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Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA. Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. Nat Chem Biol 2024:10.1038/s41589-024-01671-9. [PMID: 38965385 DOI: 10.1038/s41589-024-01671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.
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Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marco Barone
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eunju Nam
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah E DuBois-Coyne
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jonatan Caroli
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy
| | - Katherine Neal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brian Ibeabuchi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zuzer Dhoondia
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samuel Beck
- Department of Dermatology, Boston University School of Medicine & Boston Medical Center, Boston, MA, USA.
| | - Andrea Mattevi
- Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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2
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Lu Y, Sun J, Wang L, Wang M, Wu Y, Getachew A, Matthews RC, Li H, Peng WG, Zhang J, Lu R, Zhou Y. ELM2-SANT Domain-Containing Scaffolding Protein 1 Regulates Differentiation and Maturation of Cardiomyocytes Derived From Human-Induced Pluripotent Stem Cells. J Am Heart Assoc 2024; 13:e034816. [PMID: 38904247 PMCID: PMC11255699 DOI: 10.1161/jaha.124.034816] [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: 01/31/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND ELMSAN1 (ELM2-SANT domain-containing scaffolding protein 1) is a newly identified scaffolding protein of the MiDAC (mitotic deacetylase complex), playing a pivotal role in early embryonic development. Studies on Elmsan1 knockout mice showed that its absence results in embryo lethality and heart malformation. However, the precise function of ELMSAN1 in heart development and formation remains elusive. To study its potential role in cardiac lineage, we employed human-induced pluripotent stem cells (hiPSCs) to model early cardiogenesis and investigated the function of ELMSAN1. METHODS AND RESULTS We generated ELMSAN1-deficient hiPSCs through knockdown and knockout techniques. During cardiac differentiation, ELMSAN1 depletion inhibited pluripotency deactivation, decreased the expression of cardiac-specific markers, and reduced differentiation efficiency. The impaired expression of genes associated with contractile sarcomere structure, calcium handling, and ion channels was also noted in ELMSAN1-deficient cardiomyocytes derived from hiPSCs. Additionally, through a series of structural and functional assessments, we found that ELMSAN1-null hiPSC cardiomyocytes are immature, exhibiting incomplete sarcomere Z-line structure, decreased calcium handling, and impaired electrophysiological properties. Of note, we found that the cardiac-specific role of ELMSAN1 is likely associated with histone H3K27 acetylation level. The transcriptome analysis provided additional insights, indicating maturation reduction with the energy metabolism switch and restored cell proliferation in ELMSAN1 knockout cardiomyocytes. CONCLUSIONS In this study, we address the significance of the direct involvement of ELMSAN1 in the differentiation and maturation of hiPSC cardiomyocytes. We first report the impact of ELMSAN1 on multiple aspects of hiPSC cardiomyocyte generation, including cardiac differentiation, sarcomere formation, calcium handling, electrophysiological maturation, and proliferation.
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Affiliation(s)
- Yu‐An Lu
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Jiacheng Sun
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Lu Wang
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Meimei Wang
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Yalin Wu
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Anteneh Getachew
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Rachel C. Matthews
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Hui Li
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - William Gao Peng
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
| | - Jianyi Zhang
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
- Department of Medicine, Division of Cardiovascular Disease, Heersink School of MedicineUniversity of Alabama at BirminghamBirminghamAL
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, Heersink School of MedicineUniversity of Alabama at BirminghamBirminghamAL
- O’Neal Comprehensive Cancer CenterUniversity of Alabama at BirminghamBirminghamAL
| | - Yang Zhou
- Department of Biomedical Engineering, Heersink School of Medicine, School of EngineeringUniversity of Alabama at BirminghamBirminghamAL
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3
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Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Mol Cell 2024; 84:2238-2254.e11. [PMID: 38870936 PMCID: PMC11193646 DOI: 10.1016/j.molcel.2024.05.017] [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: 09/12/2023] [Revised: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their association and function in gene regulation. More recently, IDRs have been shown to promote multivalent protein-protein interactions between coregulators and TFs to drive their association into condensates. By contrast, here we demonstrate how the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the protein's structured domains with TF condensates. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil alternative mechanisms by which disordered regions and their dynamic crosstalk with structured regions can shape coregulator-TF interactions to control cis-regulatory landscapes and cell fate.
