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Zhou P, Liu W, Ma J. Roles of Menin in T cell differentiation and function: Current knowledge and perspectives. Immunology 2024. [PMID: 39011567 DOI: 10.1111/imm.13837] [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: 04/17/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
The commitment to specific T lymphocytes (T cell) lineages is governed by distinct transcription factors, whose expression is modulated through epigenetic mechanisms. Unravelling these epigenetic mechanisms that regulate T cell differentiation and function holds significant importance for understanding T cells. Menin, a multifunctional scaffolding protein, is implicated in various cellular processes, such as cell proliferation, cell cycle control, DNA repair and transcriptional regulation, primarily through epigenetic mechanisms. Existing research indicates Menin's impact on T cell differentiation and function, while a comprehensive and systematic review is currently lacking to consolidate these findings. In the current review, we have highlighted recent studies on the role of Menin in T cell differentiation and function, focusing mainly on its impact on the memory Th2 maintenance, Th17 differentiation and maintenance, CD4+ T cell senescence, and effector CD8+ T cell survival. Considering Menin's crucial function in maintaining effector T cell function, the potential of inhibiting Menin activity in mitigating inflammatory diseases associated with excessive T cell activation has also been emphasised.
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Affiliation(s)
- Pingping Zhou
- Department of Immunology, Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Weiru Liu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jian Ma
- Department of Immunology, Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
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2
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Furuya H, Toda Y, Iwata A, Kanai M, Kato K, Kumagai T, Kageyama T, Tanaka S, Fujimura L, Sakamoto A, Hatano M, Suto A, Suzuki K, Nakajima H. Stage-specific GATA3 induction promotes ILC2 development after lineage commitment. Nat Commun 2024; 15:5610. [PMID: 38969652 PMCID: PMC11226602 DOI: 10.1038/s41467-024-49881-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: 03/27/2023] [Accepted: 06/24/2024] [Indexed: 07/07/2024] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) are a subset of innate lymphocytes that produce type 2 cytokines, including IL-4, IL-5, and IL-13. GATA3 is a critical transcription factor for ILC2 development at multiple stages. However, when and how GATA3 is induced to the levels required for ILC2 development remains unclear. Herein, we identify ILC2-specific GATA3-related tandem super-enhancers (G3SE) that induce high GATA3 in ILC2-committed precursors. G3SE-deficient mice exhibit ILC2 deficiency in the bone marrow, lung, liver, and small intestine with minimal impact on other ILC lineages or Th2 cells. Single-cell RNA-sequencing and subsequent flow cytometry analysis show that GATA3 induction mechanism, which is required for entering the ILC2 stage, is lost in IL-17RB+PD-1- late ILC2-committed precursor stage in G3SE-deficient mice. Cnot6l, part of the CCR4-NOT deadenylase complex, is a possible GATA3 target during ILC2 development. Our findings implicate a stage-specific regulatory mechanism for GATA3 expression during ILC2 development.
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Affiliation(s)
- Hiroki Furuya
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yosuke Toda
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Arifumi Iwata
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Mizuki Kanai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kodai Kato
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takashi Kumagai
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Kageyama
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shigeru Tanaka
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Lisa Fujimura
- Biomedical Research Center, Chiba University, Chiba, Japan
| | - Akemi Sakamoto
- Biomedical Research Center, Chiba University, Chiba, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiko Hatano
- Biomedical Research Center, Chiba University, Chiba, Japan
- Department of Biomedical Science, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akira Suto
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kotaro Suzuki
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroshi Nakajima
- Department of Allergy and Clinical Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Chiba, Japan.
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Wang Y, Liu Q, Deng L, Ma X, Gong Y, Wang Y, Zhou F. The roles of epigenetic regulation in graft-versus-host disease. Biomed Pharmacother 2024; 175:116652. [PMID: 38692061 DOI: 10.1016/j.biopha.2024.116652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Allogeneic hematopoietic stem cell transplantation (aHSCT) is utilized as a potential curative treatment for various hematologic malignancies. However, graft-versus-host disease (GVHD) post-aHSCT is a severe complication that significantly impacts patients' quality of life and overall survival, becoming a major cause of non-relapse mortality. In recent years, the association between epigenetics and GVHD has garnered increasing attention. Epigenetics focuses on studying mechanisms that affect gene expression without altering DNA sequences, primarily including DNA methylation, histone modifications, non-coding RNAs (ncRNAs) regulation, and RNA modifications. This review summarizes the role of epigenetic regulation in the pathogenesis of GVHD, with a focus on DNA methylation, histone modifications, ncRNA, RNA modifications and their involvement and applications in the occurrence and development of GVHD. It also highlights advancements in relevant diagnostic markers and drugs, aiming to provide new insights for the clinical diagnosis and treatment of GVHD.
