environmental processes, where they thus remain in water. Exposure via water can affect both human and aquatic wildlife. PFASs easily cross the placenta, exposing the fetus at critical windows of development. Little is known about the effects of low-level exposure during this period; even less is known about the potential for multi- and transgenerational effects. We examined the effects of ultra-low, very low, and low-level PFAS exposure (7, 70, and 700 ng/L PFOA; 24, 240, 2400 ng/L PFOS; and stepwise mixtures) from 0–5 days post-fertilization (dpf) on larval zebrafish (Danio rerio) mortality, morphology, behavior and gene expression and fecundity in adult F0 and F1 fish. As expected, environmentally relevant PFAS levels did not affect survival. Morphological abnormalities were not observed until the F1 and F2 generations. Behavior was affected differentially by each chemical and generation. Gene expression was increasingly perturbed in each generation but consistently showed lipid pathway disruption across all generations. Dysregulation of behavior and gene expression is heritable, even in larvae with no direct or indirect exposure. This is the first report of the transgenerational effects of PFOA, PFOS, and their mixture in terms of zebrafish behavior and untargeted gene expression.
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31
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Huang D, Zhao Q, Zhang M, Weng Q, Zhang Q, Wang K, Dong F, Cheng H, Hu F, Wang J. Hoxb5 reprogrammes murine multipotent blood progenitors into haematopoietic stem cell-like cells. Cell Prolif 2022; 55:e13235. [PMID: 35582777 PMCID: PMC9201374 DOI: 10.1111/cpr.13235] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives The expression of transcription factor Hoxb5 specifically marks the functional haematopoietic stem cells (HSC) in mice. However, our recent work demonstrated that ectopic expression of Hoxb5 exerted little effect on HSC but could convert B‐cell progenitors into functional T cells in vivo. Thus, cell type‐ and development stage‐specific roles of Hoxb5 in haematopoietic hierarchy await more extensive exploration. In this study, we aim to investigate the effect of Hoxb5 expression in multipotent blood progenitor cells. Materials and Methods A Mx1cre/RosaLSL‐Hoxb5‐EGFP/+ mouse model was used to evaluate the effect of Hoxb5 expression in blood multipotent progenitor cells (MPP). Golden standard serial transplantation experiments were used to test the long‐term haematopoiesis potential of Hoxb5‐expressing MPP. Single‐cell RNA‐seq analysis was used to characterize the gained molecular features of Hoxb5‐expressing MPP and to compare with the global transcriptome features of natural adult HSC and fetal liver HSC (FL HSC). Results Here, with a mouse strain engineered with conditional expression of Hoxb5, we unveiled that induced expression of Hoxb5 in MPP led to the generation of a de novo Sca1+c‐kit+CD11b+CD48+ (CD11b+CD48+SK) cell type, which can repopulate long‐term multilineage haematopoiesis in serial transplantations. RNA‐seq analysis showed that CD11b+CD48+SK cells exhibited acquired features of DNA replication and cell division. Conclusions Our current study uncovers that Hoxb5 can empower MPP with self‐renewal ability and indicates an alternative approach for generating HSC‐like cells in vivo from blood lineage cells.
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Affiliation(s)
- Dehao Huang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qianhao Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, China
| | - Mengyun Zhang
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qitong Weng
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaitao Wang
- School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology & National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Center for Stem Cell Medicine & Department of Stem Cell and Regenerative Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Fangxiao Hu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jinyong Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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32
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He Z, Li Y, Feng G, Yuan X, Lu Z, Dai M, Hu Y, Zhang Y, Zhou Q, Li W. Pharmacological Perturbation of Mechanical Contractility Enables Robust Transdifferentiation of Human Fibroblasts into Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104682. [PMID: 35240008 PMCID: PMC9069193 DOI: 10.1002/advs.202104682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/27/2022] [Indexed: 05/08/2023]
Abstract
Direct cell reprogramming, also called transdifferentiation, is valuable for cell fate studies and regenerative medicine. Current approaches to transdifferentiation are usually achieved by directly targeting the nuclear functions, such as manipulating the lineage-specific transcriptional factors, microRNAs, and epigenetic modifications. Here, a robust method to convert fibroblasts to neurons through targeting the cytoskeleton followed by exposure to lineage-specification surroundings is reported. Treatment of human foreskin fibroblasts with a single molecule inhibitor of the actomyosin contraction, can disrupt the cytoskeleton, promote cell softening and nuclear export of YAP/TAZ, and induce a neuron-like state. These neuron-like cells can be further converted into mature neurons, while single-cell RNA-seq shows the homogeneity of these cells during the induction process. Finally, transcriptomic analysis shows that cytoskeletal disruption collapses the original lineage expression profile and evokes an intermediate state. These findings shed a light on the underestimated role of the cytoskeleton in maintaining cell identity and provide a paradigm for lineage conversion through the regulation of mechanical properties.
