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Madan V, Shyamsunder P, Dakle P, Woon TW, Han L, Cao Z, Nordin HBM, Jizhong S, Shuizhou Y, Hossain MZ, Koeffler HP. Dissecting the role of SWI/SNF component ARID1B in steady-state hematopoiesis. Blood Adv 2023; 7:6553-6566. [PMID: 37611161 PMCID: PMC10632677 DOI: 10.1182/bloodadvances.2023009946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The adenosine triphosphate (ATP)-dependent chromatin remodeling complex, SWItch/Sucrose Non-Fermentable (SWI/SNF), has been implicated in normal hematopoiesis. The AT-rich interaction domain 1B (ARID1B) and its paralog, ARID1A, are mutually exclusive, DNA-interacting subunits of the BRG1/BRM-associated factor (BAF) subclass of SWI/SNF complex. Although the role of several SWI/SNF components in hematopoietic differentiation and stem cell maintenance has been reported, the function of ARID1B in hematopoietic development has not been defined. To this end, we generated a mouse model of Arid1b deficiency specifically in the hematopoietic compartment. Unlike the extensive phenotype observed in mice deficient in its paralog, ARID1A, Arid1b knockout (KO) mice exhibited a modest effect on steady-state hematopoiesis. Nonetheless, transplantation experiments showed that the reconstitution of myeloid cells in irradiated recipient mice was dependent on ARID1B. Furthermore, to assess the effect of the complete loss of ARID1 proteins in the BAF complex, we generated mice lacking both ARID1A and ARID1B in the hematopoietic compartment. The double-KO mice succumbed to acute bone marrow failure resulting from complete loss of BAF-mediated chromatin remodeling activity. Our Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analyses revealed that >80% of loci regulated by ARID1B were distinct from those regulated by ARID1A; and ARID1B controlled expression of genes crucial in myelopoiesis. Overall, loss of ARID1B affected chromatin dynamics in murine hematopoietic stem and progenitor cells, albeit to a lesser extent than cells lacking ARID1A.
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Affiliation(s)
- Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Shi Jizhong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Shuizhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Md Zakir Hossain
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - H. Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA
- Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore
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2
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [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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Martin EW, Rodriguez y Baena A, Reggiardo RE, Worthington AK, Mattingly CS, Poscablo DM, Krietsch J, McManus MT, Carpenter S, Kim DH, Forsberg EC. Dynamics of Chromatin Accessibility During Hematopoietic Stem Cell Differentiation Into Progressively Lineage-Committed Progeny. Stem Cells 2023; 41:520-539. [PMID: 36945732 PMCID: PMC10183972 DOI: 10.1093/stmcls/sxad022] [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: 02/06/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Mapping the chromatin dynamics of functionally defined cell populations will shed mechanistic insight into 2 major, unanswered questions in stem cell biology: how does epigenetic identity contribute to a cell type's lineage potential, and how do cascades of chromatin remodeling dictate ensuing fate decisions? Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. Oligopotent progenitor populations operating between the HSCs and unipotent cells play essential roles in effecting hematopoietic homeostasis. To test the hypothesis that selective HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during progenitor differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points. Additionally, quantification of genome-wide peak count and size revealed overall greater chromatin accessibility in HSCs, allowing us to identify HSC-unique peaks as putative regulators of self-renewal and multilineage potential. Finally, CRISPRi-mediated targeting of ATACseq-identified putative CREs in HSCs allowed us to demonstrate the functional role of selective CREs in lineage-specific gene expression. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.
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Affiliation(s)
- Eric W Martin
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alessandra Rodriguez y Baena
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Roman E Reggiardo
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Atesh K Worthington
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Connor S Mattingly
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Donna M Poscablo
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jana Krietsch
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, Diabetes Center, W.M. Keck Center for Noncoding RNAs, University of California San Francisco, San Francisco, CA, USA
| | - Susan Carpenter
- Institute for the Biology of Stem Cells, Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Kim
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - E Camilla Forsberg
- Institute for the Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
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Xiao C, Hou J, Wang F, Song Y, Zheng J, Luo L, Wang J, Ding W, Zhu X, Xiong JW. Endothelial Brg1 fine-tunes Notch signaling during zebrafish heart regeneration. NPJ Regen Med 2023; 8:21. [PMID: 37029137 PMCID: PMC10082087 DOI: 10.1038/s41536-023-00293-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
Myocardial Brg1 is essential for heart regeneration in zebrafish, but it remains unknown whether and how endothelial Brg1 plays a role in heart regeneration. Here, we found that both brg1 mRNA and protein were induced in cardiac endothelial cells after ventricular resection and endothelium-specific overexpression of dominant-negative Xenopus Brg1 (dn-xbrg1) inhibited myocardial proliferation and heart regeneration and increased cardiac fibrosis. RNA-seq and ChIP-seq analysis revealed that endothelium-specific overexpression of dn-xbrg1 changed the levels of H3K4me3 modifications in the promoter regions of the zebrafish genome and induced abnormal activation of Notch family genes upon injury. Mechanistically, Brg1 interacted with lysine demethylase 7aa (Kdm7aa) to fine-tune the level of H3K4me3 within the promoter regions of Notch family genes and thus regulated notch gene transcription. Together, this work demonstrates that the Brg1-Kdm7aa-Notch axis in cardiac endothelial cells, including the endocardium, regulates myocardial proliferation and regeneration via modulating the H3K4me3 of the notch promoters in zebrafish.
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Affiliation(s)
- Chenglu Xiao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, 100193, Beijing, China
| | - Junjie Hou
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China
| | - Fang Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Yabing Song
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Jiyuan Zheng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Southwest University, Beibei, 400715, Chongqing, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Wanqiu Ding
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China.
| | - Xiaojun Zhu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China.
| | - Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 100871, Beijing, China.
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5
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Li N, Liu H, Xue Y, Xu Z, Miao X, Guo Y, Li Z, Fan Z, Xu Y. Targetable Brg1-CXCL14 axis contributes to alcoholic liver injury by driving neutrophil trafficking. EMBO Mol Med 2023; 15:e16592. [PMID: 36722664 PMCID: PMC9994483 DOI: 10.15252/emmm.202216592] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/02/2023] Open
Abstract
Alcoholic liver disease (ALD) accounts for a large fraction of patients with cirrhosis and hepatocellular carcinoma. In the present study we investigated the involvement of Brahma-related gene 1 (Brg1) in ALD pathogenesis and implication in ALD intervention. We report that Brg1 expression was elevated in mouse models of ALD, in hepatocyte exposed to alcohol, and in human ALD specimens. Manipulation of Brg1 expression in hepatocytes influenced the development of ALD in mice. Flow cytometry showed that Brg1 deficiency specifically attenuated hepatic infiltration of Ly6G+ neutrophils in the ALD mice. RNA-seq identified C-X-C motif chemokine ligand 14 (CXCL14) as a potential target for Brg1. CXCL14 knockdown alleviated whereas CXCL14 over-expression enhanced ALD pathogenesis in mice. Importantly, pharmaceutical inhibition of Brg1 with a small-molecule compound PFI-3 or administration of an antagonist to the CXCL14 receptor ameliorated ALD pathogenesis in mice. Finally, a positive correlation between Brg1 expression, CXCL14 expression, and neutrophil infiltration was detected in ALD patients. In conclusion, our data provide proof-of-concept for targeting the Brg1-CXCL14 axis in ALD intervention.
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Affiliation(s)
- Nan Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of PathophysiologyNanjing Medical UniversityNanjingChina
| | - Hong Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of PathophysiologyNanjing Medical UniversityNanjingChina
| | - Yujia Xue
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of PathophysiologyNanjing Medical UniversityNanjingChina
| | - Zheng Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of PathophysiologyNanjing Medical UniversityNanjingChina
| | - Xiulian Miao
- Collage of Life Sciences and Institute of Biomedical Research, Liaocheng UniversityLiaochengChina
| | - Yan Guo
- Collage of Life Sciences and Institute of Biomedical Research, Liaocheng UniversityLiaochengChina
| | - Zilong Li
- State Key Laboratory of Natural Medicines, Department of PharmacologyChina Pharmaceutical UniversityNanjingChina
| | - Zhiwen Fan
- Department of PathologyNanjing Drum Tower Hospital Affiliated to Nanjing University Medical SchoolNanjingChina
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of PathophysiologyNanjing Medical UniversityNanjingChina
- Collage of Life Sciences and Institute of Biomedical Research, Liaocheng UniversityLiaochengChina
- State Key Laboratory of Natural Medicines, Department of PharmacologyChina Pharmaceutical UniversityNanjingChina
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6
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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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7
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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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8
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Hashemi Karoii D, Azizi H, Skutella T. Microarray and in silico analysis of DNA repair genes between human testis of patients with nonobstructive azoospermia and normal cells. Cell Biochem Funct 2022; 40:865-879. [PMID: 36121211 DOI: 10.1002/cbf.3747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/16/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022]
Abstract
DNA repair processes are critical to maintaining genomic integrity. As a result, dysregulation of repair genes is likely to be linked with health implications, such as an increased prevalence of infertility and an accelerated rate of aging. We evaluated all the DNA repair genes (322 genes) by microarray. This study has provided insight into the connection between DNA repair genes, including RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, INO80, PMS2L1, CHEK2, TRIP13, and POLD4. The microarray analysis of six human cases with different nonobstructive azoospermia revealed that RAD23B, OBFC2A, PMS1, UBE2V1, ERCC5, SMUG1, RFC4, PMS2L5, MMS19, SHFM1, and INO80 were upregulated, and expression of PMS2L1, CHEK2, TRIP13, and POLD4 was downregulated versus the normal case. For this purpose, Enrich Shiny GO, STRING, and Cytoscape online evaluation was applied to predict proteins' functional and molecular interactions and then performed to recognize the master pathways. Functional enrichment analysis revealed that the biological process (BP) terms "base-excision repair, AP site formation," "nucleotide-excision repair, DNA gap filling," and "nucleotide-excision repair, preincision complex assembly" was significantly overexpressed in upregulated differentially expressed genes (DEGs). BP analysis of downregulated DEGs highlighted "histone phosphorylation," "DNA damage response, detection DNA response," "mitotic cell cycle checkpoint signaling," and "double-strand break repair." Overrepresented molecular function (MF) terms in upregulated DEGs included "Oxidized base lesion DNA N-glycosylase activity," "uracil DNA N-glycosylase activity," "bubble DNA binding" and "DNA clamp loader activity." Interestingly, MF investigation of downregulated DEGs showed overexpression in "heterotrimeric G-protein complex," "5'-deoxyribose-5-phosphate lyase activity," "minor groove of adenine-thymine-rich DNA binding," and "histone kinase activity." Our findings suggest that these genes and their interacting hub proteins could help determine the pathophysiology of germ cell abnormalities and infertility.