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Affiliation(s)
- Yimin Wang
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qi Liu
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lei Deng
- Department of Hematology, the 960th Hospital of the People's Liberation Army Joint Logistics Support Force, Jinan, China
| | - Xiting Ma
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuling Gong
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yifei Wang
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China.
| | - Fang Zhou
- Department of Hematology, the 960th Hospital of the People's Liberation Army Joint Logistics Support Force, Jinan, China.
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Kumagai J, Kiuchi M, Kokubo K, Yagyu H, Nemoto M, Tsuji K, Nagahata K, Sasaki A, Hishiya T, Onoue M, Shinmi R, Sonobe Y, Iinuma T, Yonekura S, Shinga J, Hanazawa T, Koseki H, Nakayama T, Yokote K, Hirahara K. The USP7-STAT3-granzyme-Par-1 axis regulates allergic inflammation by promoting differentiation of IL-5-producing Th2 cells. Proc Natl Acad Sci U S A 2023; 120:e2302903120. [PMID: 38015852 PMCID: PMC10710068 DOI: 10.1073/pnas.2302903120] [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: 02/20/2023] [Accepted: 09/11/2023] [Indexed: 11/30/2023] Open
Abstract
Uncontrolled type 2 immunity by type 2 helper T (Th2) cells causes intractable allergic diseases; however, whether the interaction of CD4+ T cells shapes the pathophysiology of allergic diseases remains unclear. We identified a subset of Th2 cells that produced the serine proteases granzyme A and B early in differentiation. Granzymes cleave protease-activated receptor (Par)-1 and induce phosphorylation of p38 mitogen-activated protein kinase (MAPK), resulting in the enhanced production of IL-5 and IL-13 in both mouse and human Th2 cells. Ubiquitin-specific protease 7 (USP7) regulates IL-4-induced phosphorylation of STAT3, resulting in granzyme production during Th2 cell differentiation. Genetic deletion of Usp7 or Gzma and pharmacological blockade of granzyme B ameliorated allergic airway inflammation. Furthermore, PAR-1+ and granzyme+ Th2 cells were colocalized in nasal polyps from patients with eosinophilic chronic rhinosinusitis. Thus, the USP7-STAT3-granzymes-Par-1 pathway is a potential therapeutic target for intractable allergic diseases.
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Grants
- JP19H05650 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H03685 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 17K08876 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 18K07164 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19K16683 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21H05121 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19K23858 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22K15485 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP21H05120 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20ek0410060 Japan Agency for Medical Research and Development (AMED)
- JP22ek0410092 Japan Agency for Medical Research and Development (AMED)
- JP20gm1210003 Japan Agency for Medical Research and Development (AMED)
- JPMJFR200R JST FORREST program
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Affiliation(s)
- Jin Kumagai
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Hiroyuki Yagyu
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Masahiro Nemoto
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Kaori Tsuji
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Ken Nagahata
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Department of Rheumatology, Sapporo Medical University, Sapporo060-8556, Japan
| | - Atsushi Sasaki
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Takahisa Hishiya
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Miki Onoue
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Rie Shinmi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Yuri Sonobe
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Tomohisa Iinuma
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Syuji Yonekura
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa230-0045, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Haruhiko Koseki
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Chiba University Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba260-8670, Japan
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Aisagbonhi O, Bui T, Nasamran CA, St Louis H, Pizzo D, Meads M, Mulholland M, Magallanes C, Lamale-Smith L, Laurent LC, Morey R, Jacobs MB, Fisch KM, Horii M. High placental expression of FLT1, LEP, PHYHIP and IL3RA - In persons of African ancestry with severe preeclampsia. Placenta 2023; 144:13-22. [PMID: 37949031 PMCID: PMC10843761 DOI: 10.1016/j.placenta.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
INTRODUCTION Mortality from preeclampsia (PE) and PE-associated morbidities are 3-to 5-fold higher in persons of African ancestry than in those of Asian and European ancestries. METHODS To elucidate placental contribution to worse PE outcomes in African ancestry pregnancies, we performed bulk RNA sequencing on 50 placentas from persons with severe PE (sPE) of African (n = 9), Asian (n = 18) and European (n = 23) ancestries and 73 normotensive controls of African (n = 10), Asian (n = 15) and European (n = 48) ancestries. RESULTS Previously described canonical preeclampsia genes, involved in metabolism and hypoxia/angiogenesis including: LEP, HK2, FSTL3, FLT1, ENG, TMEM45A, ARHGEF4 and HTRA1 were upregulated sPE versus normotensive placentas across ancestries. LTF, NPR3 and PHYHIP were higher in African vs. Asian ancestry sPE placentas. Allograft rejection/adaptive immune response genes were upregulated in placentas from African but not in Asian or European ancestry sPE patients; IL3RA was of particular interest because the patient with the highest placental IL3RA expression, a person of African ancestry with sPE, developed postpartum cardiomyopathy, and was the only patient out of 123, that developed this condition. Interestingly, the sPE patients with the highest IL3RA expression among persons of Asian and European ancestries developed unexplained tachycardia peripartum, necessitating echocardiography in the European ancestry patient. The association between elevated placental IL3RA levels and unexplained tachycardia or peripartum cardiomyopathy was found to be significant in the 50 sPE patients (p = .0005). DISCUSSION High placental upregulation of both canonical preeclampsia and allograft rejection/adaptive immune response genes may contribute to worse PE outcomes in African ancestry sPE patients.
