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Asmamaw MD, He A, Zhang LR, Liu HM, Gao Y. Histone deacetylase complexes: Structure, regulation and function. Biochim Biophys Acta Rev Cancer 2024; 1879:189150. [PMID: 38971208 DOI: 10.1016/j.bbcan.2024.189150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Histone deacetylases (HDACs) are key epigenetic regulators, and transcriptional complexes with deacetylase function are among the epigenetic corepressor complexes in the nucleus that target the epigenome. HDAC-bearing corepressor complexes such as the Sin3 complex, NuRD complex, CoREST complex, and SMRT/NCoR complex are common in biological systems. These complexes activate the otherwise inactive HDACs in a solitary state. HDAC complexes play vital roles in the regulation of key biological processes such as transcription, replication, and DNA repair. Moreover, deregulated HDAC complex function is implicated in human diseases including cancer. Therapeutic strategies targeting HDAC complexes are being sought actively. Thus, illustration of the nature and composition of HDAC complexes is vital to understanding the molecular basis of their functions under physiologic and pathologic conditions, and for designing targeted therapies. This review presents key aspects of large multiprotein HDAC-bearing complexes including their structure, function, regulatory mechanisms, implication in disease development, and role in therapeutics.
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Affiliation(s)
- Moges Dessale Asmamaw
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Ang He
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
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2
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Wang C, Chu C, Guo Z, Zhan X. Structures and dynamics of Rpd3S complex bound to nucleosome. SCIENCE ADVANCES 2024; 10:eadk7678. [PMID: 38598631 PMCID: PMC11006229 DOI: 10.1126/sciadv.adk7678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/07/2024] [Indexed: 04/12/2024]
Abstract
The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
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Affiliation(s)
- Chengcheng Wang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chen Chu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Zhouyan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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3
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Zhang T, Zhou C, Lv M, Yu J, Cheng S, Cui X, Wan X, Ahmad M, Xu B, Qin J, Meng X, Luo H. Trifluoromethyl quinoline derivative targets inhibiting HDAC1 for promoting the acetylation of histone in cervical cancer cells. Eur J Pharm Sci 2024; 194:106706. [PMID: 38244809 DOI: 10.1016/j.ejps.2024.106706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
Cervical cancer is the leading cause of death among gynecological malignant tumors, especially due to the poor prognosis of patients with advanced tumors due to recurrence, metastasis, and chemotherapy resistance. Therefore, exploring new antineoplastic drugs with high efficacy and low toxicity may bring new expectations in patients with cervical cancer. Natural products and their derivatives exert an antitumor activity. Therefore, in this work, combined with network pharmacology analysis and experimental validation, we investigated the anti-cervical cancer activity and molecular mechanism of a new trifluoromethyl quinoline (FKL) derivative in vivo and in vitro. FKL117 inhibited the proliferation of cervical cancer cells in a dose and time-dependent manner, induced apoptosis in HeLa cells, arrested the cell cycle in the G2/M phase, and regulated the expression of the apoptotic and cell cycle-related proteins Bcl-2, Bax, cyclin B1, and CDC2. We used online databases to obtain HDAC1 as one of the possible targets of FKL117 and the target binding and binding affinity were modeled by molecular docking. The results showed that FKL117 formed a hydrogen bond with HDAC1 and had good binding ability. We found that FKL117 targeted to inhibit the expression and function of HDAC1 and increased the acetylation of histone H3 and H4, which was also confirmed in vivo. The migration of HMGB1 from the nucleus to the cytoplasm further verified the above results. In conclusion, our study suggested that FKL117 might be used as a novel candidate for targeting the inhibition of HDAC1 against cervical cancer.
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Affiliation(s)
- Ting Zhang
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
| | - Changhua Zhou
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China
| | - Mengfan Lv
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Jia Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Sha Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Xudong Cui
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Xinwei Wan
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Mashaal Ahmad
- Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Bixue Xu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China
| | - Juan Qin
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; The Maternal and Child Health Care Hospital of Guizhou Medical University, Guiyang, China.
| | - Xueling Meng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China.
| | - Heng Luo
- College of Clinical Medicine, Guizhou Medical University, Guiyang 550004, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China; Guizhou Provincial Engineering Research Center for Natural Drugs, Guiyang 550014, China.