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Affiliation(s)
- Zheng‐Quan He
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Yu‐Huan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- The First Hospital of Jilin UniversityChangchunJilin130021China
| | - Gui‐Hai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Xue‐Wei Yuan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Zong‐Bao Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Min Dai
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Yan‐Ping Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of ZoologyChinese Academy of SciencesBeijing100101China
- Institute for Stem Cell and Regenerative MedicineChinese Academy of SciencesBeijing100100China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100100China
- University of Chinese Academy of SciencesBeijing100149China
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33
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Ozawa T, Fujii K, Sudo T, Doi Y, Nakai R, Shingai Y, Ueda T, Baba Y, Hosen N, Yokota T. Special AT-Rich Sequence-Binding Protein 1 Supports Survival and Maturation of Naive B Cells Stimulated by B Cell Receptors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1937-1946. [PMID: 35379742 DOI: 10.4049/jimmunol.2101097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/09/2022] [Indexed: 11/19/2022]
Abstract
Epigenetic mechanisms underpin the elaborate activities of essential transcription factors in lymphocyte development. Special AT-rich sequence-binding protein 1 (SATB1) is a chromatin remodeler that orchestrates the spatial and temporal actions of transcription factors. Previous studies have revealed the significance of SATB1 in T cell lineage. However, whether and how SATB1 controls B cell lineage development is yet to be clarified. In this study, we show that SATB1 is an important factor during splenic B cell maturation. By analyzing SATB1/Tomato reporter mice, we determined the dynamic fluctuation of SATB1 expression in the B cell lineage. Although SATB1 expression decreased to minimal levels during B cell differentiation in the bone marrow, it resurged markedly in naive B cells in the spleen. The expression was dramatically downregulated upon Ag-induced activation. Splenic naive B cells were subdivided into two categories, namely SATB1high and SATB1-/low, according to their SATB1 expression levels. SATB1high naive B cells were less susceptible to death and greater proliferative than were SATB1-/low cells during incubation with an anti-IgM Ab. Additionally, SATB1high cells tended to induce the expression of MHC class II, CD86, and CD83. Accordingly, naive B cells from B lineage-specific SATB1 conditional knockout mice were more susceptible to apoptosis than that in the control group upon anti-IgM Ab stimulation in vitro. Furthermore, conditional knockout mice were less capable of producing Ag-specific B cells after immunization. Collectively, our findings suggest that SATB1 expression increases in naive B cells and plays an important role in their survival and maturation.
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Affiliation(s)
- Takayuki Ozawa
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kentaro Fujii
- Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Takao Sudo
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yukiko Doi
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ritsuko Nakai
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuhiro Shingai
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tomoaki Ueda
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshihiro Baba
- Division of Immunology and Genome Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Naoki Hosen
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory of Cellular Immunotherapy, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan; and.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Takafumi Yokota
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Osaka, Japan;
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Bell RAV, Al-Khalaf MH, Brunette S, Alsowaida D, Chu A, Bandukwala H, Dechant G, Apostolova G, Dilworth FJ, Megeney LA. Chromatin Reorganization during Myoblast Differentiation Involves the Caspase-Dependent Removal of SATB2. Cells 2022; 11:cells11060966. [PMID: 35326417 PMCID: PMC8946544 DOI: 10.3390/cells11060966] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 11/17/2022] Open
Abstract
The induction of lineage-specific gene programs are strongly influenced by alterations in local chromatin architecture. However, key players that impact this genome reorganization remain largely unknown. Here, we report that the removal of the special AT-rich binding protein 2 (SATB2), a nuclear protein known to bind matrix attachment regions, is a key event in initiating myogenic differentiation. The deletion of myoblast SATB2 in vitro initiates chromatin remodeling and accelerates differentiation, which is dependent on the caspase 7-mediated cleavage of SATB2. A genome-wide analysis indicates that SATB2 binding within chromatin loops and near anchor points influences both loop and sub-TAD domain formation. Consequently, the chromatin changes that occur with the removal of SATB2 lead to the derepression of differentiation-inducing factors while also limiting the expression of genes that inhibit this cell fate change. Taken together, this study demonstrates that the temporal control of the SATB2 protein is critical in shaping the chromatin environment and coordinating the myogenic differentiation program.