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Affiliation(s)
- Danial Hashemi Karoii
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Thomas Skutella
- Institute for Anatomy and Cell Biology, Medical Faculty, University of Heidelberg, Heidelberg, Germany
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9
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Wu T, Kong M, Xin XJ, Liu RQ, Wang HD, Song MZ, Xu WP, Yuan YB, Yang YY, Xiao PX. Epigenetic repression of THBD transcription by BRG1 contributes to deep vein thrombosis. Thromb Res 2022; 219:121-132. [PMID: 36162255 DOI: 10.1016/j.thromres.2022.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Deep vein thrombosis (DVT) with its major complication, pulmonary embolism, is a global health problem. Endothelial dysfunction is involved in the pathogenesis of DVT. We have previously demonstrated that endothelial specific deletion of Brahma-related gene 1 (BRG1) ameliorates atherosclerosis and aneurysm in animal models. Whether endothelial BRG1 contributes to DVT development remains undetermined. METHODS DVT was induced in mice by ligation of inferior vena cava. Deletion of BRG1 in endothelial cells was achieved by crossing the Cdh5-ERT-Cre mice with the Brg1loxp/loxp mice. RESULTS Here we report that compared to the wild type mice, BRG1 conditional knockout (CKO) mice displayed substantially decreased DVT susceptibility characterized by decreased weight and size of thrombus and reduced immune infiltration. In endothelial cells, thrombomodulin (THBD) expression was significantly decreased by TNF-α stimulation, while BRG1 knockdown or inhibition recovered THBD expression. Further analysis revealed that BRG1 deficiency decreased the CpG methylation levels of the THBD promoter induced by TNF-α. Mechanistically, BRG1 directly upregulated DNMT1 expression after TNF-α treatment in endothelial cells. More importantly, administration of a small-molecule BRG1 inhibitor PFI-3 displayed potent preventive and therapeutic potentials in the DVT model. CONCLUSIONS Our findings implicate BRG1 as an important regulator of DVT pathogenesis likely through epigenetic regulation of THBD expression in endothelial cells and provide translational proof-of-concept for targeting BRG1 in DVT intervention.
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Affiliation(s)
- Teng Wu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Center for Experimental Medicine, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China; Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou, China
| | - Ming Kong
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Xiao-Jun Xin
- Department of Cardiology, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui-Qi Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Hui-di Wang
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Ming-Zi Song
- Laboratory Center for Experimental Medicine and Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Wen-Ping Xu
- Laboratory Center for Experimental Medicine and Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Yi-Biao Yuan
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Center for Experimental Medicine, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China.
| | - Yu-Yu Yang
- Jiangsu Key Laboratory for Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
| | - Ping-Xi Xiao
- Department of Cardiology, the Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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10
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Tu Z, Fan C, Davis AK, Hu M, Wang C, Dandamudi A, Seu KG, Kalfa TA, Lu QR, Zheng Y. Autism-associated chromatin remodeler CHD8 regulates erythroblast cytokinesis and fine-tunes the balance of Rho GTPase signaling. Cell Rep 2022; 40:111072. [PMID: 35830790 PMCID: PMC9302451 DOI: 10.1016/j.celrep.2022.111072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
CHD8 is an ATP-dependent chromatin-remodeling factor whose monoallelic mutation defines a subtype of autism spectrum disorders (ASDs). Previous work found that CHD8 is required for the maintenance of hematopoiesis by integrating ATM-P53-mediated survival of hematopoietic stem/progenitor cells (HSPCs). Here, by using Chd8F/FMx1-Cre combined with a Trp53F/F mouse model that suppresses apoptosis of Chd8−/− HSPCs, we identify CHD8 as an essential regulator of erythroid differentiation. Chd8−/−P53−/− mice exhibited severe anemia conforming to congenital dyserythropoietic anemia (CDA) phenotypes. Loss of CHD8 leads to drastically decreased numbers of orthochromatic erythroblasts and increased binucleated and multinucleated basophilic erythroblasts with a cytokinesis failure in erythroblasts. CHD8 binds directly to the gene bodies of multiple Rho GTPase signaling genes in erythroblasts, and loss of CHD8 results in their dysregulated expression, leading to decreased RhoA and increased Rac1 and Cdc42 activities. Our study shows that autism-associated CHD8 is essential for erythroblast cytokinesis. Tu et al. report that CHD8, an autism-related chromatin remodeler, is essential for erythroid differentiation. Loss of CHD8 leads to unbalanced Rho GTPase signaling and defective erythroblast cytokinesis, mimicking that of congenital dyserythropoietic anemia.
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Affiliation(s)
- Zhaowei Tu
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory for Major Obstetric Diseases, Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Cuiqing Fan
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Ashely K Davis
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Mengwen Hu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Chen Wang
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Akhila Dandamudi
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Katie G Seu
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Theodosia A Kalfa
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Q Richard Lu
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Yi Zheng
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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11
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Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis. Blood 2022; 139:3532-3545. [PMID: 35297980 DOI: 10.1182/blood.2021014308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/15/2022] [Indexed: 11/20/2022] Open
Abstract
Hemogen, also known as EDAG, is a hematopoietic tissue-specific gene that regulates the proliferation and differentiation of hematopoietic cells. However, the mechanism underlying hemogen function in erythropoiesis is unknown. We found that depletion of hemogen in human CD34+ erythroid progenitor cells and HUDEP2 cells significantly reduced the expression of genes associated with heme and hemoglobin synthesis, supporting a positive role of hemogen in erythroid maturation. In human K562 cells, hemogen antagonized the occupancy of co-repressors NuRD complex and facilitated LDB1 complex-mediated chromatin looping. Hemogen recruited SWI/SNF complex ATPase BRG1 as a co-activator to regulate nucleosome accessibility and H3K27ac enrichment for promoter and enhancer activity. To ask if hemogen/BRG1 cooperativity is conserved in mammalian systems, we generated hemogen KO/KI mice and investigated hemogen/BRG1 function in murine erythropoiesis. Loss of hemogen in E12.5-E16.5 fetal liver cells impeded erythroid differentiation through reducing the production of mature erythroblasts. ChIP-seq in WT and hemogen KO animal revealed BRG1 is largely dependent on hemogen to regulate chromatin accessibility at erythroid gene promoters and enhancers. In summary, hemogen/BRG1 interaction in mammals is essential for fetal erythroid maturation and hemoglobin production through its active role in promoter and enhancer activity and chromatin organization.
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12
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Rago F, Rodrigues LU, Bonney M, Sprouffske K, Kurth E, Elliott G, Ambrose J, Aspesi P, Oborski J, Chen JT, McDonald ER, Mapa FA, Ruddy DA, Kauffmann A, Abrams T, Bhang HEC, Jagani Z. Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia. Mol Cancer Res 2021; 20:361-372. [PMID: 34799403 DOI: 10.1158/1541-7786.mcr-21-0390] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 10/03/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Various subunits of mammalian SWI/SNF chromatin remodeling complexes display loss-of-function mutations characteristic of tumor suppressors in different cancers, but an additional role for SWI/SNF supporting cell survival in distinct cancer contexts is emerging. In particular, genetic dependence on the catalytic subunit BRG1/SMARCA4 has been observed in acute myeloid leukemia (AML), yet the feasibility of direct therapeutic targeting of SWI/SNF catalytic activity in leukemia remains unknown. Here, we evaluated the activity of dual BRG1/BRM ATPase inhibitors across a genetically diverse panel of cancer cell lines and observed that hematopoietic cancer cell lines were among the most sensitive compared to other lineages. This result was striking in comparison to data from pooled short hairpin RNA screens, which showed that only a subset of leukemia cell lines display sensitivity to BRG1 knockdown. We demonstrate that combined genetic knockdown of BRG1 and BRM is required to recapitulate the effects of dual inhibitors, suggesting that SWI/SNF dependency in human leukemia extends beyond a predominantly BRG1-driven mechanism. Through gene expression and chromatin accessibility studies, we show that the dual inhibitors act at genomic loci associated with oncogenic transcription factors, and observe a downregulation of leukemic pathway genes including MYC, a well-established target of BRG1 activity in AML. Overall, small molecule inhibition of BRG1/BRM induced common transcriptional responses across leukemia models resulting in a spectrum of cellular phenotypes. Implications: Our studies reveal the breadth of SWI/SNF dependency in leukemia and support targeting SWI/SNF catalytic function as a potential therapeutic strategy in AML.
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Affiliation(s)
| | | | - Megan Bonney
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Esther Kurth
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Jessi Ambrose
- Oncology, Novartis Institutes for Biomedical Research
| | - Peter Aspesi
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Justin Oborski
- High Throughput Biology, Novartis Institutes for Biomedical Research
| | - Julie T Chen
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Felipa A Mapa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - David A Ruddy
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research
| | - Audrey Kauffmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research
| | - Tinya Abrams
- Disease Area Oncology, Novartis Institutes for BioMedical Research
| | | | - Zainab Jagani
- Oncology, Novartis Institutes for Biomedical Research
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13
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Ding Y, Li Y, Zhao Z, Cliff Zhang Q, Liu F. The chromatin-remodeling enzyme Smarca5 regulates erythrocyte aggregation via Keap1-Nrf2 signaling. eLife 2021; 10:72557. [PMID: 34698638 PMCID: PMC8594921 DOI: 10.7554/elife.72557] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/23/2021] [Indexed: 12/30/2022] Open
Abstract
Although thrombosis has been extensively studied using various animal models, our understanding of the underlying mechanism remains elusive. Here, using zebrafish model, we demonstrated that smarca5-deficient red blood cells (RBCs) formed blood clots in the caudal vein plexus. We further used the anti-thrombosis drugs to treat smarca5zko1049a embryos and found that a thrombin inhibitor, argatroban, partially prevented blood clot formation in smarca5zko1049a. To explore the regulatory mechanism of smarca5 in RBC homeostasis, we profiled the chromatin accessibility landscape and transcriptome features in RBCs from smarca5zko1049a and their siblings and found that both the chromatin accessibility at the keap1a promoter and expression of keap1a were decreased. Keap1 is a suppressor protein of Nrf2, which is a major regulator of oxidative responses. We further identified that the expression of hmox1a, a downstream target of Keap1-Nrf2 signaling pathway, was markedly increased upon smarca5 deletion. Importantly, overexpression of keap1a or knockdown of hmox1a partially rescued the blood clot formation, suggesting that the disrupted Keap1-Nrf2 signaling is responsible for the RBC aggregation in smarca5 mutants. Together, our study using zebrafish smarca5 mutants characterizes a novel role for smarca5 in RBC aggregation, which may provide a new venous thrombosis animal model to support drug screening and pre-clinical therapeutic assessments to treat thrombosis.
