1
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Priam P, Krasteva V, Rousseau P, Polsinelli A, Côté L, Desanlis I, Farah A, Lavallée VP, Kmita M, Lessard JA. Smarcd1 subunit of SWI/SNF chromatin-remodeling complexes collaborates with E2a to promote murine lymphoid specification. Dev Cell 2024:S1534-5807(24)00490-8. [PMID: 39232562 DOI: 10.1016/j.devcel.2024.08.007] [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: 07/21/2022] [Revised: 05/02/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Lymphocyte development from murine hematopoietic stem cells (HSCs) entails a loss of self-renewal capacity and a progressive restriction of developmental potential. Previous research from our laboratory suggests that specialized assemblies of ATP-dependent SWI/SNF chromatin-remodeling complexes play lineage-specific roles during murine hematopoiesis. Here, we demonstrate that the Smarcd1 subunit is essential for specification of lymphoid cell fate from multipotent progenitors. Acute deletion of Smarcd1 in murine adult hematopoiesis leads to lymphopenia, characterized by a near-complete absence of early lymphoid progenitors and mature B and T cells, while the myeloid and erythroid lineages remain unaffected. Mechanistically, we demonstrate that Smarcd1 is essential for the coordinated activation of a lymphoid gene signature in murine multipotent progenitors. This is achieved by interacting with the E2a transcription factor at proximal promoters and by regulating the activity of distal enhancers. Globally, these findings identify Smarcd1 as an essential chromatin remodeler that governs lymphoid cell fate.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Alexandre Polsinelli
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Laurence Côté
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ines Desanlis
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Azer Farah
- Centre de Recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | | | - Marie Kmita
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, QC H2W 1R7, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
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2
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Liu X, Liu K, Wang Y, Meng X, Wang Q, Tao S, Xu Q, Shen X, Gao X, Hong S, Jin H, Wang JQ, Wang D, Lu L, Meng Z, Wang L. SWI/SNF chromatin remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cell migration. Cell Rep 2024; 43:114458. [PMID: 38996070 DOI: 10.1016/j.celrep.2024.114458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Regulatory T (Treg) cells play a critical regulatory role in the immune system by suppressing excessive immune responses and maintaining immune balance. The effective migration of Treg cells is crucial for controlling the development and progression of inflammatory diseases. However, the mechanisms responsible for directing Treg cells into the inflammatory tissue remain incompletely elucidated. In this study, we identified BAF60b, a subunit of switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complexes, as a positive regulator of Treg cell migration that inhibits the progression of inflammation in experimental autoimmune encephalomyelitis (EAE) and colitis animal models. Mechanistically, transcriptome and genome-wide chromatin-landscaped analyses demonstrated that BAF60b interacts with the transcription factor RUNX1 to promote the expression of CCR9 on Treg cells, which in turn affects their ability to migrate to inflammatory tissues. Our work provides insights into the essential role of BAF60b in regulating Treg cell migration and its impact on inflammatory diseases.
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MESH Headings
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Animals
- Cell Movement
- Mice
- Mice, Inbred C57BL
- Inflammation/pathology
- Inflammation/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/metabolism
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Humans
- Transcription Factors/metabolism
- Core Binding Factor Alpha 2 Subunit/metabolism
- Core Binding Factor Alpha 2 Subunit/genetics
- Colitis/metabolism
- Colitis/pathology
- Colitis/immunology
- Colitis/genetics
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Affiliation(s)
- Xiaoqian Liu
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Kuai Liu
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yuxi Wang
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Meng
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qianqian Wang
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Sijue Tao
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Qianying Xu
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Shen
- Co-Facility Center, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xianzhi Gao
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shenghui Hong
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - Huihui Jin
- Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China
| | - James Q Wang
- Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China
| | - Di Wang
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Linrong Lu
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhuoxian Meng
- Department of Pathology and Pathophysiology and Department of Cardiology, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou 310009, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 311100, China; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311100, China; Zhejiang University School of Medicine, Hangzhou 310058, China; Laboratory Animal Center, Zhejiang University, Hangzhou 310058, China; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining 314400, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China.
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3
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Ren G, Ku WL, Ge G, Hoffman JA, Kang JY, Tang Q, Cui K, He Y, Guan Y, Gao B, Liu C, Archer TK, Zhao K. Acute depletion of BRG1 reveals its primary function as an activator of transcription. Nat Commun 2024; 15:4561. [PMID: 38811575 PMCID: PMC11137027 DOI: 10.1038/s41467-024-48911-z] [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: 05/24/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
The mammalian SWI/SNF-like BAF complexes play critical roles during animal development and pathological conditions. Previous gene deletion studies and characterization of human gene mutations implicate that the complexes both repress and activate a large number of genes. However, the direct function of the complexes in cells remains largely unclear due to the relatively long-term nature of gene deletion or natural mutation. Here we generate a mouse line by knocking in the auxin-inducible degron tag (AID) to the Smarca4 gene, which encodes BRG1, the essential ATPase subunit of the BAF complexes. We show that the tagged BRG1 can be efficiently depleted by osTIR1 expression and auxin treatment for 6 to 10 h in CD4 + T cells, hepatocytes, and fibroblasts isolated from the knock-in mice. The acute depletion of BRG1 leads to decreases in nascent RNAs and RNA polymerase II binding at a large number of genes, which are positively correlated with the loss of BRG1. Further, these changes are correlated with diminished accessibility at DNase I Hypersensitive Sites (DHSs) and p300 binding. The acute BRG1 depletion results in three major patterns of nucleosome shifts leading to narrower nucleosome spacing surrounding transcription factor motifs and at enhancers and transcription start sites (TSSs), which are correlated with loss of BRG1, decreased chromatin accessibility and decreased nascent RNAs. Acute depletion of BRG1 severely compromises the Trichostatin A (TSA) -induced histone acetylation, suggesting a substantial interplay between the chromatin remodeling activity of BRG1 and histone acetylation. Our data suggest BRG1 mainly plays a direct positive role in chromatin accessibility, RNAPII binding, and nascent RNA production by regulating nucleosome positioning and facilitating transcription factor binding to their target sites.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
- College of Animal Science and Technology, Northwest Agriculture and Forest University, Yangling, Xianyang, Shaanxi, China
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Guangzhe Ge
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Jee Youn Kang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Qingsong Tang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yong He
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Yukun Guan
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.
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4
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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5
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Mathies LD, Kim AC, Soukup EM, Thomas AE, Bettinger JC. PBRM-1/PBAF-regulated genes in a multipotent progenitor in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkad297. [PMID: 38150396 PMCID: PMC10917506 DOI: 10.1093/g3journal/jkad297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The 2 SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates, and the other dies by programmed cell death. The polybromo-associated BAF (PBAF) chromatin remodeling complex promotes the multipotent SGP fate. The complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1,955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 that are normally expressed at higher levels in SGP vs hmc and positively regulated by pbrm-1 and 53 that are normally expressed at higher levels in hmc vs SGP and are negatively regulated by pbrm-1; these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; the hsp-12.3 reporter was derepressed in SGPs in pbrm-1 mutants, suggesting that hsp-12.3 expression is normally repressed by pbrm-1 in SGPs.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew C Kim
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Evan M Soukup
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alan’da E Thomas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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6
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Li K, Wang B, Hu H. Research progress of SWI/SNF complex in breast cancer. Epigenetics Chromatin 2024; 17:4. [PMID: 38365747 PMCID: PMC10873968 DOI: 10.1186/s13072-024-00531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
In the past decade, numerous epigenetic mechanisms have been discovered to be associated with cancer. The mammalian SWI/SNF complex is an ATP-dependent chromatin remodeling complex whose mutations are associated with various malignancies including breast cancer. As the SWI/SNF complex has become one of the most commonly mutated complexes in cancer, targeting epigenetic mutations acquired during breast cancer progress is a potential means of improving clinical efficacy in treatment strategies. This article reviews the composition of the SWI/SNF complex, its main roles and research progress in breast cancer, and links these findings to the latest discoveries in cancer epigenomics to discuss the potential mechanisms and therapeutic potential of SWI/SNF in breast cancer.
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Affiliation(s)
- Kexuan Li
- School of Medicine, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
| | - Haolin Hu
- Breast Center, Zhongda Hospital, School of Medicine, Southeast University, 87 Dingjiaqiao Road, Nanjing, 210009, Jiangsu, China.
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7
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Liu H, Zhao Y, Zhao G, Deng Y, Chen YE, Zhang J. SWI/SNF Complex in Vascular Smooth Muscle Cells and Its Implications in Cardiovascular Pathologies. Cells 2024; 13:168. [PMID: 38247859 PMCID: PMC10814623 DOI: 10.3390/cells13020168] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Mature vascular smooth muscle cells (VSMC) exhibit a remarkable degree of plasticity, a characteristic that has intrigued cardiovascular researchers for decades. Recently, it has become increasingly evident that the chromatin remodeler SWItch/Sucrose Non-Fermentable (SWI/SNF) complex plays a pivotal role in orchestrating chromatin conformation, which is critical for gene regulation. In this review, we provide a summary of research related to the involvement of the SWI/SNF complexes in VSMC and cardiovascular diseases (CVD), integrating these discoveries into the current landscape of epigenetic and transcriptional regulation in VSMC. These novel discoveries shed light on our understanding of VSMC biology and pave the way for developing innovative therapeutic strategies in CVD treatment.