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4
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Cai W, Liu Y, Zhang T, Ji P, Tian C, Liu J, Zheng Z. GDNF facilitates the differentiation of ADSCs to Schwann cells and enhances nerve regeneration through GDNF/MTA1/Hes1 axis. Arch Biochem Biophys 2024; 753:109893. [PMID: 38309681 DOI: 10.1016/j.abb.2024.109893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/05/2024]
Abstract
Adipose tissue-derived stem cells (ADSCs) are a kind of stem cells with multi-directional differentiation potential, which mainly restore tissue repair function and promote cell regeneration. It can be directionally differentiated into Schwann-like cells to promote the repair of peripheral nerve injury. Glial cell line-derived neurotrophic factor (GDNF) plays an important role in the repair of nerve injury, but the underlying mechanism remains unclear, which seriously limits its further application.The study aimed to identify the molecular mechanism by which overexpression of glial cell line-derived neurotrophic factor (GDNF) facilitates the differentiation of ADSCs into Schwann cells, enhancing nerve regeneration after injury. In vitro, ADSCs overexpressing GDNF for 48 h exhibited changes in their morphology, with 80% of the cells having two or more prominences. Compared with that of ADSCs, GDNF-ADSCs exhibited increased expression of the Schwann cell marker S100, nerve damage repair-related factors.ADSC cells in normal culture and ADSC cells were overexpressing GDNF(GDNF-ADSCs) were analysed using TMT-Based Proteomic Analysis and revealed a significantly higher expression of MTA1 in GDNF-ADSCs than in control ADSCs. Hes1 expression was significantly higher in GDNF-ADSCs than in ADSCs and decreased by MTA1 silencing, along with a simultaneous decrease in the expression of S100 and nerve damage repair factors. These findings indicate that GDNF promotes the differentiation of ADSCs into Schwann cells and induces factors that accelerate peripheral nerve damage repair.
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Affiliation(s)
- Weixia Cai
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China
| | - Yang Liu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China
| | - Ting Zhang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China
| | - Peng Ji
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China
| | - Chenyang Tian
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China
| | - Jiaqi Liu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China.
| | - Zhao Zheng
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, 127 Changle West Road, Xi'an, Shaanxi, 710032, China.
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5
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Moreno-Yruela C, Fierz B. Revealing chromatin-specific functions of histone deacylases. Biochem Soc Trans 2024; 52:353-365. [PMID: 38189424 DOI: 10.1042/bst20230693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Abstract
Histone deacylases are erasers of Nε-acyl-lysine post-translational modifications and have been targeted for decades for the treatment of cancer, neurodegeneration and other disorders. Due to their relatively promiscuous activity on peptide substrates in vitro, it has been challenging to determine the individual targets and substrate identification mechanisms of each isozyme, and they have been considered redundant regulators. In recent years, biochemical and biophysical studies have incorporated the use of reconstituted nucleosomes, which has revealed a diverse and complex arsenal of recognition mechanisms by which histone deacylases may differentiate themselves in vivo. In this review, we first present the peptide-based tools that have helped characterize histone deacylases in vitro to date, and we discuss the new insights that nucleosome tools are providing into their recognition of histone substrates within chromatin. Then, we summarize the powerful semi-synthetic approaches that are moving forward the study of chromatin-associated factors, both in vitro by detailed single-molecule mechanistic studies, and in cells by live chromatin modification. We finally offer our perspective on how these new techniques would advance the study of histone deacylases. We envision that such studies will help elucidate the role of individual isozymes in disease and provide a platform for the development of the next generation of therapeutics.
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Affiliation(s)
- Carlos Moreno-Yruela
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department of Drug Design and Pharmacology (ILF), Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules (LCBM), Institute of Chemical Sciences and Engineering (ISIC), School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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6
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Leighton GO, Shang S, Hageman S, Ginder GD, Williams DC. Analysis of the complex between MBD2 and the histone deacetylase core of NuRD reveals key interactions critical for gene silencing. Proc Natl Acad Sci U S A 2023; 120:e2307287120. [PMID: 37552759 PMCID: PMC10433457 DOI: 10.1073/pnas.2307287120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex modifies nucleosome positioning and chromatin compaction to regulate gene expression. The methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) play a critical role in complex formation; however, the molecular details of how they interact with other NuRD components have yet to be fully elucidated. We previously showed that an intrinsically disordered region (IDR) of MBD2 is necessary and sufficient to bind to the histone deacetylase core of NuRD. Building on that work, we have measured the inherent structural propensity of the MBD2-IDR using solvent and site-specific paramagnetic relaxation enhancement measurements. We then used the AlphaFold2 machine learning software to generate a model of the complex between MBD2 and the histone deacetylase core of NuRD. This model is remarkably consistent with our previous studies, including the current paramagnetic relaxation enhancement data. The latter suggests that the free MBD2-IDR samples conformations similar to the bound structure. We tested this model of the complex extensively by mutating key contact residues and measuring binding using an intracellular bioluminescent resonance energy transfer assay. Furthermore, we identified protein contacts that, when mutated, disrupted gene silencing by NuRD in a cell model of fetal hemoglobin regulation. Hence, this work provides insights into the formation of NuRD and highlights critical binding pockets that may be targeted to block gene silencing for therapy. Importantly, we show that AlphaFold2 can generate a credible model of a large complex that involves an IDR that folds upon binding.
