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Wu J, Fan C, Kabir AU, Krchma K, Kim M, Kwon Y, Xing X, Wang T, Choi K. Baf155 controls hematopoietic differentiation and regeneration through chromatin priming. Cell Rep 2024; 43:114558. [PMID: 39088321 DOI: 10.1016/j.celrep.2024.114558] [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: 10/12/2023] [Revised: 05/06/2024] [Accepted: 07/14/2024] [Indexed: 08/03/2024] Open
Abstract
Chromatin priming promotes cell-type-specific gene expression, lineage differentiation, and development. The mechanism of chromatin priming has not been fully understood. Here, we report that mouse hematopoietic stem and progenitor cells (HSPCs) lacking the Baf155 subunit of the BAF (BRG1/BRM-associated factor) chromatin remodeling complex produce a significantly reduced number of mature blood cells, leading to a failure of hematopoietic regeneration upon transplantation and 5-fluorouracil (5-FU) injury. Baf155-deficient HSPCs generate particularly fewer neutrophils, B cells, and CD8+ T cells at homeostasis, supporting a more immune-suppressive tumor microenvironment and enhanced tumor growth. Single-nucleus multiomics analysis reveals that Baf155-deficient HSPCs fail to establish accessible chromatin in selected regions that are enriched for putative enhancers and binding motifs of hematopoietic lineage transcription factors. Our study provides a fundamental mechanistic understanding of the role of Baf155 in hematopoietic lineage chromatin priming and the functional consequences of Baf155 deficiency in regeneration and tumor immunity.
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Affiliation(s)
- Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashraf Ul Kabir
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Minseo Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yoojung Kwon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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2
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Wang B, Bian Q. Regulation of 3D genome organization during T cell activation. FEBS J 2024. [PMID: 38944686 DOI: 10.1111/febs.17211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/23/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024]
Abstract
Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.
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Affiliation(s)
- Bao Wang
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
| | - Qian Bian
- Shanghai lnstitute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, China
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3
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Melnick AF, Mullin C, Lin K, McCarter AC, Liang S, Liu YE, Wang Q, Jerome NA, Choe E, Kunnath N, Bodanapu G, Akter F, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. Blood 2023; 142:2159-2174. [PMID: 37616559 PMCID: PMC10733839 DOI: 10.1182/blood.2023020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
ABSTRACT Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL), but pan-Notch inhibitors showed excessive toxicity in clinical trials. To find alternative ways to target Notch signals, we investigated cell division cycle 73 (Cdc73), which is a Notch cofactor and key component of the RNA polymerase-associated transcriptional machinery, an emerging target in T-ALL. Although we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, chromatin and nascent gene expression profiling showed that Cdc73 intersects with Ets1 and Notch at chromatin within enhancers to activate expression of known T-ALL oncogenes through its enhancer functions. Cdc73 also intersects with these factors within promoters to activate transcription of genes that are important for DNA repair and oxidative phosphorylation through its gene body functions. Consistently, Cdc73 deletion induced DNA damage and apoptosis and impaired mitochondrial function. The CDC73-induced DNA repair expression program co-opted by NOTCH1 is more highly expressed in T-ALL than in any other cancer. These data suggest that Cdc73 might induce a gene expression program that was eventually intersected and hijacked by oncogenic Notch to augment proliferation and mitigate the genotoxic and metabolic stresses of elevated Notch signaling. Our report supports studying factors such as CDC73 that intersect with Notch to derive a basic scientific understanding on how to combat Notch-dependent cancers without directly targeting the Notch complex.