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Affiliation(s)
- Hongyu Liu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Molecular & Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Vascular Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yang Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Guizhen Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Yongjie Deng
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Cardiac Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
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8
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Ho PJ, Kweon J, Blumensaadt LA, Neely AE, Kalika E, Leon DB, Oh S, Stringer CWP, Lloyd SM, Ren Z, Bao X. Multi-omics integration identifies cell-state-specific repression by PBRM1-PIAS1 cooperation. CELL GENOMICS 2024; 4:100471. [PMID: 38190100 PMCID: PMC10794847 DOI: 10.1016/j.xgen.2023.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024]
Abstract
PBRM1 is frequently mutated in cancers of epithelial origin. How PBRM1 regulates normal epithelial homeostasis, prior to cancer initiation, remains unclear. Here, we show that PBRM1's gene regulatory roles differ drastically between cell states, leveraging human skin epithelium (epidermis) as a research platform. In progenitors, PBRM1 predominantly functions to repress terminal differentiation to sustain progenitors' regenerative potential; in the differentiation state, however, PBRM1 switches toward an activator. Between these two cell states, PBRM1 retains its genomic binding but associates with differential interacting proteins. Our targeted screen identified the E3 SUMO ligase PIAS1 as a key interactor. PIAS1 co-localizes with PBRM1 on chromatin to directly repress differentiation genes in progenitors, and PIAS1's chromatin binding drastically diminishes in differentiation. Furthermore, SUMOylation contributes to PBRM1's repressive function in progenitor maintenance. Thus, our findings highlight PBRM1's cell-state-specific regulatory roles influenced by its protein interactome despite its stable chromatin binding.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Junghun Kweon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Laura A Blumensaadt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Elizabeth Kalika
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Daniel B Leon
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sanghyon Oh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Cooper W P Stringer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Ziyou Ren
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Dermatology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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9
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Yu Y, Wang S, Wang Z, Gao R, Lee J. Arabidopsis thaliana: a powerful model organism to explore histone modifications and their upstream regulations. Epigenetics 2023; 18:2211362. [PMID: 37196184 DOI: 10.1080/15592294.2023.2211362] [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: 11/24/2022] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Histones are subjected to extensive covalent modifications that affect inter-nucleosomal interactions as well as alter chromatin structure and DNA accessibility. Through switching the corresponding histone modifications, the level of transcription and diverse downstream biological processes can be regulated. Although animal systems are widely used in studying histone modifications, the signalling processes that occur outside the nucleus prior to histone modifications have not been well understood due to the limitations including non viable mutants, partial lethality, and infertility of survivors. Here, we review the benefits of using Arabidopsis thaliana as the model organism to study histone modifications and their upstream regulations. Similarities among histones and key histone modifiers such as the Polycomb group (PcG) and Trithorax group (TrxG) in Drosophila, Human, and Arabidopsis are examined. Furthermore, prolonged cold-induced vernalization system has been well-studied and revealed the relationship between the controllable environment input (duration of vernalization), its chromatin modifications of FLOWERING LOCUS C (FLC), following gene expression, and the corresponding phenotypes. Such evidence suggests that research on Arabidopsis can bring insights into incomplete signalling pathways outside of the histone box, which can be achieved through viable reverse genetic screenings based on the phenotypes instead of direct monitoring of histone modifications among individual mutants. The potential upstream regulators in Arabidopsis can provide cues or directions for animal research based on the similarities between them.
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Affiliation(s)
- Yang Yu
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Sihan Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Ziqin Wang
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Renwei Gao
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Joohyun Lee
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
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10
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Lu S, Duan R, Cong L, Song Y. The effects of ARID1A mutation in gastric cancer and its significance for treatment. Cancer Cell Int 2023; 23:296. [PMID: 38008753 PMCID: PMC10676575 DOI: 10.1186/s12935-023-03154-8] [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: 03/24/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023] Open
Abstract
Gastric cancer (GC) has emerged as a significant issue in public health all worldwide as a result of its high mortality rate and dismal prognosis. AT-rich interactive domain 1 A (ARID1A) is a vital component of the switch/sucrose-non-fermentable (SWI/SNF) chromatin remodeling complex, and ARID1A mutations occur in various tumors, leading to protein loss and decreased expression; it then affects the tumor biological behavior or prognosis. More significantly, ARID1A mutations will likely be biological markers for immune checkpoint blockade (ICB) treatment and selective targeted therapy. To provide theoretical support for future research on the stratification of individuals with gastric cancer with ARID1A as a biomarker to achieve precision therapy, we have focused on the clinical significance, predictive value, underlying mechanisms, and possible treatment strategies for ARID1A mutations in gastric cancer in this review.
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Affiliation(s)
- Shan Lu
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Ruifeng Duan
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Liang Cong
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China
| | - Ying Song
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, China.
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11
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Chen X, Li B, Wang Y, Jin J, Yang Y, Huang L, Yang M, Zhang J, Wang B, Shao Z, Ni T, Huang S, Hu X, Tao Z. Low level of ARID1A contributes to adaptive immune resistance and sensitizes triple-negative breast cancer to immune checkpoint inhibitors. Cancer Commun (Lond) 2023; 43:1003-1026. [PMID: 37434394 PMCID: PMC10508140 DOI: 10.1002/cac2.12465] [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: 12/19/2022] [Revised: 04/22/2023] [Accepted: 07/04/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) shed new light on triple-negative breast cancer (TNBC), but only a minority of patients demonstrate response. Therefore, adaptive immune resistance (AIR) needs to be further defined to guide the development of ICI regimens. METHODS Databases, including The Cancer Genome Atlas, Gene Ontology Resource, University of California Santa Cruz Genome Browser, and Pubmed, were used to screen epigenetic modulators, regulators for CD8+ T cells, and transcriptional regulators of programmed cell death-ligand 1 (PD-L1). Human peripheral blood mononuclear cell (Hu-PBMC) reconstruction mice were adopted for xenograft transplantation. Tumor specimens from a TNBC cohort and the clinical trial CTR20191353 were retrospectively analyzed. RNA-sequencing, Western blotting, qPCR and immunohistochemistry were used to assess gene expression. Coculture assays were performed to evaluate the regulation of TNBC cells on T cells. Chromatin immunoprecipitation and transposase-accessible chromatin sequencing were used to determine chromatin-binding and accessibility. RESULTS The epigenetic modulator AT-rich interaction domain 1A (ARID1A) gene demonstrated the highest expression association with AIR relative to other epigenetic modulators in TNBC patients. Low ARID1A expression in TNBC, causing an immunosuppressive microenvironment, promoted AIR and inhibited CD8+ T cell infiltration and activity through upregulating PD-L1. However, ARID1A did not directly regulate PD-L1 expression. We found that ARID1A directly bound the promoter of nucleophosmin 1 (NPM1) and that low ARID1A expression increased NPM1 chromatin accessibility as well as gene expression, further activating PD-L1 transcription. In Hu-PBMC mice, atezolizumab demonstrated the potential to reverse ARID1A deficiency-induced AIR in TNBC by reducing tumor malignancy and activating anti-tumor immunity. In CTR20191353, ARID1A-low patients derived more benefit from pucotenlimab compared to ARID1A-high patients. CONCLUSIONS In AIR epigenetics, low ARID1A expression in TNBC contributed to AIR via the ARID1A/NPM1/PD-L1 axis, leading to poor outcome but sensitivity to ICI treatment.
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Affiliation(s)
- Xin‐Yu Chen
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Bin Li
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Ye Wang
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Juan Jin
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Yu Yang
- State Key Laboratory of Genetic EngineeringCollaborative Innovation Center of Genetics and DevelopmentHuman Phenome InstituteSchool of Life SciencesFudan UniversityShanghaiP. R. China
| | - Lei‐Huan Huang
- State Key Laboratory of Genetic EngineeringCollaborative Innovation Center of Genetics and DevelopmentHuman Phenome InstituteSchool of Life SciencesFudan UniversityShanghaiP. R. China
| | - Meng‐Di Yang
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Jian Zhang
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Bi‐Yun Wang
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Zhi‐Ming Shao
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
- Key Laboratory of Breast Cancer in ShanghaiDepartment of Breast SurgeryFudan University Shanghai Cancer CenterShanghaiP. R. China
- Precision Cancer Medicine CenterFudan University Shanghai Cancer CenterShanghaiP. R. China
| | - Ting Ni
- State Key Laboratory of Genetic EngineeringCollaborative Innovation Center of Genetics and DevelopmentHuman Phenome InstituteSchool of Life SciencesFudan UniversityShanghaiP. R. China
| | - Sheng‐Lin Huang
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
- Shanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Xi‐Chun Hu
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Zhong‐Hua Tao
- Department of Breast and Urologic Medical OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiP. R. China
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12
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Kang JS, Kim D, Rhee J, Seo JY, Park I, Kim JH, Lee D, Lee W, Kim YL, Yoo K, Bae S, Chung J, Seong RH, Kong YY. Baf155 regulates skeletal muscle metabolism via HIF-1a signaling. PLoS Biol 2023; 21:e3002192. [PMID: 37478146 PMCID: PMC10396025 DOI: 10.1371/journal.pbio.3002192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/12/2023] [Indexed: 07/23/2023] Open
Abstract
During exercise, skeletal muscle is exposed to a low oxygen condition, hypoxia. Under hypoxia, the transcription factor hypoxia-inducible factor-1α (HIF-1α) is stabilized and induces expressions of its target genes regulating glycolytic metabolism. Here, using a skeletal muscle-specific gene ablation mouse model, we show that Brg1/Brm-associated factor 155 (Baf155), a core subunit of the switch/sucrose non-fermentable (SWI/SNF) complex, is essential for HIF-1α signaling in skeletal muscle. Muscle-specific ablation of Baf155 increases oxidative metabolism by reducing HIF-1α function, which accompanies the decreased lactate production during exercise. Furthermore, the augmented oxidation leads to high intramuscular adenosine triphosphate (ATP) level and results in the enhancement of endurance exercise capacity. Mechanistically, our chromatin immunoprecipitation (ChIP) analysis reveals that Baf155 modulates DNA-binding activity of HIF-1α to the promoters of its target genes. In addition, for this regulatory function, Baf155 requires a phospho-signal transducer and activator of transcription 3 (pSTAT3), which forms a coactivator complex with HIF-1α, to activate HIF-1α signaling. Our findings reveal the crucial role of Baf155 in energy metabolism of skeletal muscle and the interaction between Baf155 and hypoxia signaling.
