1
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Bergwell M, Park J, Kirkland JG. Differential modulation of polycomb-associated histone marks by cBAF, pBAF, and gBAF complexes. Life Sci Alliance 2024; 7:e202402715. [PMID: 39209535 PMCID: PMC11361369 DOI: 10.26508/lsa.202402715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Chromatin regulators alter the physical properties of chromatin to make it more or less permissive to transcription by modulating another protein's access to a specific DNA sequence through changes in nucleosome occupancy or histone modifications at a particular locus. Mammalian SWI/SNF complexes are a group of ATPase-dependent chromatin remodelers. In mouse embryonic stem cells, there are three primary forms of mSWI/SNF: canonical BAF (cBAF), polybromo-associated BAF (pBAF), and GLTSCR-associated BAF (gBAF). Nkx2-9 is bivalent, meaning nucleosomes at the locus have active and repressive modifications. In this study, we used unique BAF subunits to recruit each of the three complexes to Nkx2-9 using dCas9-mediated inducible recruitment (FIRE-Cas9). We show that recruitment of cBAF complexes leads to a significant loss of the polycomb repressive-2 H3K27me3 histone mark and polycomb repressive-1 and repressive-2 complex proteins, whereas gBAF and pBAF do not. Moreover, nucleosome occupancy alone cannot explain the loss of these marks. Our results demonstrate that cBAF has a unique role in the direct opposition of polycomb-associated histone modifications that gBAF and pBAF do not share.
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Affiliation(s)
- Mary Bergwell
- https://ror.org/035z6xf33 Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - JinYoung Park
- https://ror.org/035z6xf33 Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Jacob G Kirkland
- https://ror.org/035z6xf33 Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
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2
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Manolakos P, Boccuto L, Ivankovic DS. A Critical Review of the Impact of SMARCA4 Mutations on Survival Outcomes in Non-Small Cell Lung Cancer. J Pers Med 2024; 14:684. [PMID: 39063938 PMCID: PMC11278206 DOI: 10.3390/jpm14070684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
This critical review investigates the impact of SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4) mutations on survival outcomes in non-small cell lung cancer (NSCLC) through an analysis of 21 peer-reviewed articles. Survival analyses across this review demonstrated consistently worse outcomes for SMARCA4-mutated vs. SMARCA4 wild-type NSCLC patients, specifically emphasizing class 1 truncating mutations as an independent factor for poor overall survival. In addition, this review explores the clinicopathologic characteristics of SMARCA4 mutations and their impact on various treatment modalities, including immune checkpoint inhibitors (ICIs) both with and without Kirsten rat sarcoma viral oncogene homolog (KRAS) co-mutations. The potential ineffectiveness of ICI treatment in NSCLC is explored through the impact of SMARCA4/KRAS co-mutations on the tumor microenvironment. Moreover, this NSCLC review consistently reported statistically worse overall survival outcomes for SMARCA4/KRAS co-mutations than SMARCA4 wild-type/KRAS-mutated cohorts, extending across ICIs, chemo-immunotherapy (CIT), and KRAS G12C inhibitors. Designing prospective clinical SMARCA4-mutated or SMARCA4/KRAS co-mutated NSCLC trials to evaluate targeted therapies and immunotherapy may lead to a better understanding of how to improve cancer patients' outcomes and survival rates.
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Affiliation(s)
- Peter Manolakos
- Healthcare Genetics and Genomics PhD Program, Clemson University, Clemson, SC 29634, USA; (L.B.); (D.S.I.)
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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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Innis SM, Cabot RA. Chromatin profiling and state predictions reveal insights into epigenetic regulation during early porcine development. Epigenetics Chromatin 2024; 17:16. [PMID: 38773546 PMCID: PMC11106951 DOI: 10.1186/s13072-024-00542-w] [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: 11/09/2023] [Accepted: 05/16/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Given their physiological similarities to humans, pigs are increasingly used as model organisms in human-oriented biomedical studies. Additionally, their value to animal agriculture across the globe has led to the development of numerous studies to investigate how to improve livestock welfare and production efficiency. As such, pigs are uniquely poised as compelling models that can yield findings with potential implications in both human and animal contexts. Despite this, many gaps remain in our knowledge about the foundational mechanisms that govern gene expression in swine across different developmental stages, particularly in early development. To address some of these gaps, we profiled the histone marks H3K4me3, H3K27ac, and H3K27me3 and the SWI/SNF central ATPase BRG1 in two porcine cell lines representing discrete early developmental time points and used the resulting information to construct predicted chromatin state maps for these cells. We combined this approach with analysis of publicly available RNA-seq data to examine the relationship between epigenetic status and gene expression in these cell types. RESULTS In porcine fetal fibroblast (PFF) and trophectoderm cells (PTr2), we saw expected patterns of enrichment for each of the profiled epigenetic features relative to specific genomic regions. H3K4me3 was primarily enriched at and around global gene promoters, H3K27ac was enriched in promoter and intergenic regions, H3K27me3 had broad stretches of enrichment across the genome and narrower enrichment patterns in and around the promoter regions of some genes, and BRG1 primarily had detectable enrichment at and around promoter regions and in intergenic stretches, with many instances of H3K27ac co-enrichment. We used this information to perform genome-wide chromatin state predictions for 10 different states using ChromHMM. Using the predicted chromatin state maps, we identified a subset of genomic regions marked by broad H3K4me3 enrichment, and annotation of these regions revealed that they were highly associated with essential developmental processes and consisted largely of expressed genes. We then compared the identities of the genes marked by these regions to genes identified as cell-type-specific using transcriptome data and saw that a subset of broad H3K4me3-marked genes was also specifically expressed in either PFF or PTr2 cells. CONCLUSIONS These findings enhance our understanding of the epigenetic landscape present in early swine development and provide insight into how variabilities in chromatin state are linked to cell identity. Furthermore, this data captures foundational epigenetic details in two valuable porcine cell lines and contributes to the growing body of knowledge surrounding the epigenetic landscape in this species.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Ryan A Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Gonzalez Pisfil M, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol 2024:10.1038/s41594-024-01290-x. [PMID: 38664566 DOI: 10.1038/s41594-024-01290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- ViraTherapeutics GmbH, Rum, Austria
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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Göbel C, Schoof M, Holdhof D, Spohn M, Schüller U. SMARCA4 Loss and Mutated β-Catenin Induce Proliferative Lesions in the Murine Embryonic Cerebellum. J Neurosci 2024; 44:e1605232024. [PMID: 38383496 PMCID: PMC11007475 DOI: 10.1523/jneurosci.1605-23.2024] [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: 08/24/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Almost all medulloblastomas (MB) of the Wingless/Int-1 (WNT) type are characterized by hotspot mutations in CTNNB1, and mouse models have convincingly demonstrated the tumor-initiating role of these mutations. Additional alterations in SMARCA4 are detected in ∼20% of WNT MB, but their functional role is mostly unknown. We, therefore, amended previously described brain lipid binding protein (Blbp)-cre::Ctnnb1(ex3)fl/wt mice by the introduction of floxed Smarca4 alleles. Unexpectedly, mutated and thereby stabilized β-catenin on its own induced severe developmental phenotypes in male and female Blbp-cre::Ctnnb1(ex3)fl/wt mice in our hands, including a thinned cerebral cortex, hydrocephalus, missing cerebellar layering, and cell accumulations in the brainstem and cerebellum. An additional loss of SMARCA4 even resulted in prenatal death for most mice. Respective Blbp-cre::Ctnnb1(ex3)fl/wt::Smarca4fl/rec mutants (male and female) developed large proliferative lesions in the cerebellum evolving from E13.5 to E16.5. Histological and molecular analysis of these lesions by DNA methylation profiling and single-cell RNA sequencing suggested an origin in early undifferentiated SOX2-positive cerebellar progenitors. Furthermore, upregulated WNT signaling, altered actin/cytoskeleton organization, and reduced neuronal differentiation were evident in mutant cells. In vitro, cells harboring alterations in both Ctnnb1 and Smarca4 were negatively selected and did not show tumorigenic potential after transplantation in adult female recipient mice. However, in cerebellar explant cultures, mutant cells displayed significantly increased proliferation, suggesting an important role of the embryonic microenvironment in the development of lesions. Altogether, these results represent an important first step toward the unraveling of tumorigenic mechanisms induced by aberrant WNT signaling and SMARCA4 deficiency.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
| | - Michael Spohn
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg D-20251, Germany
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7
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Cheng Y, Song Z, Fang X, Tang Z. Polycomb repressive complex 2 and its core component EZH2: potential targeted therapeutic strategies for head and neck squamous cell carcinoma. Clin Epigenetics 2024; 16:54. [PMID: 38600608 PMCID: PMC11007890 DOI: 10.1186/s13148-024-01666-2] [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: 12/15/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
The polycomb group (PcG) comprises a set of proteins that exert epigenetic regulatory effects and play crucial roles in diverse biological processes, ranging from pluripotency and development to carcinogenesis. Among these proteins, enhancer of zeste homolog 2 (EZH2) stands out as a catalytic component of polycomb repressive complex 2 (PRC2), which plays a role in regulating the expression of homologous (Hox) genes and initial stages of x chromosome inactivation. In numerous human cancers, including head and neck squamous cell carcinoma (HNSCC), EZH2 is frequently overexpressed or activated and has been identified as a negative prognostic factor. Notably, EZH2 emerges as a significant gene involved in regulating the STAT3/HOTAIR axis, influencing HNSCC proliferation, differentiation, and promoting metastasis by modulating related oncogenes in oral cancer. Currently, various small molecule compounds have been developed as inhibitors specifically targeting EZH2 and have gained approval for treating refractory tumors. In this review, we delve into the epigenetic regulation mediated by EZH2/PRC2 in HNSCC, with a specific focus on exploring the potential roles and mechanisms of EZH2, its crucial contribution to targeted drug therapy, and its association with cancer markers and epithelial-mesenchymal transition. Furthermore, we aim to unravel its potential as a therapeutic strategy for oral squamous cell carcinoma.
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Affiliation(s)
- Yuxi Cheng
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center of Oral Major Diseases and Oral Health & Academician, Central South University, Changsha, 410008, Hunan, China
| | - Zhengzheng Song
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China
- Clinical Research Center of Oral Major Diseases and Oral Health & Academician, Central South University, Changsha, 410008, Hunan, China
| | - Xiaodan Fang
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center of Oral Major Diseases and Oral Health & Academician, Central South University, Changsha, 410008, Hunan, China.
| | - Zhangui Tang
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, 410008, Hunan, China.