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Affiliation(s)
- Yanyan Ding
- The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory, Guangzhou, China.,State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuzhe Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ziqian Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Yang C, Wang Y, Sims MM, He Y, Miller DD, Pfeffer LM. Targeting the Bromodomain of BRG-1/BRM Subunit of the SWI/SNF Complex Increases the Anticancer Activity of Temozolomide in Glioblastoma. Pharmaceuticals (Basel) 2021; 14:ph14090904. [PMID: 34577604 PMCID: PMC8467157 DOI: 10.3390/ph14090904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Glioblastoma (GBM) is a deadly and incurable brain cancer with limited therapeutic options. PFI-3 is a small-molecule bromodomain (BRD) inhibitor of the BRM/BRG1 subunits of the SWI/SNF chromatin remodeling complex. The objective of this study is to determine the efficacy of PFI-3 as a potential GBM therapy. We report that PFI-3 binds to these BRDs when expressed in GBM cells. PFI-3 markedly enhanced the antiproliferative and cell death-inducing effects of temozolomide (TMZ) in TMZ-sensitive GBM cells as well as overcame the chemoresistance of highly TMZ-resistant GBM cells. PFI-3 also altered gene expression in GBM and enhanced the basal and interferon-induced expression of a subset of interferon-responsive genes. Besides the effects of PFI-3 on GBM cells in vitro, we found that PFI-3 markedly potentiated the anticancer effect of TMZ in an intracranial GBM animal model, resulting in a marked increase in survival of animals bearing GBM tumors. Taken together, we identified the BRG1 and BRM subunits of SWI/SNF as novel targets in GBM and revealed the therapeutic potential of applying small molecule inhibitors of SWI/SNF to improve the clinical outcome in GBM using standard-of-care chemotherapy.
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Affiliation(s)
- Chuanhe Yang
- Department of Pathology and Laboratory Medicine, Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.Y.); (Y.W.); (M.M.S.)
| | - Yinan Wang
- Department of Pathology and Laboratory Medicine, Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.Y.); (Y.W.); (M.M.S.)
| | - Michelle M. Sims
- Department of Pathology and Laboratory Medicine, Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.Y.); (Y.W.); (M.M.S.)
| | - Yali He
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (Y.H.); (D.D.M.)
| | - Duane D. Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (Y.H.); (D.D.M.)
| | - Lawrence M. Pfeffer
- Department of Pathology and Laboratory Medicine, Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.Y.); (Y.W.); (M.M.S.)
- Correspondence:
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15
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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16
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Wang Y, Yang CH, Schultz AP, Sims MM, Miller DD, Pfeffer LM. Brahma-Related Gene-1 (BRG1) promotes the malignant phenotype of glioblastoma cells. J Cell Mol Med 2021; 25:2956-2966. [PMID: 33528916 PMCID: PMC7957270 DOI: 10.1111/jcmm.16330] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive malignant brain tumour that is resistant to existing therapeutics. Identifying signalling pathways deregulated in GBM that can be targeted therapeutically is critical to improve the present dismal prognosis for GBM patients. In this report, we have identified that the BRG1 (Brahma‐Related Gene‐1) catalytic subunit of the SWI/SNF chromatin remodelling complex promotes the malignant phenotype of GBM cells. We found that BRG1 is ubiquitously expressed in tumour tissue from GBM patients, and high BRG1 expression levels are localized to specific brain tumour regions. Knockout (KO) of BRG1 by CRISPR‐Cas9 gene editing had minimal effects on GBM cell proliferation, but significantly inhibited GBM cell migration and invasion. BRG1‐KO also sensitized GBM cells to the anti‐proliferative effects of the anti‐cancer agent temozolomide (TMZ), which is used to treat GBM patients in the clinic, and selectively altered STAT3 tyrosine phosphorylation and gene expression. These results demonstrate that BRG‐1 promotes invasion and migration, and decreases chemotherapy sensitivity, indicating that it functions in an oncogenic manner in GBM cells. Taken together, our findings suggest that targeting BRG1 in GBM may have therapeutic benefit in the treatment of this deadly form of brain cancer.
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Affiliation(s)
- Yinan Wang
- Department of Pathology and Laboratory Medicine (College of Medicine), and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Chuan He Yang
- Department of Pathology and Laboratory Medicine (College of Medicine), and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Andrew P Schultz
- Department of Pathology and Laboratory Medicine (College of Medicine), and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michelle M Sims
- Department of Pathology and Laboratory Medicine (College of Medicine), and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Duane D Miller
- Department of Pharmaceutical Sciences (College of Pharmacy), University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lawrence M Pfeffer
- Department of Pathology and Laboratory Medicine (College of Medicine), and the Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
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17
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Bluemn T, Schmitz J, Chen Y, Zheng Y, Zhang Y, Zheng S, Burns R, DeJong J, Christiansen L, Izaguirre-Carbonell J, Wang D, Zhu N. Arid2 regulates hematopoietic stem cell differentiation in normal hematopoiesis. Exp Hematol 2021; 94:37-46. [PMID: 33346030 PMCID: PMC10041880 DOI: 10.1016/j.exphem.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 01/25/2023]
Abstract
The switch/sugar nonfermenting (SWI/SNF) family of chromatin remodeling complexes have been implicated in normal hematopoiesis. The ARID2 protein is a component of the polybromo-associated BAF (PBAF), one of the two main SWI/SNF complexes. In the current study, we used a conditional Arid2 knockout mouse model to determine its role in normal hematopoiesis. We found that the loss of Arid2 has no discernable effects on steady-state hematopoiesis, with the exception of a modest effect on erythropoiesis. On bone marrow transplantation, however, the loss of Arid2 affects HSC differentiation in a cell-autonomous manner, resulting in significant decreases in the ability to reconstitute the lymphoid lineage. Gene expression analysis of Arid2 knockout cells revealed enrichment of myeloid-biased multipotent progenitor (MPP) cell signatures, while the lymphoid-biased MPPs are enriched in the wild type, consistent with the observed phenotype. Moreover, Arid2 knockout cells revealed enrichment of inflammatory pathways with upregulation of TLR receptors, as well as downstream signaling cascade genes. Furthermore, under lymphocyte-biased growth conditions in vitro, Arid2 null bone marrow cells have significantly impaired proliferation, which decreased further on lipopolysaccharide stimulation. Overall, these data suggest that the loss of Arid2 impairs HSC differentiation ability, and this effect may be mediated through upregulation of inflammatory pathways.
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Affiliation(s)
- Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Yuhong Chen
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | | | - Shikan Zheng
- Blood Research Institute, Versiti, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | - Luke Christiansen
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI.
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18
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Wang Y, Yu L, Engel JD, Singh SA. Epigenetic activities in erythroid cell gene regulation. Semin Hematol 2020; 58:4-9. [PMID: 33509442 DOI: 10.1053/j.seminhematol.2020.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/27/2020] [Indexed: 01/20/2023]
Abstract
Interest in the role of epigenetic mechanisms in human biology has exponentially increased over the past several decades. The multitude of opposing and context-dependent chromatin-modifying enzymes/coregulator complexes is just beginning to be understood at a molecular level. This science has benefitted tremendously from studies of erythropoiesis, in which a series of β-globin genes are in sequence turned "on" and "off," serving as a fascinating model of coordinated gene expression. We, therefore, describe here epigenetic complexes about which we know most, using erythropoiesis as the context. The biochemical insights lay the foundation for proposing and developing novel treatments for diseases of red cells and of erythropoiesis, identifying for example epigenetic enzymes that can be drugged to manipulate β-globin locus regulation, to favor activation of unmutated fetal hemoglobin over mutated adult β-globin genes to treat sickle cell disease and β-thalassemias. Other potential translational applications are in redirecting hematopoietic commitment decisions, as treatment for bone marrow failure syndromes.
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Affiliation(s)
- Yu Wang
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Lei Yu
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI.
| | - Sharon A Singh
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI
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19
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Clapier CR, Verma N, Parnell TJ, Cairns BR. Cancer-Associated Gain-of-Function Mutations Activate a SWI/SNF-Family Regulatory Hub. Mol Cell 2020; 80:712-725.e5. [PMID: 33058778 PMCID: PMC7853424 DOI: 10.1016/j.molcel.2020.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/17/2023]
Abstract
SWI/SNF-family remodelers (BAF/PBAF in mammals) are essential chromatin regulators, and mutations in human BAF/PBAF components are associated with ∼20% of cancers. Cancer-associated missense mutations in human BRG1 (encoding the catalytic ATPase) have been characterized previously as conferring loss-of-function. Here, we show that cancer-associated missense mutations in BRG1, when placed into the orthologous Sth1 ATPase of the yeast RSC remodeler, separate into two categories: loss-of-function enzymes, or instead, gain-of-function enzymes that greatly improve DNA translocation efficiency and nucleosome remodeling in vitro. Our work identifies a structural "hub," formed by the association of several Sth1 domains, that regulates ATPase activity and DNA translocation efficiency. Remarkably, all gain-of-function cancer-associated mutations and all loss-of-function mutations physically localize to distinct adjacent regions in the hub, which specifically regulate and implement DNA translocation, respectively. In vivo, only gain-of-function cancer-associated mutations conferred precocious chromatin accessibility. Taken together, we provide a structure-function mechanistic basis for cancer-associated hyperactivity.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Naveen Verma
- Department of Oncological Sciences and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bradley R Cairns
- Department of Oncological Sciences and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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20
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Fernando TM, Piskol R, Bainer R, Sokol ES, Trabucco SE, Zhang Q, Trinh H, Maund S, Kschonsak M, Chaudhuri S, Modrusan Z, Januario T, Yauch RL. Functional characterization of SMARCA4 variants identified by targeted exome-sequencing of 131,668 cancer patients. Nat Commun 2020; 11:5551. [PMID: 33144586 PMCID: PMC7609548 DOI: 10.1038/s41467-020-19402-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic studies performed in cancer patients and tumor-derived cell lines have identified a high frequency of alterations in components of the mammalian switch/sucrose non-fermentable (mSWI/SNF or BAF) chromatin remodeling complex, including its core catalytic subunit, SMARCA4. Cells exhibiting loss of SMARCA4 rely on its paralog, SMARCA2, making SMARCA2 an attractive therapeutic target. Here we report the genomic profiling of solid tumors from 131,668 cancer patients, identifying 9434 patients with one or more SMARCA4 gene alterations. Homozygous SMARCA4 mutations were highly prevalent in certain tumor types, notably non-small cell lung cancer (NSCLC), and associated with reduced survival. The large sample size revealed previously uncharacterized hotspot missense mutations within the SMARCA4 helicase domain. Functional characterization of these mutations demonstrated markedly reduced remodeling activity. Surprisingly, a few SMARCA4 missense variants partially or fully rescued paralog dependency, underscoring that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations who may benefit from SMARCA2-targeted therapy.