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Affiliation(s)
- Jong-Seol Kang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Dongha Kim
- Department of Anatomy, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Joonwoo Rhee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Yun Seo
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Inkuk Park
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ji-Hoon Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Daewon Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - WonUk Lee
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ye Lynne Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Kyusang Yoo
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Sunghwan Bae
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jongkyeong Chung
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Rho Hyun Seong
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Young-Yun Kong
- School of Biological Sciences, Seoul National University, Seoul, South Korea
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13
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Rive Le Gouard N, Nicolle R, Lefebvre M, Gelot A, Heide S, Gerasimenko A, Grigorescu R, Derive N, Jouannic JM, Garel C, Valence S, Quenum-Miraillet G, Chantot-Bastaraud S, Keren B, Heron D, Attie-Bitach T. First reports of fetal SMARCC1 related hydrocephalus. Eur J Med Genet 2023:104797. [PMID: 37285932 DOI: 10.1016/j.ejmg.2023.104797] [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: 11/27/2022] [Revised: 03/11/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
The SMARCC1 gene has been involved in congenital ventriculomegaly with aqueduct stenosis but only a few patients have been reported so far, with no antenatal cases, and it is currently not annotated as a morbid gene in OMIM nor in the Human Phenotype Ontology. Most of the reported variants are loss of function (LoF) and are often inherited from unaffected parents. SMARCC1 encodes a subunit of the mSWI/SNF complex and affects the chromatin structure and expression of several genes. Here, we report the two first antenatal cases of SMARCC1 LoF variants detected by Whole Genome Sequencing (WGS). Ventriculomegaly is the common feature in those fetuses. Both identified variants are inherited from a healthy parent, which supports the reported incomplete penetrance of this gene. This makes the identification of this condition in WGS as well as the genetic counseling challenging.
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Affiliation(s)
- Nicolas Rive Le Gouard
- UF de Génomique du Développement, Département de Génétique médicale, Groupe Hospitalier Pitié-Salpêtrière, AP-HP Sorbonne Université, Paris, France.
| | - Romain Nicolle
- Service de Médecine Génomique des maladies rares, UF MP5, Hôpital Necker-Enfants Malades, AP-HP Université Paris Cité, Paris, France
| | | | - Antoinette Gelot
- Service de Foetopathologie, Hôpital Armand Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Solveig Heide
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique médicale, Groupe Hospitalier Pitié-Salpêtrière, AP-HP Sorbonne Université, Paris, France
| | - Anna Gerasimenko
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique médicale, Groupe Hospitalier Pitié-Salpêtrière, AP-HP Sorbonne Université, Paris, France
| | - Romulus Grigorescu
- Service de Foetopathologie, Hôpital Armand Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Nicolas Derive
- Laboratoire de Biologie Médicale Multisites SeqOIA, Paris, France
| | - Jean-Marie Jouannic
- Gynécologie obstétrique, Hôpital Trousseau, Centre de Référence C-MAVEM, AP-HP Sorbonne Université, Paris, France
| | - Catherine Garel
- Service de Radiologie Pédiatrique, Hôpital Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Stéphanie Valence
- Service de Neurologie Pédiatrique, Hôpital Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Geneviève Quenum-Miraillet
- UF de Génomique Chromosomique, Département de Génétique médicale, Hôpital Armand Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Sandra Chantot-Bastaraud
- UF de Génomique Chromosomique, Département de Génétique médicale, Hôpital Armand Trousseau, AP-HP Sorbonne Université, Paris, France
| | - Boris Keren
- UF de Génomique du Développement, Département de Génétique médicale, Groupe Hospitalier Pitié-Salpêtrière, AP-HP Sorbonne Université, Paris, France; Laboratoire de Biologie Médicale Multisites SeqOIA, Paris, France
| | - Delphine Heron
- UF de Génétique Médicale et CRMR « Déficience intellectuelle », Département de Génétique médicale, Groupe Hospitalier Pitié-Salpêtrière, AP-HP Sorbonne Université, Paris, France
| | - Tania Attie-Bitach
- Service de Médecine Génomique des maladies rares, UF MP5, Hôpital Necker-Enfants Malades, AP-HP Université Paris Cité, Paris, France; Laboratoire de Biologie Médicale Multisites SeqOIA, Paris, France.
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14
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Jolly AJ, Lu S, Dubner AM, Strand KA, Mutryn MF, Pilotti-Riley A, Danis EP, Nemenoff RA, Moulton KS, Majesky MW, Weiser-Evans MC. Redistribution of the chromatin remodeler Brg1 directs smooth muscle-derived adventitial progenitor-to-myofibroblast differentiation and vascular fibrosis. JCI Insight 2023; 8:e164862. [PMID: 36976650 PMCID: PMC10243795 DOI: 10.1172/jci.insight.164862] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Vascular smooth muscle-derived Sca1+ adventitial progenitor (AdvSca1-SM) cells are tissue-resident, multipotent stem cells that contribute to progression of vascular remodeling and fibrosis. Upon acute vascular injury, AdvSca1-SM cells differentiate into myofibroblasts and are embedded in perivascular collagen and the extracellular matrix. While the phenotypic properties of AdvSca1-SM-derived myofibroblasts have been defined, the underlying epigenetic regulators driving the AdvSca1-SM-to-myofibroblast transition are unclear. We show that the chromatin remodeler Smarca4/Brg1 facilitates AdvSca1-SM myofibroblast differentiation. Brg1 mRNA and protein were upregulated in AdvSca1-SM cells after acute vascular injury, and pharmacological inhibition of Brg1 by the small molecule PFI-3 attenuated perivascular fibrosis and adventitial expansion. TGF-β1 stimulation of AdvSca1-SM cells in vitro reduced expression of stemness genes while inducing expression of myofibroblast genes that was associated with enhanced contractility; PFI blocked TGF-β1-induced phenotypic transition. Similarly, genetic knockdown of Brg1 in vivo reduced adventitial remodeling and fibrosis and reversed AdvSca1-SM-to-myofibroblast transition in vitro. Mechanistically, TGF-β1 promoted redistribution of Brg1 from distal intergenic sites of stemness genes and recruitment to promoter regions of myofibroblast-related genes, which was blocked by PFI-3. These data provide insight into epigenetic regulation of resident vascular progenitor cell differentiation and support that manipulating the AdvSca1-SM phenotype will provide antifibrotic clinical benefits.
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Affiliation(s)
- Austin J. Jolly
- Department of Medicine, Division of Renal Diseases and Hypertension
- Medical Scientist Training Program
| | - Sizhao Lu
- Department of Medicine, Division of Renal Diseases and Hypertension
- School of Medicine, Consortium for Fibrosis Research and Translation
| | | | - Keith A. Strand
- Department of Medicine, Division of Renal Diseases and Hypertension
| | - Marie F. Mutryn
- Department of Medicine, Division of Renal Diseases and Hypertension
| | | | | | - Raphael A. Nemenoff
- Department of Medicine, Division of Renal Diseases and Hypertension
- School of Medicine, Consortium for Fibrosis Research and Translation
- Cardiovascular Pulmonary Research Program, and
| | - Karen S. Moulton
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mark W. Majesky
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, USA
- Departments of Pediatrics and Pathology, University of Washington, Seattle, Washington, USA
| | - Mary C.M. Weiser-Evans
- Department of Medicine, Division of Renal Diseases and Hypertension
- School of Medicine, Consortium for Fibrosis Research and Translation
- Cardiovascular Pulmonary Research Program, and
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15
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Andrades A, Peinado P, Alvarez-Perez JC, Sanjuan-Hidalgo J, García DJ, Arenas AM, Matia-González AM, Medina PP. SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities. Mol Cancer 2023; 22:39. [PMID: 36810086 PMCID: PMC9942420 DOI: 10.1186/s12943-023-01736-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.
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Affiliation(s)
- Alvaro Andrades
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Paola Peinado
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain ,grid.451388.30000 0004 1795 1830Present Address: The Francis Crick Institute, London, UK
| | - Juan Carlos Alvarez-Perez
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Juan Sanjuan-Hidalgo
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Daniel J. García
- grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.4489.10000000121678994Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Alberto M. Arenas
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Ana M. Matia-González
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Pedro P. Medina
- grid.4489.10000000121678994Department of Biochemistry and Molecular Biology I. Faculty of Sciences, University of Granada, Granada, Spain ,grid.470860.d0000 0004 4677 7069GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain ,grid.507088.2Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
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16
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Ferguson LP, Gatchalian J, McDermott ML, Nakamura M, Chambers K, Rajbhandari N, Lytle NK, Rosenthal SB, Hamilton M, Albini S, Wartenberg M, Zlobec I, Galván JA, Karamitopoulou E, Vavinskaya V, Wascher A, Lowy AM, Schürch CM, Puri PL, Bruneau BG, Hargreaves DC, Reya T. Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma. Nat Commun 2023; 14:292. [PMID: 36653361 PMCID: PMC9849267 DOI: 10.1038/s41467-023-35796-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Pancreatic cancer is characterized by extensive resistance to conventional therapies, making clinical management a challenge. Here we map the epigenetic dependencies of cancer stem cells, cells that preferentially evade therapy and drive progression, and identify SWI/SNF complex member SMARCD3 as a regulator of pancreatic cancer cells. Although SWI/SNF subunits often act as tumor suppressors, we show that SMARCD3 is amplified in cancer, enriched in pancreatic cancer stem cells and upregulated in the human disease. Diverse genetic mouse models of pancreatic cancer and stage-specific Smarcd3 deletion reveal that Smarcd3 loss preferentially impacts established tumors, improving survival especially in context of chemotherapy. Mechanistically, SMARCD3 acts with FOXA1 to control lipid and fatty acid metabolism, programs associated with therapy resistance and poor prognosis in cancer. These data identify SMARCD3 as an epigenetic modulator responsible for establishing the metabolic landscape in aggressive pancreatic cancer cells and a potential target for new therapies.