- Clinical Research Center of Oral Major Diseases and Oral Health & Academician, Central South University, Changsha, 410008, Hunan, China.
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Aoki K, Hyuga M, Tarumoto Y, Nishibuchi G, Ueda A, Ochi Y, Sugino S, Mikami T, Kobushi H, Kato I, Akahane K, Inukai T, Takaori-Kondo A, Takita J, Ogawa S, Yusa K. Canonical BAF complex regulates the oncogenic program in human T-cell acute lymphoblastic leukemia. Blood 2024; 143:604-618. [PMID: 37922452 DOI: 10.1182/blood.2023020857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Acute leukemia cells require bone marrow microenvironments, known as niches, which provide leukemic cells with niche factors that are essential for leukemic cell survival and/or proliferation. However, it remains unclear how the dynamics of the leukemic cell-niche interaction are regulated. Using a genome-wide CRISPR screen, we discovered that canonical BRG1/BRM-associated factor (cBAF), a variant of the switch/sucrose nonfermenting chromatin remodeling complex, regulates the migratory response of human T-cell acute lymphoblastic leukemia (T-ALL) cells to a niche factor CXCL12. Mechanistically, cBAF maintains chromatin accessibility and allows RUNX1 to bind to CXCR4 enhancer regions. cBAF inhibition evicts RUNX1 from the genome, resulting in CXCR4 downregulation and impaired migration activity. In addition, cBAF maintains chromatin accessibility preferentially at RUNX1 binding sites, ensuring RUNX1 binding at these sites, and is required for expression of RUNX1-regulated genes, such as CDK6; therefore, cBAF inhibition negatively impacts cell proliferation and profoundly induces apoptosis. This anticancer effect was also confirmed using T-ALL xenograft models, suggesting cBAF as a promising therapeutic target. Thus, we provide novel evidence that cBAF regulates the RUNX1-driven leukemic program and governs migration activity toward CXCL12 and cell-autonomous growth in human T-ALL.
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Affiliation(s)
- Kazunari Aoki
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mizuki Hyuga
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Tarumoto
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Gohei Nishibuchi
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Atsushi Ueda
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Seiichi Sugino
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takashi Mikami
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hirokazu Kobushi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Itaru Kato
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kosuke Yusa
- Stem Cell Genetics, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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9
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Dreier MR, Walia J, de la Serna IL. Targeting SWI/SNF Complexes in Cancer: Pharmacological Approaches and Implications. EPIGENOMES 2024; 8:7. [PMID: 38390898 PMCID: PMC10885108 DOI: 10.3390/epigenomes8010007] [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: 12/29/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
SWI/SNF enzymes are heterogeneous multi-subunit complexes that utilize the energy from ATP hydrolysis to remodel chromatin structure, facilitating transcription, DNA replication, and repair. In mammalian cells, distinct sub-complexes, including cBAF, ncBAF, and PBAF exhibit varying subunit compositions and have different genomic functions. Alterations in the SWI/SNF complex and sub-complex functions are a prominent feature in cancer, making them attractive targets for therapeutic intervention. Current strategies in cancer therapeutics involve the use of pharmacological agents designed to bind and disrupt the activity of SWI/SNF complexes or specific sub-complexes. Inhibitors targeting the catalytic subunits, SMARCA4/2, and small molecules binding SWI/SNF bromodomains are the primary approaches for suppressing SWI/SNF function. Proteolysis-targeting chimeras (PROTACs) were generated by the covalent linkage of the bromodomain or ATPase-binding ligand to an E3 ligase-binding moiety. This engineered connection promotes the degradation of specific SWI/SNF subunits, enhancing and extending the impact of this pharmacological intervention in some cases. Extensive preclinical studies have underscored the therapeutic potential of these drugs across diverse cancer types. Encouragingly, some of these agents have progressed from preclinical research to clinical trials, indicating a promising stride toward the development of effective cancer therapeutics targeting SWI/SNF complex and sub-complex functions.
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Affiliation(s)
- Megan R Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Jasmine Walia
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
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10
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Bergwell M, Park J, Kirkland JG. Differential Modulation of Polycomb-Associated Histone Marks by cBAF, pBAF, and gBAF Complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.23.557848. [PMID: 37790495 PMCID: PMC10542518 DOI: 10.1101/2023.09.23.557848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Chromatin regulators are a group of proteins that can alter the physical properties of chromatin to make it more or less permissive to transcription by modulating another protein's access to a specific DNA sequence through changes in nucleosome occupancy or histone modifications at a particular locus. Mammalian SWI/SNF complexes (mSWI/SNF) are a group of ATPase-dependent chromatin remodelers that alter chromatin states. In mouse embryonic stem cells (mESCs), there are three primary forms of mSWI/SNF: canonical BAF (cBAF), polybromo-associated BAF (pBAF), and GLTSCR-associated BAF (gBAF or ncBAF). While cBAF and gBAF contain the SS18 protein subunit, pBAF lacks SS18. Previous studies used a novel dCas9-mediated inducible recruitment (FIRE-Cas9) of mSWI/SNF complexes via SS18 to the Nkx2.9 locus. Nkx2.9 is a developmentally regulated gene that requires mSWI/SNF for transcriptional activation during neural differentiation. However, in mESCs, Nkx2.9 is bivalent, meaning nucleosomes at the locus have both active and polycomb-associated repressive modifications. Upon recruitment of SS18-containing complexes, polycomb-associated histone marks are removed, followed by transcriptional activation of Nkx2.9. However, since both cBAF and gBAF share the SS18 subunit, it is unclear whether one or both complexes oppose the polycomb repressive marks. The ability of pBAF to do the same also remains unknown. In this study, we used unique subunits to recruit each of the three complexes to the Nkx2.9 locus individually. Here, we show that cBAF most effectively opposes polycomb repressive marks at Nkx2.9, leading to transcriptional activation of the gene. Recruitment of cBAF complexes leads to a significant loss of the polycomb repressive-2 H3K27me3 and polycomb repressive-1 H2AK119ub histone marks, whereas gBAF and pBAF do not. Moreover, nucleosome occupancy alone cannot explain the loss of these marks. Our results demonstrate that cBAF has a unique role in the direct opposition of polycomb-associated histone modifications that gBAF and pBAF do not share.
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Cermakova K, Tao L, Dejmek M, Sala M, Montierth MD, Chan YS, Patel I, Chambers C, Loeza Cabrera M, Hoffman D, Parchem RJ, Wang W, Nencka R, Barbieri E, Hodges HC. Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNF. Nucleic Acids Res 2024; 52:4-21. [PMID: 37993417 PMCID: PMC10783513 DOI: 10.1093/nar/gkad1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/29/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023] Open
Abstract
Several cancer core regulatory circuitries (CRCs) depend on the sustained generation of DNA accessibility by SWI/SNF chromatin remodelers. However, the window when SWI/SNF is acutely essential in these settings has not been identified. Here we used neuroblastoma (NB) cells to model and dissect the relationship between cell-cycle progression and SWI/SNF ATPase activity. We find that SWI/SNF inactivation impairs coordinated occupancy of non-pioneer CRC members at enhancers within 1 hour, rapidly breaking their autoregulation. By precisely timing inhibitor treatment following synchronization, we show that SWI/SNF is dispensable for survival in S and G2/M, but becomes acutely essential only during G1 phase. We furthermore developed a new approach to analyze the oscillating patterns of genome-wide DNA accessibility across the cell cycle, which revealed that SWI/SNF-dependent CRC binding sites are enriched at enhancers with peak accessibility during G1 phase, where they activate genes involved in cell-cycle progression. SWI/SNF inhibition strongly impairs G1-S transition and potentiates the ability of retinoids used clinically to induce cell-cycle exit. Similar cell-cycle effects in diverse SWI/SNF-addicted settings highlight G1-S transition as a common cause of SWI/SNF dependency. Our results illustrate that deeper knowledge of the temporal patterns of enhancer-related dependencies may aid the rational targeting of addicted cancers.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Ling Tao
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew D Montierth
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Yuen San Chan
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Ivanshi Patel
- Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Courtney Chambers
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Translational Biology and Molecular Medicine Graduate Program, Houston, TX, USA
| | - Mario Loeza Cabrera
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Development, Disease Models and Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Dane Hoffman
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Ronald J Parchem
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Center for Cell and Gene Therapy, and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eveline Barbieri
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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12
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Wang A, Jin Y, Cao Z, Lu L, Li Z. Clinicopathological characteristics and treatment outcomes of advanced SMARCA4-deficient thoracic tumors. Cancer Med 2024; 13:e6809. [PMID: 38124509 PMCID: PMC10807565 DOI: 10.1002/cam4.6809] [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: 08/24/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE SMARCA4-deficient thoracic tumors, characterized by distinct clinicopathological, morphological, immunohistochemical, and genetic features, differ significantly from conventional non-small-cell lung carcinomas (NSCLCs). This group encompasses both SMARCA4-deficient NSCLCs (SMARCA4-NSCLCs) and SMARCA4-deficient undifferentiated tumors (SMARCA4-UTs). The efficacy of PD-1 inhibitors in treating SMARCA4-deficient thoracic tumors remains uncertain. METHODS Medical records of 36 patients diagnosed with stage IIIB, IIIC, or IV SMARCA4-deficient thoracic tumors were analyzed. We assessed the clinical, pathological, and genetic features of these patients through immunohistochemistry (IHC) and a 68-gene panel next-generation sequencing (NGS). We compared the differences between SMARCA4-NSCLCs and SMARCA4-UTs, and evaluated the impact of chemotherapy and immunotherapy on patient outcomes. RESULTS The majority of patients with SMARCA4-deficient thoracic tumors were heavy-smoking males, averaging 64.6 years in age. IHC predominantly showed weak or negative staining for markers such as TTF-1, CK5/6, p40, synaptophysin, chromogranin A, and CD56, which are often associated with adenocarcinoma, squamous cell carcinoma, and neuroendocrine tumors. The most common genetic mutations identified via NGS included TP53, CDKN2A, KRAS, STK11, NF1, and PTEN. No significant overall survival (OS) difference was observed between SMARCA4-NSCLCs and SMARCA4-UTs (p = 0.366). The median OS for patients treated with chemotherapy (n = 9) was 447 days, while the median OS for patients undergoing PD-1-inhibitor-based therapy (n = 16) was not reached (p = 0.105). CONCLUSION SMARCA4-deficient thoracic tumors exhibit distinct characteristics from conventional NSCLCs, and PD-1 inhibitors show promise in treating advanced SMARCA4-deficient thoracic tumors.