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Affiliation(s)
- Omonigho Aisagbonhi
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA.
| | - Tony Bui
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Hailee St Louis
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Donald Pizzo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Morgan Meads
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Megan Mulholland
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Celestine Magallanes
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robert Morey
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marni B Jacobs
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Mariko Horii
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Center for Perinatal Discovery, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
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Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M. An intrinsically interpretable neural network architecture for sequence-to-function learning. Bioinformatics 2023; 39:i413-i422. [PMID: 37387140 PMCID: PMC10311317 DOI: 10.1093/bioinformatics/btad271] [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] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post hoc analyses, and even then, one can often not explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called totally interpretable sequence-to-function model (tiSFM). tiSFM improves upon the performance of standard multilayer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multilayer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. RESULTS We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state-of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context-specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM's model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. AVAILABILITY AND IMPLEMENTATION The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv, implemented in Python.
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Affiliation(s)
- Ali Tuğrul Balcı
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Mark Maher Ebeid
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, FL 32610, United States
| | - Dennis Kostka
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Maria Chikina
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Pittsburgh, PA 15213, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
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Onodera A, Kokubo K, Okano M, Onoue M, Kiuchi M, Iwamura C, Iinuma T, Kimura MY, Ebihara N, Hanazawa T, Nakayama T, Hirahara K. Pathogenic helper T cells as the novel therapeutic targets for immune-mediated intractable diseases. Pharmacol Ther 2023; 247:108445. [PMID: 37201737 DOI: 10.1016/j.pharmthera.2023.108445] [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: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
Allergic diseases arise from a complex interplay between immune system and environmental factors. A link between the pathogenesis of allergic diseases and type 2 immune responses has become evident, with conventional and pathogenic type 2 helper T (Th2) cells involved in both. Recently, there has been a significant development in therapeutic agents for allergic diseases: IL-5 and IL-5 receptor antagonists, Janus kinase (JAK) inhibitors, and sublingual immunotherapy (SLIT). Mepolizumab, an IL-5, and Benralizumab, an IL-5 receptor antagonist, modulate eosinophilic inflammation mediated by IL-5-producing Th2 cells. Delgocitinib shows that JAK-associated signaling is essential for the inflammatory reaction in atopic dermatitis, one of the common allergic diseases. SLIT has a significant effect on allergic rhinitis by reducing pathogenic Th2 cell numbers. More recently, novel molecules that are involved in pathogenic Th2 cell-mediated allergic diseases have been identified. These include calcitonin gene-related peptide (CGRP), reactive oxygen species (ROS) scavenging machinery regulated by the Txnip-Nrf2-Blvrb axis, and myosin light chain 9 (Myl9), which interacts with CD69. This review provides an updated view of the recent research on treatment of allergic diseases and their cause: conventional and pathogenic Th2 cells.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Institute for Advanced Academic Research, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mikiko Okano
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Miki Onoue
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Chiaki Iwamura
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Tomohisa Iinuma
- Department of Experimental Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoko Y Kimura
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Chiba University "Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED), Chiba, Japan
| | - Nobuyuki Ebihara
- Department of Ophthalmology, Juntendo University Urayasu Hospital, Chiba 279-0021, Japan
| | - Toyoyuki Hanazawa
- Department of Experimental Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Chiba University "Synergy Institute for Futuristic Mucosal Vaccine Research and Development (cSIMVa), Japan Initiative for World-leading Vaccine Research and Development Centers, Japan Agency for Medical Research and Development (AMED), Chiba, Japan.