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Affiliation(s)
- L Paige Ferguson
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | | | - Matthew L McDermott
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Mari Nakamura
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Kendall Chambers
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Nirakar Rajbhandari
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Nikki K Lytle
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sara Brin Rosenthal
- Center for Computational Biology and Bioinformatics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Hamilton
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Sonia Albini
- Genethon, 91000, EVRY, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Martin Wartenberg
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - José A Galván
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Eva Karamitopoulou
- Institute of Pathology, University of Bern, Murtenstrasse 31, 3008, Bern, Switzerland
| | - Vera Vavinskaya
- Department of Pathology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Alexis Wascher
- Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Surgery, Division of Surgical Oncology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Andrew M Lowy
- Moores Cancer Center, University of California San Diego School of Medicine, La Jolla, CA, USA
- Department of Surgery, Division of Surgical Oncology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Christian M Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Tannishtha Reya
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Physiology and Cellular Biophysics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
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17
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Celen C, Chuang JC, Shen S, Li L, Maggiore G, Jia Y, Luo X, Moore A, Wang Y, Otto JE, Collings CK, Wang Z, Sun X, Nassour I, Park J, Ghaben A, Wang T, Wang SC, Scherer PE, Kadoch C, Zhu H. Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling. Cell Rep 2022; 41:111581. [DOI: 10.1016/j.celrep.2022.111581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/18/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
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18
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Yadav N, Nagar P, Rakhi R, Kumar A, Rai A, Mustafiz A. Transcript profiling of Polycomb gene family in Oryza sativa indicates their abiotic stress-specific response. Funct Integr Genomics 2022; 22:1211-1227. [PMID: 36197542 DOI: 10.1007/s10142-022-00906-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/16/2022] [Accepted: 09/27/2022] [Indexed: 11/27/2022]
Abstract
The precise regulation of gene expression is required for the determination of cell fate, differentiation, and developmental programs in eukaryotes. The Polycomb Group (PcG) genes are the key transcriptional regulators that constitute the repressive system, with two major protein complexes, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2). Previous studies have demonstrated the significance of these proteins in regulation of normal growth and development processes. However, the role of PcG in adaptation of crops to abiotic stress is still not well understood. The present study aimed to a comprehensive genome-wide identification of the PcG gene family in one of the economically important staple crops, Oryza sativa. Here, a total of 14 PcG genes have been identified, which were distributed over eight chromosomes. Protein structure analysis revealed that both the complexes have distinct domain and motifs that are conserved within the complexes. In silico promoter analysis showed that PcG gene promoters have abundance of abiotic stress-responsive elements. RNA-seq based expression analysis revealed that PcG genes are differentially expressed in different tissues and responded variably in different environmental stress. Validation of gene expression by qRT-PCR showed that most of the genes were upregulated at 1-h time point in shoot tissue and at 24-h time point in root tissue under the drought and salinity stress conditions. These findings provide important and extensive information on the PcG family of O. sativa, which will pave the path for understanding their role in stress signaling in plants.
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Affiliation(s)
- Nikita Yadav
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Preeti Nagar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - R Rakhi
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Ashish Kumar
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Archita Rai
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India
| | - Ananda Mustafiz
- Plant Molecular Biology Laboratory, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, 110021, India.
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Ota T, Ishikawa T, Yasuda R, Yasuda T, Okayama T, Inoue K, Dohi O, Yoshida N, Kamada K, Uchiyama K, Takagi T, Konishi H, Naito Y, Matsuyama K, Yamaguchi T, Ootsuka K, Yoshida A, Kishimoto M, Itoh Y. The first case of SMARCA4-deficient sarcoma of stomach. Clin J Gastroenterol 2022; 15:531-536. [PMID: 35175571 DOI: 10.1007/s12328-022-01606-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/05/2022] [Indexed: 11/24/2022]
Abstract
SMARCA4-deficient sarcoma was first reported in the chest and recently in the uterus, but not in the stomach. Here, we present a patient diagnosed with SMARCA4-deficient sarcoma of the stomach, using histochemistry. An emergency operation was performed due to perforation of the tumor. However, one month after the operation, two nodes recurred, and six cycles of combination chemotherapy consisting of adriamycin and ifosfamide were administered. The combination chemotherapy showed a remarkable effect, and complete remission was achieved. The patient was alive without recurrence after 48-month follow-up. SMARCA4-deficient sarcoma is an exceedingly rare tumor with an extremely poor therapeutic response to anticancer drugs. Herein, we present the first case of SMARCA4-deficient sarcoma of the stomach, where a complete response to chemotherapy was achieved.
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Affiliation(s)
- Takayuki Ota
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Takeshi Ishikawa
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan.
| | - Ritsu Yasuda
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomoyo Yasuda
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tetsuya Okayama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Ken Inoue
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Osamu Dohi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Naohisa Yoshida
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiro Kamada
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kazuhiko Uchiyama
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Tomohiro Takagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Hideyuki Konishi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yuji Naito
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Kiichi Matsuyama
- Ijinkai Takeda General Hospital, 28-1 Moriminami-cho, Ishida, Fushimi-ku, Kyoto-shi, 601-1495, Japan
| | - Tomohiro Yamaguchi
- General Internal Medicine, Ijinkai Takeda General Hospital, 28-1 Moriminami-cho, Ishida, Fushimi-ku, Kyoto-shi, 601-1495, Japan
| | - Kazuo Ootsuka
- Digestive Surgery, Ijinkai Takeda General Hospital, 28-1 Moriminami-cho, Ishida, Fushimi-ku, Kyoto-shi, 601-1495, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Mitsuo Kishimoto
- Department of Pathology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Yoshito Itoh
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho Hirokoji Kawaramachi Kamigyo-ku, Kyoto, 602-8566, Japan
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20
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Kito Y, Kawashima K, Saigo C, Hasegawa M, Nomura S, Mikamo T, Hanamatsu Y, Matsuo Y, Takeuchi T. Thorahcic SMARCA4-deficient undifferentiated tumors with ganglioneuroma and enchondroma: implications for SLC7A11 and ARID1A expression: a case report. Diagn Pathol 2022; 17:29. [PMID: 35151345 PMCID: PMC8840641 DOI: 10.1186/s13000-022-01205-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Background SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4-deficient thoracic sarcoma (SMARCA4-DTS) is a rare disease that has recently been described as an entity. It is characterized by an aggressive clinical course and specific genetic alterations. As an immunohistological feature, the tumors are deficient in SMARCA4 and SMARCA2 and express sex-determining region Y (SRY)-box 2 (SOX2). Occasionally, there are cases that are less frequent and difficult to distinguish from SMARCA4-deficient non-small cell lung carcinoma (SMARCA4-dNSCLC). Therefore, the 5th edition of the World Health Organization (WHO) classification describes thoracic SMARCA 4-deficient undifferentiated tumors (SMARCA4-UT). In contrast, Carney’s triad is a syndrome that combines three rare soft tissue tumors: gastric leiomyosarcoma, pulmonary chondroma, and extra-adrenal paraganglioma. Protein kinase cAMP-dependent type I regulatory subunit alpha (PRKAR1A) has been proposed as the causative gene. Both diseases are valuable cases; moreover, there have been no previous reports of their coexistence. Case presentation A 43-year-old man visited our hospital because of respiratory distress. Computed tomography revealed a large mass measuring 55 mm in the upper lobe of the right lung and front mediastinum, with metastases in the surrounding lymph nodes. Needle biopsy was performed for diagnosis, and histological examination of the samples revealed monotonous epithelioid-like cells with loose binding and sheet-form proliferation. The tumor cells had distinct nuclei with some rhabdoid-like cells. Immunohistochemical analysis revealed that the tumor cells were positive for AE1AE3, SOX2, CD34, and p53 and negative for SMARCA4 and SMARCA2. The patient died 6 months after admission, without any treatment. Autopsy revealed ganglioneuroma and enchondroma suggestive of an incomplete Carney complex. Conclusion SMARCA4-UT is a rare and recently established disease. While it is difficult to diagnose, it is necessary to distinguish undifferentiated carcinoma, large cell carcinoma, Ewing sarcoma, and epithelioid sarcoma when diagnosing tumors involving the mediastinum. Moreover, cases of SMARCA4-UT with ganglioneuroma and enchondroma are very rare. We discuss and report a case of SMARCA4-UT in which we also examined ARID1A and SLC7A11expression.
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Differential requirements for different subfamilies of the mammalian SWI/SNF chromatin remodeling enzymes in myoblast cell cycle progression and expression of the Pax7 regulator. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194801. [PMID: 35217218 PMCID: PMC8948540 DOI: 10.1016/j.bbagrm.2022.194801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/29/2022] [Accepted: 02/14/2022] [Indexed: 11/21/2022]
Abstract
The mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) families of ATP-dependent chromatin remodeling enzymes are established co-regulators of gene expression. mSWI/SNF complexes can be assembled into three major subfamilies: BAF (BRG1 or BRM-Associated Factor), PBAF (Polybromo containing BAF), or ncBAF (non-canonical BAF) that are distinguished by the presence of mutually exclusive subunits. The mechanisms by which each subfamily contributes to the establishment or function of specific cell lineages are poorly understood. Here, we determined the contributions of the BAF, ncBAF, and PBAF complexes to myoblast proliferation via knock down (KD) of distinguishing subunits from each complex. KD of subunits unique to the BAF or the ncBAF complexes reduced myoblast proliferation rate, while KD of PBAF-specific subunits did not affect proliferation. RNA-seq from proliferating KD myoblasts targeting Baf250A (BAF complex), Brd9 (ncBAF complex), or Baf180 (PBAF complex) showed mis-regulation of a limited number of genes. KD of Baf250A specifically reduced the expression of Pax7, which is required for myoblast proliferation, concomitant with decreased binding of Baf250A to and impaired chromatin remodeling at the Pax7 gene promoter. Although Brd9 also bound to the Pax7 promoter, suggesting occupancy by the ncBAF complex, no changes were detected in Pax7 gene expression, Pax7 protein expression or chromatin remodeling at the Pax7 promoter upon Brd9 KD. The data indicate that the BAF subfamily of the mSWI/SNF enzymes is specifically required for myoblast proliferation via regulation of Pax7 expression.
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22
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Chang CY, Shipony Z, Lin SG, Kuo A, Xiong X, Loh KM, Greenleaf WJ, Crabtree GR. Increased ACTL6A occupancy within mSWI/SNF chromatin remodelers drives human squamous cell carcinoma. Mol Cell 2021; 81:4964-4978.e8. [PMID: 34687603 PMCID: PMC8761479 DOI: 10.1016/j.molcel.2021.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodelers play dosage-sensitive roles in many human malignancies and neurologic disorders. The gene encoding the BAF subunit actin-like 6a (ACTL6A) is amplified early in the development of many squamous cell carcinomas (SCCs), but its oncogenic role remains unclear. Here we demonstrate that ACTL6A overexpression leads to its stoichiometric assembly into BAF complexes and drives their interaction and engagement with specific regulatory regions in the genome. In normal epithelial cells, ACTL6A was substoichiometric to other BAF subunits. However, increased ACTL6A levels by ectopic expression or in SCC cells led to near saturation of ACTL6A within BAF complexes. Increased ACTL6A occupancy enhanced polycomb opposition genome-wide to activate SCC genes and facilitated the co-dependent loading of BAF and TEAD-YAP complexes on chromatin. Both mechanisms appeared to be critical and function as a molecular AND gate for SCC initiation and maintenance, thereby explaining the specificity of the role of ACTL6A amplification in SCCs.