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Affiliation(s)
- Tharu M Fernando
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert Piskol
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Russell Bainer
- Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Ethan S Sokol
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Sally E Trabucco
- Cancer Genomics Research, Foundation Medicine, Cambridge, MA, 02141, USA
| | - Qing Zhang
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Huong Trinh
- Product Development Personalized Healthcare Data Science, Genentech, South San Francisco, CA, 94080, USA
| | - Sophia Maund
- Oncology Biomarker Development, Genentech, South San Francisco, CA, 94080, USA
| | - Marc Kschonsak
- Structural Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Thomas Januario
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA
| | - Robert L Yauch
- Discovery Oncology, Genentech, South San Francisco, CA, 94080, USA.
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21
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ATP-Dependent Chromatin Remodeling Complex in the Lineage Specification of Mesenchymal Stem Cells. Stem Cells Int 2020; 2020:8839703. [PMID: 32963551 PMCID: PMC7499328 DOI: 10.1155/2020/8839703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) present in multiple tissues can self-renew and differentiate into multiple lineages including the bone, cartilage, muscle, cardiac tissue, and connective tissue. Key events, including cell proliferation, lineage commitment, and MSC differentiation, are ensured by precise gene expression regulation. ATP-dependent chromatin alteration is one form of epigenetic modifications that can regulate the transcriptional level of specific genes by utilizing the energy from ATP hydrolysis to reorganize chromatin structure. ATP-dependent chromatin remodeling complexes consist of a variety of subunits that together perform multiple functions in self-renewal and lineage specification. This review highlights the important role of ATP-dependent chromatin remodeling complexes and their different subunits in modulating MSC fate determination and discusses the proposed mechanisms by which ATP-dependent chromatin remodelers function.
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22
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Wu E, Vastenhouw NL. From mother to embryo: A molecular perspective on zygotic genome activation. Curr Top Dev Biol 2020; 140:209-254. [PMID: 32591075 DOI: 10.1016/bs.ctdb.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In animals, the early embryo is mostly transcriptionally silent and development is fueled by maternally supplied mRNAs and proteins. These maternal products are important not only for survival, but also to gear up the zygote's genome for activation. Over the last three decades, research with different model organisms and experimental approaches has identified molecular factors and proposed mechanisms for how the embryo transitions from being transcriptionally silent to transcriptionally competent. In this chapter, we discuss the molecular players that shape the molecular landscape of ZGA and provide insights into their mode of action in activating the transcription program in the developing embryo.
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Affiliation(s)
- Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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23
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Li Z, Lv F, Dai C, Wang Q, Jiang C, Fang M, Xu Y. Activation of Galectin-3 (LGALS3) Transcription by Injurious Stimuli in the Liver Is Commonly Mediated by BRG1. Front Cell Dev Biol 2019; 7:310. [PMID: 31850346 PMCID: PMC6901944 DOI: 10.3389/fcell.2019.00310] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/13/2019] [Indexed: 01/13/2023] Open
Abstract
Galectin-3 (encoded by LGALS3) is a glycan-binding protein that regulates a diverse range of pathophysiological processes contributing to the pathogenesis of human diseases. Previous studies have found that galectin-3 levels are up-regulated in the liver by a host of different injurious stimuli. The underlying epigenetic mechanism, however, is unclear. Here we report that conditional knockout of Brahma related gene (BRG1), a chromatin remodeling protein, in hepatocytes attenuated induction of galectin-3 expression in several different animal models of liver injury. Similarly, BRG1 depletion or pharmaceutical inhibition in cultured hepatocytes suppressed the induction of galectin-3 expression by treatment with LPS plus free fatty acid (palmitate). Further analysis revealed that BRG1 interacted with AP-1 to bind to the proximal galectin-3 promoter and activate transcription. Mechanistically, DNA demethylation surrounding the galectin-3 promoter appeared to be a rate-limiting step in BRG1-mediated activation of galectin-3 transcription. BRG1 recruited the DNA 5-methylcytosine dioxygenase TET1 to the galectin-3 to promote active DNA demethylation thereby activating galectin-3 transcription. Finally, TET1 silencing abrogated induction of galectin-3 expression by LPS plus palmitate in cultured hepatocytes. In conclusion, our data unveil a novel epigenetic pathway that contributes to injury-associated activation of galectin-3 transcription in hepatocytes.
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Affiliation(s)
- Zilong Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Fangqiao Lv
- Department of Cell Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Congxin Dai
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Qiong Wang
- Department of Surgical Oncology, the Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Chao Jiang
- Department of Surgical Oncology, the Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Mingming Fang
- Department of Clinical Medicine, Laboratory Center for Basic Medical Sciences, Jiangsu Health Vocational College, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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24
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Han L, Madan V, Mayakonda A, Dakle P, Woon TW, Shyamsunder P, Nordin HBM, Cao Z, Sundaresan J, Lei I, Wang Z, Koeffler HP. Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice. Leukemia 2019; 33:2291-2305. [PMID: 30858552 PMCID: PMC6756219 DOI: 10.1038/s41375-019-0438-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/17/2022]
Abstract
Precise regulation of chromatin architecture is vital to physiological processes including hematopoiesis. ARID1A is a core component of the mammalian SWI/SNF complex, which is one of the ATP-dependent chromatin remodeling complexes. To uncover the role of ARID1A in hematopoietic development, we utilized hematopoietic cell-specific deletion of Arid1a in mice. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impairs the differentiation of both myeloid and lymphoid lineages. ARID1A deficiency led to a global reduction in open chromatin and ensuing transcriptional changes affected key genes involved in hematopoietic development. We also observed that silencing of ARID1A affected ATRA-induced differentiation of NB4 cells, suggesting its role in granulocytic differentiation of human leukemic cells. Overall, our study provides a comprehensive elucidation of the function of ARID1A in hematopoiesis and highlights the central role of ARID1A-containing SWI/SNF complex in maintaining chromatin dynamics in hematopoietic cells.
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Affiliation(s)
- Lin Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vikas Madan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Teoh Weoi Woon
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - Zeya Cao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Janani Sundaresan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ienglam Lei
- Department of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Zhong Wang
- Department of Cardiac Surgery, Cardiovascular Research Center, University of Michigan, Ann Arbor, MI, USA
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA, USA.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Hospital, Singapore, Singapore
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25
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The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting. Nat Genet 2019; 51:618-626. [PMID: 30858614 PMCID: PMC6755913 DOI: 10.1038/s41588-019-0363-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/29/2019] [Indexed: 12/02/2022]
Abstract
Perturbations to mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complexes have been widely implicated as driving events in cancer1. One such perturbation is the dual loss of the SMARCA4 and SMARCA2 ATPase subunits in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)2–5, SMARCA4-deficient thoracic sarcomas6 and dedifferentiated endometrial carcinomas7. However, the consequences of dual ATPase subunit loss on mSWI/SNF complex subunit composition, chromatin targeting, DNA accessibility and gene expression remain unknown. Here we identify an ATPase module of subunits that is required for functional specification of BAF and PBAF subcomplexes. Using SMARCA4/2 ATPase mutant variants, we define the catalytic activity -dependent and -independent contributions of the ATPase module to the targeting of BAF and PBAF complexes on chromatin genome-wide. Finally, by linking distinct mSWI/SNF complex target sites to tumor-suppressive gene expression programs, we clarify the transcriptional consequences of SMARCA4/2 dual loss in SCCOHT.
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26
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Wang B, Kaufmann B, Engleitner T, Lu M, Mogler C, Olsavszky V, Öllinger R, Zhong S, Geraud C, Cheng Z, Rad RR, Schmid RM, Friess H, Hüser N, Hartmann D, von Figura G. Brg1 promotes liver regeneration after partial hepatectomy via regulation of cell cycle. Sci Rep 2019; 9:2320. [PMID: 30787318 PMCID: PMC6382836 DOI: 10.1038/s41598-019-38568-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/21/2018] [Indexed: 12/29/2022] Open
Abstract
Brahma-related gene 1 (Brg1), a catalytic subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, is known to be involved in proliferative cell processes. Liver regeneration is initiated spontaneously after injury and leads to a strong proliferative response. In this study, a hepatocyte-specific Brg1 gene knockout mouse model was used to analyse the role of Brg1 in liver regeneration by performing a 70% partial hepatectomy (PH). After PH, Brg1 was significantly upregulated in wildtype mice. Mice with hepatocyte-specific Brg1 gene knockout showed a significantly lower liver to body weight ratio 48 h post-PH concomitant with a lower hepatocellular proliferation rate compared to wildtype mice. RNA sequencing demonstrated that Brg1 controlled hepatocyte proliferation through the regulation of the p53 pathway and several cell cycle genes. The data of this study reveal a crucial role of Brg1 for liver regeneration by promoting hepatocellular proliferation through modulation of cell cycle genes and, thus, identify Brg1 as potential target for therapeutic approaches.
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Affiliation(s)
- Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Benedikt Kaufmann
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Miao Lu
- Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Carolin Mogler
- Institute of Pathology, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Victor Olsavszky
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University and Center of Excellence in Dermatology, Mannheim, 68135, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Suyang Zhong
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Cyrill Geraud
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University and Center of Excellence in Dermatology, Mannheim, 68135, Germany
| | - Zhangjun Cheng
- Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Roland R Rad
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Roland M Schmid
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Helmut Friess
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Norbert Hüser
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Daniel Hartmann
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.
| | - Guido von Figura
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.
