1
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Qin Y, Dong X, Lu M, Jing L, Chen Q, Guan F, Xiang Z, Huang J, Yang C, He X, Qu J, Yang Z. PARP1 interacts with WDR5 to enhance target gene recognition and facilitate tumorigenesis. Cancer Lett 2024; 593:216952. [PMID: 38750719 DOI: 10.1016/j.canlet.2024.216952] [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: 01/02/2024] [Revised: 04/18/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a nuclear protein that attaches negatively charged poly (ADP-ribose) (PAR) to itself and other target proteins. While its function in DNA damage repair is well established, its role in target chromatin recognition and regulation of gene expression remains to be better understood. This study showed that PARP1 interacts with SET1/MLL complexes by binding directly to WDR5. Notably, although PARP1 does not modulate WDR5 PARylation or the global level of H3K4 methylation, it exerts locus-specific effects on WDR5 binding and H3K4 methylation. Interestingly, PARP1 and WDR5 show extensive co-localization on chromatin, with WDR5 facilitating the recognition and expression of target genes regulated by PARP1. Furthermore, we demonstrated that inhibition of the WDR5 Win site impedes the interaction between PARP1 and WDR5, thereby inhibiting PARP1 from binding to target genes. Finally, the combined inhibition of the WDR5 Win site and PARP shows a profound inhibitory effect on the proliferation of cancer cells. These findings illuminate intricate mechanisms underlying chromatin recognition, gene transcription, and tumorigenesis, shedding light on previously unrecognized roles of PARP1 and WDR5 in these processes.
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Affiliation(s)
- Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaochuan Dong
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Manman Lu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lingyun Jing
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qingchuan Chen
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fei Guan
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhengkai Xiang
- Department of Thoracic Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430079, China
| | - Jiaojuan Huang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chengxuan Yang
- Department of Galactophore, Xinxiang First People's Hospital, Xinxiang, 453000, China
| | - Ximiao He
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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2
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Terzi Çizmecioğlu N. Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1470:73-96. [PMID: 38231346 DOI: 10.1007/5584_2023_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.
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3
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Liu Z, Hu W, Qin Y, Sun L, Jing L, Lu M, Li Y, Qu J, Yang Z. Isl1 promotes gene transcription through physical interaction with Set1/Mll complexes. Eur J Cell Biol 2023; 102:151295. [PMID: 36758343 DOI: 10.1016/j.ejcb.2023.151295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023] Open
Abstract
Histone H3 lysine 4 (H3K4) methylation is generally recognized as a prominent marker of gene activation. While Set1/Mll complexes are major methyltransferases that are responsible for H3K4 methylation, the mechanism of how these complexes are recruited into the target gene promotor is still unclear. Here, starting with an affinity purification-mass spectrometry approach, we have found that Isl1, a highly tissue-specific expressed LIM/homeodomain transcription factor, is physically associated with Set1/Mll complexes. We then show that Wdr5 directly binds to Isl1. And this binding is likely mediated by the homeodomain of Isl1. Functionally, using mouse β-cell and human neuroblastoma tumor cell lines, we show that both Wdr5 binding and H3K4 methylation level at promoters of some Isl1 target genes are significantly reduced upon depletion of Isl1, suggesting Isl1 is required for efficient locus-specific H3K4 methylation. Taken together, our results establish a critical role of Set1/Mll complexes in regulating the target gene expression of Isl1.
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Affiliation(s)
- Zhe Liu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weijing Hu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yali Qin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Sun
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lingyun Jing
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Manman Lu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yan Li
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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4
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Su WC, Mao XM, Li SY, Luo CY, Fan R, Jiang HF, Zhang LJ, Wang YT, Su GQ, Shen DY. DPY30 Promotes Proliferation and Cell Cycle Progression of Colorectal Cancer Cells via Mediating H3K4 Trimethylation. Int J Med Sci 2023; 20:901-917. [PMID: 37324189 PMCID: PMC10266052 DOI: 10.7150/ijms.80073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/25/2023] [Indexed: 06/17/2023] Open
Abstract
DPY30, a core subunit of the SET1/MLL histone H3K4 methyltransferase complexes, plays an important role in diverse biological functions through the epigenetic regulation of gene transcription, especially in cancer development. However, its involvement in human colorectal carcinoma (CRC) has not been elucidated yet. Here we demonstrated that DPY30 was overexpressed in CRC tissues, and significantly associated with pathological grading, tumor size, TNM stage, and tumor location. Furthermore, DPY30 knockdown remarkably suppressed the CRC cell proliferation through downregulation of PCNA and Ki67 in vitro and in vivo, simultaneously induced cell cycle arrest at S phase by downregulating Cyclin A2. In the mechanistic study, RNA-Seq analysis revealed that enriched gene ontology of cell proliferation and cell growth was significantly affected. And ChIP result indicated that DPY30 knockdown inhibited H3 lysine 4 trimethylation (H3K4me3) and attenuated interactions between H3K4me3 with PCNA, Ki67 and cyclin A2 respectively, which led to the decrease of H3K4me3 establishment on their promoter regions. Taken together, our results demonstrate overexpression of DPY30 promotes CRC cell proliferation and cell cycle progression by facilitating the transcription of PCNA, Ki67 and cyclin A2 via mediating H3K4me3. It suggests that DPY30 may serve as a potential therapeutic molecular target for CRC.
