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Carrasco-Wong I, Längst G, Sobrevia L, Casanello P. Nrf2 pre-recruitment at Enhancer 2 is a hallmark of H 2O 2-induced epigenetic transcriptional memory in the HMOX1 gene in human umbilical artery endothelial cells. J Cell Physiol 2024; 239:e31243. [PMID: 38465708 DOI: 10.1002/jcp.31243] [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: 02/01/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in arterial endothelium. However, specific mechanisms by which the pro-oxidant fetal environment in MO could modulate the vascular gene expression and function during the offspring's postnatal life are elusive. We tested if oxidative stress could reprogram the antioxidant-coding gene's response to a pro-oxidant challenge through an epigenetic transcriptional memory (ETM) mechanism. A pro-oxidant double-hit protocol was applied to human umbilical artery endothelial cells (HUAECs) and EA.hy 926 endothelial cell lines. The ETM acquisition in the HMOX1 gene was analyzed by RT-qPCR. HMOX1 mRNA decay was evaluated by Actinomycin-D treatment and RT-qPCR. To assess the chromatin accessibility and the enrichment of NRF2, RNAP2, and phosphorylation at serin-5 of RNAP2, at HMOX1 gene regulatory regions, were used DNase HS-qPCR and ChIP-qPCR assays, respectively. The CpG methylation pattern at the HMOX1 core promoter was analyzed by DNA bisulfite conversion and Sanger sequencing. Data were analyzed using two-way ANOVA, and p < 0.05 was statistically significant. Using a pro-oxidant double-hit protocol, we found that the Heme Oxygenase gene (HMOX1) presents an ETM response associated with changes in the chromatin structure at the promoter and gene regulatory regions. The ETM response was characterized by a paused-RNA Polymerase 2 and NRF2 enrichment at the transcription start site and Enhancer 2 of the HMOX1 gene, respectively. Changes in DNA methylation pattern at the HMOX1 promoter were not a hallmark of this oxidative stress-induced ETM. These data suggest that a pro-oxidant milieu could trigger an ETM at the vascular level, indicating a potential epigenetic mechanism involved in the increased cardiovascular risk in the offspring of women with obesity.
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Affiliation(s)
- Ivo Carrasco-Wong
- Cellular Signaling and Differentiation Laboratory (CSDL), School of Medical Technology, Medicine and Science Faculty, Universidad San Sebastian, Santiago, Chile
| | - Gernot Längst
- Biochemistry III, Biochemistry Centre Regensburg (BCR), University of Regensburg, Regensburg, Germany
| | - Luis Sobrevia
- Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrics, Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Physiology, Faculty of Pharmacy, Universidad de Sevilla, Seville, Spain
- Medical School, Faculty of Medicine, Sao Paulo State University (UNESP), Sao Paulo, Sao Paulo, Brazil
- University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine and Biomedical Sciences, University of Queensland, Herston, Brisbane, Queensland, Australia
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Faculty of Excellence, Institute for Obesity Research, School of Medicine and Health Sciences, Monterrey, Nuevo León, Mexico, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Paola Casanello
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
- Department of Neonatology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Obstetrics, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
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2
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Shanley M, Daher M, Dou J, Li S, Basar R, Rafei H, Dede M, Gumin J, Pantaleόn Garcίa J, Nunez Cortes AK, He S, Jones CM, Acharya S, Fowlkes NW, Xiong D, Singh S, Shaim H, Hicks SC, Liu B, Jain A, Zaman MF, Miao Q, Li Y, Uprety N, Liu E, Muniz-Feliciano L, Deyter GM, Mohanty V, Zhang P, Evans SE, Shpall EJ, Lang FF, Chen K, Rezvani K. Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD. Cancer Cell 2024; 42:1450-1466.e11. [PMID: 39137729 PMCID: PMC11370652 DOI: 10.1016/j.ccell.2024.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024]
Abstract
Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21. Using multiple in vivo models, IL-21 NK cells were superior to IL-15 NK cells both in terms of safety and long-term anti-tumor activity, with locoregionally administered IL-15 NK cells proving toxic and ineffective at tumor control. IL-21 NK cells displayed a unique chromatin accessibility signature, with CCAAT/enhancer-binding proteins (C/EBP), especially CEBPD, serving as key transcription factors regulating their enhanced function. Deletion of CEBPD resulted in loss of IL-21 NK cell potency while its overexpression increased NK cell long-term cytotoxicity and metabolic fitness. These results suggest that IL-21, through C/EBP transcription factors, drives epigenetic reprogramming of NK cells, enhancing their anti-tumor efficacy against GBM.