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Affiliation(s)
- Ryan A. V. Bell
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mohammad H. Al-Khalaf
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada
| | - Steve Brunette
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
| | - Dalal Alsowaida
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alphonse Chu
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Hina Bandukwala
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
| | - Georg Dechant
- Institute of Neuroscience, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (G.D.); (G.A.)
| | - Galina Apostolova
- Institute of Neuroscience, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (G.D.); (G.A.)
| | - F. Jeffrey Dilworth
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Lynn A. Megeney
- Regenerative Medicine Program, Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada; (R.A.V.B.); (M.H.A.-K.); (S.B.); (D.A.); (A.C.); (H.B.); (F.J.D.)
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Correspondence:
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35
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Yu W, Ma Y, Shrivastava SK, Srivastava RK, Shankar S. Chronic alcohol exposure induces hepatocyte damage by inducing oxidative stress, SATB2 and stem cell‐like characteristics, and activating lipogenesis. J Cell Mol Med 2022; 26:2119-2131. [PMID: 35152538 PMCID: PMC8980954 DOI: 10.1111/jcmm.17235] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Alcohol is a risk factor for hepatocellular carcinoma (HCC). However, the molecular mechanism by which chronic alcohol consumption contributes to HCC is not well understood. The purpose of the study was to demonstrate the effects of chronic ethanol exposure on the damage of human normal hepatocytes. Our data showed that chronic exposure of hepatocytes with ethanol induced changes similar to transformed hepatocytes that is, exhibited colonies and anchorage‐independent growth. These damaged hepatocytes contained high levels of reactive oxygen species (ROS) and showed induction of the SATB2 gene. Furthermore, damaged hepatocytes gained the phenotypes of CSCs which expressed stem cell markers (CD133, CD44, CD90, EpCAM, AFP and LGR5), and pluripotency maintaining factors (Sox‐2, POU5F1/Oct4 and KLF‐4). Ethanol exposure also induced Nanog, a pluripotency maintaining transcription factor that functions in concert with Oct4 and SOX‐2. Furthermore, ethanol induced expression of EMT‐related transcription factors (Snail, Slug and Zeb1), N‐Cadherin, and inhibited E‐cadherin expression in damaged hepatocytes. Ethanol enhanced recruitment of SATB2 to promoters of Bcl‐2, Nanog, c‐Myc, Klf4 and Oct4. Ethanol also induced activation of the Wnt/TCF‐LEF1 pathway and its targets (Bcl‐2, Cyclin D1, AXIN2 and Myc). Finally, ethanol induced hepatocellular steatosis, SREBP1 transcription, and modulated the expression of SREBP1c, ACAC, ACLY, FASN, IL‐1β, IL‐6, TNF‐α, GPC3, FLNB and p53. These data suggest that chronic alcohol consumption may contribute towards the development of HCC by damaging normal hepatocytes with the generation of inflammatory environment, induction of SATB2, stem cell‐like characteristics, and cellular steatosis.