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8
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Balcı AT, Ebeid MM, Benos PV, Kostka D, Chikina M. An intrinsically interpretable neural network architecture for sequence to function learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525572. [PMID: 36747873 PMCID: PMC9900791 DOI: 10.1101/2023.01.25.525572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Motivation Sequence-based deep learning approaches have been shown to predict a multitude of functional genomic readouts, including regions of open chromatin and RNA expression of genes. However, a major limitation of current methods is that model interpretation relies on computationally demanding post-hoc analyses, and even then, we often cannot explain the internal mechanics of highly parameterized models. Here, we introduce a deep learning architecture called tiSFM (totally interpretable sequence to function model). tiSFM improves upon the performance of standard multi-layer convolutional models while using fewer parameters. Additionally, while tiSFM is itself technically a multi-layer neural network, internal model parameters are intrinsically interpretable in terms of relevant sequence motifs. Results tiSFM's model architecture makes use of convolutions with a fixed set of kernel weights representing known transcription factor (TF) binding site motifs. We analyze published open chromatin measurements across hematopoietic lineage cell-types and demonstrate that tiSFM outperforms a state- of-the-art convolutional neural network model custom-tailored to this dataset. We also show that it correctly identifies context specific activities of transcription factors with known roles in hematopoietic differentiation, including Pax5 and Ebf1 for B-cells, and Rorc for innate lymphoid cells. tiSFM's model parameters have biologically meaningful interpretations, and we show the utility of our approach on a complex task of predicting the change in epigenetic state as a function of developmental transition. Availability and implementation The source code, including scripts for the analysis of key findings, can be found at https://github.com/boooooogey/ATAConv , implemented in Python. Contact atb44@pitt.edu.
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Affiliation(s)
- Ali Tuğrul Balcı
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States
| | - Mark Maher Ebeid
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States
| | - Panayiotis V Benos
- Department of Epidemiology, University of Florida, Gainesville, 32610, Unites States
| | - Dennis Kostka
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States, (D.K.) and (M.C.)
| | - Maria Chikina
- Joint Carnegie Mellon University-University of Pittsburgh Program in Computational Biology, Institution, Pittsburgh, 15213, United States,Department of Computational and Systems Biology University of Pittsburgh, Pittsburgh, 15213, Unites States, (D.K.) and (M.C.)
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9
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Kokubo K, Onodera A, Kiuchi M, Tsuji K, Hirahara K, Nakayama T. Conventional and pathogenic Th2 cells in inflammation, tissue repair, and fibrosis. Front Immunol 2022; 13:945063. [PMID: 36016937 PMCID: PMC9395650 DOI: 10.3389/fimmu.2022.945063] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/18/2022] [Indexed: 12/15/2022] Open
Abstract
Type 2 helper T (Th2) cells, a subset of CD4+ T cells, play an important role in the host defense against pathogens and allergens by producing Th2 cytokines, such as interleukin-4 (IL-4), IL-5, and IL-13, to trigger inflammatory responses. Emerging evidence reveals that Th2 cells also contribute to the repair of injured tissues after inflammatory reactions. However, when the tissue repair process becomes chronic, excessive, or uncontrolled, pathological fibrosis is induced, leading to organ failure and death. Thus, proper control of Th2 cells is needed for complete tissue repair without the induction of fibrosis. Recently, the existence of pathogenic Th2 (Tpath2) cells has been revealed. Tpath2 cells produce large amounts of Th2 cytokines and induce type 2 inflammation when activated by antigen exposure or tissue injury. In recent studies, Tpath2 cells are suggested to play a central role in the induction of type 2 inflammation whereas the role of Tpath2 cells in tissue repair and fibrosis has been less reported in comparison to conventional Th2 cells. In this review, we discuss the roles of conventional Th2 cells and pathogenic Th2 cells in the sequence of tissue inflammation, repair, and fibrosis.