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27
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The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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28
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Jiang L, Gao Y, Wang G, Zhong J. Retracted Article: PKM2 overexpression protects against 6-hydroxydopamine-induced cell injury in the PC12 cell model of Parkinson's disease via regulation of the brahma-related gene 1/STAT3 pathway. RSC Adv 2019; 9:14834-14840. [PMID: 35516344 PMCID: PMC9064332 DOI: 10.1039/c9ra01760g] [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: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 11/26/2022] Open
Abstract
According to published estimates, pyruvate kinase isoform M2 (PKM2) was expressed in low amounts in patients with Parkinson's disease (PD). However, the function and molecular mechanism of PKM2 in PD remain largely unknown. The main purpose of our study was to reveal the function and mechanism of PKM2 in the in vitro model of PD. Here, we show that PKM2 decreased in PC12 cells after 6-hydroxydopamine (6-OHDA) treatment, which inhibited PC12 cell survival and induced its apoptosis. PKM2 overexpression is required for 6-OHDA-induced PC12 cell survival. Moreover, up-regulated PKM2 expression suppressed PC12 cell apoptosis and caspase-3 activity compared with the 6-OHDA treatment alone group. Increased brahma-related gene 1 (Brg1) and p-STAT3 expression was observed in PKM2-overexpressed PC12 cells compared to those in 6-OHDA treated PC12 cells. Further studies suggested that Brg1 knockdown impeded the high expression of p-STAT3, which was induced by PKM2 overexpression. Finally, the STAT3 inhibitor reversed the effects of PKM2 on cell survival and apoptosis in 6-OHDA-induced PC12 cells. Our results suggest that PKM2 was involved in 6-OHDA-induced PC12 cell injury by mediating the Brg1/STAT3 pathway. According to published estimates, pyruvate kinase isoform M2 (PKM2) was expressed in low amounts in patients with Parkinson's disease (PD) compared with the control health humans.![]()
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Affiliation(s)
- Lei Jiang
- The First Ward of Neurology Department
- Kaifeng Central Hospital
- Kaifeng 475000
- China
| | - Yuanlin Gao
- The First Ward of Neurology Department
- Kaifeng Central Hospital
- Kaifeng 475000
- China
| | - Gaiying Wang
- The Second Ward of Neurology Department
- Kaifeng Central Hospital
- Kaifeng 475000
- China
| | - Jie Zhong
- Department of Nursing
- Kaifeng Central Hospital
- Kaifeng 475000
- China
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29
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Marian CA, Stoszko M, Wang L, Leighty MW, de Crignis E, Maschinot CA, Gatchalian J, Carter BC, Chowdhury B, Hargreaves DC, Duvall JR, Crabtree GR, Mahmoudi T, Dykhuizen EC. Small Molecule Targeting of Specific BAF (mSWI/SNF) Complexes for HIV Latency Reversal. Cell Chem Biol 2018; 25:1443-1455.e14. [PMID: 30197195 PMCID: PMC6404985 DOI: 10.1016/j.chembiol.2018.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 05/24/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022]
Abstract
The persistence of a pool of latently HIV-1-infected cells despite combination anti-retroviral therapy treatment is the major roadblock for a cure. The BAF (mammalian SWI/SNF) chromatin remodeling complex is involved in establishing and maintaining viral latency, making it an attractive drug target for HIV-1 latency reversal. Here we report a high-throughput screen for inhibitors of BAF-mediated transcription in cells and the subsequent identification of a 12-membered macrolactam. This compound binds ARID1A-specific BAF complexes, prevents nucleosomal positioning, and relieves transcriptional repression of HIV-1. Through this mechanism, these compounds are able to reverse HIV-1 latency in an in vitro T cell line, an ex vivo primary cell model of HIV-1 latency, and in patient CD4+ T cells without toxicity or T cell activation. These macrolactams represent a class of latency reversal agents with unique mechanism of action, and can be combined with other latency reversal agents to improve reservoir targeting.
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Affiliation(s)
- Christine A Marian
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Mateusz Stoszko
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands
| | - Lili Wang
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Matthew W Leighty
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands
| | - Chad A Maschinot
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Jovylyn Gatchalian
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin C Carter
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Basudev Chowdhury
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Diana C Hargreaves
- Department of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeremy R Duvall
- The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Gerald R Crabtree
- HHMI and the Departments of Developmental Biology and Pathology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA.
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Ee634, P.O. Box 2040, 3000CA Rotterdam, the Netherlands.
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA.
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30
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Ganguly D, Sims M, Cai C, Fan M, Pfeffer LM. Chromatin Remodeling Factor BRG1 Regulates Stemness and Chemosensitivity of Glioma Initiating Cells. Stem Cells 2018; 36:1804-1815. [PMID: 30171737 DOI: 10.1002/stem.2909] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/23/2018] [Accepted: 08/18/2018] [Indexed: 12/13/2022]
Abstract
Glioblastoma multiforme (GBM) is a highly aggressive and malignant brain tumor that is refractory to existing therapeutic regimens, which reflects the presence of stem-like cells, termed glioma-initiating cells (GICs). The complex interactions between different signaling pathways and epigenetic regulation of key genes may be critical in the maintaining GICs in their stem-like state. Although several signaling pathways have been identified as being dysregulated in GBM, the prognosis of GBM patients remains miserable despite improvements in targeted therapies. In this report, we identified that BRG1, the catalytic subunit of the SWI/SNF chromatin remodeling complex, plays a fundamental role in maintaining GICs in their stem-like state. In addition, we identified a novel mechanism by which BRG1 regulates glycolysis genes critical for GICs. BRG1 downregulates the expression of TXNIP, a negative regulator of glycolysis. BRG1 knockdown also triggered the STAT3 pathway, which led to TXNIP activation. We further identified that TXNIP is an STAT3-regulated gene. Moreover, BRG1 suppressed the expression of interferon-stimulated genes, which are negatively regulated by STAT3 and regulate tumorigenesis. We further demonstrate that BRG1 plays a critical role in the drug resistance of GICs and in GIC-induced tumorigenesis. By genetic and pharmacological means, we found that inhibiting BRG1 can sensitize GICs to chemotherapeutic drugs, temozolomide and carmustine. Our studies suggest that BRG1 may be a novel therapeutic target in GBM. The identification of the critical role that BRG1 plays in GIC stemness and chemosensitivity will inform the development of better targeted therapies in GBM and possibly other cancers. Stem Cells 2018;36:1806-12.
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Affiliation(s)
- Debolina Ganguly
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Michelle Sims
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Chun Cai
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Meiyun Fan
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Lawrence M Pfeffer
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee
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31
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An actin-based nucleoskeleton involved in gene regulation and genome organization. Biochem Biophys Res Commun 2018; 506:378-386. [DOI: 10.1016/j.bbrc.2017.11.206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/30/2017] [Indexed: 12/21/2022]
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32
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Chu X, Wang Y, Pang L, Huang J, Sun X, Chen X. miR-130 aggravates acute myocardial infarction-induced myocardial injury by targeting PPAR-γ. J Cell Biochem 2018; 119:7235-7244. [PMID: 29761875 DOI: 10.1002/jcb.26903] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 12/26/2022]
Abstract
Cardiac remodeling is a common pathophysiological change associated with acute myocardial infarction (AMI). Recent evidence indicates that microRNAs are strong posttranscriptional regulators which play an important role in regulating the microenvironment of myocardial tissue after AMI. In this study, we sought to explore the potential role and underlying mechanism of miR-130 in AMI. H9c2 cells were cultured under hypoxic conditions to simulate myocardial infarction. The influence of aberrantly expressed miR-130 on H9c2 cells under hypoxia was also estimated with RT-PCR, western blot and enzyme-linked immunosorbent assay. Using bioinformatics methods, of miR-130 target genes were verified with luciferase reporter assay. Then, the effects of miR-130 on AMI were identified in an induced myocardial injury model in rats. The results show that miR-130 downregulation remarkably decreased hypoxia-induced inflammation and fibrosis related protein expression in H9c2 cells and reversed hypoxia-induced peroxisome proliferator-activated receptor γ (PPAR-γ) inhibition. A bifluorescein reporter assay further confirmed that PPAR-γ was a target gene of miR-130. This study verified that PPAR-γ has a cardioprotective effect by inhibiting NFκB-mediated inflammation and TGF-β1-mediated fibrosis. In vivo experiments confirmed that downregulation of miR-130 expression promotes PPAR-γ-mediated cardioprotective effects by suppressing inflammation and myocardial fibrosis. Taken together, these findings suggest that miR-130 knockdown alleviates infarction-induced myocardial injury by promoting PPAR-γ expression.
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Affiliation(s)
- Xianglin Chu
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiqing Wang
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Liewen Pang
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiechun Huang
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaotian Sun
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofeng Chen
- Department of Cardiothoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
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33
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Nakagawa T, Yoneda M, Higashi M, Ohkuma Y, Ito T. Enhancer function regulated by combinations of transcription factors and cofactors. Genes Cells 2018; 23:808-821. [PMID: 30092612 DOI: 10.1111/gtc.12634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
Regulation of the expression of diverse genes is essential for making possible the complexity of higher organisms, and the temporal and spatial regulation of gene expression allows for the alteration of cell types and growth patterns. A critical component of this regulation is the DNA sequence-specific binding of transcription factors (TFs). However, most TFs do not independently participate in gene transcriptional regulation, because they lack an effector function. Instead, TFs are thought to work by recruiting cofactors, including Mediator complex (Mediator), chromatin-remodeling complexes (CRCs), and histone-modifying complexes (HMCs). Mediator associates with the majority of transcribed genes and acts as an integrator of multiple signals. On the other hand, CRCs and HMCs are selectively recruited by TFs. Although all the pairings between TFs and CRCs or HMCs are not fully known, there are a growing number of established TF-CRC and TF-HMC combinations. In this review, we focused on the most important of these pairings and discuss how they control gene expression.