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Affiliation(s)
- Wei-Chao Su
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Xiao-Mei Mao
- School of Pharmaceutical Science and Technology, Suzhou Chien-Shiung Institute of Technology, Suzhou 215411, Jiangsu Province, P.R. China
| | - Si-Yang Li
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Chun-Ying Luo
- Department of Pathology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise 533000, Guangxi Province, P.R. China
- Medical College, Guangxi University, Nanning 530004, Guangxi Province, P.R. China
| | - Rui Fan
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Hai-Feng Jiang
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Lin-Jun Zhang
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Ya-Tao Wang
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
| | - Guo-Qiang Su
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
- Medical College, Guangxi University, Nanning 530004, Guangxi Province, P.R. China
| | - Dong-Yan Shen
- Xiamen Cell Therapy Research Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, P.R. China
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5
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Mei Q, Yang Z, Xiang Z, Zuo H, Zhou Z, Dong X, Zhang L, Song W, Wang Y, Hu Q, Zhou Y, Qu J. Pharmacological inhibition of MDM4 alleviates pulmonary fibrosis. Theranostics 2023; 13:2787-2799. [PMID: 37284444 PMCID: PMC10240813 DOI: 10.7150/thno.81993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease of unknown etiology with no cure. A better understanding of the disease processes and identification of druggable targets will benefit the development of effective therapies for IPF. We previously reported that MDM4 promoted lung fibrosis through the MDM4-p53-dependent pathway. However, it remained unclear whether targeting this pathway would have any therapeutic potential. In this study, we evaluated the efficacy of XI-011, a small molecular inhibitor of MDM4, for treating lung fibrosis. We found that XI-011 significantly reduced MDM4 expression and increased the expression of total and acetylated p53 in primary human myofibroblasts and a murine fibrotic model. XI-011 treatment resulted in the resolution of lung fibrosis in mice with no notable impact on normal fibroblast death or the morphology of healthy lungs. Based on these findings, we propose that XI-011 might be a promising therapeutic drug candidate for treating pulmonary fibrosis.
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Affiliation(s)
- Qianru Mei
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhengkai Xiang
- Department of Thoracic Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430079, China
| | - He Zuo
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zijing Zhou
- Department of Pulmonary and Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiaochuan Dong
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ludan Zhang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenhui Song
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Wang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qinghua Hu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yong Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, the University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jing Qu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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6
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Jin ML, Yang L, Jeong KW. SETD1A-SOX2 axis is involved in tamoxifen resistance in estrogen receptor α-positive breast cancer cells. Theranostics 2022; 12:5761-5775. [PMID: 35966598 PMCID: PMC9373809 DOI: 10.7150/thno.72599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/02/2022] [Indexed: 12/03/2022] Open
Abstract
Rationale: Approximately 30-40% of estrogen receptor (ER)-positive breast cancer (BC) cases recur after tamoxifen therapy. Thus, additional studies on the mechanisms underlying tamoxifen resistance and more specific prognostic biomarkers are required. In this study, we investigated the role of the SET domain containing 1A (SETD1A), a histone H3-lysine 4 (H3K4) methyltransferase, in the development of tamoxifen resistance in BC. Methods: The relationship between tamoxifen resistance and SETD1A protein level was investigated using resistant cell lines derived from the parent BC cells. Biochemical and molecular assays, such as RNA-sequencing, reverse transcription-quantitative polymerase chain reaction, chromatin-immunoprecipitation, and protein-binding assays, were used to identify the SETD1A target gene in tamoxifen-resistant BC cells. Additionally, the role of SETD1A in cancer stem cells (CSCs) was investigated using CSCs isolated from tamoxifen-resistant BC cells. Comprehensive transcriptome analysis and immunofluorescence staining using clinical datasets and tissue microarray were performed to determine the correlation between the expression of the SETD1A-SRY-box transcription factor 2 (SOX2) pair and recurrence in tamoxifen-treated patients with BC. Results: SETD1A was expressed at higher levels in tamoxifen-resistant BC cells than in primary BC cells. Notably, SETD1A-depleted tamoxifen-resistant MCF-7 cells showed restored sensitivity to tamoxifen, whereas SETD1A overexpression in MCF-7 cells resulted in decreased sensitivity. SETD1A is recruited to the SOX2 gene via its interaction with SOX2, thereby enhancing the expression of SOX2 genes in tamoxifen-resistant BC cells. The growth of tamoxifen-resistant cells and CSCs was effectively suppressed by SETD1A knockdown. In addition, high levels of SETD1A and SOX2 were significantly correlated with a low survival rate in patients with ER-positive tamoxifen-resistant BC. Conclusion: Our findings provide the first evidence of the critical role of the SETD1A-SOX2 axis in tamoxifen-resistant BC cells, implying that SETD1A may serve as a molecular target and prognostic indicator of a therapeutic response in patients with tamoxifen-resistant BC.