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Affiliation(s)
- Anni Wang
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Yueping Jin
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Zhengqi Cao
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Li Lu
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
| | - Ziming Li
- Shanghai Lung Cancer Center, Shanghai Chest HospitalShanghai Jiao Tong University, School of MedicineShanghaiChina
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13
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Pisfil MG, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569516. [PMID: 38106060 PMCID: PMC10723341 DOI: 10.1101/2023.12.04.569516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. We investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with our data. We speculate that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Nicola Hepp
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Epigenetics Institute & Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia (PA), USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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Martin BJE, Ablondi EF, Goglia C, Mimoso CA, Espinel-Cabrera PR, Adelman K. Global identification of SWI/SNF targets reveals compensation by EP400. Cell 2023; 186:5290-5307.e26. [PMID: 37922899 PMCID: PMC11307202 DOI: 10.1016/j.cell.2023.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/11/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.
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Affiliation(s)
- Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA
| | - Eileen F Ablondi
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christine Goglia
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Piero R Espinel-Cabrera
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center at Harvard, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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15
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Göbel C, Godbole S, Schoof M, Holdhof D, Kresbach C, Loose C, Neumann J, Schüller U. MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice. Acta Neuropathol Commun 2023; 11:174. [PMID: 37919824 PMCID: PMC10621315 DOI: 10.1186/s40478-023-01654-2] [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: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4-negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Carolin Loose
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Julia Neumann
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
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Giordano G, Ferioli E, Guareschi D, Tafuni A. Dedifferentiated Endometrial Carcinoma: A Rare Aggressive Neoplasm-Clinical, Morphological and Immunohistochemical Features. Cancers (Basel) 2023; 15:5155. [PMID: 37958329 PMCID: PMC10647464 DOI: 10.3390/cancers15215155] [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: 10/09/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Dedifferentiated endometrioid adenocarcinoma is characterised by the coexistence of an undifferentiated carcinoma and a low-grade endometrioid adenocarcinoma. The low-grade component in this subtype of endometrial carcinoma is Grade 1 or 2 according to the Federation of Gynaecology and Obstetrics (FIGO) grading system. The coexistence of low-grade endometrial carcinoma and solid undifferentiated carcinoma can cause diagnostic problems on histological examination. In fact, this combination can often be mistaken for a more common Grade 2 or Grade 3 endometrial carcinoma. Therefore, this subtype of uterine carcinoma can often go under-recognised. An accurate diagnosis of dedifferentiated endometrial carcinoma is mandatory because of its poorer prognosis compared to Grade 3 endometrial carcinoma, with a solid undifferentiated component that can amount to as much as 20% of the entire tumour. The aim of this review is to provide clinical, immunohistochemical, and molecular data to aid with making an accurate histological diagnosis and to establish whether there are any findings which could have an impact on the prognosis or therapeutic implications of this rare and aggressive uterine neoplasm.
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Affiliation(s)
- Giovanna Giordano
- Department of Medicine and Surgery, Pathology Unit, University of Parma, Viale A. Gramsci, 14, 43126 Parma, Italy; (E.F.); (A.T.)
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Xu J, Zhou X, Zhang T, Zhang B, Xu PX. Smarca4 deficiency induces Pttg1 oncogene upregulation and hyperproliferation of tubular and interstitial cells during kidney development. Front Cell Dev Biol 2023; 11:1233317. [PMID: 37727504 PMCID: PMC10506413 DOI: 10.3389/fcell.2023.1233317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/17/2023] [Indexed: 09/21/2023] Open
Abstract
Kidney formation and nephrogenesis are controlled by precise spatiotemporal gene expression programs, which are coordinately regulated by cell-cycle, cell type-specific transcription factors and epigenetic/chromatin regulators. However, the roles of epigenetic/chromatin regulators in kidney development and disease remain poorly understood. In this study, we investigated the impact of deleting the chromatin remodeling factor Smarca4 (Brg1), a human Wilms tumor-associated gene, in Wnt4-expressing cells. Smarca4 deficiency led to severe tubular defects and a shortened medulla. Through unbiased single-cell RNA sequencing analyses, we identified multiple types of Wnt4 Cre-labeled interstitial cells, along with nephron-related cells. Smarca4 deficiency increased interstitial cells but markedly reduced tubular cells, resulting in cells with mixed identity and elevated expression of cell-cycle regulators and genes associated with extracellular matrix and epithelial-to-mesenchymal transition/fibrosis. We found that Smarca4 loss induced a significant upregulation of the oncogene Pttg1 and hyperproliferation of Wnt4 Cre-labeled cells. These changes in the cellular state could hinder the cellular transition into characteristic tubular structures, eventually leading to fibrosis. In conclusion, our findings shed light on novel cell types and genes associated with Wnt4 Cre-labeled cells and highlight the critical role of Smarca4 in regulating tubular cell differentiation and the expression of the cancer-causing gene Pttg1 in the kidney. These findings may provide valuable insights into potential therapeutic strategies for renal cell carcinoma resulting from SMARCA4 deficiency.
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Affiliation(s)
- Jinshu Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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18
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Yang C, He Y, Wang Y, McKinnon PJ, Shahani V, Miller DD, Pfeffer LM. Next-generation bromodomain inhibitors of the SWI/SNF complex enhance DNA damage and cell death in glioblastoma. J Cell Mol Med 2023; 27:2770-2781. [PMID: 37593885 PMCID: PMC10494295 DOI: 10.1111/jcmm.17907] [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: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive brain cancer with a poor prognosis. While surgical resection is the primary treatment, adjuvant temozolomide (TMZ) chemotherapy and radiotherapy only provide slight improvement in disease course and outcome. Unfortunately, most treated patients experience recurrence of highly aggressive, therapy-resistant tumours and eventually succumb to the disease. To increase chemosensitivity and overcome therapy resistance, we have modified the chemical structure of the PFI-3 bromodomain inhibitor of the BRG1 and BRM catalytic subunits of the SWI/SNF chromatin remodelling complex. Our modifications resulted in compounds that sensitized GBM to the DNA alkylating agent TMZ and the radiomimetic bleomycin. We screened these chemical analogues using a cell death ELISA with GBM cell lines and a cellular thermal shift assay using epitope tagged BRG1 or BRM bromodomains expressed in GBM cells. An active analogue, IV-129, was then identified and further modified, resulting in new generation of bromodomain inhibitors with distinct properties. IV-255 and IV-275 had higher bioactivity than IV-129, with IV-255 selectively binding to the bromodomain of BRG1 and not BRM, while IV-275 bound well to both BRG1 and BRM bromodomains. In contrast, IV-191 did not bind to either bromodomain or alter GBM chemosensitivity. Importantly, both IV-255 and IV-275 markedly increased the extent of DNA damage induced by TMZ and bleomycin as determined by nuclear γH2AX staining. Our results demonstrate that these next-generation inhibitors selectively bind to the bromodomains of catalytic subunits of the SWI/SNF complex and sensitize GBM to the anticancer effects of TMZ and bleomycin. This approach holds promise for improving the treatment of GBM.
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Affiliation(s)
- Chuanhe Yang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yali He
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Yinan Wang
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - Vijay Shahani
- Recursion Pharmaceuticals IncTorontoOntarioM5V 2A2Canada
| | - Duane D. Miller
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory MedicineCollege of Medicine, University of Tennessee Health Science CenterMemphisTennesseeUSA
- The Center for Cancer ResearchUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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19
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Hong L, Williams NL, Jaffe M, Shields CE, Haynes KA. Synthetic Reader-Actuators Targeted to Polycomb-Silenced Genes Block Triple-Negative Breast Cancer Proliferation and Invasion. GEN BIOTECHNOLOGY 2023; 2:301-316. [PMID: 37928406 PMCID: PMC10623628 DOI: 10.1089/genbio.2023.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/06/2023] [Indexed: 11/07/2023]
Abstract
Scientists have used pharmacological inhibitors of polycomb proteins to restore the expression of tumor suppressor genes and stop cancer proliferation and invasion. A major limitation of this approach is that key transcriptional activators, such as TP53 and BAF SWI/SNF, are often mutated in cancer. Poor clinical results for polycomb-targeting therapies in solid cancers, including triple-negative breast cancer (TNBC), could discourage the further development of epigenetic monotherapies. Here, we performed epigenome actuation with a synthetic reader-actuator (SRA) that binds trimethylated histone H3 lysine 27 in polycomb chromatin and modulates core transcriptional activators. In SRA-expressing TNBC BT-549 cells, 122 genes become upregulated ≥2-fold, including the genes involved in cell death, cell cycle arrest, and migration inhibition. The SRA-expressing spheroids showed reduced size in Matrigel and loss of invasion. Therefore, targeting Mediator-recruiting regulators to silenced chromatin can activate tumor suppressors and stimulate anti-cancer phenotypes, and further development of robust gene regulators might benefit TNBC patients.
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Affiliation(s)
- Lauren Hong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA; and Emory University, Atlanta, Georgia, USA
| | - Natecia L. Williams
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, Georgia, USA
| | - Maya Jaffe
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA; and Emory University, Atlanta, Georgia, USA
| | - Cara E. Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, Georgia, USA
| | - Karmella A. Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA; and Emory University, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, Georgia, USA
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20
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Navickas SM, Giles KA, Brettingham-Moore KH, Taberlay PC. The role of chromatin remodeler SMARCA4/BRG1 in brain cancers: a potential therapeutic target. Oncogene 2023:10.1038/s41388-023-02773-9. [PMID: 37433987 PMCID: PMC10374441 DOI: 10.1038/s41388-023-02773-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
The chromatin remodeler SMARCA4/BRG1 is a key epigenetic regulator with diverse roles in coordinating the molecular programs that underlie brain tumour development. BRG1 function in brain cancer is largely specific to the tumour type and varies further between tumour subtypes, highlighting its complexity. Altered SMARCA4 expression has been linked to medulloblastoma, low-grade gliomas such as oligodendroglioma, high-grade gliomas such as glioblastoma and atypical/teratoid rhabdoid tumours. SMARCA4 mutations in brain cancer predominantly occur in the crucial catalytic ATPase domain, which is associated with tumour suppressor activity. However, SMARCA4 is opposingly seen to promote tumourigenesis in the absence of mutation and through overexpression in other brain tumours. This review explores the multifaceted interaction between SMARCA4 and various brain cancer types, highlighting its roles in tumour pathogenesis, the pathways it regulates, and the advances that have been made in understanding the functional relevance of mutations. We discuss developments made in targeting SMARCA4 and the potential to translate these to adjuvant therapies able to enhance current methods of brain cancer treatment.