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Affiliation(s)
- Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Domenic N Narducci
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shaunak Raval
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew H Reiter
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - William Hawkins
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiaming Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anders S Hansen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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4
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Yang M, Wu Y, Yang XB, Liu T, Zhang Y, Zhuo Y, Luo Y, Zhang N. Establishing a prediction model of severe acute mountain sickness using machine learning of support vector machine recursive feature elimination. Sci Rep 2023; 13:4633. [PMID: 36944699 PMCID: PMC10030784 DOI: 10.1038/s41598-023-31797-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023] Open
Abstract
Severe acute mountain sickness (sAMS) can be life-threatening, but little is known about its genetic basis. The study was aimed to explore the genetic susceptibility of sAMS for the purpose of prediction, using microarray data from 112 peripheral blood mononuclear cell (PBMC) samples of 21 subjects, who were exposed to very high altitude (5260 m), low barometric pressure (406 mmHg), and hypobaric hypoxia (VLH) at various timepoints. We found that exposure to VLH activated gene expression in leukocytes, resulting in an inverted CD4/CD8 ratio that interacted with other phenotypic risk factors at the genetic level. A total of 2286 underlying risk genes were input into the support vector machine recursive feature elimination (SVM-RFE) system for machine learning, and a model with satisfactory predictive accuracy and clinical applicability was established for sAMS screening using ten featured genes with significant predictive power. Five featured genes (EPHB3, DIP2B, RHEBL1, GALNT13, and SLC8A2) were identified upstream of hypoxia- and/or inflammation-related pathways mediated by microRNAs as potential biomarkers for sAMS. The established prediction model of sAMS holds promise for clinical application as a genetic screening tool for sAMS.
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Affiliation(s)
- Min Yang
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China.
| | - Yang Wu
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Xing-Biao Yang
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Tao Liu
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Ya Zhang
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Yue Zhuo
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Yong Luo
- Department of Traditional Chinese Medicine, Rheumatology Center of Integrated Medicine, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
| | - Nan Zhang
- Department of Hematology, The General Hospital of Western Theater Command, PLA, Chengdu, 610083, China
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5
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Herchenröther A, Gossen S, Friedrich T, Reim A, Daus N, Diegmüller F, Leers J, Sani HM, Gerstner S, Schwarz L, Stellmacher I, Szymkowiak LV, Nist A, Stiewe T, Borggrefe T, Mann M, Mackay JP, Bartkuhn M, Borchers A, Lan J, Hake SB. The H2A.Z and NuRD associated protein HMG20A controls early head and heart developmental transcription programs. Nat Commun 2023; 14:472. [PMID: 36709316 PMCID: PMC9884267 DOI: 10.1038/s41467-023-36114-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/17/2023] [Indexed: 01/30/2023] Open
Abstract
Specialized chromatin-binding proteins are required for DNA-based processes during development. We recently established PWWP2A as a direct histone variant H2A.Z interactor involved in mitosis and craniofacial development. Here, we identify the H2A.Z/PWWP2A-associated protein HMG20A as part of several chromatin-modifying complexes, including NuRD, and show that it localizes to distinct genomic regulatory regions. Hmg20a depletion causes severe head and heart developmental defects in Xenopus laevis. Our data indicate that craniofacial malformations are caused by defects in neural crest cell (NCC) migration and cartilage formation. These developmental failures are phenocopied in Hmg20a-depleted mESCs, which show inefficient differentiation into NCCs and cardiomyocytes (CM). Consequently, loss of HMG20A, which marks open promoters and enhancers, results in chromatin accessibility changes and a striking deregulation of transcription programs involved in epithelial-mesenchymal transition (EMT) and differentiation processes. Collectively, our findings implicate HMG20A as part of the H2A.Z/PWWP2A/NuRD-axis and reveal it as a key modulator of intricate developmental transcription programs that guide the differentiation of NCCs and CMs.
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Affiliation(s)
| | - Stefanie Gossen
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Tobias Friedrich
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Nadine Daus
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Felix Diegmüller
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Jörg Leers
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Hakimeh Moghaddas Sani
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Sarah Gerstner
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Leah Schwarz
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany
| | - Inga Stellmacher
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Laura Victoria Szymkowiak
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Institute for Physiological Chemistry, Technical University Dresden, Dresden, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Universities of Giessen and Marburg Lung Center, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, Marburg, Germany
| | - Tilman Borggrefe
- Institute for Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, Australia
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Institute for lung health, Justus-Liebig University Giessen, Giessen, Germany.
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps University Marburg, Marburg, Germany.
| | - Jie Lan
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, Giessen, Germany.
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6
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Christensen LM, Hancock WW. Nuclear Coregulatory Complexes in Tregs as Targets to Promote Anticancer Immune Responses. Front Immunol 2022; 13:909816. [PMID: 35795673 PMCID: PMC9251111 DOI: 10.3389/fimmu.2022.909816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/18/2022] [Indexed: 12/17/2022] Open
Abstract
T-regulatory (Treg) cells display considerable heterogeneity in their responses to various cancers. The functional differences among this cell type are heavily influenced by multiprotein nuclear complexes that control their gene expression. Many such complexes act mechanistically by altering epigenetic profiles of genes important to Treg function, including the forkhead P3 (Foxp3) transcription factor. Complexes that form with certain members of the histone/protein deacetylase (HDAC) class of enzymes, like HDACs 1, 2, and 3, along with histone methyltransferase complexes, are important in the induction and stabilization of Foxp3 and Treg identity. The functional behavior of both circulating and intratumoral Tregs greatly impacts the antitumor immune response and can be predictive of patient outcome. Thus, targeting these regulatory complexes within Tregs may have therapeutic potential, especially in personalized immunotherapies.
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Affiliation(s)
- Lanette M. Christensen
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Wayne W. Hancock
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Wayne W. Hancock,
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