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Affiliation(s)
- Wei Yu
- Kansas City VA Medical Center Kansas City Missouri USA
| | - Yiming Ma
- Kansas City VA Medical Center Kansas City Missouri USA
| | - Sushant K. Shrivastava
- Department of Pharmaceutics Indian Institute of Technology Banaras Hindu University Varanasi U.P. India
| | - Rakesh K. Srivastava
- Kansas City VA Medical Center Kansas City Missouri USA
- Department of Genetics Louisiana State University Health Sciences Center New Orleans Louisina USA
- Stanley S. Scott Cancer Center Department of Genetics Louisiana State University Health Sciences Center New Orleans Louisina USA
- A.B. Freeman School of Business Tulane University New Orleans Louisina USA
| | - Sharmila Shankar
- Kansas City VA Medical Center Kansas City Missouri USA
- John W. Deming Department of Medicine Tulane University School of Medicine New Orleans Louisina USA
- Southeast Louisiana Veterans Health Care System New Orleans Louisina USA
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36
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Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Cell Stem Cell 2022; 29:101-115.e10. [PMID: 34582804 PMCID: PMC8741647 DOI: 10.1016/j.stem.2021.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/13/2021] [Accepted: 09/08/2021] [Indexed: 01/09/2023]
Abstract
Adult stem cells maintain regenerative tissue structure and function by producing tissue-specific progeny, but the factors that preserve their tissue identities are not well understood. The small and large intestines differ markedly in cell composition and function, reflecting their distinct stem cell populations. Here we show that SATB2, a colon-restricted chromatin factor, singularly preserves LGR5+ adult colonic stem cell and epithelial identity in mice and humans. Satb2 loss in adult mice leads to stable conversion of colonic stem cells into small intestine ileal-like stem cells and replacement of the colonic mucosa with one that resembles the ileum. Conversely, SATB2 confers colonic properties on the mouse ileum. Human colonic organoids also adopt ileal characteristics upon SATB2 loss. SATB2 regulates colonic identity in part by modulating enhancer binding of the intestinal transcription factors CDX2 and HNF4A. Our study uncovers a conserved core regulator of colonic stem cells able to mediate cross-tissue plasticity in mature intestines.
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Affiliation(s)
- Wei Gu
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Hua Wang
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA
| | - Xiaofeng Huang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Judith Kraiczy
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Pratik N. P. Singh
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Charles Ng
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Sezin Dagdeviren
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Sean Houghton
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ying Lan
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Yaohui Nie
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Jiaoyue Zhang
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Kushal K Banerjee
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Emily J. Onufer
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, 660 S Euclid Avenue, St. Louis, MO, 63110, USA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, 1500 E Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Ellen Scherl
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Shahin Rafii
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Richard T. Lee
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Michael P. Verzi
- Department of Genetics, Rutgers University, 145 Bevier Road, Piscataway, NJ, 08854, USA
| | - David Redmond
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Randy Longman
- Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, 1283 York Avenue, New York, NY, 10065, USA
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, 430 E 67th Street, New York, NY, 10065, USA,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen N 2200 Denmark,The Novo Nordisk Foundation for Stem Cell Biology (Danstem), University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ramesh A. Shivdasani
- Department of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA,Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Qiao Zhou
- Division of Regenerative Medicine & Ansary Stem Cell Institute, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA,Lead Contact ()
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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Kuwabara T, Ishikawa F, Ikeda M, Ide T, Kohwi-Shigematsu T, Tanaka Y, Kondo M. SATB1-dependent mitochondrial ROS production controls TCR signaling in CD4 T cells. Life Sci Alliance 2021; 4:4/11/e202101093. [PMID: 34583974 PMCID: PMC8500228 DOI: 10.26508/lsa.202101093] [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: 04/14/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022] Open
Abstract
SATB1 regulates mitochondrial function and reactive oxygen species (ROS) production through the expression of mitochondrial transcription factor A. SATB1-mediated ROS production is necessary for TCR stimulation and T-cell function. Special AT-rich sequence binding protein-1 (SATB1) is localized to the nucleus and remodels chromatin structure in T cells. SATB1-deficient CD4 T cells cannot respond to TCR stimulation; however, the cause of this unresponsiveness is to be clarified. Here, we demonstrate that SATB1 is indispensable to proper mitochondrial functioning and necessary for the activation of signal cascades via the TCR in CD4 T cells. Naïve SATB1-deficient CD4 T cells contain fewer mitochondria than WT T cells, as the former do not express mitochondrial transcription factor A (TFAM). Impaired mitochondrial function in SATB1-deficient T cells subverts mitochondrial ROS production and SHP-1 inactivation by constitutive oxidization. Ectopic TFAM expression increases mitochondrial mass and mitochondrial ROS production and rescues defects in the antigen-specific response in the SATB1-deficient T cells. Thus, SATB1 is vital for maintaining mitochondrial mass and function by regulating TFAM expression, which is necessary for TCR signaling.