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Affiliation(s)
- Chiung-Ying Chang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zohar Shipony
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sherry G Lin
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ann Kuo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle M Loh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Gerald R Crabtree
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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23
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Wang X, Wang Y, Fang Z, Wang H, Zhang J, Zhang L, Huang H, Jiang Z, Jin Y, Han X, Hou S, Zhou B, Meng F, Chen L, Wong KK, Liu J, Zhang Z, Zhang X, Chen H, Sun Y, Hu L, Ji H. Targeting HSPA1A in ARID2-deficient lung adenocarcinoma. Natl Sci Rev 2021; 8:nwab014. [PMID: 34858604 PMCID: PMC8566174 DOI: 10.1093/nsr/nwab014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/23/2020] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Somatic mutations of the chromatin remodeling gene ARID2 are observed in ∼7% of human lung adenocarcinomas (LUADs). However, the role of ARID2 in the pathogenesis of LUADs remains largely unknown. Here we find that ARID2 expression is decreased during the malignant progression of both human and mice LUADs. Using two KrasG12D-based genetically engineered murine models, we demonstrate that ARID2 knockout significantly promotes lung cancer malignant progression and shortens overall survival. Consistently, ARID2 knockdown significantly promotes cell proliferation in human and mice lung cancer cells. Through integrative analyses of ChIP-Seq and RNA-Seq data, we find that Hspa1a is up-regulated by Arid2 loss. Knockdown of Hspa1a specifically inhibits malignant progression of Arid2-deficient but not Arid2-wt lung cancers in both cell lines as well as animal models. Treatment with an HSPA1A inhibitor could significantly inhibit the malignant progression of lung cancer with ARID2 deficiency. Together, our findings establish ARID2 as an important tumor suppressor in LUADs with novel mechanistic insights, and further identify HSPA1A as a potential therapeutic target in ARID2-deficient LUADs.
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuetong Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhaoyuan Fang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hua Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Longfu Zhang
- Department of Pulmonary Medicine, ZhongShan Hospital, Fudan University, Shanghai 200032, China
| | - Hsinyi Huang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhonglin Jiang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yujuan Jin
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiangkun Han
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shenda Hou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Feilong Meng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jinfeng Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Zhiqi Zhang
- Shanghai University of Medicine and Health Sciences, Shanghai Sixth People's Hospital East Campus, Shanghai 201306, China
| | - Xin Zhang
- Department of Pulmonary Medicine, ZhongShan Hospital, Fudan University, Shanghai 200032, China
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Liang Hu
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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Li J, Xu J, Jiang H, Zhang T, Ramakrishnan A, Shen L, Xu PX. Chromatin Remodelers Interact with Eya1 and Six2 to Target Enhancers to Control Nephron Progenitor Cell Maintenance. J Am Soc Nephrol 2021; 32:2815-2833. [PMID: 34716243 PMCID: PMC8806105 DOI: 10.1681/asn.2021040525] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/26/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Eya1 is a critical regulator of nephron progenitor cell specification and interacts with Six2 to promote NPC self-renewal. Haploinsufficiency of these genes causes kidney hypoplasia. However, how the Eya1-centered network operates remains unknown. METHODS We engineered a 2×HA-3×Flag-Eya1 knock-in mouse line and performed coimmunoprecipitation with anti-HA or -Flag to precipitate the multitagged-Eya1 and its associated proteins. Loss-of-function, transcriptome profiling, and genome-wide binding analyses for Eya1's interacting chromatin-remodeling ATPase Brg1 were carried out. We assayed the activity of the cis-regulatory elements co-occupied by Brg1/Six2 in vivo. RESULTS Eya1 and Six2 interact with the Brg1-based SWI/SNF complex during kidney development. Knockout of Brg1 results in failure of metanephric mesenchyme formation and depletion of nephron progenitors, which has been linked to loss of Eya1 expression. Transcriptional profiling shows conspicuous downregulation of important regulators for nephrogenesis in Brg1-deficient cells, including Lin28, Pbx1, and Dchs1-Fat4 signaling, but upregulation of podocyte lineage, oncogenic, and cell death-inducing genes, many of which Brg1 targets. Genome-wide binding analysis identifies Brg1 occupancy to a distal enhancer of Eya1 that drives nephron progenitor-specific expression. We demonstrate that Brg1 enrichment to two distal intronic enhancers of Pbx1 and a proximal promoter region of Mycn requires Six2 activity and that these Brg1/Six2-bound enhancers govern nephron progenitor-specific expression in response to Six2 activity. CONCLUSIONS Our results reveal an essential role for Brg1, its downstream pathways, and its interaction with Eya1-Six2 in mediating the fine balance among the self-renewal, differentiation, and survival of nephron progenitors.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huihui Jiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aarthi Ramakrishnan
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Li Shen
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York
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25
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Kumar S. SWI/SNF (BAF) complexes: From framework to a functional role in endothelial mechanotransduction. CURRENT TOPICS IN MEMBRANES 2021; 87:171-198. [PMID: 34696885 DOI: 10.1016/bs.ctm.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Endothelial cells (ECs) are constantly subjected to an array of mechanical cues, especially shear stress, due to their luminal placement in the blood vessels. Blood flow can regulate various aspects of endothelial biology and pathophysiology by regulating the endothelial processes at the transcriptomic, proteomic, miRNomic, metabolomics, and epigenomic levels. ECs sense, respond, and adapt to altered blood flow patterns and shear profiles by specialized mechanisms of mechanosensing and mechanotransduction, resulting in qualitative and quantitative differences in their gene expression. Chromatin-regulatory proteins can regulate transcriptional activation by modifying the organization of nucleosomes at promoters, enhancers, silencers, insulators, and locus control regions. Recent research efforts have illustrated that SWI/SNF (SWItch/Sucrose Non-Fermentable) or BRG1/BRM-associated factor (BAF) complex regulates DNA accessibility and chromatin structure. Since the discovery, the gene-regulatory mechanisms of the BAF complex associated with chromatin remodeling have been intensively studied to investigate its role in diverse disease phenotypes. Thus far, it is evident that (1) the SWI/SNF complex broadly regulates the activity of transcriptional enhancers to control lineage-specific differentiation and (2) mutations in the BAF complex proteins lead to developmental disorders and cancers. It is unclear if blood flow can modulate the activity of SWI/SNF complex to regulate EC differentiation and reprogramming. This review emphasizes the integrative role of SWI/SNF complex from a structural and functional standpoint with a special reference to cardiovascular diseases (CVDs). The review also highlights how regulation of this complex by blood flow can lead to the discovery of new therapeutic interventions for the treatment of endothelial dysfunction in vascular diseases.
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Affiliation(s)
- Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Institute of Technology, Atlanta, GA, United States.
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26
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Li J, Ouyang T, Li M, Hong T, Alriashy M, Meng W, Zhang N. CBX7 is Dualistic in Cancer Progression Based on its Function and Molecular Interactions. Front Genet 2021; 12:740794. [PMID: 34659360 PMCID: PMC8517511 DOI: 10.3389/fgene.2021.740794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
Chromobox protein homolog 7 (CBX7) is a member of the Chromobox protein family and participates in the formation of the polycomb repressive complex 1(PRC1). In cells, CBX7 often acts as an epigenetic regulator to regulate gene expression. However, pathologically, abnormal expression of CBX7 can lead to an imbalance of gene expression, which is closely related to the occurrence and progression of cancers. In cancers, CBX7 plays a dual role; On the one hand, it contributes to cancer progression in some cancers by inhibiting oncosuppressor genes. On the other hand, it suppresses cancer progression by interacting with different molecules to regulate the synthesis of cell cycle-related proteins. In addition, CBX7 protein may interact with different RNAs (microRNAs, long noncoding RNAs, circular RNAs) in different cancer environments to participate in a variety of pathways, affecting the development of cancers. Furthermore, CBX7 is involved in cancer-related immune response and DNA repair. In conclusion, CBX7 expression is a key factor in the occurrence and progression of cancers.
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Affiliation(s)
- Jun Li
- Department of the Second Clinical Medical College of Nanchang University, Jiangxi Province, China
| | - Taohui Ouyang
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Meihua Li
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Tao Hong
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Mhs Alriashy
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Wei Meng
- Department of Neurosurgery, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
| | - Na Zhang
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Jiangxi Province, China
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Mullen J, Kato S, Sicklick JK, Kurzrock R. Targeting ARID1A mutations in cancer. Cancer Treat Rev 2021; 100:102287. [PMID: 34619527 DOI: 10.1016/j.ctrv.2021.102287] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/22/2022]
Abstract
Genes encoding SWI/SNF chromatin remodeling complex subunits are collectively mutated in approximately 20% of human cancers. ARID1A is a SWI/SNF subunit gene whose protein product binds DNA. ARID1A gene alterations result in loss of function. It is the most commonly mutated member of the SWI/SNF complex, being aberrant in ∼6% of cancers overall, including ovarian clear cell cancers (∼45% of patients) and uterine endometrioid cancers (∼37%). ARID1A has a crucial role in regulating gene expression that drives oncogenesis or tumor suppression. In particular, ARID1A participates in control of the PI3K/AKT/mTOR pathway, immune responsiveness to cancer, EZH2 methyltransferase activity, steroid receptor modulation, DNA damage checkpoints, and regulation of p53 targets and KRAS signaling. A variety of compounds may be of benefit in ARID1A-altered cancers: immune checkpoint blockade, and inhibitors of mTOR, EZH2, histone deacetylases, ATR and/or PARP. ARID1A alterations may also mediate resistance to platinum chemotherapy and estrogen receptor degraders/modulators.