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Affiliation(s)
- Gage O. Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
| | - Shengzhe Shang
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298
| | - Sean Hageman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
| | - Gordon D. Ginder
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA23298
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA23298
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA23298
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
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Wang S, Fairall L, Pham TK, Ragan TJ, Vashi D, Collins M, Dominguez C, Schwabe JR. A potential histone-chaperone activity for the MIER1 histone deacetylase complex. Nucleic Acids Res 2023; 51:6006-6019. [PMID: 37099381 PMCID: PMC10325919 DOI: 10.1093/nar/gkad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 04/27/2023] Open
Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
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Affiliation(s)
- Siyu Wang
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Trong Khoa Pham
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Timothy J Ragan
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dipti Vashi
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Cyril Dominguez
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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Schmolka N, Karemaker ID, Cardoso da Silva R, Recchia DC, Spegg V, Bhaskaran J, Teske M, de Wagenaar NP, Altmeyer M, Baubec T. Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation. Nat Commun 2023; 14:3848. [PMID: 37385984 PMCID: PMC10310694 DOI: 10.1038/s41467-023-39551-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
The Nucleosome Remodeling and Deacetylation (NuRD) complex is a crucial regulator of cellular differentiation. Two members of the Methyl-CpG-binding domain (MBD) protein family, MBD2 and MBD3, are known to be integral, but mutually exclusive subunits of the NuRD complex. Several MBD2 and MBD3 isoforms are present in mammalian cells, resulting in distinct MBD-NuRD complexes. Whether these different complexes serve distinct functional activities during differentiation is not fully explored. Based on the essential role of MBD3 in lineage commitment, we systematically investigated a diverse set of MBD2 and MBD3 variants for their potential to rescue the differentiation block observed for mouse embryonic stem cells (ESCs) lacking MBD3. While MBD3 is indeed crucial for ESC differentiation to neuronal cells, it functions independently of its MBD domain. We further identify that MBD2 isoforms can replace MBD3 during lineage commitment, however with different potential. Full-length MBD2a only partially rescues the differentiation block, while MBD2b, an isoform lacking an N-terminal GR-rich repeat, fully rescues the Mbd3 KO phenotype. In case of MBD2a, we further show that removing the methylated DNA binding capacity or the GR-rich repeat enables full redundancy to MBD3, highlighting the synergistic requirements for these domains in diversifying NuRD complex function.
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Affiliation(s)
- Nina Schmolka
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Richard Cardoso da Silva
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Davide C Recchia
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jahnavi Bhaskaran
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- MRC London Institute of Medical Sciences, London, UK
| | - Michael Teske
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nathalie P de Wagenaar
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
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9
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Ping W, Sheng Y, Hu G, Zhong H, Li Y, Liu Y, Luo W, Yan C, Wen Y, Wang X, Li Q, Guo R, Zhang J, Liu A, Pan G, Yao H. RBBP4 is an epigenetic barrier for the induced transition of pluripotent stem cells into totipotent 2C-like cells. Nucleic Acids Res 2023; 51:5414-5431. [PMID: 37021556 PMCID: PMC10287929 DOI: 10.1093/nar/gkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/07/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Cellular totipotency is critical for whole-organism generation, yet how totipotency is established remains poorly illustrated. Abundant transposable elements (TEs) are activated in totipotent cells, which is critical for embryonic totipotency. Here, we show that the histone chaperone RBBP4, but not its homolog RBBP7, is indispensable for maintaining the identity of mouse embryonic stem cells (mESCs). Auxin-induced degradation of RBBP4, but not RBBP7, reprograms mESCs to the totipotent 2C-like cells. Also, loss of RBBP4 enhances transition from mESCs to trophoblast cells. Mechanistically, RBBP4 binds to the endogenous retroviruses (ERVs) and functions as an upstream regulator by recruiting G9a to deposit H3K9me2 on ERVL elements, and recruiting KAP1 to deposit H3K9me3 on ERV1/ERVK elements, respectively. Moreover, RBBP4 facilitates the maintenance of nucleosome occupancy at the ERVK and ERVL sites within heterochromatin regions through the chromatin remodeler CHD4. RBBP4 depletion leads to the loss of the heterochromatin marks and activation of TEs and 2C genes. Together, our findings illustrate that RBBP4 is required for heterochromatin assembly and is a critical barrier for inducing cell fate transition from pluripotency to totipotency.
