1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Cis-regulatory evolution of the recently expanded Ly49 gene family. Nat Commun 2024; 15:4839. [PMID: 38844462 PMCID: PMC11156856 DOI: 10.1038/s41467-024-48990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
Collapse
Affiliation(s)
- Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Samuel J H Murphy
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA.
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63110, USA.
| |
Collapse
|
3
|
Fiskus W, Piel J, Collins M, Hentemann M, Cuglievan B, Mill CP, Birdwell CE, Das K, Davis JA, Hou H, Jain A, Malovannaya A, Kadia TM, Daver N, Sasaki K, Takahashi K, Hammond D, Reville PK, Wang J, Loghavi S, Sen R, Ruan X, Su X, Flores LB, DiNardo CD, Bhalla KN. BRG1/BRM inhibitor targets AML stem cells and exerts superior preclinical efficacy combined with BET or menin inhibitor. Blood 2024; 143:2059-2072. [PMID: 38437498 DOI: 10.1182/blood.2023022832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
ABSTRACT BRG1 (SMARCA4) and BRM (SMARCA2) are the mutually exclusive core ATPases of the chromatin remodeling BAF (BRG1/BRM-associated factor) complexes. They enable transcription factors/cofactors to access enhancers/promoter and modulate gene expressions responsible for cell growth and differentiation of acute myeloid leukemia (AML) stem/progenitor cells. In AML with MLL1 rearrangement (MLL1r) or mutant NPM1 (mtNPM1), although menin inhibitor (MI) treatment induces clinical remissions, most patients either fail to respond or relapse, some harboring menin mutations. FHD-286 is an orally bioavailable, selective inhibitor of BRG1/BRM under clinical development in AML. Present studies show that FHD-286 induces differentiation and lethality in AML cells with MLL1r or mtNPM1, concomitantly causing perturbed chromatin accessibility and repression of c-Myc, PU.1, and CDK4/6. Cotreatment with FHD-286 and decitabine, BET inhibitor (BETi) or MI, or venetoclax synergistically induced in vitro lethality in AML cells with MLL1r or mtNPM1. In models of xenografts derived from patients with AML with MLL1r or mtNPM1, FHD-286 treatment reduced AML burden, improved survival, and attenuated AML-initiating potential of stem-progenitor cells. Compared with each drug, cotreatment with FHD-286 and BETi, MI, decitabine, or venetoclax significantly reduced AML burden and improved survival, without inducing significant toxicity. These findings highlight the FHD-286-based combinations as a promising therapy for AML with MLL1r or mtNPM1.
Collapse
Affiliation(s)
- Warren Fiskus
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | - Kaberi Das
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John A Davis
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hanxi Hou
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Tapan M Kadia
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Naval Daver
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Koji Sasaki
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jian Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sanam Loghavi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Xinjia Ruan
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xiaoping Su
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren B Flores
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Kapil N Bhalla
- The University of Texas MD Anderson Cancer Center, Houston, TX
| |
Collapse
|
4
|
Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Ermis E, Kaiser C, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS. PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape. Nat Immunol 2024; 25:860-872. [PMID: 38632339 PMCID: PMC11089574 DOI: 10.1038/s41590-024-01807-y] [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: 06/27/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
Adaptive immunity relies on specialized effector functions elicited by lymphocytes, yet how antigen recognition activates appropriate effector responses through nonspecific signaling intermediates is unclear. Here we examined the role of chromatin priming in specifying the functional outputs of effector T cells and found that most of the cis-regulatory landscape active in effector T cells was poised early in development before the expression of the T cell antigen receptor. We identified two principal mechanisms underpinning this poised landscape: the recruitment of the nucleosome remodeler mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) by the transcription factors RUNX1 and PU.1 to establish chromatin accessibility at T effector loci; and a 'relay' whereby the transcription factor BCL11B succeeded PU.1 to maintain occupancy of the chromatin remodeling complex mSWI/SNF together with RUNX1, after PU.1 silencing during lineage commitment. These mechanisms define modes by which T cells acquire the potential to elicit specialized effector functions early in their ontogeny and underscore the importance of integrating extrinsic cues to the developmentally specified intrinsic program.