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Affiliation(s)
- Jaren Mullen
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Jason K Sicklick
- Center for Personalized Cancer Therapy, UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, USA; Department of Surgery, Division of Surgical Oncology, UC San Diego School of Medicine, San Diego, CA, USA
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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29
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D'Souza L, Channakkar AS, Muralidharan B. Chromatin remodelling complexes in cerebral cortex development and neurodevelopmental disorders. Neurochem Int 2021; 147:105055. [PMID: 33964373 PMCID: PMC7611358 DOI: 10.1016/j.neuint.2021.105055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/11/2021] [Accepted: 04/24/2021] [Indexed: 12/19/2022]
Abstract
The diverse number of neurons in the cerebral cortex are generated during development by neural stem cells lining the ventricle, and they continue maturing postnatally. Dynamic chromatin regulation in these neural stem cells is a fundamental determinant of the emerging property of the functional neural network, and the chromatin remodellers are critical determinants of this process. Chromatin remodellers participate in several steps of this process from proliferation, differentiation, migration leading to complex network formation which forms the basis of higher-order functions of cognition and behaviour. Here we review the role of these ATP-dependent chromatin remodellers in cortical development in health and disease and highlight several key mouse mutants of the subunits of the complexes which have revealed how the remodelling mechanisms control the cortical stem cell chromatin landscape for expression of stage-specific transcripts. Consistent with their role in cortical development, several putative risk variants in the subunits of the remodelling complexes have been identified as the underlying causes of several neurodevelopmental disorders. A basic understanding of the detailed molecular mechanism of their action is key to understating how mutations in the same networks lead to disease pathologies and perhaps pave the way for therapeutic development for these complex multifactorial disorders.
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Affiliation(s)
- Leora D'Souza
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Asha S Channakkar
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India
| | - Bhavana Muralidharan
- Brain Development and Disease Mechanisms, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore Life Science Cluster, Bangalore, India.
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30
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Lo YH, Kolahi KS, Du Y, Chang CY, Krokhotin A, Nair A, Sobba WD, Karlsson K, Jones SJ, Longacre TA, Mah AT, Tercan B, Sockell A, Xu H, Seoane JA, Chen J, Shmulevich I, Weissman JS, Curtis C, Califano A, Fu H, Crabtree GR, Kuo CJ. A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation. Cancer Discov 2021; 11:1562-1581. [PMID: 33451982 PMCID: PMC8346515 DOI: 10.1158/2159-8290.cd-20-1109] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/02/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022]
Abstract
Mutations in ARID1A rank among the most common molecular aberrations in human cancer. However, oncogenic consequences of ARID1A mutation in human cells remain poorly defined due to lack of forward genetic models. Here, CRISPR/Cas9-mediated ARID1A knockout (KO) in primary TP53-/- human gastric organoids induced morphologic dysplasia, tumorigenicity, and mucinous differentiation. Genetic WNT/β-catenin activation rescued mucinous differentiation, but not hyperproliferation, suggesting alternative pathways of ARID1A KO-mediated transformation. ARID1A mutation induced transcriptional regulatory modules characteristic of microsatellite instability and Epstein-Barr virus-associated subtype human gastric cancer, including FOXM1-associated mitotic genes and BIRC5/survivin. Convergently, high-throughput compound screening indicated selective vulnerability of ARID1A-deficient organoids to inhibition of BIRC5/survivin, functionally implicating this pathway as an essential mediator of ARID1A KO-dependent early-stage gastric tumorigenesis. Overall, we define distinct pathways downstream of oncogenic ARID1A mutation, with nonessential WNT-inhibited mucinous differentiation in parallel with essential transcriptional FOXM1/BIRC5-stimulated proliferation, illustrating the general utility of organoid-based forward genetic cancer analysis in human cells. SIGNIFICANCE: We establish the first human forward genetic modeling of a commonly mutated tumor suppressor gene, ARID1A. Our study integrates diverse modalities including CRISPR/Cas9 genome editing, organoid culture, systems biology, and small-molecule screening to derive novel insights into early transformation mechanisms of ARID1A-deficient gastric cancers.See related commentary by Zafra and Dow, p. 1327.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Yuan-Hung Lo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
| | - Kevin S Kolahi
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia
| | - Chiung-Ying Chang
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Andrey Krokhotin
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
| | - Ajay Nair
- Department of Systems Biology, Columbia University, New York, New York
| | - Walter D Sobba
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
| | - Kasper Karlsson
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Sunny J Jones
- Department of Systems Biology, Columbia University, New York, New York
| | - Teri A Longacre
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Amanda T Mah
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
| | - Bahar Tercan
- Institute for Systems Biology, Seattle, Washington
| | - Alexandra Sockell
- Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Hang Xu
- Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Jose A Seoane
- Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Jin Chen
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Jonathan S Weissman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
| | - Christina Curtis
- Division of Oncology, Stanford University School of Medicine, Stanford, California
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, New York
| | - Haian Fu
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California.
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31
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Chromatin phosphoproteomics unravels a function for AT-hook motif nuclear localized protein AHL13 in PAMP-triggered immunity. Proc Natl Acad Sci U S A 2021; 118:2004670118. [PMID: 33419940 DOI: 10.1073/pnas.2004670118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In many eukaryotic systems during immune responses, mitogen-activated protein kinases (MAPKs) link cytoplasmic signaling to chromatin events by targeting transcription factors, chromatin remodeling complexes, and the RNA polymerase machinery. So far, knowledge on these events is scarce in plants and no attempts have been made to focus on phosphorylation events of chromatin-associated proteins. Here we carried out chromatin phosphoproteomics upon elicitor-induced activation of Arabidopsis The events in WT were compared with those in mpk3, mpk4, and mpk6 mutant plants to decipher specific MAPK targets. Our study highlights distinct signaling networks involving MPK3, MPK4, and MPK6 in chromatin organization and modification, as well as in RNA transcription and processing. Among the chromatin targets, we characterized the AT-hook motif containing nuclear localized (AHL) DNA-binding protein AHL13 as a substrate of immune MAPKs. AHL13 knockout mutant plants are compromised in pathogen-associated molecular pattern (PAMP)-induced reactive oxygen species production, expression of defense genes, and PAMP-triggered immunity. Transcriptome analysis revealed that AHL13 regulates key factors of jasmonic acid biosynthesis and signaling and affects immunity toward Pseudomonas syringae and Botrytis cinerea pathogens. Mutational analysis of the phosphorylation sites of AHL13 demonstrated that phosphorylation regulates AHL13 protein stability and thereby its immune functions.
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32
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Yang QQ, Zhai YQ, Wang HF, Cai YC, Ma XY, Yin YQ, Li YD, Zhou GM, Zhang X, Hu G, Zhou JW. Nuclear isoform of FGF13 regulates post-natal neurogenesis in the hippocampus through an epigenomic mechanism. Cell Rep 2021; 35:109127. [PMID: 34010636 DOI: 10.1016/j.celrep.2021.109127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 02/13/2021] [Accepted: 04/22/2021] [Indexed: 10/21/2022] Open
Abstract
The hippocampus is one of two niches in the mammalian brain with persistent neurogenesis into adulthood. The neurogenic capacity of hippocampal neural stem cells (NSCs) declines with age, but the molecular mechanisms of this process remain unknown. In this study, we find that fibroblast growth factor 13 (FGF13) is essential for the post-natal neurogenesis in mouse hippocampus, and FGF13 deficiency impairs learning and memory. In particular, we find that FGF13A, the nuclear isoform of FGF13, is involved in the maintenance of NSCs and the suppression of neuronal differentiation during post-natal hippocampal development. Furthermore, we find that FGF13A interacts with ARID1B, a unit of Brahma-associated factor chromatin remodeling complex, and suppresses the expression of neuron differentiation-associated genes through chromatin modification. Our results suggest that FGF13A is an important regulator for maintaining the self-renewal and neurogenic capacity of NSCs in post-natal hippocampus, revealing an epigenomic regulatory function of FGFs in neurogenesis.
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Affiliation(s)
- Qiao-Qiao Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ying-Qi Zhai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hai-Fang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Chen Cai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Yue Ma
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yan-Qing Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan-Dong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Min Zhou
- Department of Anatomy, Histology and Embryology, Shanghai Medical School of Fudan University, Shanghai 200032, China
| | - Xu Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 210029, China; Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China.
| | - Jia-Wei Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China; Co-innovation Center of Neuroregeneration, School of Medicine, Nantong University, Nantong, Jiangsu 226001, China.
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33
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Mou PK, Yang EJ, Shi C, Ren G, Tao S, Shim JS. Aurora kinase A, a synthetic lethal target for precision cancer medicine. Exp Mol Med 2021; 53:835-847. [PMID: 34050264 PMCID: PMC8178373 DOI: 10.1038/s12276-021-00635-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/01/2023] Open
Abstract
Recent advances in high-throughput sequencing technologies and data science have facilitated the development of precision medicine to treat cancer patients. Synthetic lethality is one of the core methodologies employed in precision cancer medicine. Synthetic lethality describes the phenomenon of the interplay between two genes in which deficiency of a single gene does not abolish cell viability but combined deficiency of two genes leads to cell death. In cancer treatment, synthetic lethality is leveraged to exploit the dependency of cancer cells on a pathway that is essential for cell survival when a tumor suppressor is mutated. This approach enables pharmacological targeting of mutant tumor suppressors that are theoretically undruggable. Successful clinical introduction of BRCA-PARP synthetic lethality in cancer treatment led to additional discoveries of novel synthetic lethal partners of other tumor suppressors, including p53, PTEN, and RB1, using high-throughput screening. Recent work has highlighted aurora kinase A (AURKA) as a synthetic lethal partner of multiple tumor suppressors. AURKA is a serine/threonine kinase involved in a number of central biological processes, such as the G2/M transition, mitotic spindle assembly, and DNA replication. This review introduces synthetic lethal interactions between AURKA and its tumor suppressor partners and discusses the potential of AURKA inhibitors in precision cancer medicine.
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Affiliation(s)
- Pui Kei Mou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Eun Ju Yang
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Changxiang Shi
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Guowen Ren
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Shishi Tao
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Joong Sup Shim
- Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China.
- MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau SAR, China.
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34
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Yan S, Lu J, Jiao K. Epigenetic Regulation of Cardiac Neural Crest Cells. Front Cell Dev Biol 2021; 9:678954. [PMID: 33968946 PMCID: PMC8097001 DOI: 10.3389/fcell.2021.678954] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 01/02/2023] Open
Abstract
The cardiac neural crest cells (cNCCs) is a transient, migratory cell population that contribute to the formation of major arteries and the septa and valves of the heart. Abnormal development of cNCCs leads to a spectrum of congenital heart defects that mainly affect the outflow region of the hearts. Signaling molecules and transcription factors are the best studied regulatory events controlling cNCC development. In recent years, however, accumulated evidence supports that epigenetic regulation also plays an important role in cNCC development. Here, we summarize the functions of epigenetic regulators during cNCC development as well as cNCC related cardiovascular defects. These factors include ATP-dependent chromatin remodeling factors, histone modifiers and DNA methylation modulators. In many cases, mutations in the genes encoding these factors are known to cause inborn heart diseases. A better understanding of epigenetic regulators, their activities and their roles during heart development will ultimately contribute to the development of new clinical applications for patients with congenital heart disease.