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Affiliation(s)
- Ming Li Jin
- Gachon Research Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 21936, Republic of Korea
| | - Liu Yang
- Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-Constructed by Henan Province & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Kwang Won Jeong
- Gachon Research Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 21936, Republic of Korea
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7
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Hagey DW, Bergsland M, Muhr J. SOX2 transcription factor binding and function. Development 2022; 149:276045. [DOI: 10.1242/dev.200547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The transcription factor SOX2 is a vital regulator of stem cell activity in various developing and adult tissues. Mounting evidence has demonstrated the importance of SOX2 in regulating the induction and maintenance of stemness as well as in controlling cell proliferation, lineage decisions and differentiation. Recent studies have revealed that the ability of SOX2 to regulate these stem cell features involves its function as a pioneer factor, with the capacity to target nucleosomal DNA, modulate chromatin accessibility and prepare silent genes for subsequent activation. Moreover, although SOX2 binds to similar DNA motifs in different stem cells, its multifaceted and cell type-specific functions are reliant on context-dependent features. These cell type-specific properties include variations in partner factor availability and SOX2 protein expression levels. In this Primer, we discuss recent findings that have increased our understanding of how SOX2 executes its versatile functions as a master regulator of stem cell activities.
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Affiliation(s)
- Daniel W. Hagey
- Karolinska Institutet 1 Department of Laboratory Medicine , , SE-171 77 Stockholm , Sweden
| | - Maria Bergsland
- Karolinska Institutet 2 Department of Cell and Molecular Biology , , Solnavägen 9, SE-171 65 Stockholm , Sweden
| | - Jonas Muhr
- Karolinska Institutet 2 Department of Cell and Molecular Biology , , Solnavägen 9, SE-171 65 Stockholm , Sweden
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8
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Poreba E, Lesniewicz K, Durzynska J. Histone-lysine N-methyltransferase 2 (KMT2) complexes - a new perspective. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108443. [PMID: 36154872 DOI: 10.1016/j.mrrev.2022.108443] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/25/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Histone H3 Lys4 (H3K4) methylation is catalyzed by the Histone-Lysine N-Methyltransferase 2 (KMT2) protein family, and its members are required for gene expression control. In vertebrates, the KMT2s function in large multisubunit complexes known as COMPASS or COMPASS-like complexes (COMplex of Proteins ASsociated with Set1). The activity of these complexes is critical for proper development, and mutation-induced defects in their functioning have frequently been found in human cancers. Moreover, inherited or de novo mutations in KMT2 genes are among the etiological factors in neurodevelopmental disorders such as Kabuki and Kleefstra syndromes. The canonical role of KMT2s is to catalyze H3K4 methylation, which results in a permissive chromatin environment that drives gene expression. However, current findings described in this review demonstrate that these enzymes can regulate processes that are not dependent on methylation: noncatalytic functions of KMT2s include DNA damage response, cell division, and metabolic activities. Moreover, these enzymes may also methylate non-histone substrates and play a methylation-dependent function in the DNA damage response. In this review, we present an overview of the new, noncanonical activities of KMT2 complexes in a variety of cellular processes. These discoveries may have crucial implications for understanding the functions of these methyltransferases in developmental processes, disease, and epigenome-targeting therapeutic strategies in the future.
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Affiliation(s)
- Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Julia Durzynska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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9
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Dixit D, Prager BC, Gimple RC, Miller TE, Wu Q, Yomtoubian S, Kidwell RL, Lv D, Zhao L, Qiu Z, Zhang G, Lee D, Park DE, Wechsler-Reya RJ, Wang X, Bao S, Rich JN. Glioblastoma stem cells reprogram chromatin in vivo to generate selective therapeutic dependencies on DPY30 and phosphodiesterases. Sci Transl Med 2022; 14:eabf3917. [PMID: 34985972 DOI: 10.1126/scitranslmed.abf3917] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glioblastomas are universally fatal cancers and contain self-renewing glioblastoma stem cells (GSCs) that initiate tumors. Traditional anticancer drug discovery based on in vitro cultures tends to identify targets with poor therapeutic indices and fails to accurately model the effects of the tumor microenvironment. Here, leveraging in vivo genetic screening, we identified the histone H3 lysine 4 trimethylation (H3K4me3) regulator DPY30 (Dpy-30 histone methyltransferase complex regulatory subunit) as an in vivo–specific glioblastoma dependency. On the basis of the hypothesis that in vivo epigenetic regulation may define critical GSC dependencies, we interrogated active chromatin landscapes of GSCs derived from intracranial patient-derived xenografts (PDXs) and cell culture through H3K4me3 chromatin immunoprecipitation and transcriptome analyses. Intracranial-specific genes marked by H3K4me3 included FOS, NFκB, and phosphodiesterase (PDE) family members. In intracranial PDX tumors, DPY30 regulated angiogenesis and hypoxia pathways in an H3K4me3-dependent manner but was dispensable in vitro in cultured GSCs. PDE4B was a key downstream effector of DPY30, and the PDE4 inhibitor rolipram preferentially targeted DPY30-expressing cells and impaired PDX tumor growth in mice without affecting tumor cells cultured in vitro. Collectively, the MLL/SET1 (mixed lineage leukemia/SET domain-containing 1, histone lysine methyltransferase) complex member DPY30 selectively regulates H3K4me3 modification on genes critical to support angiogenesis and tumor growth in vivo, suggesting the DPY30-PDE4B axis as a specific therapeutic target in glioblastoma.