Collapse
Affiliation(s)
- Noah Gamble
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Alexandra Bradu
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Jason A Caldwell
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Joshua McKeever
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Molecular Metabolism and Nutrition, University of Chicago, Chicago, IL, USA
| | - Olubusayo Bolonduro
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, Systems Biology, University of Chicago, Chicago, IL, USA
| | - Ebru Ermis
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Caroline Kaiser
- Department of Pathology, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - YeEun Kim
- Immunology Program, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benjamin Parks
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Andrew S Koh
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
5
|
Chambers C, Cermakova K, Chan YS, Kurtz K, Wohlan K, Lewis AH, Wang C, Pham A, Dejmek M, Sala M, Loeza Cabrera M, Aguilar R, Nencka R, Lacorazza HD, Rau RE, Hodges HC. SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia. Cancer Res 2023; 83:983-996. [PMID: 36662812 PMCID: PMC10071820 DOI: 10.1158/0008-5472.can-22-2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/09/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
In acute myeloid leukemia (AML), SWI/SNF chromatin remodeling complexes sustain leukemic identity by driving high levels of MYC. Previous studies have implicated the hematopoietic transcription factor PU.1 (SPI1) as an important target of SWI/SNF inhibition, but PU.1 is widely regarded to have pioneer-like activity. As a result, many questions have remained regarding the interplay between PU.1 and SWI/SNF in AML as well as normal hematopoiesis. Here we found that PU.1 binds to most of its targets in a SWI/SNF-independent manner and recruits SWI/SNF to promote accessibility for other AML core regulatory factors, including RUNX1, LMO2, and MEIS1. SWI/SNF inhibition in AML cells reduced DNA accessibility and binding of these factors at PU.1 sites and redistributed PU.1 to promoters. Analysis of nontumor hematopoietic cells revealed that similar effects also impair PU.1-dependent B-cell and monocyte populations. Nevertheless, SWI/SNF inhibition induced profound therapeutic response in an immunocompetent AML mouse model as well as in primary human AML samples. In vivo, SWI/SNF inhibition promoted leukemic differentiation and reduced the leukemic stem cell burden in bone marrow but also induced leukopenia. These results reveal a variable therapeutic window for SWI/SNF blockade in AML and highlight important off-tumor effects of such therapies in immunocompetent settings. SIGNIFICANCE Disruption of PU.1-directed enhancer programs upon SWI/SNF inhibition causes differentiation of AML cells and induces leukopenia of PU.1-dependent B cells and monocytes, revealing the on- and off-tumor effects of SWI/SNF blockade.
Collapse
Affiliation(s)
- Courtney Chambers
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Yuen San Chan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Kristen Kurtz
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
| | - Andrew Henry Lewis
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Christiana Wang
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Anh Pham
- Department of Bioengineering, Rice University, Houston, Texas
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mario Loeza Cabrera
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Rogelio Aguilar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - H. Daniel Lacorazza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Rachel E. Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - H. Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| |
Collapse
|
6
|
Wang Y, Huang Z, Sun M, Huang W, Xia L. ETS transcription factors: Multifaceted players from cancer progression to tumor immunity. Biochim Biophys Acta Rev Cancer 2023; 1878:188872. [PMID: 36841365 DOI: 10.1016/j.bbcan.2023.188872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.