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Affiliation(s)
| | | | - Kai Jiao
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, United States
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35
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Pipkin ME. Runx proteins and transcriptional mechanisms that govern memory CD8 T cell development. Immunol Rev 2021; 300:100-124. [PMID: 33682165 DOI: 10.1111/imr.12954] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
Adaptive immunity to intracellular pathogens and tumors is mediated by antigen-experienced CD8 T cells. Individual naive CD8 T cells have the potential to differentiate into a diverse array of antigen-experienced subsets that exhibit distinct effector functions, life spans, anatomic positioning, and potential for regenerating an entirely new immune response during iterative pathogenic exposures. The developmental process by which activated naive cells undergo diversification involves regulation of chromatin structure and transcription but is not entirely understood. This review examines how alterations in chromatin structure, transcription factor binding, extracellular signals, and single-cell gene expression explain the differential development of distinct effector (TEFF ) and memory (TMEM ) CD8 T cell subsets. Special emphasis is placed on how Runx proteins function with additional transcription factors to pioneer changes in chromatin accessibility and drive transcriptional programs that establish the core attributes of cytotoxic T lymphocytes, subdivide circulating and non-circulating TMEM cell subsets, and govern terminal differentiation. The discussion integrates the roles of specific cytokine signals, transcriptional circuits and how regulation of individual nucleosomes and RNA polymerase II activity can contribute to the process of differentiation. A model that integrates many of these features is discussed to conceptualize how activated CD8 T cells arrive at their fates.
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Affiliation(s)
- Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute - FL, Jupiter, FL, USA
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36
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Braun SMG, Petrova R, Tang J, Krokhotin A, Miller EL, Tang Y, Panagiotakos G, Crabtree GR. BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex. Genes Dev 2021; 35:335-353. [PMID: 33602870 PMCID: PMC7919417 DOI: 10.1101/gad.342345.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/08/2021] [Indexed: 12/28/2022]
Abstract
mSWI/SNF or BAF chromatin regulatory complexes are dosage-sensitive regulators of human neural development frequently mutated in autism spectrum disorders and intellectual disability. Cell cycle exit and differentiation of neural stem/progenitor cells is accompanied by BAF subunit switching to generate neuron-specific nBAF complexes. We manipulated the timing of BAF subunit exchange in vivo and found that early loss of the npBAF subunit BAF53a stalls the cell cycle to disrupt neurogenesis. Loss of BAF53a results in decreased chromatin accessibility at specific neural transcription factor binding sites, including the pioneer factors SOX2 and ASCL1, due to Polycomb accumulation. This results in repression of cell cycle genes, thereby blocking cell cycle progression and differentiation. Cell cycle block upon Baf53a deletion could be rescued by premature expression of the nBAF subunit BAF53b but not by other major drivers of proliferation or differentiation. WNT, EGF, bFGF, SOX2, c-MYC, or PAX6 all fail to maintain proliferation in the absence of BAF53a, highlighting a novel mechanism underlying neural progenitor cell cycle exit in the continued presence of extrinsic proliferative cues.
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Affiliation(s)
- Simon M G Braun
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Ralitsa Petrova
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jiong Tang
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
- Singapore Bioimaging Consortium, Agency for Science Technology and Research (A*STAR), Singapore 138667, Singapore
| | - Andrey Krokhotin
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
| | - Erik L Miller
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
| | - Yitai Tang
- Department of Pathology, Stanford University, California 94305, USA
| | - Georgia Panagiotakos
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California at San Francisco, San Francisco, California 94143, USA
| | - Gerald R Crabtree
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
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37
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Lupo BE, Chu P, Harms MJ, Morrison EA, Musselman CA. Evolutionary Conservation of Structural and Functional Coupling between the BRM AT-Hook and Bromodomain. J Mol Biol 2021; 433:166845. [PMID: 33539881 PMCID: PMC8184587 DOI: 10.1016/j.jmb.2021.166845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/13/2023]
Abstract
The BAF chromatin remodeling complex is critical for genome regulation. The central ATPase of BAF is either BRM or BRG1, both of which contain a C-terminal bromodomain, known to associate with acetylated lysines. We have recently demonstrated that in addition to acetyl-lysine binding, the BRG1/BRM bromodomain can associate with DNA through a lysine/arginine rich patch that is adjacent to the acetyl-lysine binding pocket. Flanking the bromodomain is an AT-hook separated by a short, proline-rich linker. We previously found that the AT-hook and bromodomain can associate with DNA in a multivalent manner. Here, we investigate the conservation of this composite module and find that the AT-hook, linker, and lysine/arginine rich bromodomain patch are ancient, conserved over ~1 billion years. We utilize extensive mutagenesis, NMR spectroscopy, and fluorescence anisotropy to dissect the contribution of each of these conserved elements in association of this module with DNA. Our results reveal a structural and functional coupling of the AT-hook and bromodomain mediated by the linker. The lysine/arginine rich patch on the bromodomain and the conserved elements of the AT-hook are critical for robust affinity for DNA, while the conserved elements of the linker are dispensable for overall DNA affinity but critical for maintaining the relative conformation of the AT-hook and bromodomain in binding to DNA. This supports that the coupled action of the AT-hook and bromodomain are important for BAF activity.
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Affiliation(s)
- Brianna E Lupo
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States
| | - Peirou Chu
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States
| | - Michael J Harms
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, United States; Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, United States
| | - Emma A Morrison
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States; Medical College of Wisconsin, Department of Biochemistry, Milwaukee, WI 53226, United States.
| | - Catherine A Musselman
- University of Iowa, Carver College of Medicine, Department of Biochemistry, Iowa City, IA 52242, United States; University of Colorado Anschutz Medical Campus, Department of Biochemistry and Molecular Genetics, Aurora, CO 80045, United States.
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38
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Tsuda M, Fukuda A, Kawai M, Araki O, Seno H. The role of the SWI/SNF chromatin remodeling complex in pancreatic ductal adenocarcinoma. Cancer Sci 2021; 112:490-497. [PMID: 33301642 PMCID: PMC7894000 DOI: 10.1111/cas.14768] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes are a group of epigenetic regulators that can alter the assembly of nucleosomes and regulate the accessibility of transcription factors to DNA in order to modulate gene expression. One of these complexes, the SWI/SNF chromatin remodeling complex is mutated in more than 20% of human cancers. We have investigated the roles of the SWI/SNF complex in pancreatic ductal adenocarcinoma (PDA), which is the most lethal type of cancer. Here, we reviewed the recent literature regarding the role of the SWI/SNF complex in pancreatic tumorigenesis and current knowledge about therapeutic strategies targeting the SWI/SNF complex in PDA. The subunits of the SWI/SNF complex are mutated in 14% of human PDA. Recent studies have shown that they have context-dependent oncogenic or tumor-suppressive roles in pancreatic carcinogenesis. To target its tumor-suppressive properties, synthetic lethal strategies have recently been developed. In addition, their oncogenic properties could be novel therapeutic targets. The SWI/SNF subunits are potential therapeutic targets for PDA, and further understanding of the precise role of the SWI/SNF complex subunits in PDA is required for further development of novel strategies targeting SWI/SNF subunits against PDA.
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Affiliation(s)
- Motoyuki Tsuda
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
- Department of Gastroenterology and HepatologyKindai University Faculty of MedicineOsaka‐sayama CityJapan
| | - Akihisa Fukuda
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Munenori Kawai
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Osamu Araki
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
| | - Hiroshi Seno
- Department of Gastroenterology and HepatologyKyoto University Graduate School of MedicineKyotoJapan
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Emerging role of SWI/SNF complex deficiency as a target of immune checkpoint blockade in human cancers. Oncogenesis 2021; 10:3. [PMID: 33419967 PMCID: PMC7794300 DOI: 10.1038/s41389-020-00296-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Mammalian SWI/SNF complex is a key chromatin remodeler that reshapes nucleosomes and regulates DNA accessibility. Mutations in SWI/SNF subunits are found in a broad spectrum of human cancers; however, the mechanisms of how these aberrations of SWI/SNF complex would impact tumorigenesis and cancer therapeutics remain to be elucidated. Studies have demonstrated that immune checkpoint blockade (ICB) therapy is promising in cancer treatment. Nevertheless, suitable biomarkers that reliably predict the clinical response to ICB are still lacking. Emerging evidence has suggested that SWI/SNF components play novel roles in the regulation of anti-tumor immunity, and SWI/SNF deficiency can be therapeutically targeted by ICB. These findings manifest the prominence of the SWI/SNF complex as a stratification biomarker that predicts treatment (therapeutic) response to ICB. In this review, we summarize the recent advances in ICB therapy by harnessing the cancer-specific vulnerability elicited by SWI/SNF deficiency. We provide novel insights into a comprehensive understanding of the underlying mechanisms by which SWI/SNF functions as a modulator of anti-tumor immunity.
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Zhu X, Liao Y, Tang L. Targeting BRD9 for Cancer Treatment: A New Strategy. Onco Targets Ther 2020; 13:13191-13200. [PMID: 33380808 PMCID: PMC7769155 DOI: 10.2147/ott.s286867] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/12/2020] [Indexed: 01/01/2023] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a newly identified subunit of the non-canonical barrier-to-autointegration factor (ncBAF) complex and a member of the bromodomain family IV. Studies have confirmed that BRD9 plays an oncogenic role in multiple cancer types, by regulating tumor cell growth. The tumor biological functions of BRD9 are mainly due to epigenetic modification mediated by its bromodomain. The bromodomain recruits the ncBAF complex to the promoter to regulate gene transcription. This review summarizes the potential mechanisms of action of BRD9 in carcinogenesis and the emerging strategies for targeting BRD9 for cancer therapeutics. Although the therapeutic potential of BRD9 has been exploited to some extent, research on the detailed biological mechanisms of BRD9 is still in its infancy. Therefore, targeting BRD9 to study its biological roles will be an attractive tool for cancer diagnosis and treatment, but it remains a great challenge.