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Affiliation(s)
- Mayra Shanley
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - May Daher
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sufang Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Rafet Basar
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Hind Rafei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Joy Gumin
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Jezreel Pantaleόn Garcίa
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ana Karen Nunez Cortes
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Shan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Corry M Jones
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sunil Acharya
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Natalie W Fowlkes
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Donghai Xiong
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Sanjay Singh
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Hila Shaim
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Samantha Claire Hicks
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Bin Liu
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Mohammad Fayyad Zaman
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ye Li
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Nadima Uprety
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Enli Liu
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Luis Muniz-Feliciano
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Gary M Deyter
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Patrick Zhang
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Frederick F Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030-4009, USA.
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3
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Luchtel RA. ETS1 Function in Leukemia and Lymphoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:359-378. [PMID: 39017852 DOI: 10.1007/978-3-031-62731-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
ETS proto-oncogene 1 (ETS1) is a transcription factor (TF) critically involved in lymphoid cell development and function. ETS1 expression is tightly regulated throughout differentiation and activation in T-cells, natural killer (NK) cells, and B-cells. It has also been described as an oncogene in a range of solid and hematologic cancer types. Among hematologic malignancies, its role has been best studied in T-cell acute lymphoblastic leukemia (T-ALL), adult T-cell leukemia/lymphoma (ATLL), and diffuse large B-cell lymphoma (DLBCL). Aberrant expression of ETS1 in these malignancies is driven primarily by chromosomal amplification and enhancer-driven transcriptional regulation, promoting the ETS1 transcriptional program. ETS1 also facilitates aberrantly expressed or activated transcriptional complexes to drive oncogenic pathways. Collectively, ETS1 functions to regulate cell growth, differentiation, signaling, response to stimuli, and viral interactions in these malignancies. A tumor suppressor role has also been indicated for ETS1 in select lymphoma types, emphasizing the importance of cellular context in ETS1 function. Research is ongoing to further characterize the clinical implications of ETS1 dysregulation in hematologic malignancies, to further resolve binding complexes and transcriptional targets, and to identify effective therapeutic targeting approaches.
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Affiliation(s)
- Rebecca A Luchtel
- Division of Hematology and Oncology, Department of Medicine, Northwestern University, Chicago, IL, USA.
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4
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Schoonhoven AOV, de Bruijn MJ, Stikker B, Brouwer RW, Braunstahl GJ, van IJcken WF, Graf T, Huylebroeck D, Hendriks RW, Stik G, Stadhouders R. 3D chromatin reprogramming primes human memory T H2 cells for rapid recall and pathogenic dysfunction. Sci Immunol 2023; 8:eadg3917. [PMID: 37418545 PMCID: PMC7617366 DOI: 10.1126/sciimmunol.adg3917] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/13/2023] [Indexed: 07/09/2023]
Abstract
Memory T cells provide long-lasting defense responses through their ability to rapidly reactivate, but how they efficiently "recall" an inflammatory transcriptional program remains unclear. Here, we show that human CD4+ memory T helper 2 (TH2) cells carry a chromatin landscape synergistically reprogrammed at both one-dimensional (1D) and 3D levels to accommodate recall responses, which is absent in naive T cells. In memory TH2 cells, recall genes were epigenetically primed through the maintenance of transcription-permissive chromatin at distal (super)enhancers organized in long-range 3D chromatin hubs. Precise transcriptional control of key recall genes occurred inside dedicated topologically associating domains ("memory TADs"), in which activation-associated promoter-enhancer interactions were preformed and exploited by AP-1 transcription factors to promote rapid transcriptional induction. Resting memory TH2 cells from patients with asthma showed premature activation of primed recall circuits, linking aberrant transcriptional control of recall responses to chronic inflammation. Together, our results implicate stable multiscale reprogramming of chromatin organization as a key mechanism underlying immunological memory and dysfunction in T cells.