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Affiliation(s)
- Deobrat Dixit
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Briana C Prager
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ryan C Gimple
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Qiulian Wu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Shira Yomtoubian
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Reilly L Kidwell
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Deguan Lv
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Linjie Zhao
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Zhixin Qiu
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Guoxin Zhang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Derrick Lee
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
| | - Donglim Esther Park
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiuxing Wang
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Shideng Bao
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44106, USA
| | - Jeremy N Rich
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, San Diego, CA 92037, USA.,University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA
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10
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Shah K, King GD, Jiang H. A chromatin modulator sustains self-renewal and enables differentiation of postnatal neural stem and progenitor cells. J Mol Cell Biol 2021; 12:4-16. [PMID: 31065682 PMCID: PMC7052987 DOI: 10.1093/jmcb/mjz036] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/31/2019] [Accepted: 04/07/2019] [Indexed: 12/17/2022] Open
Abstract
It remains unknown whether H3K4 methylation, an epigenetic modification associated with gene activation, regulates fate determination of the postnatal neural stem and progenitor cells (NSPCs). By inactivating the Dpy30 subunit of the major H3K4 methyltransferase complexes in specific regions of mouse brain, we demonstrate a crucial role of efficient H3K4 methylation in maintaining both the self-renewal and differentiation capacity of postnatal NSPCs. Dpy30 deficiency disrupts development of hippocampus and especially the dentate gyrus and subventricular zone, the major regions for postnatal NSC activities. Dpy30 is indispensable for sustaining the self-renewal and proliferation of NSPCs in a cell-intrinsic manner and also enables the differentiation of mouse and human neural progenitor cells to neuronal and glial lineages. Dpy30 directly regulates H3K4 methylation and the induction of several genes critical in neurogenesis. These findings link a prominent epigenetic mechanism of gene expression to the fundamental properties of NSPCs and may have implications in neurodevelopmental disorders.
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Affiliation(s)
- Kushani Shah
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gwendalyn D King
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
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11
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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12
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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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13
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Pacelli C, Adipietro I, Malerba N, Squeo GM, Piccoli C, Amoresano A, Pinto G, Pucci P, Lee JE, Ge K, Capitanio N, Merla G. Loss of Function of the Gene Encoding the Histone Methyltransferase KMT2D Leads to Deregulation of Mitochondrial Respiration. Cells 2020; 9:cells9071685. [PMID: 32668765 PMCID: PMC7407568 DOI: 10.3390/cells9071685] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
KMT2D encodes a methyltransferase responsible for histone 3 lysine 4 (H3K4) mono-/di-methylation, an epigenetic mark correlated with active transcription. Here, we tested the hypothesis that KMT2D pathogenic loss-of-function variants, which causes the Kabuki syndrome type 1, could affect the mitochondrial metabolic profile. By using Seahorse technology, we showed a significant reduction of the mitochondrial oxygen consumption rate as well as a reduction of the glycolytic flux in both Kmt2d knockout MEFs and skin fibroblasts of Kabuki patients harboring heterozygous KMT2D pathogenic variants. Mass-spectrometry analysis of intermediate metabolites confirmed alterations in the glycolytic and TCA cycle pathways. The observed metabolic phenotype was accompanied by a significant increase in the production of reactive oxygen species. Measurements of the specific activities of the mitochondrial respiratory chain complexes revealed significant inhibition of CI (NADH dehydrogenase) and CIV (cytochrome c oxidase); this result was further supported by a decrease in the protein content of both complexes. Finally, we unveiled an impaired oxidation of glucose and larger reliance on long-chain fatty acids oxidation. Altogether, our findings clearly indicate a rewiring of the mitochondrial metabolic phenotype in the KMT2D-null or loss-of-function context that might contribute to the development of Kabuki disease, and represents metabolic reprogramming as a potential new therapeutic approach.
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Affiliation(s)
- Consiglia Pacelli
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy; (C.P.); (C.P.)
| | - Iolanda Adipietro
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy; (I.A.); (N.M.); (G.M.S.)
| | - Natascia Malerba
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy; (I.A.); (N.M.); (G.M.S.)
| | - Gabriella Maria Squeo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy; (I.A.); (N.M.); (G.M.S.)
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy; (C.P.); (C.P.)