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Affiliation(s)
- Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Miki Higashi
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Yoshiaki Ohkuma
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
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34
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Kovač K, Sauer A, Mačinković I, Awe S, Finkernagel F, Hoffmeister H, Fuchs A, Müller R, Rathke C, Längst G, Brehm A. Tumour-associated missense mutations in the dMi-2 ATPase alters nucleosome remodelling properties in a mutation-specific manner. Nat Commun 2018; 9:2112. [PMID: 29844320 PMCID: PMC5974244 DOI: 10.1038/s41467-018-04503-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/30/2018] [Indexed: 12/20/2022] Open
Abstract
ATP-dependent chromatin remodellers are mutated in more than 20% of human cancers. The consequences of these mutations on enzyme function are poorly understood. Here, we characterise the effects of CHD4 mutations identified in endometrial carcinoma on the remodelling properties of dMi-2, the highly conserved Drosophila homologue of CHD4. Mutations from different patients have surprisingly diverse defects on nucleosome binding, ATPase activity and nucleosome remodelling. Unexpectedly, we identify both mutations that decrease and increase the enzyme activity. Our results define the chromodomains and a novel regulatory region as essential for nucleosome remodelling. Genetic experiments in Drosophila demonstrate that expression of cancer-derived dMi-2 mutants misregulates differentiation of epithelial wing structures and produces phenotypes that correlate with their nucleosome remodelling properties. Our results help to define the defects of CHD4 in cancer at the mechanistic level and provide the basis for the development of molecular approaches aimed at restoring their activity. ATP-dependent chromatin remodelers are often found mutated in human cancers. Here, the authors characterize the nucleosome remodelling properties of cancer-associated mutants of the Drosophila Chd4 homolog dMi-2.
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Affiliation(s)
- Kristina Kovač
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Anja Sauer
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Igor Mačinković
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Stephan Awe
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany
| | - Florian Finkernagel
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Rolf Müller
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.,Center for Tumour Biology and Immunology, University of Marburg, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043, Marburg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Alexander Brehm
- Institute for Molecular Biology and Tumour Research, University of Marburg, 35043, Marburg, Germany.
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35
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Liu L, Wan X, Zhou P, Zhou X, Zhang W, Hui X, Yuan X, Ding X, Zhu R, Meng G, Xiao H, Ma F, Huang H, Song X, Zhou B, Xiong S, Zhang Y. The chromatin remodeling subunit Baf200 promotes normal hematopoiesis and inhibits leukemogenesis. J Hematol Oncol 2018; 11:27. [PMID: 29482581 PMCID: PMC5828314 DOI: 10.1186/s13045-018-0567-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 11/10/2022] Open
Abstract
Background Adenosine triphosphate (ATP)-dependent chromatin remodeling SWI/SNF-like BAF and PBAF complexes have been implicated in the regulation of stem cell function and cancers. Several subunits of BAF or PBAF, including BRG1, BAF53a, BAF45a, BAF180, and BAF250a, are known to be involved in hematopoiesis. Baf200, a subunit of PBAF complex, plays a pivotal role in heart morphogenesis and coronary artery angiogenesis. However, little is known on the importance of Baf200 in normal and malignant hematopoiesis. Methods Utilizing Tie2-Cre-, Vav-iCre-, and Mx1-Cre-mediated Baf200 gene deletion combined with fetal liver/bone marrow transplantation, we investigated the function of Baf200 in fetal and adult hematopoiesis. In addition, a mouse model of MLL-AF9-driven leukemogenesis was used to study the role of Baf200 in malignant hematopoiesis. We also explored the potential mechanism by using RNA-seq, RT-qPCR, cell cycle, and apoptosis assays. Results Tie2-Cre-mediated loss of Baf200 causes perinatal death due to defective erythropoiesis and impaired hematopoietic stem cell expansion in the fetal liver. Vav-iCre-mediated loss of Baf200 causes only mild anemia and enhanced extramedullary hematopoiesis. Fetal liver hematopoietic stem cells from Tie2-Cre+, Baf200f/f or Vav-iCre+, Baf200f/f embryos and bone marrow hematopoietic stem cells from Vav-iCre+, Baf200f/f mice exhibited impaired long-term reconstitution potential in vivo. A cell-autonomous requirement of Baf200 for hematopoietic stem cell function was confirmed utilizing the interferon-inducible Mx1-Cre mouse strain. Transcriptomes analysis revealed that expression of several erythropoiesis- and hematopoiesis-associated genes were regulated by Baf200. In addition, loss of Baf200 in a mouse model of MLL-AF9-driven leukemogenesis accelerates the tumor burden and shortens the host survival. Conclusion Our current studies uncover critical roles of Baf200 in both normal and malignant hematopoiesis and provide a potential therapeutic target for suppressing the progression of leukemia without interfering with normal hematopoiesis. Electronic supplementary material The online version of this article (10.1186/s13045-018-0567-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lulu Liu
- Institute of Biology and Medical Sciences, Soochow University, No. 199 Ren'ai Rd, Suzhou, China.,Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China
| | - Xiaoling Wan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peipei Zhou
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Zhou
- University of Chinese Academy of Sciences, Beijing, China.,CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Xinhui Hui
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,School of Life Sciences, Shanghai University, Shanghai, China
| | - Xiujie Yuan
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaodan Ding
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ruihong Zhu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangxun Meng
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Xiao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - He Huang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianmin Song
- Department of Hematology, Shanghai Jiao Tong University Affiliated Shanghai General Hospital, Shanghai, China
| | - Bin Zhou
- The State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China.
| | - Sidong Xiong
- Institute of Biology and Medical Sciences, Soochow University, No. 199 Ren'ai Rd, Suzhou, China.
| | - Yan Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, China. .,University of Chinese Academy of Sciences, Beijing, China.
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36
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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37
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Kokavec J, Zikmund T, Savvulidi F, Kulvait V, Edelmann W, Skoultchi AI, Stopka T. The ISWI ATPase Smarca5 (Snf2h) Is Required for Proliferation and Differentiation of Hematopoietic Stem and Progenitor Cells. Stem Cells 2017; 35:1614-1623. [PMID: 28276606 DOI: 10.1002/stem.2604] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 12/14/2016] [Accepted: 01/09/2017] [Indexed: 12/17/2022]
Abstract
The imitation switch nuclear ATPase Smarca5 (Snf2h) is one of the most conserved chromatin remodeling factors. It exists in a variety of oligosubunit complexes that move DNA with respect to the histone octamer to generate regularly spaced nucleosomal arrays. Smarca5 interacts with different accessory proteins and represents a molecular motor for DNA replication, repair, and transcription. We deleted Smarca5 at the onset of definitive hematopoiesis (Vav1-iCre) and observed that animals die during late fetal development due to anemia. Hematopoietic stem and progenitor cells accumulated but their maturation toward erythroid and myeloid lineages was inhibited. Proerythroblasts were dysplastic while basophilic erythroblasts were blocked in G2/M and depleted. Smarca5 deficiency led to increased p53 levels, its activation at two residues, one associated with DNA damage (S15Ph °s ) second with CBP/p300 (K376Ac ), and finally activation of the p53 targets. We also deleted Smarca5 in committed erythroid cells (Epor-iCre) and observed that animals were anemic postnatally. Furthermore, 4-hydroxytamoxifen-mediated deletion of Smarca5 in the ex vivo cultures confirmed its requirement for erythroid cell proliferation. Thus, Smarca5 plays indispensable roles during early hematopoiesis and erythropoiesis. Stem Cells 2017;35:1614-1623.
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Affiliation(s)
- Juraj Kokavec
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tomas Zikmund
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Filipp Savvulidi
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Vojtech Kulvait
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tomas Stopka
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
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38
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The BAF45a/PHF10 subunit of SWI/SNF-like chromatin remodeling complexes is essential for hematopoietic stem cell maintenance. Exp Hematol 2017; 48:58-71.e15. [DOI: 10.1016/j.exphem.2016.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/12/2016] [Accepted: 11/25/2016] [Indexed: 11/22/2022]
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39
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Stanton BZ, Hodges C, Crabtree GR, Zhao K. A General Non-Radioactive ATPase Assay for Chromatin Remodeling Complexes. ACTA ACUST UNITED AC 2017; 9:1-10. [PMID: 28253434 DOI: 10.1002/cpch.16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromatin remodeling complexes couple the energy released from ATP hydrolysis to facilitate transcription, recombination, and repair mechanisms essential for a wide variety of biologic responses. While recombinant expression of the regulatory subunits of these enzymes is possible, measuring catalytic (ATPase) activity of the intact complexes recovered from normal or mutant cells is critical for understanding their mechanisms. SWI/SNF-like remodeling complexes can be megadaltons in size and include many regulatory subunits, making reconstitution of purified subunits challenging for recapitulating in vivo function. The protocol in this article defines the first highly quantitative ATPase assay for intact remodeling complexes that does not require radiation or reconstitution of recombinantly expressed subunits. This protocol is specifically useful for defining the catalytic role of active-site mutations in the context of other regulatory subunits and quantitatively rank-ordering inactivating catalytic-site mutations. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin Z Stanton
- Department of Pathology, Stanford University School of Medicine, Stanford, California.,Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Courtney Hodges
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Gerald R Crabtree
- Department of Pathology, Stanford University School of Medicine, Stanford, California.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Keji Zhao
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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40
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Xiao C, Gao L, Hou Y, Xu C, Chang N, Wang F, Hu K, He A, Luo Y, Wang J, Peng J, Tang F, Zhu X, Xiong JW. Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nat Commun 2016; 7:13787. [PMID: 27929112 PMCID: PMC5476829 DOI: 10.1038/ncomms13787] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
The zebrafish possesses a remarkable capacity of adult heart regeneration, but the underlying mechanisms are not well understood. Here we report that chromatin remodelling factor Brg1 is essential for adult heart regeneration. Brg1 mRNA and protein are induced during heart regeneration. Transgenic over-expression of dominant-negative Xenopus Brg1 inhibits the formation of BrdU+/Mef2C+ and Tg(gata4:EGFP) cardiomyocytes, leading to severe cardiac fibrosis and compromised myocardial regeneration. RNA-seq and RNAscope analyses reveal that inhibition of Brg1 increases the expression of cyclin-dependent kinase inhibitors such as cdkn1a and cdkn1c in the myocardium after ventricular resection; and accordingly, myocardial-specific expression of dn-xBrg1 blunts myocardial proliferation and regeneration. Mechanistically, injury-induced Brg1, via its interaction with Dnmt3ab, suppresses the expression of cdkn1c by increasing the methylation level of CpG sites at the cdkn1c promoter. Taken together, our results suggest that Brg1 promotes heart regeneration by repressing cyclin-dependent kinase inhibitors partly through Dnmt3ab-dependent DNA methylation.