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Affiliation(s)
- Sophie M Navickas
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Katherine A Giles
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Kate H Brettingham-Moore
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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21
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Shi Y, Shin DS. Dysregulation of SWI/SNF Chromatin Remodelers in NSCLC: Its Influence on Cancer Therapies including Immunotherapy. Biomolecules 2023; 13:984. [PMID: 37371564 DOI: 10.3390/biom13060984] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Molecularly targeted therapeutics and immunotherapy revolutionized the clinical care of NSCLC patients. However, not all NSCLC patients harbor molecular targets (e.g., mutated EGFR), and only a subset benefits from immunotherapy. Moreover, we are lacking reliable biomarkers for immunotherapy, although PD-L1 expression has been mainly used for guiding front-line therapeutic options. Alterations of the SWI/SNF chromatin remodeler occur commonly in patients with NSCLC. This subset of NSCLC tumors tends to be undifferentiated and presents high heterogeneity in histology, and it shows a dismal prognosis because of poor response to the current standard therapies. Catalytic subunits SMARCA4/A2 and DNA binding subunits ARID1A/ARID1B/ARID2 as well as PBRM1 were identified to be the most commonly mutated subunits of SWI/SNF complexes in NSCLC. Mechanistically, alteration of these SWI/SNF subunits contributes to the tumorigenesis of NSCLC through compromising the function of critical tumor suppressor genes, enhancing oncogenic activity as well as impaired DNA repair capacity related to genomic instability. Several vulnerabilities of NSCLCS with altered SWI/SNF subunits were detected and evaluated clinically using EZH2 inhibitors, PROTACs of mutual synthetic lethal paralogs of the SWI/SNF subunits as well as PARP inhibitors. The response of NSCLC tumors with an alteration of SWI/SNF to ICIs might be confounded by the coexistence of mutations in genes capable of influencing patients' response to ICIs. High heterogenicity in the tumor with SWI/SNF deficiency might also be responsible for the seemingly conflicting results of ICI treatment of NSCLC patients with alterations of SWI/SNF. In addition, an alteration of each different SWI/SNF subunit might have a unique impact on the response of NSCLC with deficient SWI/SNF subunits. Prospective studies are required to evaluate how the alterations of the SWI/SNF in the subset of NSCLC patients impact the response to ICI treatment. Finally, it is worthwhile to point out that combining inhibitors of other chromatin modulators with ICIs has been proven to be effective for the treatment of NSCLC with deficient SWI/SNF chromatin remodelers.
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Affiliation(s)
- Yijiang Shi
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
| | - Daniel Sanghoon Shin
- Division of Hematology/Oncology, Department of Medicine, Los Angeles, CA 90073, USA
- Division of Hematology/Oncology, Department of Medicine, VA Greater Los Angeles Healthcare System, 11301 Wilshire Blvd, Los Angeles, CA 90073, USA
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22
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Reddy D, Bhattacharya S, Workman JL. (mis)-Targeting of SWI/SNF complex(es) in cancer. Cancer Metastasis Rev 2023; 42:455-470. [PMID: 37093326 PMCID: PMC10349013 DOI: 10.1007/s10555-023-10102-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF (also called BAF) is critical for the regulation of gene expression. During the evolution from yeast to mammals, the BAF complex has evolved an enormous complexity that contains a high number of subunits encoded by various genes. Emerging studies highlight the frequent involvement of altered mammalian SWI/SNF chromatin-remodeling complexes in human cancers. Here, we discuss the recent advances in determining the structure of SWI/SNF complexes, highlight the mechanisms by which mutations affecting these complexes promote cancer, and describe the promising emerging opportunities for targeted therapies.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
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23
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Neil AJ, Zhao L, Isidro RA, Srivastava A, Cleary JM, Dong F. SMARCA4 Mutations in Carcinomas of the Esophagus, Esophagogastric Junction, and Stomach. Mod Pathol 2023; 36:100183. [PMID: 37054973 DOI: 10.1016/j.modpat.2023.100183] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Deficiency of SMARCA4, a member of the SWI/SNF chromatin remodeling complex, has been described in a subset of undifferentiated gastroesophageal carcinomas with an aggressive clinical course. The full spectrum and frequency of SMARCA4 mutations in gastroesophageal cancer are unknown. We interrogated our institutional database and identified patients with gastroesophageal carcinomas who underwent cancer next-generation sequencing. We classified SMARCA4 mutations, assessed histologic features, and correlated SMARCA4 mutations with SMARCA4 protein expression by immunohistochemistry. SMARCA4 mutations were identified in gastroesophageal carcinomas from 107 (9.1%) of 1174 patients. Forty-nine SMARCA4 mutations, including 26 missense variants and 23 protein-truncating variants, were interpreted as pathogenic in 42 (3.6%) of 1174 patients. Thirty (71%) of 42 cancers with pathogenic SMARCA4 mutations were located in the esophagus or esophagogastric junction, and 12 cancers (29%) were located in the stomach. Sixty-four percent of carcinomas with pathogenic truncating SMARCA4 variants were poorly differentiated or undifferentiated compared with 25% of carcinomas with pathogenic missense variants. Eight of 12 carcinomas with truncating SMARCA4 variants and none of the 7 carcinomas with pathogenic SMARCA4 missense variants showed loss of SMARCA4 expression by immunohistochemistry. Four carcinomas with pathogenic truncating SMARCA4 variants were associated with Barrett esophagus. SMARCA4-mutated gastroesophageal cancers were enriched for APC (31%) and CTNNB1 (14%) mutations and exhibited similar frequency of TP53 (76%) and ARID1A (31%) mutations compared with gastroesophageal cancers without pathogenic SMARCA4 mutations. The median overall survival was 13.6 months for patients who presented with metastasis at diagnosis and 22.7 months for patients without metastasis. Overall, SMARCA4-mutated gastroesophageal cancers exhibit a spectrum of histologic grade, an association with Barrett esophagus, and a concurrent mutational pattern similar to SMARCA4-wild-type gastroesophageal adenocarcinomas. Although SMARCA4-deficient gastroesophageal carcinomas are associated with poorly differentiated and undifferentiated histology, the spectrum of histologic and molecular features suggests overlapping pathogenic pathways with conventional gastroesophageal adenocarcinomas.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lei Zhao
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Raymond A Isidro
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Amitabh Srivastava
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Now with Department of Pathology, Memorial Sloan Kettering Cancer Center, New York
| | - James M Cleary
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
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24
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Zhu Z, Chen X, Guo A, Manzano T, Walsh PJ, Wills KM, Halliburton R, Radko-Juettner S, Carter RD, Partridge JF, Green DR, Zhang J, Roberts CWM. Mitotic bookmarking by SWI/SNF subunits. Nature 2023; 618:180-187. [PMID: 37225980 PMCID: PMC10303083 DOI: 10.1038/s41586-023-06085-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2023] [Indexed: 05/26/2023]
Abstract
For cells to initiate and sustain a differentiated state, it is necessary that a 'memory' of this state is transmitted through mitosis to the daughter cells1-3. Mammalian switch/sucrose non-fermentable (SWI/SNF) complexes (also known as Brg1/Brg-associated factors, or BAF) control cell identity by modulating chromatin architecture to regulate gene expression4-7, but whether they participate in cell fate memory is unclear. Here we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but are bound to promoters during mitosis, and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 has a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.
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Affiliation(s)
- Zhexin Zhu
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Xiaolong Chen
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Trishabelle Manzano
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick J Walsh
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kendall M Wills
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rebecca Halliburton
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sandi Radko-Juettner
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
- St Jude Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Raymond D Carter
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Janet F Partridge
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA.
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25
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Lear BP, Thompson EAN, Rodriguez K, Arndt ZP, Khullar S, Klosa PC, Lu RJ, Morrow CS, Risgaard R, Peterson ER, Teefy BB, Bhattacharyya A, Sousa AMM, Wang D, Benayoun BA, Moore DL. Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541995. [PMID: 37292613 PMCID: PMC10245848 DOI: 10.1101/2023.05.23.541995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Injury to adult mammalian central nervous system (CNS) axons results in limited regeneration. Rodent studies have revealed a developmental switch in CNS axon regenerative ability, yet whether this is conserved in humans is unknown. Using human fibroblasts from 8 gestational-weeks to 72 years-old, we performed direct reprogramming to transdifferentiate fibroblasts into induced neurons (Fib-iNs), avoiding pluripotency which restores cells to an embryonic state. We found that early gestational Fib-iNs grew longer neurites than all other ages, mirroring the developmental switch in regenerative ability in rodents. RNA-sequencing and screening revealed ARID1A as a developmentally-regulated modifier of neurite growth in human neurons. These data suggest that age-specific epigenetic changes may drive the intrinsic loss of neurite growth ability in human CNS neurons during development. One-Sentence Summary: Directly-reprogrammed human neurons demonstrate a developmental decrease in neurite growth ability.