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Affiliation(s)
- Wangfang Ping
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yingliang Sheng
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Gongcheng Hu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hongxin Zhong
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yaoyi Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - YanJiang Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Wei Luo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Chenghong Yan
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yulin Wen
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xinxiu Wang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Qing Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Rong Guo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Hongjie Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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10
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Wang B, Li C, Ming J, Wu L, Fang S, Huang Y, Lin L, Liu H, Kuang J, Zhao C, Huang X, Feng H, Guo J, Yang X, Guo L, Zhang X, Chen J, Liu J, Zhu P, Pei D. The NuRD complex cooperates with SALL4 to orchestrate reprogramming. Nat Commun 2023; 14:2846. [PMID: 37208322 DOI: 10.1038/s41467-023-38543-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
Cell fate decision involves rewiring of the genome, but remains poorly understood at the chromatin level. Here, we report that chromatin remodeling complex NuRD participates in closing open chromatin in the early phase of somatic reprogramming. Sall4, Jdp2, Glis1 and Esrrb can reprogram MEFs to iPSCs efficiently, but only Sall4 is indispensable capable of recruiting endogenous components of NuRD. Yet knocking down NuRD components only reduces reprogramming modestly, in contrast to disrupting the known Sall4-NuRD interaction by mutating or deleting the NuRD interacting motif at its N-terminus that renders Sall4 inept to reprogram. Remarkably, these defects can be partially rescured by grafting NuRD interacting motif onto Jdp2. Further analysis of chromatin accessibility dynamics demonstrates that the Sall4-NuRD axis plays a critical role in closing the open chromatin in the early phase of reprogramming. Among the chromatin loci closed by Sall4-NuRD encode genes resistant to reprogramming. These results identify a previously unrecognized role of NuRD in reprogramming, and may further illuminate chromatin closing as a critical step in cell fate control.
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Affiliation(s)
- Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chen Li
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Wu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shicai Fang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Joint School of Life Science, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yi Huang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Joint School of Life Science, Guangzhou Medical University-Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lihui Lin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences, Guangzhou, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- Guangzhou Branch of the Supercomputing Center of Chinese Academy of Sciences, Guangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xingnan Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huijian Feng
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Guo
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Xuejie Yang
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Liman Guo
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Xiaofei Zhang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Jing Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institutes for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academic of Sciences, Guangzhou, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou Key Laboratory of Cardiac Pathogenesis and Prevention, Guangzhou, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
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11
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Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C. Structure of a SIN3-HDAC complex from budding yeast. Nat Struct Mol Biol 2023:10.1038/s41594-023-00975-z. [PMID: 37081318 DOI: 10.1038/s41594-023-00975-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/23/2023] [Indexed: 04/22/2023]
Abstract
SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 Å. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.