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Affiliation(s)
- Chenglu Xiao
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Lu Gao
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Yu Hou
- Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China.,College of Life Sciences, Peking University, Beijing 100871, China
| | - Congfei Xu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Nannan Chang
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Fang Wang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Keping Hu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China.,Peking Union Medical College, Beijing 100730, China
| | - Aibin He
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Ying Luo
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Jun Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, Peking University, Beijing 100871, China.,College of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaojun Zhu
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, Beijing 100871, China
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41
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He S, Limi S, McGreal RS, Xie Q, Brennan LA, Kantorow WL, Kokavec J, Majumdar R, Hou H, Edelmann W, Liu W, Ashery-Padan R, Zavadil J, Kantorow M, Skoultchi AI, Stopka T, Cvekl A. Chromatin remodeling enzyme Snf2h regulates embryonic lens differentiation and denucleation. Development 2016; 143:1937-47. [PMID: 27246713 PMCID: PMC4920164 DOI: 10.1242/dev.135285] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/21/2016] [Indexed: 12/30/2022]
Abstract
Ocular lens morphogenesis is a model for investigating mechanisms of cellular differentiation, spatial and temporal gene expression control, and chromatin regulation. Brg1 (Smarca4) and Snf2h (Smarca5) are catalytic subunits of distinct ATP-dependent chromatin remodeling complexes implicated in transcriptional regulation. Previous studies have shown that Brg1 regulates both lens fiber cell differentiation and organized degradation of their nuclei (denucleation). Here, we employed a conditional Snf2h(flox) mouse model to probe the cellular and molecular mechanisms of lens formation. Depletion of Snf2h induces premature and expanded differentiation of lens precursor cells forming the lens vesicle, implicating Snf2h as a key regulator of lens vesicle polarity through spatial control of Prox1, Jag1, p27(Kip1) (Cdkn1b) and p57(Kip2) (Cdkn1c) gene expression. The abnormal Snf2h(-/-) fiber cells also retain their nuclei. RNA profiling of Snf2h(-/) (-) and Brg1(-/-) eyes revealed differences in multiple transcripts, including prominent downregulation of those encoding Hsf4 and DNase IIβ, which are implicated in the denucleation process. In summary, our data suggest that Snf2h is essential for the establishment of lens vesicle polarity, partitioning of prospective lens epithelial and fiber cell compartments, lens fiber cell differentiation, and lens fiber cell nuclear degradation.
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Grants
- R01 EY012200 NEI NIH HHS
- R01 CA079057 NCI NIH HHS
- R01 DK096266 NIDDK NIH HHS
- R01 GM116143 NIGMS NIH HHS
- R01 EY013022 NEI NIH HHS
- R01 CA076329 NCI NIH HHS
- T32 GM007491 NIGMS NIH HHS
- R56 CA079057 NCI NIH HHS
- R01 EY014237 NEI NIH HHS
- 001 World Health Organization
- R01 EY022645 NEI NIH HHS
- Grant support: R01 EY012200 (AC), EY014237 (AC), EY014237-7S1 (AC), EY013022 (MK), CA079057 (AIS), EY022645 (WL), T32 GM007491 (SL), GACR: P305/12/1033 (TS, JK), UNCE: 204021 (TS, JK), and an unrestricted grant from Research to Prevent Blindness to the Department of Ophthalmology and Visual Sciences. TS is member of the BIOCEV ? Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (CZ.1.05/1.1.00/02.0109) supported by the European Regional Development Fund. The Israel Science Foundation 610/10, the Israel Ministry of Science 36494, the Ziegler Foundation and the Binational Science Foundation (2013016) to RAP.
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Affiliation(s)
- Shuying He
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Saima Limi
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rebecca S McGreal
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qing Xie
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lisa A Brennan
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Wanda Lee Kantorow
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Juraj Kokavec
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic
| | - Romit Majumdar
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Harry Hou
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wei Liu
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine Tel-Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Jiri Zavadil
- Department of Pathology and NYU Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY 10016, USA Mechanisms of Carcinogenesis Section, International Agency for Research on Cancer, Lyon Cedex 08 69372, France
| | - Marc Kantorow
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tomas Stopka
- First Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic
| | - Ales Cvekl
- Department of Ophthalmology & Visual Sciences and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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42
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DeVilbiss AW, Tanimura N, McIver SC, Katsumura KR, Johnson KD, Bresnick EH. Navigating Transcriptional Coregulator Ensembles to Establish Genetic Networks: A GATA Factor Perspective. Curr Top Dev Biol 2016; 118:205-44. [PMID: 27137658 DOI: 10.1016/bs.ctdb.2016.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Complex developmental programs require orchestration of intrinsic and extrinsic signals to control cell proliferation, differentiation, and survival. Master regulatory transcription factors are vital components of the machinery that transduce these stimuli into cellular responses. This is exemplified by the GATA family of transcription factors that establish cell type-specific genetic networks and control the development and homeostasis of systems including blood, vascular, adipose, and cardiac. Dysregulated GATA factor activity/expression underlies anemia, immunodeficiency, myelodysplastic syndrome, and leukemia. Parameters governing the capacity of a GATA factor expressed in multiple cell types to generate cell type-specific transcriptomes include selective coregulator usage and target gene-specific chromatin states. As knowledge of GATA-1 mechanisms in erythroid cells constitutes a solid foundation, we will focus predominantly on GATA-1, while highlighting principles that can be extrapolated to other master regulators. GATA-1 interacts with ubiquitous and lineage-restricted transcription factors, chromatin modifying/remodeling enzymes, and other coregulators to activate or repress transcription and to maintain preexisting transcriptional states. Major unresolved issues include: how does a GATA factor selectively utilize diverse coregulators; do distinct epigenetic landscapes and nuclear microenvironments of target genes dictate coregulator requirements; and do gene cohorts controlled by a common coregulator ensemble function in common pathways. This review will consider these issues in the context of GATA factor-regulated hematopoiesis and from a broader perspective.
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Affiliation(s)
- A W DeVilbiss
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - N Tanimura
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - S C McIver
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - K R Katsumura
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - K D Johnson
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States
| | - E H Bresnick
- UW-Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; UW-Madison Blood Research Program, Madison, WI, United States.
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43
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Cheng CK, Chan NPH, Wan TSK, Lam LY, Cheung CHY, Wong THY, Ip RKL, Wong RSM, Ng MHL. Helicase-like transcription factor is a RUNX1 target whose downregulation promotes genomic instability and correlates with complex cytogenetic features in acute myeloid leukemia. Haematologica 2016; 101:448-57. [PMID: 26802049 DOI: 10.3324/haematol.2015.137125] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/13/2016] [Indexed: 12/27/2022] Open
Abstract
Helicase-like transcription factor is a SWI/SNF chromatin remodeling factor involved in various biological processes. However, little is known about its role in hematopoiesis. In this study, we measured helicase-like transcription factor mRNA expression in the bone marrow of 204 adult patients with de novo acute myeloid leukemia. Patients were dichotomized into low and high expression groups at the median level for clinicopathological correlations. Helicase-like transcription factor levels were dramatically reduced in the low expression patient group compared to those in the normal controls (n=40) (P<0.0001). Low helicase-like transcription factor expression correlated positively with French-American-British M4/M5 subtypes (P<0.0001) and complex cytogenetic abnormalities (P=0.02 for ≥3 abnormalities;P=0.004 for ≥5 abnormalities) but negatively with CEBPA double mutations (P=0.012). Also, low expression correlated with poorer overall (P=0.005) and event-free (P=0.006) survival in the intermediate-risk cytogenetic subgroup. Consistent with the more aggressive disease associated with low expression, helicase-like transcription factor knockdown in leukemic cells promoted proliferation and chromosomal instability that was accompanied by downregulation of mitotic regulators and impaired DNA damage response. The significance of helicase-like transcription factor in genome maintenance was further indicated by its markedly elevated expression in normal human CD34(+)hematopoietic stem cells. We further demonstrated that helicase-like transcription factor was a RUNX1 target and transcriptionally repressed by RUNX1-ETO and site-specific DNA methylation through a duplicated RUNX1 binding site in its promoter. Taken together, our findings provide new mechanistic insights on genomic instability linked to helicase-like transcription factor deregulation, and strongly suggest a tumor suppressor function of the SWI/SNF protein in acute myeloid leukemia.
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Affiliation(s)
- Chi Keung Cheng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Natalie P H Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Thomas S K Wan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Lai Ying Lam
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Coty H Y Cheung
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Terry H Y Wong
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Rosalina K L Ip
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina
| | - Raymond S M Wong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina Sir Y. K. Pao Centre for Cancer, Prince of Wales Hospital, Hong Kong, Cina
| | - Margaret H L Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Cina State Key Laboratory in Oncology in South China, The Chinese University of Hong Kong, Cina
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44
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Padilla-Benavides T, Nasipak BT, Imbalzano AN. Brg1 Controls the Expression of Pax7 to Promote Viability and Proliferation of Mouse Primary Myoblasts. J Cell Physiol 2015; 230:2990-7. [PMID: 26036967 DOI: 10.1002/jcp.25031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 12/29/2022]
Abstract
Brg1 (Brahma-related gene 1) is a catalytic component of the evolutionarily conserved mammalian SWI/SNF ATP-dependent chromatin remodeling enzymes that disrupt histone-DNA contacts on the nucleosome. While the requirement for the SWI/SNF enzymes in cell differentiation has been extensively studied, its role in precursor cell proliferation and survival is not as well defined. Muscle satellite cells constitute the stem cell pool that sustains and regenerates myofibers in adult skeletal muscle. Here, we show that deletion of Brg1 in primary mouse myoblasts derived from muscle satellite cells cultured ex vivo leads to a cell proliferation defect and apoptosis. We determined that Brg1 regulates cell proliferation and survival by controlling chromatin remodeling and activating transcription at the Pax7 promoter, which is expressed during somite development and is required for controlling viability of the satellite cell population. Reintroduction of catalytically active Brg1 or of Pax7 into Brg1-deficient satellite cells rescued the apoptotic phenotype and restored proliferation. These data demonstrate that Brg1 functions as a positive regulator for cellular proliferation and survival of primary myoblasts. Therefore, the regulation of gene expression through Brg1-mediated chromatin remodeling is critical not just for skeletal muscle differentiation but for maintaining the myoblast population as well.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Brian T Nasipak
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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45
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Skulte KA, Phan L, Clark SJ, Taberlay PC. Chromatin remodeler mutations in human cancers: epigenetic implications. Epigenomics 2015; 6:397-414. [PMID: 25333849 DOI: 10.2217/epi.14.37] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chromatin remodeler complexes exhibit the ability to alter nucleosome composition and positions, with seemingly divergent roles in the regulation of chromatin architecture and gene expression. The outcome is directed by subunit variation and interactions with accessory factors. Recent studies have revealed that subunits of chromatin remodelers display an unexpectedly high mutation rate and/or are inactivated in a number of cancers. Consequently, a repertoire of epigenetic processes are likely to be affected, including interactions with histone modifying factors, as well as the ability to precisely modulate nucleosome positions, DNA methylation patterns and potentially, higher-order genome structure. However, the true significance of chromatin remodeler genetic aberrations in promoting a cascade of epigenetic changes, particularly during initiation and progression of cancer, remains largely unknown.