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26
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Pan M, Jiang C, Zhang Z, Achacoso N, Solorzano-Pinto AV, Tse P, Chung E, Suga JM, Thomas S, Habel LA. Sex- and Co-Mutation-Dependent Prognosis in Patients with SMARCA4-Mutated Malignancies. Cancers (Basel) 2023; 15:2665. [PMID: 37345003 DOI: 10.3390/cancers15102665] [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: 03/07/2023] [Revised: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Whether sex and co-mutations impact prognosis of patients with SMARCA4-mutated (mutSMARCA4) malignancies is not clear. METHODS This cohort included patients from Northern California Kaiser Permanente with next-generation sequencing (NGS) performed from August 2020 to October 2022. We used Cox regression modeling to examine the association between sex and overall survival (OS), adjusting for demographics, performance status, Charlson comorbidity index, receipt of treatment, tumor mutation burden (TMB), and TP53, KRAS, CDKN2A, STK11, and Keap1 co-mutations. RESULTS Out of 9221 cases with NGS performed, 125 cases (1.4%) had a mutSMARCA4. The most common malignancies with a mutSMARCA4 were non-small cell lung cancer (NSCLC, 35.2%), esophageal and stomach adenocarcinoma (12.8%), and cancer of unknown primary (11.2%). The most common co-mutations were p53 (mutp53, 59.2%), KRAS (mutKRAS, 28.8%), CDKN2A (mutCDKN2A, 31.2%), STK11 (mutSTK11, 12.8%), and Keap1 (mutKeap1, 8.8%) mutations. Male patients had substantially worse OS than female patients both among the entire mutSMARCA4 cohort (HR = 1.71, [95% CI 0.92-3.18]) with a median OS of 3.0 versus 43.3 months (p < 0.001), and among the NSCLC subgroup (HR = 14.2, [95% CI 2.76-73.4]) with a median OS of 2.75 months versus un-estimable (p = 0.02). Among all patients with mutSMARCA4, mutp53 versus wtp53 (HR = 2.12, [95% CI 1.04-4.29]) and mutSTK11 versus wtSTK11 (HR = 2.59, [95% CI 0.87-7.73]) were associated with worse OS. Among the NSCLC subgroup, mutp53 versus wtp53 (HR = 0.35, [0.06-1.97]) and mutKRAS versus wtKRAS (HR = 0.04, [0.003-.45]) were associated with better OS, while mutCDKN2A versus wtCDKN2A (HR = 5.04, [1.12-22.32]), mutSTK11 versus wtSTK11 (HR = 13.10, [95% CI 1.16-148.26]), and mutKeap1 versus wtKeap1 (HR = 5.06, [95% CI 0.89-26.61}) were associated with worse OS. CONCLUSION In our cohort of patients with mutSMARCA4, males had substantially worse prognosis than females, while mutTP53, mutKRAS, mutCDKN2A, mutSTK11 and mutKeap1were differentially associated with prognosis among all patients and among the NSCLC subgroup. Our results, if confirmed, could suggest potentially unidentified mechanisms that underly this sex and co-mutation-dependent prognostic disparity among patients whose tumor bears a mutSMARCA4.
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Affiliation(s)
- Minggui Pan
- Department of Oncology and Hematology, Kaiser Permanente, Santa Clara, CA 94051, USA
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
- Division of Oncology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Zheyang Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, and National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361102, China
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | | | - Pam Tse
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Elaine Chung
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
| | - Jennifer Marie Suga
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Sachdev Thomas
- Department of Oncology and Hematology, Kaiser Permanente, Vallejo, CA 94589, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente, Oakland, CA 94612, USA
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27
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Deng C, Deng G, Zhu X. Case Report: Nintedanib for immune-related pneumonitis triggered by anti-PD-1 treatment in a patient with SMARCA4-mutant NSCLC: a case report. Front Pharmacol 2023; 14:1177329. [PMID: 37214462 PMCID: PMC10192877 DOI: 10.3389/fphar.2023.1177329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
SMARCA4-mutant lung cancer accounts for approximately 10% of non-small-cell lung cancers (NSCLCs), has few effective treatments, and has been associated with a poor prognosis. Our case report describes a 73-year-old man who was diagnosed with SMARCA4-mutant advanced lung adenocarcinoma. Routine driver gene mutation screening was negative, and tumor tissue immunohistochemistry analysis showed the absence of the BRG1 protein (encoded by SMARCA4). In addition to the standard chemotherapy regimens, programmed cell death protein 1 (PD-1) inhibitors were administered. After three cycles of combination therapy, the focus of the primary lung tumor shrunk evidently, but radiological interstitial abnormalities emerged in the basal and subpleural areas of the bilateral lungs. The patient's clinical condition deteriorated and he was diagnosed with immune checkpoint inhibitor (ICI)-associated pneumonia. Thus, the combination regimen was discontinued, corticosteroid therapy was administered according to guidelines, and nintedanib was added, given that interstitial abnormalities were observed on chest computed tomography (CT). Following the above treatment, the patient's condition improved, the standard chemotherapy regimen was restarted, and nintedanib treatment was maintained. The patient's clinical condition continued to improve, and follow-up CT showed significant resolution of the interstitial abnormalities and stabilization of the primary tumor lesion. In summary, we report the case of a patient with SMARCA4-mutant NSCLC, which is generally considered to be associated with a poor prognosis owing to a lack of effective treatments. The patient responded favorably to initial combination therapy with ICIs, although he subsequently developed immune-related adverse events. We also found that nintedanib, a multitargeted anti-fibrotic agent, was beneficial for the treatment of immune-related lung injury and showed potential anti-tumor effects.
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28
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Strickland AL, Maniar KP, Tanner E, Shanes E, Jennings L, Wei JJ. Borderline With Bad Behavior: An Unusual Low-grade Serous Carcinoma With Dedifferentiation From a Serous Borderline Tumor. Int J Gynecol Pathol 2023; 42:241-246. [PMID: 36867463 DOI: 10.1097/pgp.0000000000000885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The pathogenesis of serous ovarian tumors has been extensively investigated, with a dualistic model dividing these cancers into 2 groups. Type I tumors, including low-grade serous carcinoma, is characteristic for concurrent presence of borderline tumors, less atypical cytology, relatively indolent biologic behavior, and molecular aberrations related to the MAPK pathway with chromosomal stability. Meanwhile, type II tumors, such as high-grade serous carcinoma, are notable for no significant association with borderline tumors, higher grade cytology, more aggressive biologic behavior, and TP53 mutations along with chromosomal instability. We describe a case of morphologic low-grade serous carcinoma with focally increased cytologic atypia arising in serous borderline tumors involving both ovaries, which demonstrated highly aggressive behavior despite several years of surgical and chemotherapeutic management. Each recurrent specimen contained more uniform higher grade morphology than what was seen in the original specimen. Immunohistochemical and molecular studies in both the original tumor and the most recent recurrence demonstrate identical mutations in the MAPK genes, but with additional mutations in the latter, notably an acquisition of a variant of possible clinical significance in the SMARCA4 gene, which is associated with dedifferentiation and aggressive biologic behavior. This case challenges our current and still evolving understanding of the pathogenesis, biologic behavior, and expected clinical outcome of low-grade serous ovarian carcinomas. It also underscores the need for further investigation into this complicated tumor.
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Affiliation(s)
- Amanda L Strickland
- Department of Pathology (A.L.S., K.P.M., E.S., L.J., J.J.W.); and Division of Gynecologic Oncology, Department of Obstetrics and Gynecology (E.T., J.J.), Northwestern University Feinberg School of Medicine, Chicago, Illinois
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29
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Klein DC, Troy K, Tripplehorn SA, Hainer SJ. The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. BMC Genomics 2023; 24:201. [PMID: 37055726 PMCID: PMC10103515 DOI: 10.1186/s12864-023-09287-4] [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: 10/25/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are consistently well-positioned, some nucleosomes and alternative nucleosome structures are more sensitive to nuclease digestion or are transitory. Fragile nucleosomes are nucleosome structures that are sensitive to nuclease digestion and may be composed of either six or eight histone proteins, making these either hexasomes or octasomes. Overlapping dinucleosomes are composed of two merged nucleosomes, lacking one H2A:H2B dimer, creating a 14-mer wrapped by ~ 250 bp of DNA. In vitro studies of nucleosome remodeling suggest that the collision of adjacent nucleosomes by sliding stimulates formation of overlapping dinucleosomes. RESULTS To better understand how nucleosome remodeling factors regulate alternative nucleosome structures, we depleted murine embryonic stem cells of the transcripts encoding remodeler ATPases BRG1 or SNF2H, then performed MNase-seq. We used high- and low-MNase digestion to assess the effects of nucleosome remodeling factors on nuclease-sensitive or "fragile" nucleosome occupancy. In parallel we gel-extracted MNase-digested fragments to enrich for overlapping dinucleosomes. We recapitulate prior identification of fragile nucleosomes and overlapping dinucleosomes near transcription start sites, and identify enrichment of these features around gene-distal DNaseI hypersensitive sites, CTCF binding sites, and pluripotency factor binding sites. We find that BRG1 stimulates occupancy of fragile nucleosomes but restricts occupancy of overlapping dinucleosomes. CONCLUSIONS Overlapping dinucleosomes and fragile nucleosomes are prevalent within the ES cell genome, occurring at hotspots of gene regulation beyond their characterized existence at promoters. Although neither structure is fully dependent on either nucleosome remodeling factor, both fragile nucleosomes and overlapping dinucleosomes are affected by knockdown of BRG1, suggesting a role for the complex in creating or removing these structures.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Kris Troy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
- Department of Quantitative and Systems Biology, University of California, 95343, Merced, Merced, CA, USA
| | - Sarah A Tripplehorn
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
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30
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Wang L, Tang J. SWI/SNF complexes and cancers. Gene 2023; 870:147420. [PMID: 37031881 DOI: 10.1016/j.gene.2023.147420] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/11/2023]
Abstract
Epigenetics refers to the study of genetic changes that can affect gene expression without altering the underlying DNA sequence, including DNA methylation, histone modification, chromatin remodelling, X chromosome inactivation and non-coding RNA regulation. Of these, DNA methylation, histone modification and chromatin remodelling constitute the three classical modes of epigenetic regulation. These three mechanisms alter gene transcription by adjusting chromatin accessibility, thereby affecting cell and tissue phenotypes in the absence of DNA sequence changes. In the presence of ATP hydrolases, chromatin remodelling alters the structure of chromatin and thus changes the transcription level of DNA-guided RNA. To date, four types of ATP-dependent chromatin remodelling complexes have been identified in humans, namely SWI/SNF, ISWI, INO80 and NURD/MI2/CHD. SWI/SNF mutations are prevalent in a wide variety of cancerous tissues and cancer-derived cell lines as discovered by next-generation sequencing technologies.. SWI/SNF can bind to nucleosomes and use the energy of ATP to disrupt DNA and histone interactions, sliding or ejecting histones, altering nucleosome structure, and changing transcriptional and regulatory mechanisms. Furthermore, mutations in the SWI/SNF complex have been observed in approximately 20% of all cancers. Together, these findings suggest that mutations targeting the SWI/SNF complex may have a positive impact on tumorigenesis and cancer progression.