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Affiliation(s)
- Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Institute for Advanced Academic Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kaori Tsuji
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kiyoshi Hirahara
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- *Correspondence: Kiyoshi Hirahara, ; Toshinori Nakayama,
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
- AMED-CREST, AMED, Chiba, Japan
- *Correspondence: Kiyoshi Hirahara, ; Toshinori Nakayama,
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10
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain‐containing proteins*. Immunol Rev 2022. [DOI: 10.1111/imr.13056
expr 964170082 + 969516512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Atsushi Onodera
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- Institute for Global Prominent Research Chiba University Chiba Japan
| | - Masahiro Kiuchi
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Kota Kokubo
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Toshinori Nakayama
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- AMED‐CREST, AMED Chiba Japan
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11
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Liu S, Ni C, Li Y, Yin H, Xing C, Yuan Y, Gong Y. The Involvement of TRIB3 and FABP1 and Their Potential Functions in the Dynamic Process of Gastric Cancer. Front Mol Biosci 2021; 8:790433. [PMID: 34957220 PMCID: PMC8696077 DOI: 10.3389/fmolb.2021.790433] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Background: Dysregulated expression of TRIB3 and FABP1 have been previously observed in human cancer tissues. However, there are little information as to their expression change in dynamic gastric diseases and the functional roles. Methods: Tissues from a total of 479 patients, including 89 GS, 102 IM-GA, 144 EGC, and 144 AGC were collected. The protein expressions of TRIB3 and FABP1 were detected by immunohistochemical staining. Meanwhile, the potential functions of TRIB3 and FABP1 in GC were further analyzed by R software and some internet public databases, such as TCGA and DAVID. Results: During this multi-stage process that go through GS to EGC, the expression trend of TRIB3 and FABP1 protein was GS > IM-GA > EGC. Besides, the expression of TRIB3 protein continued to decrease in AGC, while the expression of FABP1 was abnormally increased. Hp infection was significantly associated with the decreased expression of TRIB3 and FABP1. In addition, the diagnostic efficiency of the combination of these two indicators to diagnose EGC was higher than that of a single indicator. Survival analysis showed that higher expression of TRIB3 or FABP1 could indicate a better prognosis of GC. The protein expressions of TRIB3 and FABP1 were significantly positively correlated. Moreover, CEACAM5 and PRAP1 were positively correlated with both TRIB3 and FABP1 expressions, while GABRP and THBS4 were negatively correlated. The macrophages M0 infiltration was positively correlated with both TRIB3 and FABP1 expressions. Conclusion: The protein expressions of TRIB3 and FABP1 gradually decreased with the gastric disease progress, and was positively correlated. Hp infection may reduce the protein expression of TRIB3 and FABP1. Combing TRIB3 and FABP1 expressions can improve the diagnostic efficiency for EGC. Either a high expression of TRIB3 or FABP1 indicates a better prognosis for GC. TRIB3 and FABP1 may interact with CEACAM5, PRAP1, GABRP and THBS4, and affect tumor immune microenvironment by regulating immune cells, and participate in the development and progression of GC.
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Affiliation(s)
- Songyi Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Chuxuan Ni
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yizhi Li
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Honghao Yin
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
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12
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain-containing proteins. Immunol Rev 2021; 305:137-151. [PMID: 34935162 DOI: 10.1111/imr.13056] [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: 08/19/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system. CxxC domain-containing proteins, which basically bind to the non-methylated CpG (i.e., epigenetic "readers"), often function as "writers" of the epigenetic markers via their catalytic domain within the proteins or by interacting with other epigenetic modifiers. We herein report the most recent advances in our understanding of the functions of CxxC domain-containing proteins in the immune system and inflammation, mainly focusing on T cells and macrophages.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,AMED-CREST, AMED, Chiba, Japan
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13
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Dutta A, Venkataganesh H, Love PE. New Insights into Epigenetic Regulation of T Cell Differentiation. Cells 2021; 10:cells10123459. [PMID: 34943965 PMCID: PMC8700096 DOI: 10.3390/cells10123459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Immature CD4− CD8− thymocytes progress through several developmental steps in the thymus, ultimately emerging as mature CD4+ (helper) or CD8+ (cytotoxic) T cells. Activation of naïve CD4+ and CD8+ T cells in the presence of specific cytokines results in the induction of transcriptional programs that result in their differentiation into effector or memory cells and in the case of CD4+ T cells, the adoption of distinct T-helper fates. Previous studies have shown that histone modification and DNA methylation play important roles in each of these events. More recently, the roles of specific epigenetic regulators in T cell differentiation have been clarified. The identification of the epigenetic modifications and modifiers that control mature T cell differentiation and specification has also provided further insights into how dysregulation of these processes can lead to cancer or autoimmune diseases. In this review, we summarize recent findings that have provided new insights into epigenetic regulation of T cell differentiation in both mice and humans.
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Affiliation(s)
- Avik Dutta
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
- Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
- Correspondence:
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14
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Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
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Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
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