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Affiliation(s)
- Katherine A Skulte
- Chromatin Dynamics Group, Cancer Division, Garvan Institute of Medical Research, 394 Victoria Rd, Darlinghurst 2010, New South Wales, Australia
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46
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Alexander JM, Hota SK, He D, Thomas S, Ho L, Pennacchio LA, Bruneau BG. Brg1 modulates enhancer activation in mesoderm lineage commitment. Development 2015; 142:1418-30. [PMID: 25813539 PMCID: PMC4392595 DOI: 10.1242/dev.109496] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 02/27/2015] [Indexed: 12/28/2022]
Abstract
The interplay between different levels of gene regulation in modulating developmental transcriptional programs, such as histone modifications and chromatin remodeling, is not well understood. Here, we show that the chromatin remodeling factor Brg1 is required for enhancer activation in mesoderm induction. In an embryonic stem cell-based directed differentiation assay, the absence of Brg1 results in a failure of cardiomyocyte differentiation and broad deregulation of lineage-specific gene expression during mesoderm induction. We find that Brg1 co-localizes with H3K27ac at distal enhancers and is required for robust H3K27 acetylation at distal enhancers that are activated during mesoderm induction. Brg1 is also required to maintain Polycomb-mediated repression of non-mesodermal developmental regulators, suggesting cooperativity between Brg1 and Polycomb complexes. Thus, Brg1 is essential for modulating active and repressive chromatin states during mesoderm lineage commitment, in particular the activation of developmentally important enhancers. These findings demonstrate interplay between chromatin remodeling complexes and histone modifications that, together, ensure robust and broad gene regulation during crucial lineage commitment decisions. SUMMARY: The chromatin remodeling factor Brg1 is essential for mesoderm induction and, by modulating active and repressive chromatin states, is involved in promoting the activation of dynamic enhancers.
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Affiliation(s)
- Jeffrey M Alexander
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Daniel He
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Sean Thomas
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Lena Ho
- Institute of Medical Biology, A*STAR, Singapore 138648
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA United States Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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47
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The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia. BIOMED RESEARCH INTERNATIONAL 2015; 2015:347571. [PMID: 25789315 PMCID: PMC4348595 DOI: 10.1155/2015/347571] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/27/2015] [Indexed: 12/15/2022]
Abstract
Here, we review the role of sucrose nonfermenting (SNF2) family enzymes in blood cell development. The SNF2 family comprises helicase-like ATPases, originally discovered in yeast, that can remodel chromatin by changing chromatin structure and composition. The human genome encodes 30 different SNF2 enzymes. SNF2 family enzymes are often part of multisubunit chromatin remodeling complexes (CRCs), which consist of noncatalytic/auxiliary subunit along with the ATPase subunit. However, blood cells express a limited set of SNF2 ATPases that are necessary to maintain the pool of hematopoietic stem cells (HSCs) and drive normal blood cell development and differentiation. The composition of CRCs can be altered by the association of specific auxiliary subunits. Several auxiliary CRC subunits have specific functions in hematopoiesis. Aberrant expressions of SNF2 ATPases and/or auxiliary CRC subunit(s) are often observed in hematological malignancies. Using large-scale data from the International Cancer Genome Consortium (ICGC) we observed frequent mutations in genes encoding SNF2 helicase-like enzymes and auxiliary CRC subunits in leukemia. Hence, orderly function of SNF2 family enzymes is crucial for the execution of normal blood cell developmental program, and defects in chromatin remodeling caused by mutations or aberrant expression of these proteins may contribute to leukemogenesis.
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48
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Zhang X, Li B, Li W, Ma L, Zheng D, Li L, Yang W, Chu M, Chen W, Mailman RB, Zhu J, Fan G, Archer TK, Wang Y. Transcriptional repression by the BRG1-SWI/SNF complex affects the pluripotency of human embryonic stem cells. Stem Cell Reports 2014; 3:460-74. [PMID: 25241744 PMCID: PMC4266000 DOI: 10.1016/j.stemcr.2014.07.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 12/01/2022] Open
Abstract
The SWI/SNF complex plays an important role in mouse embryonic stem cells (mESCs), but it remains to be determined whether this complex is required for the pluripotency of human ESCs (hESCs). Using RNAi, we demonstrated that depletion of BRG1, the catalytic subunit of the SWI/SNF complex, led to impaired self-renewing ability and dysregulated lineage specification of hESCs. A unique composition of the BRG1-SWI/SNF complex in hESCs was further defined by the presence of BRG1, BAF250A, BAF170, BAF155, BAF53A, and BAF47. Genome-wide expression analyses revealed that BRG1 participated in a broad range of biological processes in hESCs through pathways different from those in mESCs. In addition, chromatin immunoprecipitation sequencing (ChIP-seq) demonstrated that BRG1 played a repressive role in transcriptional regulation by modulating the acetylation levels of H3K27 at the enhancers of lineage-specific genes. Our data thus provide valuable insights into molecular mechanisms by which transcriptional repression affects the self-renewal and differentiation of hESCs. We report a conserved but distinct role of SWI/SNF complex in hESC pluripotency Depletion of BAF170 in SWI/SNF complex leads to impaired pluripotency of hESCs BRG1 negatively regulates transcription of lineage-specific genes BRG1 downregulates H3K27ac levels at enhancers of lineage-specific genes
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Affiliation(s)
- Xiaoli Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Bing Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wenguo Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lijuan Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dongyan Zheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Leping Li
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Weijing Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Min Chu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Richard B Mailman
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-7088, USA
| | - Trevor K Archer
- Chromatin and Gene Expression Group, Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Yuan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
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49
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Hewitt KJ, Sanalkumar R, Johnson KD, Keles S, Bresnick EH. Epigenetic and genetic mechanisms in red cell biology. Curr Opin Hematol 2014; 21:155-64. [PMID: 24722192 PMCID: PMC6061918 DOI: 10.1097/moh.0000000000000034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Erythropoiesis, in which hematopoietic stem cells (HSCs) generate lineage-committed progenitors that mature into erythrocytes, is regulated by numerous chromatin modifying and remodeling proteins. We will focus on how epigenetic and genetic mechanisms mesh to establish the erythroid transcriptome and how studying erythropoiesis can yield genomic principles. RECENT FINDINGS Trans-acting factor binding to small DNA motifs (cis-elements) underlies regulatory complex assembly at specific chromatin sites, and therefore unique transcriptomes. As cis-elements are often very small, thousands or millions of copies of a given element reside in a genome. Chromatin restricts factor access in a context-dependent manner, and cis-element-binding factors recruit chromatin regulators that mediate functional outputs. Technologies to map chromatin attributes of loci in vivo, to edit genomes and to sequence whole genomes have been transformative in discovering critical cis-elements linked to human disease. SUMMARY Cis-elements mediate chromatin-targeting specificity, and chromatin regulators dictate cis-element accessibility/function, illustrating an amalgamation of genetic and epigenetic mechanisms. Cis-elements often function ectopically when studied outside of their endogenous loci, and complex strategies to identify nonredundant cis-elements require further development. Facile genome-editing technologies provide a new approach to address this problem. Extending genetic analyses beyond exons and promoters will yield a rich pipeline of cis-element alterations with importance for red cell biology and disease.
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Affiliation(s)
- Kyle J. Hewitt
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health
- UW-Madison Blood Research Program, Carbone Cancer Center
| | - Rajendran Sanalkumar
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health
- UW-Madison Blood Research Program, Carbone Cancer Center
| | - Kirby D. Johnson
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health
- UW-Madison Blood Research Program, Carbone Cancer Center
| | - Sunduz Keles
- UW-Madison Blood Research Program, Carbone Cancer Center
- Department of Biostatistics and Medical Informatics, Department of Statistics, Wisconsin Institutes for Medical Research, Madison, Wisconsin, USA
| | - Emery H. Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health
- UW-Madison Blood Research Program, Carbone Cancer Center
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Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res 2014; 24:920-9. [PMID: 24752179 PMCID: PMC4032856 DOI: 10.1101/gr.168930.113] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The SMARCA4 (also known as BRG1 in humans) chromatin remodeling factor is critical for establishing lineage-specific chromatin states during early mammalian development. However, the role of SMARCA4 in tissue-specific gene regulation during embryogenesis remains poorly defined. To investigate the genome-wide binding landscape of SMARCA4 in differentiating tissues, we engineered a Smarca4FLAG knock-in mouse line. Using ChIP-seq, we identified ∼51,000 SMARCA4-associated regions across six embryonic mouse tissues (forebrain, hindbrain, neural tube, heart, limb, and face) at mid-gestation (E11.5). The majority of these regions was distal from promoters and showed dynamic occupancy, with most distal SMARCA4 sites (73%) confined to a single or limited subset of tissues. To further characterize these regions, we profiled active and repressive histone marks in the same tissues and examined the intersection of informative chromatin states and SMARCA4 binding. This revealed distinct classes of distal SMARCA4-associated elements characterized by activating and repressive chromatin signatures that were associated with tissue-specific up- or down-regulation of gene expression and relevant active/repressed biological pathways. We further demonstrate the predicted active regulatory properties of SMARCA4-associated elements by retrospective analysis of tissue-specific enhancers and direct testing of SMARCA4-bound regions in transgenic mouse assays. Our results indicate a dual active/repressive function of SMARCA4 at distal regulatory sequences in vivo and support its role in tissue-specific gene regulation during embryonic development.
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Affiliation(s)
- Catia Attanasio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Alex S Nord
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yiwen Zhu
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Matthew J Blow
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Simon C Biddie
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; Addenbrooke's Hospital, Cambridge University NHS Trust, Cambridge CB2 0QQ, United Kingdom
| | - Eric M Mendenhall
- HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Jesse Dixon
- Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA
| | - Crystal Wright
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Roya Hosseini
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jennifer A Akiyama
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Amy Holt
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ingrid Plajzer-Frick
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Malak Shoukry
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Veena Afzal
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, UCSD School of Medicine, La Jolla, California 92093, USA
| | - Bradley E Bernstein
- HHMI and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Edward M Rubin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
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