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Affiliation(s)
- Liyuan Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Oncology and Hematology, Jinan 250000, Shandong Province, China
| | - Jinglong Tang
- Adicon Medical Laboratory Center, Molecular Genetic Diagnosis Center, Pathological Diagnosis Center, Jinan 250014, Shandong Province, China.
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31
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Chambers C, Cermakova K, Chan YS, Kurtz K, Wohlan K, Lewis AH, Wang C, Pham A, Dejmek M, Sala M, Loeza Cabrera M, Aguilar R, Nencka R, Lacorazza HD, Rau RE, Hodges HC. SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia. Cancer Res 2023; 83:983-996. [PMID: 36662812 PMCID: PMC10071820 DOI: 10.1158/0008-5472.can-22-2129] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/09/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
In acute myeloid leukemia (AML), SWI/SNF chromatin remodeling complexes sustain leukemic identity by driving high levels of MYC. Previous studies have implicated the hematopoietic transcription factor PU.1 (SPI1) as an important target of SWI/SNF inhibition, but PU.1 is widely regarded to have pioneer-like activity. As a result, many questions have remained regarding the interplay between PU.1 and SWI/SNF in AML as well as normal hematopoiesis. Here we found that PU.1 binds to most of its targets in a SWI/SNF-independent manner and recruits SWI/SNF to promote accessibility for other AML core regulatory factors, including RUNX1, LMO2, and MEIS1. SWI/SNF inhibition in AML cells reduced DNA accessibility and binding of these factors at PU.1 sites and redistributed PU.1 to promoters. Analysis of nontumor hematopoietic cells revealed that similar effects also impair PU.1-dependent B-cell and monocyte populations. Nevertheless, SWI/SNF inhibition induced profound therapeutic response in an immunocompetent AML mouse model as well as in primary human AML samples. In vivo, SWI/SNF inhibition promoted leukemic differentiation and reduced the leukemic stem cell burden in bone marrow but also induced leukopenia. These results reveal a variable therapeutic window for SWI/SNF blockade in AML and highlight important off-tumor effects of such therapies in immunocompetent settings. SIGNIFICANCE Disruption of PU.1-directed enhancer programs upon SWI/SNF inhibition causes differentiation of AML cells and induces leukopenia of PU.1-dependent B cells and monocytes, revealing the on- and off-tumor effects of SWI/SNF blockade.
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Affiliation(s)
- Courtney Chambers
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Yuen San Chan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Kristen Kurtz
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Katharina Wohlan
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
| | - Andrew Henry Lewis
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Christiana Wang
- Genetics and Genomics Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Anh Pham
- Department of Bioengineering, Rice University, Houston, Texas
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sala
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Mario Loeza Cabrera
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Rogelio Aguilar
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - H. Daniel Lacorazza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Rachel E. Rau
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas
| | - H. Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nat Genet 2023; 55:471-483. [PMID: 36894709 PMCID: PMC10011139 DOI: 10.1038/s41588-023-01307-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arya Ökten
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew McNamara
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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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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SMARCA4: Current status and future perspectives in non-small-cell lung cancer. Cancer Lett 2023; 554:216022. [PMID: 36450331 DOI: 10.1016/j.canlet.2022.216022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
SMARCA4, also known as transcription activator, is an ATP-dependent catalytic subunit of SWI/SNF (SWItch/Sucrose NonFermentable) chromatin-remodeling complexes that participates in the regulation of chromatin structure and gene expression by supplying energy. As a tumor suppressor that has aberrant expression in ∼10% of non-small-cell lung cancers (NSCLCs), SMARCA4 possesses many biological functions, including regulating gene expression, differentiation and transcription. Furthermore, NSCLC patients with SMARCA4 alterations have a weak response to conventional chemotherapy and poor prognosis. Therefore, the mechanisms of SMARCA4 in NSCLC development urgently need to be explored to identify novel biomarkers and precise therapeutic strategies for this subtype. This review systematically describes the biological functions of SMARCA4 and its role in NSCLC development, metastasis, functional epigenetics and potential therapeutic approaches for NSCLCs with SMARCA4 alterations. Additionally, this paper explores the relationship and regulatory mechanisms shared by SMARCA4 and its mutually exclusive catalytic subunit SMARCA2. We aim to provide innovative treatment strategies and improve clinical outcomes for NSCLC patients with SMARCA4 alterations.
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35
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Zhuang HH, Qu Q, Teng XQ, Dai YH, Qu J. Superenhancers as master gene regulators and novel therapeutic targets in brain tumors. Exp Mol Med 2023; 55:290-303. [PMID: 36720920 PMCID: PMC9981748 DOI: 10.1038/s12276-023-00934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/27/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Transcriptional deregulation, a cancer cell hallmark, is driven by epigenetic abnormalities in the majority of brain tumors, including adult glioblastoma and pediatric brain tumors. Epigenetic abnormalities can activate epigenetic regulatory elements to regulate the expression of oncogenes. Superenhancers (SEs), identified as novel epigenetic regulatory elements, are clusters of enhancers with cell-type specificity that can drive the aberrant transcription of oncogenes and promote tumor initiation and progression. As gene regulators, SEs are involved in tumorigenesis in a variety of tumors, including brain tumors. SEs are susceptible to inhibition by their key components, such as bromodomain protein 4 and cyclin-dependent kinase 7, providing new opportunities for antitumor therapy. In this review, we summarized the characteristics and identification, unique organizational structures, and activation mechanisms of SEs in tumors, as well as the clinical applications related to SEs in tumor therapy and prognostication. Based on a review of the literature, we discussed the relationship between SEs and different brain tumors and potential therapeutic targets, focusing on glioblastoma.
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Affiliation(s)
- Hai-Hui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410007, PR China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410007, PR China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China
| | - Ying-Huan Dai
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, 410011, PR China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, PR China.
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36
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Williams NL, Hong L, Jaffe M, Shields CE, Haynes KA. PIC recruitment by synthetic reader-actuators to polycomb-silenced genes blocks triple-negative breast cancer invasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525196. [PMID: 36747762 PMCID: PMC9900809 DOI: 10.1101/2023.01.23.525196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Scientists have used small molecule inhibitors and genetic knockdown of gene-silencing polycomb repressive complexes (PRC1/2) to determine if restoring the expression of tumor suppressor genes can block proliferation and invasion of cancer cells. A major limitation of this approach is that inhibitors can not restore key transcriptional activators that are mutated in many cancers, such as p53 and members of the BRAF SWI/SNF complex. Furthermore, small molecule inhibitors can alter the activity of, rather than inhibit, the polycomb enzyme EZH2. While chromatin has been shown to play a major role in gene regulation in cancer, poor clinical results for polycomb chromatin-targeting therapies for diseases like triple-negative breast cancer (TNBC) could discourage further development of this emerging avenue for treatment. To overcome the limitations of inhibiting polycomb to study epigenetic regulation, we developed an engineered chromatin protein to manipulate transcription. The synthetic reader-actuator (SRA) is a fusion protein that directly binds a target chromatin modification and regulates gene expression. Here, we report the activity of an SRA built from polycomb chromodomain and VP64 modules that bind H3K27me3 and subunits of the Mediator complex, respectively. In SRA-expressing BT-549 cells, we identified 122 upregulated differentially expressed genes (UpDEGs, ≥ 2-fold activation, adjusted p < 0.05). On-target epigenetic regulation was determined by identifying UpDEGs at H3K27me3-enriched, closed chromatin. SRA activity induced activation of genes involved in cell death, cell cycle arrest, and the inhibition of migration and invasion. SRA-expressing BT-549 cells showed reduced spheroid size in Matrigel over time, loss of invasion, and activation of apoptosis. These results show that Mediator-recruiting regulators broadly targeted to silenced chromatin activate silenced tumor suppressor genes and stimulate anti-cancer phenotypes. Therefore further development of gene-activating epigenetic therapies might benefit TNBC patients.
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Affiliation(s)
- Natecia L Williams
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30312 USA
| | - Lauren Hong
- Georgia Institute of Technology, Atlanta, GA 30332
| | - Maya Jaffe
- Georgia Institute of Technology, Atlanta, GA 30332
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30312 USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30312 USA
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Nguyen VT, Tessema M, Weissman BE. The SWI/SNF Complex: A Frequently Mutated Chromatin Remodeling Complex in Cancer. Cancer Treat Res 2023; 190:211-244. [PMID: 38113003 DOI: 10.1007/978-3-031-45654-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The switch/sucrose non-fermenting (SWI/SNF) chromatin remodeling complex is a global regulator of gene expression known to maintain nucleosome-depleted regions at active enhancers and promoters. The mammalian SWI/SNF protein subunits are encoded by 29 genes and 11-15 subunits including an ATPase domain of either SMARCA4 (BRG1) or SMARCA2 (BRM) are assembled into a complex. Based on the distinct subunits, SWI/SNF are grouped into 3 major types (subfamilies): the canonical BRG1/BRM-associated factor (BAF/cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (GBAF/ncBAF). Pan-cancer genome sequencing studies have shown that nearly 25% of all cancers bear mutations in subunits of the SWI/SNF complex, many of which are loss of function (LOF) mutations, suggesting a tumor suppressor role. Inactivation of SWI/SNF complex subunits causes widespread epigenetic dysfunction, including increased dependence on antagonistic components such as polycomb repressor complexes (PRC1/2) and altered enhancer regulation, likely promoting an oncogenic state leading to cancer. Despite the prevalence of mutations, most SWI/SNF-mutant cancers lack targeted therapeutic strategies. Defining the dependencies created by LOF mutations in SWI/SNF subunits will identify better targets for these cancers.
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Affiliation(s)
- Vinh The Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Mathewos Tessema
- Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Bernard Ellis Weissman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA.