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Affiliation(s)
- Taku Kuwabara
- Department of Molecular Immunology, Toho University School of Medicine, Tokyo, Japan
| | - Fumio Ishikawa
- Department of Molecular Immunology, Toho University School of Medicine, Tokyo, Japan.,Faculty of Health Sciences, Tsukuba International University, Tsuchiura, Japan
| | - Masataka Ikeda
- Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomomi Ide
- Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Terumi Kohwi-Shigematsu
- Department of Orofacial Science, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Yuriko Tanaka
- Department of Molecular Immunology, Toho University School of Medicine, Tokyo, Japan
| | - Motonari Kondo
- Department of Molecular Immunology, Toho University School of Medicine, Tokyo, Japan
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39
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Synthetic modified Fezf2 mRNA (modRNA) with concurrent small molecule SIRT1 inhibition enhances refinement of cortical subcerebral/corticospinal neuron identity from mouse embryonic stem cells. PLoS One 2021; 16:e0254113. [PMID: 34473715 PMCID: PMC8412356 DOI: 10.1371/journal.pone.0254113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/20/2021] [Indexed: 01/29/2023] Open
Abstract
During late embryonic development of the cerebral cortex, the major class of cortical output neurons termed subcerebral projection neurons (SCPN; including the predominant population of corticospinal neurons, CSN) and the class of interhemispheric callosal projection neurons (CPN) initially express overlapping molecular controls that later undergo subtype-specific refinements. Such molecular refinements are largely absent in heterogeneous, maturation-stalled, neocortical-like neurons (termed "cortical" here) spontaneously generated by established embryonic stem cell (ES) and induced pluripotent stem cell (iPSC) differentiation. Building on recently identified central molecular controls over SCPN development, we used a combination of synthetic modified mRNA (modRNA) for Fezf2, the central transcription factor controlling SCPN specification, and small molecule screening to investigate whether distinct chromatin modifiers might complement Fezf2 functions to promote SCPN-specific differentiation by mouse ES (mES)-derived cortical-like neurons. We find that the inhibition of a specific histone deacetylase, Sirtuin 1 (SIRT1), enhances refinement of SCPN subtype molecular identity by both mES-derived cortical-like neurons and primary dissociated E12.5 mouse cortical neurons. In vivo, we identify that SIRT1 is specifically expressed by CPN, but not SCPN, during late embryonic and postnatal differentiation. Together, these data indicate that SIRT1 has neuronal subtype-specific expression in the mouse cortex in vivo, and that its inhibition enhances subtype-specific differentiation of highly clinically relevant SCPN / CSN cortical neurons in vitro.
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40
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den Hoed J, Devaraju K, Fisher SE. Molecular networks of the FOXP2 transcription factor in the brain. EMBO Rep 2021; 22:e52803. [PMID: 34260143 PMCID: PMC8339667 DOI: 10.15252/embr.202152803] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
The discovery of the FOXP2 transcription factor, and its implication in a rare severe human speech and language disorder, has led to two decades of empirical studies focused on uncovering its roles in the brain using a range of in vitro and in vivo methods. Here, we discuss what we have learned about the regulation of FOXP2, its downstream effectors, and its modes of action as a transcription factor in brain development and function, providing an integrated overview of what is currently known about the critical molecular networks.
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Affiliation(s)
- Joery den Hoed
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- International Max Planck Research School for Language SciencesMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Karthikeyan Devaraju
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Simon E Fisher
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenThe Netherlands
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41
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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Zou M, Duren Z, Yuan Q, Li H, Hutchins AP, Wong WH, Wang Y. MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. Brief Bioinform 2021; 22:6309927. [PMID: 34180954 PMCID: PMC8575015 DOI: 10.1093/bib/bbab235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 11/14/2022] Open
Abstract
Multi-omics data allow us to select a small set of informative markers for the discrimination of specific cell types and study of cellular heterogeneity. However, it is often challenging to choose an optimal marker panel from the high-dimensional molecular profiles for a large amount of cell types. Here, we propose a method called Mixed Integer programming Model to Identify Cell type-specific marker panel (MIMIC). MIMIC maintains the hierarchical topology among different cell types and simultaneously maximizes the specificity of a fixed number of selected markers. MIMIC was benchmarked on the mouse ENCODE RNA-seq dataset, with 29 diverse tissues, for 43 surface markers (SMs) and 1345 transcription factors (TFs). MIMIC could select biologically meaningful markers and is robust for different accuracy criteria. It shows advantages over the standard single gene-based approaches and widely used dimensional reduction methods, such as multidimensional scaling and t-SNE, both in accuracy and in biological interpretation. Furthermore, the combination of SMs and TFs achieves better specificity than SMs or TFs alone. Applying MIMIC to a large collection of 641 RNA-seq samples covering 231 cell types identifies a panel of TFs and SMs that reveal the modularity of cell type association networks. Finally, the scalability of MIMIC is demonstrated by selecting enhancer markers from mouse ENCODE data. MIMIC is freely available at https://github.com/MengZou1/MIMIC.