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Affiliation(s)
- Zhouyan Guo
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chen Chu
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yichen Lu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiaofeng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yihang Xiao
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, China
| | - Shuaixin Gao
- Human Nutrition Program & James Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Chengcheng Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
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12
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Wang C, Guo Z, Chu C, Lu Y, Zhang X, Zhan X. Two assembly modes for SIN3 histone deacetylase complexes. Cell Discov 2023; 9:42. [PMID: 37076472 PMCID: PMC10115800 DOI: 10.1038/s41421-023-00539-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/10/2023] [Indexed: 04/21/2023] Open
Abstract
The switch-independent 3 (SIN3)/histone deacetylase (HDAC) complexes play essential roles in regulating chromatin accessibility and gene expression. There are two major types of SIN3/HDAC complexes (named SIN3L and SIN3S) targeting different chromatin regions. Here we present the cryo-electron microscopy structures of the SIN3L and SIN3S complexes from Schizosaccharomyces pombe (S. pombe), revealing two distinct assembly modes. In the structure of SIN3L, each Sin3 isoform (Pst1 and Pst3) interacts with one histone deacetylase Clr6, and one WD40-containing protein Prw1, forming two lobes. These two lobes are bridged by two vertical coiled-coil domains from Sds3/Dep1 and Rxt2/Png2, respectively. In the structure of SIN3S, there is only one lobe organized by another Sin3 isoform Pst2; each of the Cph1 and Cph2 binds to an Eaf3 molecule, providing two modules for histone recognition and binding. Notably, the Pst1 Lobe in SIN3L and the Pst2 Lobe in SIN3S adopt similar conformation with their deacetylase active sites exposed to the space; however, the Pst3 Lobe in SIN3L is in a compact state with its active center buried inside and blocked. Our work reveals two classical organization mechanisms for the SIN3/HDAC complexes to achieve specific targeting and provides a framework for studying the histone deacetylase complexes.
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Affiliation(s)
- Chengcheng Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
| | - Zhouyan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Chen Chu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China.
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13
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Reid XJ, Low JKK, Mackay JP. A NuRD for all seasons. Trends Biochem Sci 2023; 48:11-25. [PMID: 35798615 DOI: 10.1016/j.tibs.2022.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/27/2022]
Abstract
The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.
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14
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KTN1-AS1, a SOX2-mediated lncRNA, activates epithelial-mesenchymal transition process in esophageal squamous cell carcinoma. Sci Rep 2022; 12:20186. [PMID: 36418920 PMCID: PMC9684558 DOI: 10.1038/s41598-022-24743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Kinectin 1 antisense RNA 1 (KTN1-AS1), a long non-coding RNA (lncRNA), has been proved to have tumor-promoting properties and its expression is enhanced in several human tumors. However, the role of KTN1-AS1 in the pathogenesis of esophageal squamous cell carcinoma (ESCC) remains unknown. This study aimed to investigate the expression status, functional roles, and molecular mechanisms of KTN1-AS1 in the development of ESCC. Considerable upregulation of KTN1-AS1 was confirmed in esophageal cancer cells and ESCC tissues and its expression was associated with TNM stage, pathological differentiation, and lymph node metastasis. SOX2 directly activated transcription of KTN1-AS1, and overexpression of KTN1-AS1 facilitated ESCC cells proliferation and invasion in vitro and in vivo. Furthermore, KTN1-AS1 could bind to retinoblastoma binding protein 4 (RBBP4) in the nucleus and enhanced its binding with histone deacetylase 1 (HDAC1), thereby activating the epithelial-mesenchymal transition (EMT) process through downregulating E-cadherin expression at the epigenetic level. In conclusion, KTN1-AS1, induced by SOX2, acts as a tumor-promoting gene and may serve as a potential therapeutic and prognostic biomarker for ESCC.
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15
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Lee K, Whedon SD, Wang ZA, Cole PA. Distinct biochemical properties of the class I histone deacetylase complexes. Curr Opin Chem Biol 2022; 70:102179. [PMID: 35803024 PMCID: PMC10786639 DOI: 10.1016/j.cbpa.2022.102179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/25/2022] [Accepted: 05/29/2022] [Indexed: 11/22/2022]
Abstract
Classical histone deacetylases (HDACs) are enzymes that can hydrolytically cleave acetyl-Lys in histones and other proteins and serve as established drug targets in some forms of cancer. Class I HDACs 1-3 typically exist in a range of multiprotein complexes inside cells and show distinct biological functions in modulating gene expression. In recent years, it has become possible to purify and analyze the structure and enzymatic properties of several of these HDAC complexes, including CoREST, MiDAC, NuRD, Sin3, SMRT, MIER, and RERE. Here, we summarize what is experimentally established and/or computationally predicted about the structure of these complexes to describe their particular catalytic activities and site-specificities with modified nucleosome substrates.