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Affiliation(s)
- Ashley F. Melnick
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Carea Mullin
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Karena Lin
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Anna C. McCarter
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Shannon Liang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Yiran E. Liu
- Cancer Biology Program, Stanford University, Stanford, CA
| | - Qing Wang
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Nicole A. Jerome
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Elizabeth Choe
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Nicholas Kunnath
- Center for Healthcare Outcomes and Policy, University of Michigan School of Medicine, Ann Arbor, MI
| | - Geethika Bodanapu
- School of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Fatema Akter
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Brian Magnuson
- Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI
| | - Surinder Kumar
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - David B. Lombard
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - Andrew G. Muntean
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mats Ljungman
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Radiology Oncology, University of Michigan School of Medicine, Ann Arbor, MI
| | - JoAnn Sekiguchi
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI
| | - Russell J. H. Ryan
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mark Y. Chiang
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
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Marcucci F, Rumio C. On the Role of Glycolysis in Early Tumorigenesis-Permissive and Executioner Effects. Cells 2023; 12:cells12081124. [PMID: 37190033 DOI: 10.3390/cells12081124] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/26/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Reprogramming energy production from mitochondrial respiration to glycolysis is now considered a hallmark of cancer. When tumors grow beyond a certain size they give rise to changes in their microenvironment (e.g., hypoxia, mechanical stress) that are conducive to the upregulation of glycolysis. Over the years, however, it has become clear that glycolysis can also associate with the earliest steps of tumorigenesis. Thus, many of the oncoproteins most commonly involved in tumor initiation and progression upregulate glycolysis. Moreover, in recent years, considerable evidence has been reported suggesting that upregulated glycolysis itself, through its enzymes and/or metabolites, may play a causative role in tumorigenesis, either by acting itself as an oncogenic stimulus or by facilitating the appearance of oncogenic mutations. In fact, several changes induced by upregulated glycolysis have been shown to be involved in tumor initiation and early tumorigenesis: glycolysis-induced chromatin remodeling, inhibition of premature senescence and induction of proliferation, effects on DNA repair, O-linked N-acetylglucosamine modification of target proteins, antiapoptotic effects, induction of epithelial-mesenchymal transition or autophagy, and induction of angiogenesis. In this article we summarize the evidence that upregulated glycolysis is involved in tumor initiation and, in the following, we propose a mechanistic model aimed at explaining how upregulated glycolysis may play such a role.
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Affiliation(s)
- Fabrizio Marcucci
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Trentacoste 2, 20134 Milan, Italy
| | - Cristiano Rumio
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Via Trentacoste 2, 20134 Milan, Italy
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5
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Zhao X, Zhu S, Peng W, Xue HH. The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2269-2278. [PMID: 36469845 PMCID: PMC9731349 DOI: 10.4049/jimmunol.2200625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 01/04/2023]
Abstract
T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.
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Affiliation(s)
- Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ 07018
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6
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Ma H, Li N, Mo Z. Elevated Notch-1 expression promotes the lymph node metastasis of gastric cancer and the Notch-1-PTEN-ERK1/2 signalling axis promotes the progression of gastric cancer. Cytokine 2022; 159:156013. [PMID: 36067712 DOI: 10.1016/j.cyto.2022.156013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/02/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common malignant tumours and has a high fatality rate worldwide. This study investigated the role of the Notch-1 signalling pathway in the pathogenesis and progression of GC. METHODS A total of 64 patients with GC were included in this study. Immunohistochemistry staining was used to detect Notch-1 expression in tumour tissues and adjacent non-tumour tissues, and Notch-1 knockdown in GC cells was identified using short hairpin RNA. A cell scratch assay, transwell assay and flow cytometry analysis were used to analyse the effect of Notch-1 knockdown on cell proliferation, migration and cell cycle distribution. The expression of Notch-1, PTEN, Akt, ERK1/2, E-cadherin and other proteins was detected using Western blotting. RESULTS The expression level of Notch-1 in GC tissues was higher than that in adjacent non-tumour tissues (P < 0.05). High levels of Notch-1 were also found to be associated with sex (male) and lymph node metastasis (P < 0.05). Notch-1 knockdown in the AGS and BGC-823 GC cell lines inhibited the migration and proliferation of GC cells, and Notch-1 knockdown arrested the cell cycle in the G0/G1 phase. PTEN protein expression was elevated in the presence of Notch-1 knockdown, resulting in the inhibition of phosphorylated Akt protein expression. In addition, phosphorylated ERK protein levels decreased in the presence of Notch-1 knockdown. Further inhibition of ERK1/2 signalling by the MEK1/2 inhibitor U0126 decreased the proliferation of AGS cells. The results of in vivo experiments with xenotransplantation in nude mice are consistent with these results. CONCLUSIONS Notch-1 plays a key role in the development of GC and was found to promote the lymph node metastasis of GC. Notch-1 knockdown can effectively attenuate the progression of GC cells, which may function in part through the Notch-1-PTEN-ERK1/2 signalling axis.
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Affiliation(s)
- Haining Ma
- Department of Gastrointestinal-pancreatic Surgery, Shanxi Province People's Hospital, Taiyuan, China.
| | - Ning Li
- Department of Gastrointestinal-pancreatic Surgery, Shanxi Province People's Hospital, Taiyuan, China
| | - Zhenzhou Mo
- Department of Gastrointestinal-pancreatic Surgery, Shanxi Province People's Hospital, Taiyuan, China
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7
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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8
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Wang W, Chandra A, Goldman N, Yoon S, Ferrari EK, Nguyen SC, Joyce EF, Vahedi G. TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. Nat Immunol 2022; 23:1052-1062. [PMID: 35726060 PMCID: PMC9728953 DOI: 10.1038/s41590-022-01232-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.
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Affiliation(s)
- Wenliang Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Naomi Goldman
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sora Yoon
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily K Ferrari
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Son C Nguyen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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