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Affiliation(s)
- Meng Zou
- Department of Mathematics, Huazhong University of Science and Technology, Beijing 100190, China
| | - Zhana Duren
- Department of Genetics and Biochemistry, Clemson University, Beijing 100190, China
| | - Qiuyue Yuan
- Academy of Mathematics and Systems Science, CAS, Beijing 100190, China
| | - Henry Li
- Department of Health Research & Policy, Bio-X Program Stanford University, Beijing 100190, China
| | | | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program Stanford University, Beijing 100190, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, CAS, Beijing 100190, China
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44
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Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription. Epigenetics Chromatin 2021; 14:27. [PMID: 34130715 PMCID: PMC8207718 DOI: 10.1186/s13072-021-00403-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background A critical question emerging in the field of developmental toxicology is whether alterations in chromatin structure induced by toxicant exposure control patterns of gene expression or, instead, are structural changes that are part of a nuclear stress response. Previously, we used a mouse model to conduct a three-way comparison between control offspring, alcohol-exposed but phenotypically normal animals, and alcohol-exposed offspring exhibiting craniofacial and central nervous system structural defects. In the cerebral cortex of animals exhibiting alcohol-induced dysgenesis, we identified a dramatic increase in the enrichment of dimethylated histone H3, lysine 9 (H3K9me2) within the regulatory regions of key developmental factors driving histogenesis in the brain. However, whether this change in chromatin structure is causally involved in the development of structural defects remains unknown. Results Deep-sequencing analysis of the cortex transcriptome reveals that the emergence of alcohol-induced structural defects correlates with disruptions in the genetic pathways controlling oxidative phosphorylation and mitochondrial function. The majority of the affected pathways are downstream targets of the mammalian target of rapamycin complex 2 (mTORC2), indicating that this stress-responsive complex plays a role in propagating the epigenetic memory of alcohol exposure through gestation. Importantly, transcriptional disruptions of the pathways regulating oxidative homeostasis correlate with the emergence of increased H3K9me2 across genic, repetitive, and non-transcribed regions of the genome. However, although associated with gene silencing, none of the candidate genes displaying increased H3K9me2 become transcriptionally repressed, nor do they exhibit increased markers of canonical heterochromatin. Similar to studies in C. elegans, disruptions in oxidative homeostasis induce the chromatin looping factor SATB2, but in mammals, this protein does not appear to drive increased H3K9me2 or altered patterns of gene expression. Conclusions Our studies demonstrate that changes in H3K9me2 associate with alcohol-induced congenital defects, but that this epigenetic change does not correlate with transcriptional suppression. We speculate that the mobilization of SATB2 and increased enrichment of H3K9me2 may be components of a nuclear stress response that preserve chromatin integrity and interactions under prolonged oxidative stress. Further, we postulate that while this response may stabilize chromatin structure, it compromises the nuclear plasticity required for normal differentiation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00403-w.