Collapse
Affiliation(s)
- Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zhao Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
| |
Collapse
|
7
|
Tu Z, Fan C, Davis AK, Hu M, Wang C, Dandamudi A, Seu KG, Kalfa TA, Lu QR, Zheng Y. Autism-associated chromatin remodeler CHD8 regulates erythroblast cytokinesis and fine-tunes the balance of Rho GTPase signaling. Cell Rep 2022; 40:111072. [PMID: 35830790 PMCID: PMC9302451 DOI: 10.1016/j.celrep.2022.111072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
CHD8 is an ATP-dependent chromatin-remodeling factor whose monoallelic mutation defines a subtype of autism spectrum disorders (ASDs). Previous work found that CHD8 is required for the maintenance of hematopoiesis by integrating ATM-P53-mediated survival of hematopoietic stem/progenitor cells (HSPCs). Here, by using Chd8F/FMx1-Cre combined with a Trp53F/F mouse model that suppresses apoptosis of Chd8−/− HSPCs, we identify CHD8 as an essential regulator of erythroid differentiation. Chd8−/−P53−/− mice exhibited severe anemia conforming to congenital dyserythropoietic anemia (CDA) phenotypes. Loss of CHD8 leads to drastically decreased numbers of orthochromatic erythroblasts and increased binucleated and multinucleated basophilic erythroblasts with a cytokinesis failure in erythroblasts. CHD8 binds directly to the gene bodies of multiple Rho GTPase signaling genes in erythroblasts, and loss of CHD8 results in their dysregulated expression, leading to decreased RhoA and increased Rac1 and Cdc42 activities. Our study shows that autism-associated CHD8 is essential for erythroblast cytokinesis. Tu et al. report that CHD8, an autism-related chromatin remodeler, is essential for erythroid differentiation. Loss of CHD8 leads to unbalanced Rho GTPase signaling and defective erythroblast cytokinesis, mimicking that of congenital dyserythropoietic anemia.
Collapse
Affiliation(s)
- Zhaowei Tu
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory for Major Obstetric Diseases, Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Cuiqing Fan
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Ashely K Davis
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Mengwen Hu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Chen Wang
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Akhila Dandamudi
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Katie G Seu
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Theodosia A Kalfa
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Q Richard Lu
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
| |
Collapse
|
8
|
Huang X, Ferris ST, Kim S, Choudhary MNK, Belk JA, Fan C, Qi Y, Sudan R, Xia Y, Desai P, Chen J, Ly N, Shi Q, Bagadia P, Liu T, Guilliams M, Egawa T, Colonna M, Diamond MS, Murphy TL, Satpathy AT, Wang T, Murphy KM. Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. Immunity 2021; 54:1417-1432.e7. [PMID: 34004142 PMCID: PMC8282756 DOI: 10.1016/j.immuni.2021.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 04/14/2021] [Indexed: 12/11/2022]
Abstract
The transcriptional repressor ZEB2 regulates development of many cell fates among somatic, neural, and hematopoietic lineages, but the basis for its requirement in these diverse lineages is unclear. Here, we identified a 400-basepair (bp) region located 165 kilobases (kb) upstream of the Zeb2 transcriptional start site (TSS) that binds the E proteins at several E-box motifs and was active in hematopoietic lineages. Germline deletion of this 400-bp region (Zeb2Δ-165mice) specifically prevented Zeb2 expression in hematopoietic stem cell (HSC)-derived lineages. Zeb2Δ-165 mice lacked development of plasmacytoid dendritic cells (pDCs), monocytes, and B cells. All macrophages in Zeb2Δ-165 mice were exclusively of embryonic origin. Using single-cell chromatin profiling, we identified a second Zeb2 enhancer located at +164-kb that was selectively active in embryonically derived lineages, but not HSC-derived ones. Thus, Zeb2 expression in adult, but not embryonic, hematopoiesis is selectively controlled by the -165-kb Zeb2 enhancer.
Collapse
Affiliation(s)
- Xiao Huang
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Stephen T Ferris
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Changxu Fan
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Raki Sudan
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Yu Xia
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Pritesh Desai
- Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Jing Chen
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Nghi Ly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Quanming Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Prachi Bagadia
- Department of Oncology, Amgen, 1120 Veterans Boulevard, South San Francisco, CA 94080, USA
| | - Tiantian Liu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Martin Guilliams
- Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent 9000, Belgium
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|