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Affiliation(s)
- Anne Onrust-van Schoonhoven
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Marjolein J.W. de Bruijn
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Bernard Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger W.W. Brouwer
- Center for Biomics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gert-Jan Braunstahl
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Respiratory Medicine, Franciscus Gasthuis and Vlietland, Rotterdam, Netherlands
| | | | - Thomas Graf
- Centre for Genomic Regulation (CRG) and Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rudi W. Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
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5
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Zhang Z, Butler R, Koestler DC, Bell-Glenn S, Warrier G, Molinaro AM, Christensen BC, Wiencke JK, Kelsey KT, Salas LA. Comparative analysis of the DNA methylation landscape in CD4, CD8, and B memory lineages. Clin Epigenetics 2022; 14:173. [PMID: 36522672 PMCID: PMC9753273 DOI: 10.1186/s13148-022-01399-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND There is considerable evidence that epigenetic mechanisms and DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common epigenetic pathways among cell lineages. Further, it remains unclear if long-lived memory cell subtypes differentiate distinctly by cell lineages. RESULTS We used the Illumina EPIC array to investigate the consistency of DNA methylation in B cell, CD4 T, and CD8 T naïve and memory cells states. In the process of naïve to memory activation across the three lineages, we identify considerable shared epigenetic regulation at the DNA level for immune memory generation. Further, in central to effector memory differentiation, our analyses revealed specific CpG dinucleotides and genes in CD4 T and CD8 T cells with DNA methylation changes. Finally, we identified unique DNA methylation patterns in terminally differentiated effector memory (TEMRA) CD8 T cells compared to other CD8 T memory cell subtypes. CONCLUSIONS Our data suggest that epigenetic alterations are widespread and essential in generating human lymphocyte memory. Unique profiles are involved in methylation changes that accompany memory genesis in the three subtypes of lymphocytes.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Rondi Butler
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Devin C Koestler
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Shelby Bell-Glenn
- Department of Biostatistics and Data Science, University of Kansas Cancer Center, Kansas City, KS, USA
| | - Gayathri Warrier
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - John K Wiencke
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, USA
| | - Karl T Kelsey
- Department of Epidemiology, Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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6
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LINC00892 Is an lncRNA Induced by T Cell Activation and Expressed by Follicular Lymphoma-Resident T Helper Cells. Noncoding RNA 2022; 8:ncrna8030040. [PMID: 35736637 PMCID: PMC9228450 DOI: 10.3390/ncrna8030040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Successful immunotherapy in both solid tumors and in hematological malignancies relies on the ability of T lymphocytes to infiltrate the cancer tissue and mount an immune response against the tumor. Biomarkers able to discern the amount and the types of T lymphocytes infiltrating a given tumor therefore have high diagnostic and prognostic value. Given that lncRNAs are known to have a highly cell-type-specific expression pattern, we searched for lncRNAs specifically expressed by activated T cells and at the same time in a kind of lymphoma, follicular lymphoma, where the microenvironment is known to play a critical role in the regulation of antitumor immunity. We focused on a non-coding transcript, annotated as LINC00892, which reaches extremely high expression levels following cell activation in Jurkat cells. Interestingly LINC00892 has an expression pattern resembling that of genes involved in T cell memory. Accordingly, LINC00892 is mostly expressed by the effector memory and helper CD4+ T cell sub-types but not by naïve T cells. In situ analyses of LINC00892 expression in normal lymph nodes and in follicular lymphoma biopsies show that its expression is limited to CD4+ PD1hi T cells, with a subcellular localization within the germinal center matching that of follicular helper T cells. Our analysis therefore suggests that the previously uncharacterized lncRNA LINC00892 could be a useful biomarker for the detection of CD4+ memory T cells in both normal and tumor tissues.