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Abstract
The regulatory circuits that define developmental decisions of thymocytes are still incompletely resolved. SATB1 protein is predominantly expressed at the CD4+CD8+cell stage exerting its broad transcription regulation potential with both activatory and repressive roles. A series of post-translational modifications and the presence of potential SATB1 protein isoforms indicate the complexity of its regulatory potential. The most apparent mechanism of its involvement in gene expression regulation is via the orchestration of long-range chromatin loops between genes and their regulatory elements. Multiple SATB1 perturbations in mice uncovered a link to autoimmune diseases while clinical investigations on cancer research uncovered that SATB1 has a promoting role in several types of cancer and can be used as a prognostic biomarker. SATB1 is a multivalent tissue-specific factor with a broad and yet undetermined regulatory potential. Future investigations on this protein could further uncover T cell-specific regulatory pathways and link them to (patho)physiology.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete , Heraklion, Crete, Greece.,Gene Regulation & Genomics, Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas , Heraklion, Crete, Greece
| | - Charalampos Spilianakis
- Department of Biology, University of Crete , Heraklion, Crete, Greece.,Gene Regulation & Genomics, Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas , Heraklion, Crete, Greece
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46
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Maity S, Chakrabarti O. Mitochondrial protein import as a quality control sensor. Biol Cell 2021; 113:375-400. [PMID: 33870508 DOI: 10.1111/boc.202100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Mitochondria are organelles involved in various functions related to cellular metabolism and homoeostasis. Though mitochondria contain own genome, their nuclear counterparts encode most of the different mitochondrial proteins. These are synthesised as precursors in the cytosol and have to be delivered into the mitochondria. These organelles hence have elaborate machineries for the import of precursor proteins from cytosol. The protein import machineries present in both mitochondrial membrane and aqueous compartments show great variability in pre-protein recognition, translocation and sorting across or into it. Mitochondrial protein import machineries also interact transiently with other protein complexes of the respiratory chain or those involved in the maintenance of membrane architecture. Hence mitochondrial protein translocation is an indispensable part of the regulatory network that maintains protein biogenesis, bioenergetics, membrane dynamics and quality control of the organelle. Various stress conditions and diseases that are associated with mitochondrial import defects lead to changes in cellular transcriptomic and proteomic profiles. Dysfunction in mitochondrial protein import also causes over-accumulation of precursor proteins and their aggregation in the cytosol. Multiple pathways may be activated for buffering these harmful consequences. Here, we present a comprehensive picture of import machinery and its role in cellular quality control in response to defective mitochondrial import. We also discuss the pathological consequences of dysfunctional mitochondrial protein import in neurodegeneration and cancer.
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Affiliation(s)
- Sebabrata Maity
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.,Homi Bhabha National Institute, India
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47
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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48
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Lodewijk I, Nunes SP, Henrique R, Jerónimo C, Dueñas M, Paramio JM. Tackling tumor microenvironment through epigenetic tools to improve cancer immunotherapy. Clin Epigenetics 2021; 13:63. [PMID: 33761971 PMCID: PMC7992805 DOI: 10.1186/s13148-021-01046-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic alterations are known contributors to cancer development and aggressiveness. Additional to alterations in cancer cells, aberrant epigenetic marks are present in cells of the tumor microenvironment, including lymphocytes and tumor-associated macrophages, which are often overlooked but known to be a contributing factor to a favorable environment for tumor growth. Therefore, the main aim of this review is to give an overview of the epigenetic alterations affecting immune cells in the tumor microenvironment to provoke an immunosuppressive function and contribute to cancer development. Moreover, immunotherapy is briefly discussed in the context of epigenetics, describing both its combination with epigenetic drugs and the need for epigenetic biomarkers to predict response to immune checkpoint blockage. MAIN BODY Combining both topics, epigenetic machinery plays a central role in generating an immunosuppressive environment for cancer growth, which creates a barrier for immunotherapy to be successful. Furthermore, epigenetic-directed compounds may not only affect cancer cells but also immune cells in the tumor microenvironment, which could be beneficial for the clinical response to immunotherapy. CONCLUSION Thus, modulating epigenetics in combination with immunotherapy might be a promising therapeutic option to improve the success of this therapy. Further studies are necessary to (1) understand in depth the impact of the epigenetic machinery in the tumor microenvironment; (2) how the epigenetic machinery can be modulated according to tumor type to increase response to immunotherapy and (3) find reliable biomarkers for a better selection of patients eligible to immunotherapy.