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Napoli, Italy; (A.A.); (G.P.); (P.P.)
- INBB—Biostructures and Biosystems National Institute, 00136 Roma, Italy
| | - Gabriella Pinto
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Napoli, Italy; (A.A.); (G.P.); (P.P.)
| | - Pietro Pucci
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Napoli, Italy; (A.A.); (G.P.); (P.P.)
- Department of Chemical Sciences, CEINGE Advanced Biotechnology, Federico II University, 80145 Napoli, Italy
| | - Ji-Eun Lee
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.E.L.); (K.G.)
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (J.E.L.); (K.G.)
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, 71121 Foggia, Italy; (C.P.); (C.P.)
- Correspondence: (N.C.); (G.M.)
| | - Giuseppe Merla
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy; (I.A.); (N.M.); (G.M.S.)
- Correspondence: (N.C.); (G.M.)
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14
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Jiang H. The complex activities of the SET1/MLL complex core subunits in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194560. [PMID: 32302696 DOI: 10.1016/j.bbagrm.2020.194560] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/14/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022]
Abstract
In mammalian cells, the SET1/MLL complexes are the main writers of the H3K4 methyl mark that is associated with active gene expression. The activities of these complexes are critically dependent on the association of the catalytic subunit with their shared core subunits, WDR5, RBBP5, ASH2L, and DPY30, collectively referred as WRAD. In addition, some of these core subunits can bind to proteins other than the SET1/MLL complex components. This review starts with discussion of the molecular activities of these core subunits, with an emphasis on DPY30 in organizing the assembly of the SET1/MLL complexes with other associated factors. This review then focuses on the roles of the core subunits in stem cells and development, as well as in diseased cell states, mainly cancer, and ends with discussion on dissecting the responsible activities of the core subunits and how we may target them for potential disease treatment. This article is part of a Special Issue entitled: The MLL family of proteins in normal development and disease edited by Thomas A Milne.
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Affiliation(s)
- Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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15
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Tsai PH, Chien Y, Wang ML, Hsu CH, Laurent B, Chou SJ, Chang WC, Chien CS, Li HY, Lee HC, Huo TI, Hung JH, Chen CH, Chiou SH. Ash2l interacts with Oct4-stemness circuitry to promote super-enhancer-driven pluripotency network. Nucleic Acids Res 2019; 47:10115-10133. [PMID: 31555818 PMCID: PMC6821267 DOI: 10.1093/nar/gkz801] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 01/31/2023] Open
Abstract
Pluripotency and cell fates can be modulated through the regulation of super-enhancers; however, the underlying mechanisms are unclear. Here, we showed a novel mechanism in which Ash2l directly binds to super-enhancers of several stemness genes to regulate pluripotency and self-renewal in pluripotent stem cells. Ash2l recruits Oct4/Sox2/Nanog (OSN) to form Ash2l/OSN complex at the super-enhancers of Jarid2, Nanog, Sox2 and Oct4, and further drives enhancer activation, upregulation of stemness genes, and maintains the pluripotent circuitry. Ash2l knockdown abrogates the OSN recruitment to all super-enhancers and further hinders the enhancer activation. In addition, CRISPRi/dCas9-mediated blocking of Ash2l-binding motifs at these super-enhancers also prevents OSN recruitment and enhancer activation, validating that Ash2l directly binds to super-enhancers and initiates the pluripotency network. Transfection of Ash2l with W118A mutation to disrupt Ash2l–Oct4 interaction fails to rescue Ash2l-driven enhancer activation and pluripotent gene upregulation in Ash2l-depleted pluripotent stem cells. Together, our data demonstrated Ash2l formed an enhancer-bound Ash2l/OSN complex that can drive enhancer activation, govern pluripotency network and stemness circuitry.