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Affiliation(s)
- Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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16
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Archibald L, Brown EA, Millard CJ, Watson PJ, Robertson NS, Wang S, Schwabe JWR, Jamieson AG. Hydroxamic Acid-Modified Peptide Library Provides Insights into the Molecular Basis for the Substrate Selectivity of HDAC Corepressor Complexes. ACS Chem Biol 2022; 17:2572-2582. [PMID: 35973051 PMCID: PMC9488896 DOI: 10.1021/acschembio.2c00510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Targeting the lysine deacetylase activity of class I histone deacetylases (HDACs) is potentially beneficial for the treatment of several diseases including human immunodeficiency virus (HIV) infection, Alzheimer's disease, and various cancers. It is therefore important to understand the function and mechanism of action of these enzymes. Class I HDACs act as catalytic components of seven large, multiprotein corepressor complexes. Different HDAC corepressor complexes have specific, nonredundant roles in the cell. It is likely that their specific functions are at least partly influenced by the substrate specificity of the complexes. To address this, we developed chemical tools to probe the specificity of HDAC complexes. We assessed a library of acetyl-lysine-containing substrate peptides and hydroxamic acid-containing inhibitor peptides against the full range of class I HDAC corepressor complexes. The results suggest that site-specific HDAC corepressor complex activity is driven in part by the recognition of the primary amino acid sequence surrounding a particular lysine position in the histone tail.
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Affiliation(s)
- Lewis
J. Archibald
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, U.K.
| | - Edward A. Brown
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Christopher J. Millard
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Peter J. Watson
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - Naomi S. Robertson
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Siyu Wang
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.
| | - John W. R. Schwabe
- The
Leicester Institute of Structural and Chemical Biology, Department
of Molecular and Cell Biology, University
of Leicester, Leicester LE1 7RH, U.K.,
| | - Andrew G. Jamieson
- School
of Chemistry, Advanced Research Centre, University of Glasgow, Glasgow G11 6EW, U.K.,
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17
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Çalışkaner ZO. Computational discovery of novel inhibitory candidates targeting versatile transcriptional repressor MBD2. J Mol Model 2022; 28:296. [PMID: 36066769 DOI: 10.1007/s00894-022-05297-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
Abstract
Genome methylation is a key epigenetic mechanism in various biological events such as development, cellular differentiation, cancer progression, aging, and iPSC reprogramming. Crosstalk between DNA methylation and gene expression is mediated by MBD2, known as the reader of DNA methylation and suggested as a drug target. Despite its magnitude of significance, a scarcely limited number of small molecules to be used as inhibitors have been detected so far. Therefore, we screened a comprehensive compound library to elicit MBD2 inhibitor candidates. Promising molecules were subjected to computational docking analysis by targeting the methylated DNA-binding domain of human MBD2. We could detect reasonable binding energies and docking residues, presumably located in druggable pockets. Docking results were also validated via MD simulation and per-residue energy decomposition calculation. Drug-likeness of these small molecules was assessed through ADMET prediction to foresee off-target side effects for future studies. All computational approaches notably highlighted two compounds named CID3100583 and 8,8-ethylenebistheophylline. These compounds have become prominent as novel candidates, possibly disrupting MBD2MBD-DNA interaction. Consequently, these compounds have been considered prospective inhibitors with the usage potential in a wide range of applications from cancer treatment to somatic cell reprogramming protocols.
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Affiliation(s)
- Zihni Onur Çalışkaner
- Faculty of Engineering and Natural Sciences, Molecular Biology and Genetics Department, Biruni University, 34010, Istanbul, Turkey.
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18
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Arvindekar S, Jackman MJ, Low JKK, Landsberg MJ, Mackay JP, Viswanath S. Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Protein Sci 2022; 31:e4387. [PMID: 36040254 PMCID: PMC9413472 DOI: 10.1002/pro.4387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/18/2022] [Accepted: 06/19/2022] [Indexed: 11/11/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions, and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4, MTA1N -HDAC1-MBD3GATAD2CC , and MTA1-HDAC1-RBBP4-MBD3-GATAD2A [nucleosome deacetylase (NuDe)]. The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C -MTA1BAH , MTA1BAH -MBD3MBD , and HDAC160-100 -MBD3MBD . Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR , thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