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Affiliation(s)
- Iris Lodewijk
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
| | - Sandra P. Nunes
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar – University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group – Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar – University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Marta Dueñas
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jesús M. Paramio
- Molecular Oncology Unit, Centro de Investigaciones Energéticas, Medioambientales Y Tecnológicas (CIEMAT), 28040 Madrid, Spain
- Biomedical Research Institute I+12, University Hospital “12 de Octubre”, 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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Sah E, Krishnamurthy S, Ahmidouch MY, Gillispie GJ, Milligan C, Orr ME. The Cellular Senescence Stress Response in Post-Mitotic Brain Cells: Cell Survival at the Expense of Tissue Degeneration. Life (Basel) 2021; 11:life11030229. [PMID: 33799628 PMCID: PMC7998276 DOI: 10.3390/life11030229] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 01/10/2023] Open
Abstract
In 1960, Rita Levi-Montalcini and Barbara Booker made an observation that transformed neuroscience: as neurons mature, they become apoptosis resistant. The following year Leonard Hayflick and Paul Moorhead described a stable replicative arrest of cells in vitro, termed "senescence". For nearly 60 years, the cell biology fields of neuroscience and senescence ran in parallel, each separately defining phenotypes and uncovering molecular mediators to explain the 1960s observations of their founding mothers and fathers, respectively. During this time neuroscientists have consistently observed the remarkable ability of neurons to survive. Despite residing in environments of chronic inflammation and degeneration, as occurs in numerous neurodegenerative diseases, often times the neurons with highest levels of pathology resist death. Similarly, cellular senescence (hereon referred to simply as "senescence") now is recognized as a complex stress response that culminates with a change in cell fate. Instead of reacting to cellular/DNA damage by proliferation or apoptosis, senescent cells survive in a stable cell cycle arrest. Senescent cells simultaneously contribute to chronic tissue degeneration by secreting deleterious molecules that negatively impact surrounding cells. These fields have finally collided. Neuroscientists have begun applying concepts of senescence to the brain, including post-mitotic cells. This initially presented conceptual challenges to senescence cell biologists. Nonetheless, efforts to understand senescence in the context of brain aging and neurodegenerative disease and injury emerged and are advancing the field. The present review uses pre-defined criteria to evaluate evidence for post-mitotic brain cell senescence. A closer interaction between neuro and senescent cell biologists has potential to advance both disciplines and explain fundamental questions that have plagued their fields for decades.
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Affiliation(s)
- Eric Sah
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (E.S.); (S.K.); (M.Y.A.); (G.J.G.)
| | - Sudarshan Krishnamurthy
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (E.S.); (S.K.); (M.Y.A.); (G.J.G.)
- Bowman Gray Center for Medical Education, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Mohamed Y. Ahmidouch
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (E.S.); (S.K.); (M.Y.A.); (G.J.G.)
- Departments of Biology and Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Gregory J. Gillispie
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (E.S.); (S.K.); (M.Y.A.); (G.J.G.)
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Carol Milligan
- Department of Neurobiology and Anatomy, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Miranda E. Orr
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (E.S.); (S.K.); (M.Y.A.); (G.J.G.)
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
- Salisbury VA Medical Center, Salisbury, NC 28144, USA
- Correspondence:
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Lai P, Wang Y. Epigenetics of cutaneous T-cell lymphoma: biomarkers and therapeutic potentials. Cancer Biol Med 2021; 18:34-51. [PMID: 33628583 PMCID: PMC7877166 DOI: 10.20892/j.issn.2095-3941.2020.0216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/30/2020] [Indexed: 12/31/2022] Open
Abstract
Cutaneous T-cell lymphomas (CTCLs) are a heterogeneous group of skin-homing non-Hodgkin lymphomas. There are limited options for effective treatment of patients with advanced-stage CTCL, leading to a poor survival rate. Epigenetics plays a pivotal role in regulating gene expression without altering the DNA sequence. Epigenetic alterations are involved in virtually all key cancer-associated pathways and are fundamental to the genesis of cancer. In recent years, the epigenetic hallmarks of CTCL have been gradually elucidated and their potential values in the diagnosis, prognosis, and therapeutic intervention have been clarified. In this review, we summarize the current knowledge of the best-studied epigenetic modifications in CTCL, including DNA methylation, histone modifications, microRNAs, and chromatin remodelers. These epigenetic regulators are essential in the development of CTCL and provide new insights into the clinical treatments of this refractory disease.
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Affiliation(s)
- Pan Lai
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
| | - Yang Wang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, National Clinical Research Center for Skin and Immune Diseases, Beijing 100034, China
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