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7
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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8
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Roostaei T, Klein HU, Ma Y, Felsky D, Kivisäkk P, Connor SM, Kroshilina A, Yung C, Kaskow BJ, Shao X, Rhead B, Ordovás JM, Absher DM, Arnett DK, Liu J, Patsopoulos N, Barcellos LF, Weiner HL, De Jager PL. Proximal and distal effects of genetic susceptibility to multiple sclerosis on the T cell epigenome. Nat Commun 2021; 12:7078. [PMID: 34873174 PMCID: PMC8648735 DOI: 10.1038/s41467-021-27427-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/18/2021] [Indexed: 01/29/2023] Open
Abstract
Identifying the effects of genetic variation on the epigenome in disease-relevant cell types can help advance our understanding of the first molecular contributions of genetic susceptibility to disease onset. Here, we establish a genome-wide map of DNA methylation quantitative trait loci in CD4+ T-cells isolated from multiple sclerosis patients. Utilizing this map in a colocalization analysis, we identify 19 loci where the same haplotype drives both multiple sclerosis susceptibility and local DNA methylation. We also identify two distant methylation effects of multiple sclerosis susceptibility loci: a chromosome 16 locus affects PRDM8 methylation (a chromosome 4 region not previously associated with multiple sclerosis), and the aggregate effect of multiple sclerosis-associated variants in the major histocompatibility complex influences DNA methylation near PRKCA (chromosome 17). Overall, we present a new resource for a key cell type in inflammatory disease research and uncover new gene targets for the study of predisposition to multiple sclerosis.
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Affiliation(s)
- Tina Roostaei
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Hans-Ulrich Klein
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Yiyi Ma
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Daniel Felsky
- grid.17063.330000 0001 2157 2938Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, University of Toronto, Toronto, ON Canada
| | - Pia Kivisäkk
- grid.32224.350000 0004 0386 9924Alzheimer’s Clinical and Translational Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Sarah M. Connor
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Alexandra Kroshilina
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Christina Yung
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
| | - Belinda J. Kaskow
- grid.62560.370000 0004 0378 8294Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Xiaorong Shao
- grid.47840.3f0000 0001 2181 7878Genetic Epidemiology and Genomics Laboratory, University of California, Berkeley, CA USA
| | - Brooke Rhead
- grid.47840.3f0000 0001 2181 7878Genetic Epidemiology and Genomics Laboratory, University of California, Berkeley, CA USA
| | - José M. Ordovás
- grid.429997.80000 0004 1936 7531Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, Tufts University, Boston, MA USA
| | - Devin M. Absher
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Donna K. Arnett
- grid.266539.d0000 0004 1936 8438College of Public Health, University of Kentucky, Lexington, KY USA
| | - Jia Liu
- grid.212340.60000000122985718Advanced Science Research Center at the Graduate Center, Neuroscience Initiative, City University of New York, New York, NY USA
| | - Nikolaos Patsopoulos
- grid.62560.370000 0004 0378 8294Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Lisa F. Barcellos
- grid.47840.3f0000 0001 2181 7878Genetic Epidemiology and Genomics Laboratory, University of California, Berkeley, CA USA
| | - Howard L. Weiner
- grid.62560.370000 0004 0378 8294Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
| | - Philip L. De Jager
- grid.21729.3f0000000419368729Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s disease and the Aging brain, Columbia University Irving Medical Center, New York, NY USA
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9
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Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Front Immunol 2021; 12:701924. [PMID: 34421907 PMCID: PMC8377396 DOI: 10.3389/fimmu.2021.701924] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Runx proteins (also known as Runt-domain transcription factors) have been studied for a long time as key regulators of cellular differentiation. RUNX2 has been described as essential for osteogenesis, whereas RUNX1 and RUNX3 are known to control blood cell development during different stages of cell lineage specification. However, recent studies show evidence of complex relationships between RUNX proteins, chromatin-modifying machinery, the cytoskeleton and different transcription factors in various non-embryonic contexts, including mature T cell homeostasis, inflammation and cancer. In this review, we discuss the diversity of Runx functions in mature T helper cells, such as production of cytokines and chemokines by different CD4 T cell populations; apoptosis; and immunologic memory acquisition. We then briefly cover recent findings about the contribution of RUNX1, RUNX2 and RUNX3 to various immunologic diseases. Finally, we discuss areas that require further study to better understand the role that Runx proteins play in inflammation and immunity.