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Affiliation(s)
- Shreyas Arvindekar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
| | - Matthew J. Jackman
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Jason K. K. Low
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Michael J. Landsberg
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Joel P. Mackay
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Shruthi Viswanath
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBangaloreIndia
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19
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Mladek AC, Yan H, Tian S, Decker PA, Burgenske DM, Bakken K, Hu Z, He L, Connors MA, Carlson BL, Wilson J, Bommi-Reddy A, Conery A, Eckel-Passow JE, Sarkaria JN, Kitange GJ. RBBP4-p300 axis modulates expression of genes essential for cell survival and is a potential target for therapy in glioblastoma. Neuro Oncol 2022; 24:1261-1272. [PMID: 35231103 PMCID: PMC9340617 DOI: 10.1093/neuonc/noac051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RBBP4 activates transcription by histone acetylation, but the partner histone acetyltransferases are unknown. Thus, we investigated the hypothesis that RBBP4 interacts with p300 in a complex in glioblastoma (GBM). METHODS shRNA silencing of RBBP4 or p300 and RNAseq was used to identify genes co-regulated by RBBP4 and p300 in GBM43 patient-derived xenograft (PDX). RBBP4/p300 complex was demonstrated using proximity ligation assay (PLA) and ChIPseq delineated histone H3 acetylation and RBBP4/p300 complex binding in promoters/enhancers. Temozolomide (TMZ)-induced DNA double strand breaks (DSBs) were evaluated by γ-H2AX and proliferation by CyQuant and live cell monitoring assays. In vivo efficacy was based on survival of mice with orthotopic tumors. RESULTS shRBBP4 and shp300 downregulated 4768 genes among which 1485 (31%) were commonly downregulated by both shRNAs, while upregulated genes were 2484, including 863 (35%) common genes. The pro-survival genes were the top-ranked among the downregulated genes, including C-MYC. RBBP4/p300 complex was demonstrated in the nucleus, and shRBBP4 or shp300 significantly sensitized GBM cells to TMZ compared to the control shNT in vitro (P < .05). Moreover, TMZ significantly prolonged the survival of mice bearing GBM22-shRBBP4 orthotopic tumors compared with control shNT tumors (median shNT survival 52 days vs. median shRBBP4 319 days; P = .001). CREB-binding protein (CBP)/p300 inhibitor CPI-1612 suppressed H3K27Ac and RBBP4/p300 complex target proteins, including C-MYC, and synergistically sensitized TMZ in vitro. Pharmacodynamic evaluation confirmed brain penetration by CPI-1612 supporting further investigation to evaluate efficacy to sensitize TMZ. CONCLUSIONS RBBP4/p300 complex is present in GBM cells and is a potential therapeutic target.
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Affiliation(s)
- Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Huihuang Yan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul A Decker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Katrina Bakken
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Zeng Hu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lihong He
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret A Connors
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Brett L Carlson
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jonathan Wilson
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | - Andy Conery
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gaspar J Kitange
- Corresponding Author: Gaspar J. Kitange, MD, PhD, Department of Radiation Oncology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA (/)
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20
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Wang ZA, Whedon SD, Wu M, Wang S, Brown EA, Anmangandla A, Regan L, Lee K, Du J, Hong JY, Fairall L, Kay T, Lin H, Zhao Y, Schwabe JWR, Cole PA. Histone H2B Deacylation Selectivity: Exploring Chromatin's Dark Matter with an Engineered Sortase. J Am Chem Soc 2022; 144:3360-3364. [PMID: 35175758 PMCID: PMC8895396 DOI: 10.1021/jacs.1c13555] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We describe a new method to produce histone H2B by semisynthesis with an engineered sortase transpeptidase. N-Terminal tail site-specifically modified acetylated, lactylated, and β-hydroxybutyrylated histone H2Bs were incorporated into nucleosomes and investigated as substrates of histone deacetylase (HDAC) complexes and sirtuins. A wide range of rates and site-specificities were observed by these enzyme forms suggesting distinct biological roles in regulating chromatin structure and epigenetics.