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38
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Wolf BK, Zhao Y, McCray A, Hawk WH, Deary LT, Sugiarto NW, LaCroix IS, Gerber SA, Cheng C, Wang X. Cooperation of chromatin remodeling SWI/SNF complex and pioneer factor AP-1 shapes 3D enhancer landscapes. Nat Struct Mol Biol 2023; 30:10-21. [PMID: 36522426 PMCID: PMC10513740 DOI: 10.1038/s41594-022-00880-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
The mechanism controlling the dynamic targeting of SWI/SNF has long been postulated to be coordinated by transcription factors (TFs), yet demonstrating a specific TF influence has proven difficult. Here we take a multi-omics approach to interrogate transient SWI/SNF interactors, chromatin targeting and the resulting three-dimensional epigenetic landscape. We utilize the labeling technique TurboID to map the SWI/SNF interactome and identify the activator protein-1 (AP-1) family members as critical interacting partners for SWI/SNF complexes. CUT&RUN profiling demonstrates SWI/SNF targeting enrichment at AP-1 bound loci, as well as SWI/SNF-AP-1 cooperation in chromatin targeting. HiChIP reveals AP-1-SWI/SNF-dependent restructuring of the three-dimensional promoter-enhancer architecture and generation of enhancer hubs. Through interrogation of the SWI/SNF-AP-1 interaction, we demonstrate an SWI/SNF dependency on AP-1-mediated chromatin localization. We propose that pioneer factors, such as AP-1, bind and target SWI/SNF to inactive chromatin, where it restructures the genomic landscape into an active state through epigenetic rewiring spanning multiple dimensions.
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Affiliation(s)
- Bennett K Wolf
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Andrew McCray
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - William H Hawk
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Luke T Deary
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Nicholas W Sugiarto
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | - Ian S LaCroix
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Scott A Gerber
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Sciences, Baylor College of Medicine, Houston, TX, USA.
| | - Xiaofeng Wang
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA.
- Dartmouth Cancer Center, Dartmouth College, Lebanon, NH, USA.
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Cantley J, Ye X, Rousseau E, Januario T, Hamman BD, Rose CM, Cheung TK, Hinkle T, Soto L, Quinn C, Harbin A, Bortolon E, Chen X, Haskell R, Lin E, Yu SF, Del Rosario G, Chan E, Dunlap D, Koeppen H, Martin S, Merchant M, Grimmer M, Broccatelli F, Wang J, Pizzano J, Dragovich PS, Berlin M, Yauch RL. Selective PROTAC-mediated degradation of SMARCA2 is efficacious in SMARCA4 mutant cancers. Nat Commun 2022; 13:6814. [PMID: 36357397 PMCID: PMC9649729 DOI: 10.1038/s41467-022-34562-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
The mammalian SWItch/Sucrose Non-Fermentable (SWI/SNF) helicase SMARCA4 is frequently mutated in cancer and inactivation results in a cellular dependence on its paralog, SMARCA2, thus making SMARCA2 an attractive synthetic lethal target. However, published data indicates that achieving a high degree of selective SMARCA2 inhibition is likely essential to afford an acceptable therapeutic index, and realizing this objective is challenging due to the homology with the SMARCA4 paralog. Herein we report the discovery of a potent and selective SMARCA2 proteolysis-targeting chimera molecule (PROTAC), A947. Selective SMARCA2 degradation is achieved in the absence of selective SMARCA2/4 PROTAC binding and translates to potent in vitro growth inhibition and in vivo efficacy in SMARCA4 mutant models, compared to wild type models. Global ubiquitin mapping and proteome profiling reveal no unexpected off-target degradation related to A947 treatment. Our study thus highlights the ability to transform a non-selective SMARCA2/4-binding ligand into a selective and efficacious in vivo SMARCA2-targeting PROTAC, and thereby provides a potential new therapeutic opportunity for patients whose tumors contain SMARCA4 mutations.
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Affiliation(s)
- Jennifer Cantley
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Xiaofen Ye
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Emma Rousseau
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Tom Januario
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Brian D. Hamman
- HotSpot Therapeutics, Inc. 1 Deerpark Dr., Ste C, Monmouth Junction, NJ 08852 USA
| | - Christopher M. Rose
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Tommy K. Cheung
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Trent Hinkle
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Leofal Soto
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Connor Quinn
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Alicia Harbin
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Elizabeth Bortolon
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Xin Chen
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Roy Haskell
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Eva Lin
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Shang-Fan Yu
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Geoff Del Rosario
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Emily Chan
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Debra Dunlap
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Hartmut Koeppen
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Scott Martin
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Mark Merchant
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Matt Grimmer
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Fabio Broccatelli
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Jing Wang
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Jennifer Pizzano
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Peter S. Dragovich
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
| | - Michael Berlin
- grid.504169.f0000 0004 7667 0983Arvinas, LLC, 5 Science Park, New Haven, CT 06511 USA
| | - Robert L. Yauch
- grid.418158.10000 0004 0534 4718Genentech, 1 DNA Way, South San Francisco, 94080 USA
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40
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Molecular Biology and Therapeutic Perspectives for K-Ras Mutant Non-Small Cell Lung Cancers. Cancers (Basel) 2022; 14:cancers14174103. [PMID: 36077640 PMCID: PMC9454753 DOI: 10.3390/cancers14174103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/28/2022] Open
Abstract
In non-small cell lung cancer (NSCLC) the most common alterations are identified in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene, accounting for approximately 30% of cases in Caucasian patients. The majority of mutations are located in exon 2, with the c.34G > T (p.G12C) change being the most prevalent. The clinical relevance of KRAS mutations in NSCLC was not recognized until a few years ago. What is now emerging is a dual key role played by KRAS mutations in the management of NSCLC patients. First, recent data report that KRAS-mutant lung AC patients generally have poorer overall survival (OS). Second, a KRAS inhibitor specifically targeting the c.34G > T (p.G12C) variant, Sotorasib, has been approved by the U.S. Food and Drug Administration (FDA) and by the European Medicines Agency. Another KRAS inhibitor targeting c.34G > T (p.G12C), Adagrasib, is currently being reviewed by the FDA for accelerated approval. From the description of the biology of KRAS-mutant NSCLC, the present review will focus on the clinical aspects of KRAS mutations in NSCLC, in particular on the emerging efficacy data of Sotorasib and other KRAS inhibitors, including mechanisms of resistance. Finally, the interaction between KRAS mutations and immune checkpoint inhibitors will be discussed.
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41
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Ulicna L, Kimmey SC, Weber CM, Allard GM, Wang A, Bui NQ, Bendall SC, Crabtree GR, Bean GR, Van Rechem C. The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations. Cancer Res 2022; 82:2829-2837. [PMID: 35749589 PMCID: PMC9379364 DOI: 10.1158/0008-5472.can-21-1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 01/09/2023]
Abstract
Subunits from the chromatin remodelers mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) are mutated, deleted, or amplified in more than 40% of cancers. Understanding their functions in normal cells and the consequences of cancerous alterations will provide insight into developing new targeted therapies. Here we examined whether mSWI/SNF mutations increase cellular sensitivity to specific drugs. Taking advantage of the DepMap studies, we demonstrate that cancer cells harboring mutations of specific mSWI/SNF subunits exhibit a genetic dependency on translation factors and are sensitive to translation pathway inhibitors. Furthermore, mSWI/SNF subunits were present in the cytoplasm and interacted with the translation initiation machinery, and short-term inhibition and depletion of specific subunits decreased global translation, implicating a direct role for these factors in translation. Depletion of specific mSWI/SNF subunits also increased sensitivity to mTOR-PI3K inhibitors. In patient-derived breast cancer samples, mSWI/SNF subunits expression in both the nucleus and the cytoplasm was substantially altered. In conclusion, an unexpected cytoplasmic role for mSWI/SNF complexes in translation suggests potential new therapeutic opportunities for patients afflicted by cancers demonstrating alterations in their subunits. SIGNIFICANCE This work establishes direct functions for mSWI/SNF in translation and demonstrates that alterations in mSWI/SNF confer a therapeutic vulnerability to translation pathway inhibitors in cancer cells.
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Affiliation(s)
- Livia Ulicna
- Department of Pathology, Stanford University, Stanford, California
| | - Samuel C. Kimmey
- Department of Pathology, Stanford University, Stanford, California.,Department of Medicine/Oncology, Stanford University, Stanford, California
| | | | - Grace M. Allard
- Department of Pathology, Stanford University, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University, Stanford, California
| | - Nam Q. Bui
- Department of Medicine/Oncology, Stanford University, Stanford, California
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, California
| | - Gerald R. Crabtree
- Department of Pathology, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University, Stanford, California
| | - Gregory R. Bean
- Department of Pathology, Stanford University, Stanford, California
| | - Capucine Van Rechem
- Department of Pathology, Stanford University, Stanford, California.,Corresponding Author: Capucine Van Rechem, Ph.D. Stanford Medicine Department of Pathology, 269 Campus Drive, CCSR-3245C, Stanford, CA 94305-5176. Phone: 650-723-7698; E-mail:
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42
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Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature 2022; 605:166-171. [PMID: 35477757 DOI: 10.1038/s41586-022-04658-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
DNA wraps around the histone octamer to form nucleosomes1, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions2,3. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.
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43
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Liu M, Wan L, Wang C, Yuan H, Peng Y, Wan N, Tang Z, Yuan X, Chen D, Long Z, Shi Y, Qiu R, Tang B, Jiang H, Chen Z. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4. Genes Genomics 2022; 44:1061-1070. [PMID: 35353340 DOI: 10.1007/s13258-022-01231-2] [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: 10/24/2021] [Accepted: 02/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in China. OBJECTIVE The aim of the current study was to identify the causes of two Chinese patients with congenital growth deficiency and intellectual disability. METHODS Genomic DNA was extracted from the peripheral venous blood of patients and their family members. Genetic analysis included whole-exome and Sanger sequencing. Pathogenicity assessments of variants were performed according to the guideline of the American College of Medical Genetics and Genomics. The phenotypic characteristics of all CSS subtypes were summarized through literature review. RESULTS We identified two Chinese CSS patients carrying novel variants of ARID1A and SMARCA4 respectively. The cases presented most core symptoms of CSS except for the digits involvement. Additionally, we performed a review of the phenotypic characteristics in CSS, highlighting phenotypic varieties and related potential causes. CONCLUSIONS We reported the first Chinese CSS2 and CSS4 patients with novel variants of ARID1A and SMARCA4. Our study expanded the genetic and phenotypic spectrum of CSS, providing a comprehensive overview of genotype-phenotype correlations of CSS.