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Affiliation(s)
- Svetlana Korinfskaya
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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10
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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11
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HDAC inhibition prevents transgene expression downregulation and loss-of-function in T-cell-receptor-transduced T cells. MOLECULAR THERAPY-ONCOLYTICS 2021; 20:352-363. [PMID: 33614916 PMCID: PMC7878989 DOI: 10.1016/j.omto.2021.01.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/20/2021] [Indexed: 01/22/2023]
Abstract
T cells that are gene-modified with tumor-specific T cell receptors are a promising treatment for metastatic melanoma patients. In a clinical trial, we treated seven metastatic melanoma patients with autologous T cells transduced to express a tyrosinase-reactive T cell receptor (TCR) (TIL 1383I) and a truncated CD34 molecule as a selection marker. We followed transgene expression in the TCR-transduced T cells after infusion and observed that both lentiviral- and retroviral-transduced T cells lost transgene expression over time, so that by 4 weeks post-transfer, few T cells expressed either lentiviral or retroviral transgenes. Transgene expression was reactivated by stimulation with anti-CD3/anti-CD28 beads and cytokines. TCR-transduced T cell lentiviral and retroviral transgene expression was also downregulated in vitro when T cells were cultured without cytokines. Transduced T cells cultured with interleukin (IL)-15 maintained transgene expression. Culturing gene-modified T cells in the presence of histone deacetylase (HDAC) inhibitors maintained transgene expression and functional TCR-transduced T cell responses to tumor. These results implicate epigenetic processes in the loss of transgene expression in lentiviral- and retroviral-transduced T cells.
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12
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Tu WJ, McCuaig RD, Tan AHY, Hardy K, Seddiki N, Ali S, Dahlstrom JE, Bean EG, Dunn J, Forwood J, Tsimbalyuk S, Smith K, Yip D, Malik L, Prasanna T, Milburn P, Rao S. Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch. Front Immunol 2020; 11:1228. [PMID: 32612611 PMCID: PMC7309504 DOI: 10.3389/fimmu.2020.01228] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
Lysine specific demethylase 1 (LSD1) is a key epigenetic eraser enzyme implicated in cancer metastases and recurrence. Nuclear LSD1 phosphorylated at serine 111 (nLSD1p) has been shown to be critical for the development of breast cancer stem cells. Here we show that circulating tumor cells isolated from immunotherapy-resistant metastatic melanoma patients express higher levels of nLSD1p compared to responders, which is associated with co-expression of stem-like, mesenchymal genes. Targeting nLSD1p with selective nLSD1 inhibitors better inhibits the stem-like mesenchymal signature than traditional FAD-specific LSD1 catalytic inhibitors such as GSK2879552. We also demonstrate that nLSD1p is enriched in PD-1+CD8+ T cells from resistant melanoma patients and 4T1 immunotherapy-resistant mice. Targeting the LSD1p nuclear axis induces IFN-γ/TNF-α-expressing CD8+ T cell infiltration into the tumors of 4T1 immunotherapy-resistant mice, which is further augmented by combined immunotherapy. Underpinning these observations, nLSD1p is regulated by the key T cell exhaustion transcription factor EOMES in dysfunctional CD8+ T cells. EOMES co-exists with nLSD1p in PD-1+CD8+ T cells in resistant patients, and nLSD1p regulates EOMES nuclear dynamics via demethylation/acetylation switching of critical EOMES residues. Using novel antibodies to target these post-translational modifications, we show that EOMES demethylation/acetylation is reciprocally expressed in resistant and responder patients. Overall, we show for the first time that dual inhibition of metastatic cancer cells and re-invigoration of the immune system requires LSD1 inhibitors that target the nLSD1p axis.