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Affiliation(s)
- Ping-Hsing Tsai
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yueh Chien
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Mong-Lien Wang
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.,School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China
| | - Benoit Laurent
- Boston Children's Hospital and Harvard Medical School, Boston MA 02115, USA
| | - Shih-Jie Chou
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan.,School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chian-Shiu Chien
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Hsin-Yang Li
- School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan.,Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsin-Chen Lee
- Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan.,School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Teh-Ia Huo
- Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan.,Section of Gastroenterology, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Jui-Hung Hung
- Institutes of Data Science and Engineering, and Department of computer science, National Chiao-Tung University, Hsinchu 30010, Taiwan
| | | | - Shih-Hwa Chiou
- Department of Medical Research, Taipei VeteransGeneral Hospital, Taipei 11217, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei 11221, Taiwan.,School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan.,Genomic Research Center, Academia Sinica, Taipei 11529, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao-Tung University, Hsinchu 30010, Taiwan
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16
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Yang Z, Shah K, Khodadadi-Jamayran A, Jiang H. Control of Hematopoietic Stem and Progenitor Cell Function through Epigenetic Regulation of Energy Metabolism and Genome Integrity. Stem Cell Reports 2019; 13:61-75. [PMID: 31231026 PMCID: PMC6627005 DOI: 10.1016/j.stemcr.2019.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/23/2022] Open
Abstract
It remains largely unclear how stem cells regulate bioenergetics and genome integrity to ensure tissue homeostasis. Here, our integrative gene analyses suggest that metabolic and genotoxic stresses may underlie the common functional defects of both fetal and adult hematopoietic stem and progenitor cells (HSPCs) upon loss of DPY30, an epigenetic modulator that facilitates H3K4 methylation. DPY30 directly regulates expression of several key glycolytic genes, and its loss in HSPCs critically impaired energy metabolism, including both glycolytic and mitochondrial pathways. We also found significant increase in DNA breaks as a result of impaired DNA repair upon DPY30 loss, and inhibition of DNA damage response partially rescued clonogenicity of the DPY30-deficient HSPCs. Moreover, CDK inhibitor p21 was upregulated in DPY30-deficient HSPCs, and p21 deletion alleviated their functional defect. These results demonstrate that epigenetic mechanisms by H3K4 methylation play a crucial role in HSPC function through control of energy metabolism and protecting genome integrity. DPY30-deficient fetal and adult HSCs are defective in maintenance and differentiation Glycolytic and oxidative metabolism are dysregulated in DPY30-deficient HSCs Increase in DNA damage response contributes to dysfunction of DPY30-deficient HSPCs P21 increase partially mediates dysfunction of DPY30-deficient HSPCs
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Affiliation(s)
- Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA.
| | - Kushani Shah
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA; Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 JPA, Pinn Hall Room 6017, Charlottesville, VA 22908, USA.
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17
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Watts AJ, Storey KB. Hibernation impacts lysine methylation dynamics in the 13-lined ground squirrel, Ictidomys tridecemlineatus. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2019; 331:234-244. [PMID: 30767414 DOI: 10.1002/jez.2259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 11/11/2022]
Abstract
During winter hibernation in mammals, body temperature falls to near-ambient levels, metabolism shifts to favor lipid oxidation, and metabolic rate is strongly suppressed by inhibiting many ATP-expensive processes (e.g., transcription, translation) for animals in order to survive for many months on limited reserves of body fuels. Regulation of such profound changes (i.e., metabolic rate depression) requires rapid and reversible controls provided by protein posttranslational modifications. Protein lysine methylation provides one mechanism by which the functionality, activity, and stability of cellular proteins and enzymes can be modified for the needs of the hibernator. The present study reports the responses of seven lysine methyltransferases (SMYD2, SUV39H1, SET8, SET7/9, G9a, ASH2L, and RBBP5) in skeletal muscle and liver over seven stages of the torpor/arousal cycle in 13-lined ground squirrels (Ictidomys tridecemlineatus). A tissue-specific and stage-specific analysis revealed significant changes in the protein levels of lysine methyltransferases, methylation patterns on histone H3, histone methyltransferase activity, and methylation of the p53 transcription factor. Enzymes typically increased in protein amount in either torpor, arousal, or the transitory periods. Methylation of histone H3 and p53 typically followed the patterns of the methyltransferase enzymes. Overall, these data show that protein lysine methylation is an important regulator of the mammalian hibernation phenotype.
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Affiliation(s)
- Alexander J Watts
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Canada
| | - Kenneth B Storey
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Canada
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18
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Li S, Xiao F, Zhang J, Sun X, Wang H, Zeng Y, Hu J, Tang F, Gu J, Zhao Y, Jin Y, Liao B. Disruption of OCT4 Ubiquitination Increases OCT4 Protein Stability and ASH2L-B-Mediated H3K4 Methylation Promoting Pluripotency Acquisition. Stem Cell Reports 2018; 11:973-987. [PMID: 30269953 PMCID: PMC6178847 DOI: 10.1016/j.stemcr.2018.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 11/25/2022] Open
Abstract
The protein level of OCT4, a core pluripotency transcription factor, is vital for embryonic stem cell (ESC) maintenance, differentiation, and somatic cell reprogramming. However, how OCT4 protein levels are controlled during reprogramming remains largely unknown. Here, we identify ubiquitin conjugation sites of OCT4 and report that disruption of WWP2-catalyzed OCT4 ubiquitination or ablation of Wwp2 significantly promotes the efficiency of pluripotency induction from mouse embryonic fibroblasts. Mechanistically, disruption of WWP2-mediated OCT4 ubiquitination elevates OCT4 protein stability and H3K4 methylation level during the reprogramming process. Furthermore, we reveal that OCT4 directly activates expression of Ash2l-b, and that ASH2L-B is a major isoform of ASH2L highly expressed in ESCs and required for somatic cell reprogramming. Together, this study emphasizes the importance of ubiquitination manipulation of the reprogramming factor and its interplay with the epigenetic regulator for successful reprogramming, opening a new avenue to improve the efficiency of pluripotency induction. Five lysine residues are major ubiquitination sites of OCT4 catalyzed by WWP2 Disruption of OCT4 ubiquitination promotes somatic cell reprogramming Mutation of OCT4 ubiquitination sites enhances OCT4 stability and H3K4me levels ASH2L-B contributes to somatic cell reprogramming as a direct target of OCT4
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Affiliation(s)
- Shuang Li
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Feng Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Junmei Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaozhi Sun
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Han Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China
| | - Yanwu Zeng
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Jing Hu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Fan Tang
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Junjie Gu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China
| | - Yingming Zhao
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ying Jin
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200032, China.
| | - Bing Liao
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 227 South Chongqing Road, Shanghai 200025, China.