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Affiliation(s)
- Zhipeng A Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Samuel D Whedon
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Siyu Wang
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Edward A Brown
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Ananya Anmangandla
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Liam Regan
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianfeng Du
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - Jun Young Hong
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Taylor Kay
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hening Lin
- Howard Hughes Medical Institute; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yingming Zhao
- The Ben May Department for Cancer Research, Chicago, Illinois 60637, United States
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, United States.,Department of Biological Chemistry and Molecular Pharmcology, Harvard Medical School, Boston, Massachusetts 02115, United States
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21
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Blasl AT, Schulze S, Qin C, Graf LG, Vogt R, Lammers M. Post-translational lysine ac(et)ylation in health, ageing and disease. Biol Chem 2021; 403:151-194. [PMID: 34433238 DOI: 10.1515/hsz-2021-0139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022]
Abstract
The acetylation/acylation (ac(et)ylation) of lysine side chains is a dynamic post-translational modification (PTM) regulating fundamental cellular processes with implications on the organisms' ageing process: metabolism, transcription, translation, cell proliferation, regulation of the cytoskeleton and DNA damage repair. First identified to occur on histones, later studies revealed the presence of lysine ac(et)ylation in organisms of all kingdoms of life, in proteins covering all essential cellular processes. A remarkable finding showed that the NAD+-dependent sirtuin deacetylase Sir2 has an impact on replicative lifespan in Saccharomyces cerevisiae suggesting that lysine acetylation has a direct role in the ageing process. Later studies identified sirtuins as mediators for beneficial effects of caloric/dietary restriction on the organisms' health- or lifespan. However, the molecular mechanisms underlying these effects are only incompletely understood. Progress in mass-spectrometry, structural biology, synthetic and semi-synthetic biology deepened our understanding of this PTM. This review summarizes recent developments in the research field. It shows how lysine ac(et)ylation regulates protein function, how it is regulated enzymatically and non-enzymatically, how a dysfunction in this post-translational machinery contributes to disease development. A focus is set on sirtuins and lysine acyltransferases as these are direct sensors and mediators of the cellular metabolic state. Finally, this review highlights technological advances to study lysine ac(et)ylation.
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Affiliation(s)
- Anna-Theresa Blasl
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Sabrina Schulze
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Chuan Qin
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Leonie G Graf
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Robert Vogt
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
| | - Michael Lammers
- Department Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17487Greifswald, Germany
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22
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Sharifi Tabar M, Giardina C, Feng Y, Francis H, Moghaddas Sani H, Low JKK, Mackay JP, Bailey CG, Rasko JEJ. Unique protein interaction networks define the chromatin remodelling module of the NuRD complex. FEBS J 2021; 289:199-214. [PMID: 34231305 PMCID: PMC9545347 DOI: 10.1111/febs.16112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/27/2021] [Accepted: 07/06/2021] [Indexed: 01/13/2023]
Abstract
The combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1 and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodelling module of the nucleosome remodelling and deacetylase (NuRD) complex. To date, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential for defining underlying mechanisms of gene regulation. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS), we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodelling activity into both ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation-prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the nuclear receptor co-repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia
| | - Caroline Giardina
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Yue Feng
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Habib Francis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | | | - Jason K K Low
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Joel P Mackay
- School of Life & Environmental Sciences, The University of Sydney, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia.,Faculty of Medicine & Health, The University of Sydney, NSW, Australia.,Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
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23
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Liu YR, Wang JQ, Huang ZG, Chen RN, Cao X, Zhu DC, Yu HX, Wang XR, Zhou HY, Xia Q, Li J. Histone deacetylase‑2: A potential regulator and therapeutic target in liver disease (Review). Int J Mol Med 2021; 48:131. [PMID: 34013366 PMCID: PMC8136123 DOI: 10.3892/ijmm.2021.4964] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Histone acetyltransferases are responsible for histone acetylation, while histone deacetylases (HDACs) counteract histone acetylation. An unbalanced dynamic between histone acetylation and deacetylation may lead to aberrant chromatin landscape and chromosomal function. HDAC2, a member of class I HDAC family, serves a crucial role in the modulation of cell signaling, immune response and gene expression. HDAC2 has emerged as a promising therapeutic target for liver disease by regulating gene transcription, chromatin remodeling, signal transduction and nuclear reprogramming, thus receiving attention from researchers and clinicians. The present review introduces biological information of HDAC2 and its physiological and biochemical functions. Secondly, the functional roles of HDAC2 in liver disease are discussed in terms of hepatocyte apoptosis and proliferation, liver regeneration, hepatocellular carcinoma, liver fibrosis and non-alcoholic steatohepatitis. Moreover, abnormal expression of HDAC2 may be involved in the pathogenesis of liver disease, and its expression levels and pharmacological activity may represent potential biomarkers of liver disease. Finally, research on selective HDAC2 inhibitors and non-coding RNAs relevant to HDAC2 expression in liver disease is also reviewed. The aim of the present review was to improve understanding of the multifunctional role and potential regulatory mechanism of HDAC2 in liver disease.
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Affiliation(s)
- Ya-Ru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jie-Quan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, P.R. China
| | - Zhao-Gang Huang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ruo-Nan Chen
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xi Cao
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dong-Chun Zhu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Hai-Xia Yu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiu-Rong Wang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Hai-Yun Zhou
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jun Li
- The Key Laboratory of Anti‑inflammatory Immune Medicines, School of Pharmacy, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, P.R. China
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24
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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