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Affiliation(s)
- Wen Juan Tu
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Melanie Swan Memorial Translational Centre, Faculty of Science and Technology, University of Canberra, Bruce, ACT, Australia
| | - Robert D. McCuaig
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Melanie Swan Memorial Translational Centre, Faculty of Science and Technology, University of Canberra, Bruce, ACT, Australia
| | - Abel H. Y. Tan
- Melanie Swan Memorial Translational Centre, Faculty of Science and Technology, University of Canberra, Bruce, ACT, Australia
| | - Kristine Hardy
- Melanie Swan Memorial Translational Centre, Faculty of Science and Technology, University of Canberra, Bruce, ACT, Australia
| | - Nabila Seddiki
- Inserm, U955, Equipe 16, Créteil, France
- Université Paris Est, Faculté de Médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Sayed Ali
- Medical Oncology, St John of God Midland Public and Private Hospitals, Midland, WA, Australia
| | - Jane E. Dahlstrom
- Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra Health Services, Garran, ACT, Australia
- ANU Medical School, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Elaine G. Bean
- Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra Health Services, Garran, ACT, Australia
| | - Jenny Dunn
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jade Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Sofia Tsimbalyuk
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Kate Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
- Australian Synchtrotron - ANSTO, Clayton, VIC, Australia
| | - Desmond Yip
- ANU Medical School, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
- Department of Medical Oncology, The Canberra Hospital, Canberra Health Services, Garran, ACT, Australia
| | - Laeeq Malik
- ANU Medical School, College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
- Department of Medical Oncology, The Canberra Hospital, Canberra Health Services, Garran, ACT, Australia
| | - Thiru Prasanna
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
- Department of Medical Oncology, The Canberra Hospital, Canberra Health Services, Garran, ACT, Australia
| | - Peter Milburn
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sudha Rao
- Gene Regulation and Translational Medicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Melanie Swan Memorial Translational Centre, Faculty of Science and Technology, University of Canberra, Bruce, ACT, Australia
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13
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Zhao Q, Wirka R, Nguyen T, Nagao M, Cheng P, Miller CL, Kim JB, Pjanic M, Quertermous T. TCF21 and AP-1 interact through epigenetic modifications to regulate coronary artery disease gene expression. Genome Med 2019; 11:23. [PMID: 31014396 PMCID: PMC6480881 DOI: 10.1186/s13073-019-0635-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified over 160 loci that are associated with coronary artery disease. As with other complex human diseases, risk in coronary disease loci is determined primarily by altered expression of the causal gene, due to variation in binding of transcription factors and chromatin-modifying proteins that directly regulate the transcriptional apparatus. We have previously identified a coronary disease network downstream of the disease-associated transcription factor TCF21, and in work reported here extends these studies to investigate the mechanisms by which it interacts with the AP-1 transcription complex to regulate local epigenetic effects in these downstream coronary disease loci. METHODS Genomic studies, including chromatin immunoprecipitation sequencing, RNA sequencing, and protein-protein interaction studies, were performed in human coronary artery smooth muscle cells. RESULTS We show here that TCF21 and JUN regulate expression of two presumptive causal coronary disease genes, SMAD3 and CDKN2B-AS1, in part by interactions with histone deacetylases and acetyltransferases. Genome-wide TCF21 and JUN binding is jointly localized and particularly enriched in coronary disease loci where they broadly modulate H3K27Ac and chromatin state changes linked to disease-related processes in vascular cells. Heterozygosity at coronary disease causal variation, or genome editing of these variants, is associated with decreased binding of both JUN and TCF21 and loss of expression in cis, supporting a transcriptional mechanism for disease risk. CONCLUSIONS These data show that the known chromatin remodeling and pioneer functions of AP-1 are a pervasive aspect of epigenetic control of transcription, and thus, the risk in coronary disease-associated loci, and that interaction of AP-1 with TCF21 to control epigenetic features, contributes to the genetic risk in loci where they co-localize.
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Affiliation(s)
- Quanyi Zhao
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Robert Wirka
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Trieu Nguyen
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Manabu Nagao
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Paul Cheng
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Clint L Miller
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Juyong Brian Kim
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Milos Pjanic
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, 300 Pasteur Dr., Falk CVRC, Stanford, CA, 94305, USA.