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19
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Yang Z, Shah K, Busby T, Giles K, Khodadadi-Jamayran A, Li W, Jiang H. Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer. J Clin Invest 2018; 128:3605-3618. [PMID: 29870403 DOI: 10.1172/jci97072] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 05/29/2018] [Indexed: 12/14/2022] Open
Abstract
While the genomic binding of MYC protein correlates with active epigenetic marks on chromatin, it remains largely unclear how major epigenetic mechanisms functionally impact the tumorigenic potential of MYC. Here, we show that, compared with the catalytic subunits, the core subunits, including DPY30, of the major H3K4 methyltransferase complexes were frequently amplified in human cancers and selectively upregulated in Burkitt lymphoma. We show that DPY30 promoted the expression of endogenous MYC and was also functionally important for efficient binding of MYC to its genomic targets by regulating chromatin accessibility. Dpy30 heterozygosity did not affect normal animal physiology including lifespan, but significantly suppressed Myc-driven lymphomagenesis, as cells failed to combat oncogene-triggered apoptosis as a result of insufficient epigenetic modulation and expression of a subset of antiapoptotic genes. Dpy30 reduction also greatly impeded MYC-dependent cellular transformation, without affecting normal cell growth. These results suggest that MYC hijacks a major epigenetic pathway - H3K4 methylation - to facilitate its molecular activity in target binding and to coordinate its oncogenic program for efficient tumorigenesis, meanwhile creating "epigenetic vulnerability." DPY30 and the H3K4 methylation pathway are thus potential epigenetic targets for treating certain MYC-driven cancers.
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Affiliation(s)
- Zhenhua Yang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Kushani Shah
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Theodore Busby
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Keith Giles
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Wei Li
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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20
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Mittal A, Hobor F, Zhang Y, Martin SR, Gamblin SJ, Ramos A, Wilson JR. The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites. Nucleic Acids Res 2018; 46:3802-3812. [PMID: 29897600 PMCID: PMC6283417 DOI: 10.1093/nar/gky199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 03/03/2018] [Accepted: 03/07/2018] [Indexed: 12/26/2022] Open
Abstract
The multi-protein complex WRAD, formed by WDR5, RbBP5, Ash2L and Dpy30, binds to the MLL SET domain to stabilize the catalytically active conformation required for histone H3K4 methylation. In addition, the WRAD complex contributes to the targeting of the activated complex to specific sites on chromatin. RbBP5 is central to MLL catalytic activation, by making critical contacts with the other members of the complex. Interestingly its only major structural domain, a canonical WD40 repeat β-propeller, is not implicated in this function. Here, we present the structure of the RbBP5 β-propeller domain revealing a distinct, feature rich surface, dominated by clusters of Arginine residues. Our nuclear magnetic resonance binding data supports the hypothesis that in addition to the role of RbBP5 in catalytic activation, its β-propeller domain is a platform for the recruitment of the MLL complexes to chromatin targets through its direct interaction with nucleic acids.
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Affiliation(s)
| | - Fruzsina Hobor
- Institute of Structural and Molecular Biology, University College London, London WC1E 6XA, UK
| | - Ying Zhang
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, London WC1E 6XA, UK
| | - Jon R Wilson
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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21
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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22
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Abstract
Somatic cells can be reprogrammed to pluripotent stem cells or transdifferentiate to another lineage cell type. Much efforts have been made to unravel the epigenetic mechanisms underlying the cell fate conversion. Histone modifications as the major epigenetic regulator are implicated in various aspects of reprogramming and transdifferentiation. Here, we discuss the roles of histone modifications on reprogramming and transdifferentiation and hopefully provide new insights into induction and promotion of the cell fate conversion by modulating histone modifications.