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Affiliation(s)
- Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinrong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daji Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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44
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Tung HJ, Wu RC, Lin CY, Lai CH. Rare Subtype of Endometrial Cancer: Undifferentiated/Dedifferentiated Endometrial Carcinoma, from Genetic Aspects to Clinical Practice. Int J Mol Sci 2022; 23:ijms23073794. [PMID: 35409155 PMCID: PMC8999061 DOI: 10.3390/ijms23073794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 02/01/2023] Open
Abstract
Endometrial cancer (EC) is one of the most common gynecologic cancers worldwide. There were 417,367 newly diagnosed cases and 97,370 deaths due to this disease worldwide in 2020. The incidence rates have increased over time, especially in countries with rapid socioeconomic transitions, and EC has been the most prevalent gynecologic malignancy in Taiwan since 2012. The new EC molecular classifications of The Cancer Genome Atlas (TCGA) Research Network include clear-cell carcinoma, serous carcinoma, and carcinosarcoma, while undifferentiated/dedifferentiated EC (UDEC) is not mentioned, and most previous clinical trials for EC have not included UDEC. UDEC is rare, has an aggressive growth pattern, tends to be diagnosed at an advanced stage, and is resistant to conventional chemotherapy. In this review, case series or case reports on the clinical features and genomic/epigenetic and expression profiles on UDEC data are summarized in order to identify potential molecular targets for current and future research.
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Affiliation(s)
- Hsiu-Jung Tung
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
| | - Ren-Chin Wu
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
- Department of Pathology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
| | - Chyong-Huey Lai
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch and Chang Gung University College of Medicine, Taoyuan 333, Taiwan; (H.-J.T.); (C.-Y.L.)
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan 333, Taiwan;
- Correspondence: ; Tel.: +886-(3)-328-1200; Fax: +886-(3)-328-8252
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45
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Parreno V, Martinez AM, Cavalli G. Mechanisms of Polycomb group protein function in cancer. Cell Res 2022; 32:231-253. [PMID: 35046519 PMCID: PMC8888700 DOI: 10.1038/s41422-021-00606-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/10/2021] [Indexed: 02/01/2023] Open
Abstract
Cancer arises from a multitude of disorders resulting in loss of differentiation and a stem cell-like phenotype characterized by uncontrolled growth. Polycomb Group (PcG) proteins are members of multiprotein complexes that are highly conserved throughout evolution. Historically, they have been described as essential for maintaining epigenetic cellular memory by locking homeotic genes in a transcriptionally repressed state. What was initially thought to be a function restricted to a few target genes, subsequently turned out to be of much broader relevance, since the main role of PcG complexes is to ensure a dynamically choregraphed spatio-temporal regulation of their numerous target genes during development. Their ability to modify chromatin landscapes and refine the expression of master genes controlling major switches in cellular decisions under physiological conditions is often misregulated in tumors. Surprisingly, their functional implication in the initiation and progression of cancer may be either dependent on Polycomb complexes, or specific for a subunit that acts independently of other PcG members. In this review, we describe how misregulated Polycomb proteins play a pleiotropic role in cancer by altering a broad spectrum of biological processes such as the proliferation-differentiation balance, metabolism and the immune response, all of which are crucial in tumor progression. We also illustrate how interfering with PcG functions can provide a powerful strategy to counter tumor progression.
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Affiliation(s)
- Victoria Parreno
- Institute of Human Genetics, UMR 9002, CNRS-University of Montpellier, Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002, CNRS-University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS-University of Montpellier, Montpellier, France.
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46
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Duethorn B, Groll F, Rieger B, Drexler HCA, Brinkmann H, Kremer L, Stehling M, Borowski MT, Mildner K, Zeuschner D, Zernicka-Goetz M, Stemmler MP, Busch KB, Vaquerizas JM, Bedzhov I. Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism. Nat Commun 2022; 13:610. [PMID: 35105859 PMCID: PMC8807836 DOI: 10.1038/s41467-022-28139-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022] Open
Abstract
Lima1 is an extensively studied prognostic marker of malignancy and is also considered to be a tumour suppressor, but its role in a developmental context of non-transformed cells is poorly understood. Here, we characterise the expression pattern and examined the function of Lima1 in mouse embryos and pluripotent stem cell lines. We identify that Lima1 expression is controlled by the naïve pluripotency circuit and is required for the suppression of membrane blebbing, as well as for proper mitochondrial energetics in embryonic stem cells. Moreover, forcing Lima1 expression enables primed mouse and human pluripotent stem cells to be incorporated into murine pre-implantation embryos. Thus, Lima1 is a key effector molecule that mediates the pluripotency control of membrane dynamics and cellular metabolism.
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Affiliation(s)
- Binyamin Duethorn
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Fabian Groll
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Bettina Rieger
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Hannes C A Drexler
- Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Ludmila Kremer
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Marie-Theres Borowski
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Karina Mildner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, California Institute of Technology (Caltech), Pasadena, CA, 91125, USA
| | - Marc P Stemmler
- Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, FAU University Erlangen-Nürnberg, Erlangen, Germany
| | - Karin B Busch
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Schlossplatz 5, 48149, Münster, Germany
| | - Juan M Vaquerizas
- Regulatory Genomics group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.,MRC London Institute of Medical Sciences, Du Cane Road, W12 0NN, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149, Münster, Germany.
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47
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Shen M, Qi R, Ren J, Lv D, Yang H. Characterization With KRAS Mutant Is a Critical Determinant in Immunotherapy and Other Multiple Therapies for Non-Small Cell Lung Cancer. Front Oncol 2022; 11:780655. [PMID: 35070984 PMCID: PMC8766810 DOI: 10.3389/fonc.2021.780655] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a frequent type of cancer, which is mainly characterized clinically by high aggressiveness and high mortality. KRAS oncoprotein is the most common molecular protein detected in NSCLC, accounting for 25% of all oncogenic mutations. Constitutive activation of the KRAS oncoprotein triggers an intracellular cascade in cancer cells, leading to uncontrolled cell proliferation of cancer cells and aberrant cell survival states. The results of multiple clinical trials have shown that different KRAS mutation subtypes exhibit different sensitivities to different chemotherapy regimens. Meanwhile, anti-angiogenic drugs have shown differential efficacy for different subtypes of KRAS mutated lung cancer. It was explored to find if the specificity of the KRAS mutation subtype would affect PD-L1 expression, so immunotherapy would be of potential clinical value for the treatment of some types of KRAS mutations. It was discovered that the specificity of the KRAS mutation affected PD-L1, which opened up immunotherapy as a potential clinical treatment option. After several breakthrough studies, the preliminary test data of many early clinical trials showed that it is possible to directly inhibit KRAS G12C mutation, which has been proved to be a targeted treatment that is suitable for about 10%-12% of patients with advanced NSCLC, having a significant impact on the prolongation of their survival and the improvement of their quality of life. This article reviews the latest progress of treatments for NSCLC with KRAS mutation, in order to gain insight into the biological diversity of lung cancer cells and their potential clinical implications, thereby enabling individualized treatment for patients with KRAS-mutant NSCLC.
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Affiliation(s)
- Mo Shen
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Rongbin Qi
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Justin Ren
- Biological Sciences, Northwestern University, Evanston, Evanston, IL, United States
| | - Dongqing Lv
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Respiratory Medicine, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
| | - Haihua Yang
- Key Laboratory of Radiation Oncology of Taizhou, Radiation Oncology Institute of Enze Medical Health Academy, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
- Department of Radiation Oncology, Enze Hospital, Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou, China
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48
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Abstract
Actin is a highly conserved protein in mammals. The actin dynamics is regulated by actin-binding proteins and actin-related proteins. Nuclear actin and these regulatory proteins participate in multiple nuclear processes, including chromosome architecture organization, chromatin remodeling, transcription machinery regulation, and DNA repair. It is well known that the dysfunctions of these processes contribute to the development of cancer. Moreover, emerging evidence has shown that the deregulated actin dynamics is also related to cancer. This chapter discusses how the deregulation of nuclear actin dynamics contributes to tumorigenesis via such various nuclear events.
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Affiliation(s)
- Yuanjian Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengzhe Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center and Health Science Center, Houston, TX, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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49
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He Y, Yang C, Wang Y, Sacher JR, Sims MM, Pfeffer LM, Miller DD. Novel structural-related analogs of PFI-3 (SRAPs) that target the BRG1 catalytic subunit of the SWI/SNF complex increase the activity of temozolomide in glioblastoma cells. Bioorg Med Chem 2022; 53:116533. [PMID: 34863065 DOI: 10.1016/j.bmc.2021.116533] [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: 10/27/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 11/02/2022]
Abstract
Glioblastoma (GBM) is the most aggressive and treatment-refractory malignant adult brain cancer. After standard of care therapy, the overall median survival for GBM is only ∼6 months with a 5-year survival <10%. Although some patients initially respond to the DNA alkylating agent temozolomide (TMZ), unfortunately most patients become resistant to therapy and brain tumors eventually recur. We previously found that knockout of BRG1 or treatment with PFI-3, a small molecule inhibitor of the BRG1 bromodomain, enhances sensitivity of GBM cells to temozolomide in vitro and in vivo GBM animal models. Those results demonstrated that the BRG1 catalytic subunit of the SWI/SNF chromatin remodeling complex appears to play a critical role in regulating TMZ-sensitivity. In the present study we designed and synthesized Structurally Related Analogs of PFI-3 (SRAPs) and tested their bioactivity in vitro. Among of the SRAPs, 9f and 11d show better efficacy than PFI-3 in sensitizing GBM cells to the antiproliferative and cell death inducing effects of temozolomide in vitro, as well as enhancing the inhibitor effect of temozolomide on the growth of subcutaneous GBM tumors.
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Affiliation(s)
- Yali He
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Chuanhe Yang
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38103, United States
| | - Yinan Wang
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38103, United States
| | - Joshua R Sacher
- Cyclica, Inc., 207 Queens Quay West, Suite 420, Toronto, Ontario M5J 1A7, Canada
| | - Michelle M Sims
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38103, United States
| | - Lawrence M Pfeffer
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38103, United States
| | - Duane D Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, United States.
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50
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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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