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14
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Epigenetic programming of T cells impacts immune reconstitution in hematopoietic stem cell transplant recipients. Blood Adv 2019; 2:656-668. [PMID: 29563122 DOI: 10.1182/bloodadvances.2018015909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/24/2018] [Indexed: 12/31/2022] Open
Abstract
Immune reconstitution following hematopoietic stem cell transplantation (HSCT) is critical in preventing harmful sequelae in recipients with cytomegalovirus (CMV) infection. To understand the molecular mechanisms underlying immune reconstitution kinetics, we profiled the transcriptome-chromatin accessibility landscape of CMV-specific CD8+ T cells from HCST recipients with different immune reconstitution efficiencies. CMV-specific T cells from HSCT recipients with stable antiviral immunity expressed higher levels of interferon/defense response and cell cycle genes in an interconnected network involving PI3KCG, STAT5B, NFAT, RBPJ, and lower HDAC6, increasing chromatin accessibility at the enhancer regions of immune and T-cell receptor signaling pathway genes. By contrast, the transcriptional and epigenomic signatures of CMV-specific T cells from HSCT recipients with unstable immune reconstitution showed commonalities with T-cell responses in other nonresolving chronic infections. These signatures included higher levels of EGR and KLF factors that, along with lower JARID2 expression, maintained higher accessibility at promoter and CpG-rich regions of genes associated with apoptosis. Furthermore, epigenetic targeting via inhibition of HDAC6 or JARID2 enhanced the transcription of genes associated with differential responses, suggesting that drugs targeting epigenomic modifiers may have therapeutic potential for enhancing immune reconstitution in HSCT recipients. Taken together, these analyses demonstrate that transcription factors and chromatin modulators create different chromatin accessibility landscapes in T cells of HSCT recipients that not only affect immediate gene expression but also differentially prime cells for responses to additional signals. Epigenetic therapy may be a promising strategy to promote immune reconstitution in HSCT recipients.
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15
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DeLong JH, O'Hara Hall A, Rausch M, Moodley D, Perry J, Park J, Phan AT, Beiting DP, Kedl RM, Hill JA, Hunter CA. IL-27 and TCR Stimulation Promote T Cell Expression of Multiple Inhibitory Receptors. Immunohorizons 2019; 3:13-25. [PMID: 31356173 PMCID: PMC6994206 DOI: 10.4049/immunohorizons.1800083] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/26/2018] [Indexed: 12/18/2022] Open
Abstract
Inhibitory receptors (IR) are a diverse group of cell surface molecules that modulate T cell activation, but there are gaps in our knowledge of the cell-extrinsic factors that regulate their expression. The present study found that in vivo overexpression of IL-27 in mice led to increased T cell expression of PD-L1, LAG-3, TIGIT, and TIM-3. In vitro, TCR stimulation alone promoted expression of multiple IRs, whereas IL-27 alone induced expression of PD-L1. However, the combination of intermediate TCR stimulation and IL-27 resulted in synergistic induction of LAG-3, CTLA-4, and TIGIT. In vivo, infection with Toxoplasma gondii resulted in parasite-specific effector T cells that expressed high levels of IR, and at local sites of infection where IL-27 production was highest, IL-27 was required for maximal effector cell expression of PD-L1, LAG-3, CTLA-4, and TIGIT. Together, these results affirm the critical role of TCR signals in the induction of IR expression but find that during infection, IL-27 promotes T cell expression of IR.
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Affiliation(s)
- Jonathan H DeLong
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Aisling O'Hara Hall
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Immunology Discovery Research, Janssen Research and Development, LLC, Spring House, PA 19477
| | | | | | - Joseph Perry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jeongho Park
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Anthony T Phan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ross M Kedl
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045
| | | | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104;
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16
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Zhang T, Wei G, Millard CJ, Fischer R, Konietzny R, Kessler BM, Schwabe JWR, Brockdorff N. A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes. Nat Commun 2018; 9:3798. [PMID: 30228260 PMCID: PMC6143588 DOI: 10.1038/s41467-018-06235-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation by chromatin is a highly dynamic process directed through the recruitment and coordinated action of epigenetic modifiers and readers of these modifications. Using an unbiased proteomic approach to find interactors of H3K36me3, a modification enriched on active chromatin, here we identify PWWP2A and HDAC2 among the top interactors. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66α/β, and CHD3/4. PWWP2A competes with MBD3 for binding to MTA1, thus defining a new variant NuRD complex that is mutually exclusive with the MBD2/3 containing NuRD. In mESCs, PWWP2A/B is most enriched at highly transcribed genes. Loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes. Transcription regulation requires recruitment of different epigenetic regulators to the chromatin. Here the authors provide evidence that an H3K36me3 reader PWWP2A forms a variant NuRD complex and plays a role in regulating transcription and histone acetylation dynamics.
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Affiliation(s)
- Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Christopher J Millard
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - Rebecca Konietzny
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.,Agilent Technologies, Hewlett-Packard-Str. 8, 76337, Waldbronn, Germany
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
| | - John W R Schwabe
- Leicester Institute for Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom.
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