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Wu C, Zhang HF, Gupta N, Alshareef A, Wang Q, Huang YH, Lewis JT, Douglas DN, Kneteman NM, Lai R. A positive feedback loop involving the Wnt/β-catenin/MYC/Sox2 axis defines a highly tumorigenic cell subpopulation in ALK-positive anaplastic large cell lymphoma. J Hematol Oncol 2016; 9:120. [PMID: 27821172 PMCID: PMC5100098 DOI: 10.1186/s13045-016-0349-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/28/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND We have previously described the existence of two phenotypically distinct cell subsets in ALK-positive anaplastic large cell lymphoma (ALK + ALCL) based on their differential responsiveness to a Sox2 reporter (SRR2), with reporter-responsive (RR) cells being more tumorigenic and chemoresistant than reporter-unresponsive (RU) cells. However, the regulator(s) of RU/RR dichotomy are not identified. In this study, we aim to delineate the key regulator(s) of RU/RR dichotomy. METHODS JASPER motif match analysis was used to identify the putative factors binding to SRR2 sequence. SRR2 probe pull-down assay and quantitate real-time PCR were performed to analyze the regulation of Sox2 transcriptional activity by MYC. Methylcellulose colony formation assay, chemoresistance to doxorubicin and mouse xenograft study were performed to investigate the biological functions of MYC. PCR array and western blotting were executed to study related signaling pathways that regulate MYC expression. Immunofluorescence and immunohistochemistry assay were initiated to evaluate the expression of MYC and its correlation with its regulator by chi-square test analysis in human primary tumor cells. RESULTS We identified MYC as a potential regulator of RU/RR dichotomy. In support of its role, MYC was highly expressed in RR cells compared to RU cells, and inhibition of MYC substantially decreased the Sox2/SRR2 binding, Sox2 transcriptional activity, chemoresistance, and methylcellulose colony formation. In contrast, enforced expression of MYC in RU cells conferred the RR phenotype. The Wnt/β-catenin pathway, a positive regulator of MYC, was highly active in RR but not RU cells. While inhibition of this pathway in RR cells substantially decreased MYC expression and SRR2 reporter activity, experimental activation of this pathway led to the opposite effects in RU cells. Collectively, our results support a model in which a positive feedback loop involving Wnt/β-catenin/MYC and Sox2 contributes to the RR phenotype. In a mouse xenograft model, RU cells stably transfected with MYC showed upregulation of the Wnt/β-catenin/MYC/Sox2 axis and increased tumorigenecity. Correlating with these findings, there was a significant correlation between the expression of active β-catenin and MYC in ALK + ALCL primary tumor cells. CONCLUSIONS A positive feedback loop involving the Wnt/β-catenin/MYC/Sox2 axis defines a highly tumorigenic cell subset in ALK + ALCL.
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Affiliation(s)
- Chengsheng Wu
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
| | - Hai-Feng Zhang
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Nidhi Gupta
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
| | - Abdulraheem Alshareef
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
| | - Qian Wang
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
| | - Yung-Hsing Huang
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
| | - Jamie T. Lewis
- Department of Surgery, University of Alberta, Edmonton, Alberta Canada
| | - Donna N. Douglas
- Department of Surgery, University of Alberta, Edmonton, Alberta Canada
| | | | - Raymond Lai
- Department of Laboratory Medicine and Pathology, 5142J Katz Group Centre for Pharmacy and Health Research, University of Alberta, Edmonton, Alberta T6G 1Z2 Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta Canada
- DynaLIFEDX Medical Laboratories, Edmonton, Alberta Canada
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Butler JS, Qiu YH, Zhang N, Yoo SY, Coombes KR, Dent SYR, Kornblau SM. Low expression of ASH2L protein correlates with a favorable outcome in acute myeloid leukemia. Leuk Lymphoma 2016; 58:1207-1218. [PMID: 28185526 DOI: 10.1080/10428194.2016.1235272] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
ASH2L encodes a trithorax group protein that is a core component of all characterized mammalian histone H3K4 methyltransferase complexes, including mixed lineage leukemia (MLL) complexes. ASH2L protein levels in primary leukemia patient samples have not yet been defined. We analyzed ASH2L protein expression in 511 primary AML patient samples using reverse phase protein array (RPPA) technology. We discovered that ASH2L expression is significantly increased in a subset of patients carrying fms-related tyrosine kinase 3 (FLT3) mutations. Furthermore, we observed that low levels of ASH2L are associated with increased overall survival. We also compared ASH2L levels to the expression of 230 proteins previously analyzed on this array. ASH2L expression was inversely correlated with 32 proteins, mostly involved in cell adhesion and cell cycle inhibition, while a positive correlation was observed for 50 proteins, many of which promote cell proliferation. Together, these results indicate that a lower level of ASH2L protein is beneficial to AML patients.
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Affiliation(s)
- Jill S Butler
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Science Park , Smithville , TX , USA.,b Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Yi Hua Qiu
- c Division of Molecular Hematology, Department of Leukemia , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | | | - Suk-Young Yoo
- e Department of Bioinformatics and Computational Biology , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Kevin R Coombes
- f Department of Biomedical Informatics , The Ohio State University College of Medicine , Columbus , OH , USA
| | - Sharon Y R Dent
- a Department of Epigenetics and Molecular Carcinogenesis , The University of Texas MD Anderson Cancer Center , Science Park , Smithville , TX , USA.,b Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Steven M Kornblau
- c Division of Molecular Hematology, Department of Leukemia , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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Bayarsaihan D. A central role of H3K4me3 extended chromatin domains in gene regulation. Epigenomics 2016; 8:1011-4. [PMID: 27410771 DOI: 10.2217/epi-2016-0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for Systems Genomics, Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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