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Affiliation(s)
- Xiuzuo Zhu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, People's Republic of China
| | - Yi Liao
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, People's Republic of China
| | - Liling Tang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, People's Republic of China
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41
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Rezinciuc S, Tian Z, Wu S, Hengel S, Pasa-Tolic L, Smallwood HS. Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells. Viruses 2020; 12:v12121409. [PMID: 33302437 PMCID: PMC7762524 DOI: 10.3390/v12121409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Zhixin Tian
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Si Wu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Shawna Hengel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Z.T.); (S.W.); (S.H.); (L.P.-T.)
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
- Children’s Foundation Research Institute, Memphis, TN 38105, USA
- Correspondence: ; Tel.: +1-(901)-448–3068
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Martin MC, Zeng G, Yu J, Schiltz GE. Small Molecule Approaches for Targeting the Polycomb Repressive Complex 2 (PRC2) in Cancer. J Med Chem 2020; 63:15344-15370. [PMID: 33283516 DOI: 10.1021/acs.jmedchem.0c01344] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The polycomb repressive complex 2 (PRC2) is composed of three core subunits, enhancer of zeste 2 (EZH2), embryonic ectoderm development (EED), and suppressor of zeste 12 (SUZ12), along with a number of accessory proteins. It is the key enzymatic protein complex that catalyzes histone H3 lysine 27 (H3K27) methylation to mediate epigenetic silencing of target genes. PRC2 thus plays essential roles in maintaining embryonic stem cell identity and in controlling cellular differentiation. Studies in the past decade have reported frequent overexpression or mutation of PRC2 in various cancers including prostate cancer and lymphoma. Aberrant PRC2 function has been extensively studied and proven to contribute to a large number of abnormal cellular processes, including those that lead to uncontrolled proliferation and tumorigenesis. Significant efforts have recently been made to develop small molecules targeting PRC2 function for potential use as anticancer therapeutics. In this review, we describe recent approaches to identify and develop small molecules that target PRC2. These various strategies include the inhibition of the function of individual PRC2 core proteins, the disruption of PRC2 complex formation, and the degradation of its subunits.
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Affiliation(s)
- M Cynthia Martin
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Guihua Zeng
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Jindan Yu
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Gary E Schiltz
- Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States.,Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
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Kinnaman MD, Hamill D, Yabe M, Powell J, Benhamida J, Hasselblatt M, Neumann M, Vokuhl C, Koelsche C, von Deimling A, Kolb EA, Solit DB, Ladanyi M, Dogan A, Shukla N. Aggressive Hematopoietic Malignancy Characterized by Biallelic Loss of SMARCB1. JCO Precis Oncol 2020; 4:2000215. [PMID: 33163846 DOI: 10.1200/po.20.00215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Michael D Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darcy Hamill
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mariko Yabe
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jonathan Powell
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamal Benhamida
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin Hasselblatt
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin Neumann
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christian Vokuhl
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christian Koelsche
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Edward Anders Kolb
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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Wu J, Krchma K, Lee HJ, Prabhakar S, Wang X, Zhao H, Xing X, Seong RH, Fremont DH, Artyomov MN, Wang T, Choi K. Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. Cell Rep 2020; 33:108395. [PMID: 33207205 PMCID: PMC7694876 DOI: 10.1016/j.celrep.2020.108395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/25/2020] [Accepted: 10/26/2020] [Indexed: 12/21/2022] Open
Abstract
The mammalian SWitch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling BAF (BRG1/BRM-associated factor) complex plays an essential role in developmental and pathological processes. We show that the deletion of Baf155, which encodes a subunit of the BAF complex, in the Tie2(+) lineage (Baf155 (CKO) leads to defects in yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs). The chromatin of myeloid gene loci in Baf155 CKO EMPs is mostly inaccessible and enriched mainly by the ETS binding motif. BAF155 interacts with PU.1 and is recruited to PU.1 target gene loci together with p300 and KDM6a. Treatment of Baf155 CKO embryos with GSK126, an H3K27me2/3 methyltransferase EZH2 inhibitor, rescues myeloid lineage gene expression. This study uncovers indispensable BAF-mediated chromatin remodeling of myeloid gene loci at the EMP stage. Future studies exploiting epigenetics in the generation and application of EMP derivatives for tissue repair, regeneration, and disease are warranted. The mammalian chromatin-remodeling BAF (BRG1/BRM-associated factor) complex has an essential role in developmental and pathological processes. Wu et al. show that BAF-mediated chromatin remodeling and activation of the myeloid and definitive erythroid transcriptional program at the EMP stage is critical for myeloid and definitive erythroid lineage development.
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Affiliation(s)
- Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sairam Prabhakar
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Haiyong Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rho H Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA; Graduate School of Biotechnology, Kyung Hee University, Yong In, Korea.
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Reske JJ, Wilson MR, Holladay J, Wegener M, Adams M, Chandler RL. SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. Hum Mol Genet 2020; 29:3412-3430. [PMID: 33075803 PMCID: PMC7749707 DOI: 10.1093/hmg/ddaa227] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/14/2022] Open
Abstract
Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
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Affiliation(s)
- Jake J Reske
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mike R Wilson
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeanne Holladay
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Marc Wegener
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Marie Adams
- Genomics Core Facility, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ronald L Chandler
- To whom correspondence should be addressed at: Grand Rapids Research Center, 400 Monroe NW, Grand Rapids, MI 49503, USA. Tel: +1 6162340980;
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Strejčková B, Čegan R, Pecinka A, Milec Z, Šafář J. Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat. BMC PLANT BIOLOGY 2020; 20:175. [PMID: 33050875 PMCID: PMC7557041 DOI: 10.1186/s12870-020-02384-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. RESULTS Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals. CONCLUSIONS The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.
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Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Radim Čegan
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200, Brno, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic.
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ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells. Stem Cells Int 2020; 2020:8839703. [PMID: 32963551 PMCID: PMC7499328 DOI: 10.1155/2020/8839703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.
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48
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Mathies LD, Lindsay JH, Handal AP, Blackwell GG, Davies AG, Bettinger JC. SWI/SNF complexes act through CBP-1 histone acetyltransferase to regulate acute functional tolerance to alcohol. BMC Genomics 2020; 21:646. [PMID: 32957927 PMCID: PMC7507291 DOI: 10.1186/s12864-020-07059-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/10/2020] [Indexed: 01/19/2023] Open
Abstract
Background SWI/SNF chromatin remodeling genes are required for normal acute responses to alcohol in C. elegans and are associated with alcohol use disorder in two human populations. In an effort to discover the downstream genes that are mediating this effect, we identified SWI/SNF-regulated genes in C. elegans. Results To identify SWI/SNF-regulated genes in adults, we compared mRNA expression in wild type and swsn-1(os22ts) worms under conditions that produce inactive swsn-1 in mature cells. To identify SWI/SNF-regulated genes in neurons, we compared gene expression in swsn-9(ok1354) null mutant worms that harbor a neuronal rescue or a control construct. RNA sequencing was performed to an average depth of 25 million reads per sample using 50-base, paired-end reads. We found that 6813 transcripts were significantly differentially expressed between swsn-1(os22ts) mutants and wild-type worms and 2412 transcripts were significantly differentially expressed between swsn-9(ok1354) mutants and swsn-9(ok1354) mutants with neuronal rescue. We examined the intersection between these two datasets and identified 603 genes that were differentially expressed in the same direction in both comparisons; we defined these as SWI/SNF-regulated genes in neurons and in adults. Among the differentially expressed genes was cbp-1, a C. elegans homolog of the mammalian CBP/p300 family of histone acetyltransferases. CBP has been implicated in the epigenetic regulation in response to alcohol in animal models and a polymorphism in the human CBP gene, CREBBP, has been associated with alcohol-related phenotypes. We found that cbp-1 is required for the development of acute functional tolerance to alcohol in C. elegans. Conclusions We identified 603 transcripts that were regulated by two different SWI/SNF complex subunits in adults and in neurons. The SWI/SNF-regulated genes were highly enriched for genes involved in membrane rafts, suggesting an important role for this membrane microdomain in the acute alcohol response. Among the differentially expressed genes was cbp-1; CBP-1 homologs have been implicated in alcohol responses across phyla and we found that C. elegans cbp-1 was required for the acute alcohol response in worms.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA.
| | - Jonathan H Lindsay
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Amal P Handal
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - GinaMari G Blackwell
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Andrew G Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA, 23298, USA
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Jungblut A, Hopfner KP, Eustermann S. Megadalton chromatin remodelers: common principles for versatile functions. Curr Opin Struct Biol 2020; 64:134-144. [PMID: 32771531 DOI: 10.1016/j.sbi.2020.06.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
ATP-dependent chromatin remodelers are enigmatic macromolecular machines that govern the arrangement and composition of nucleosomes across eukaryotic genomes. Here, we review the recent breakthrough provided by cryo-electron microscopy that reveal the first high-resolution insights into all four families of remodelers. We highlight the emerging structural and mechanistic principles with a particular focus on multi-subunit SWI/SNF and INO80/SWR1 complexes. A conserved architecture comprising a motor, rotor, stator and grip suggests a unifying mechanism for how stepwise DNA translocation enables large scale reconfigurations of nucleosomes. A molecular circuitry involving the nuclear actin containing module establishes a framework for understanding allosteric regulation. Remodelers emerge as programable hubs that enable differential processing of genetic and epigenetic information in response to the physiological state of a cell.
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Affiliation(s)
- Anna Jungblut
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany; Candidate for joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
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Sanchez JC, Zhang L, Evoli S, Schnicker NJ, Nunez-Hernandez M, Yu L, Wereszczynski J, Pufall MA, Musselman CA. The molecular basis of selective DNA binding by the BRG1 AT-hook and bromodomain. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194566. [PMID: 32376391 PMCID: PMC7350285 DOI: 10.1016/j.bbagrm.2020.194566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
The ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to investigate the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.
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Affiliation(s)
- Julio C Sanchez
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States; Integrated DNA Technologies IDT, Coralville, IA 52241, United States
| | - Stefania Evoli
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Nicholas J Schnicker
- Protein & Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Maria Nunez-Hernandez
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Liping Yu
- Department of Biochemistry, Carver College of Medicine NMR Core Facility, University of Iowa, Iowa City, IA 52242, United States; The Iowa City Veterans Affairs Medical Center, Iowa City, IA 52242, United States
| | - Jeff Wereszczynski
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States.
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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