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Pichavaram P, Jablonowski CM, Fang J, Fleming AM, Gil HJ, Boghossian AS, Rees MG, Ronan MM, Roth JA, Morton CL, Zambetti GP, Davidoff AM, Yang J, Murphy AJ. Oncogenic Cells of Renal Embryonic Lineage Sensitive to the Small-Molecule Inhibitor QC6352 Display Depletion of KDM4 Levels and Disruption of Ribosome Biogenesis. Mol Cancer Ther 2024; 23:478-491. [PMID: 37988559 PMCID: PMC10987284 DOI: 10.1158/1535-7163.mct-23-0312] [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: 05/22/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023]
Abstract
The histone lysine demethylases KDM4A-C are involved in physiologic processes including stem cell identity and self-renewal during development, DNA damage repair, and cell-cycle progression. KDM4A-C are overexpressed and associated with malignant cell behavior in multiple human cancers and are therefore potential therapeutic targets. Given the role of KDM4A-C in development and cancer, we aimed to test the potent, selective KDM4A-C inhibitor QC6352 on oncogenic cells of renal embryonic lineage. The anaplastic Wilms tumor cell line WiT49 and the tumor-forming human embryonic kidney cell line HEK293 demonstrated low nanomolar QC6352 sensitivity. The cytostatic response to QC6352 in WiT49 and HEK293 cells was marked by induction of DNA damage, a DNA repair-associated protein checkpoint response, S-phase cell-cycle arrest, profound reduction of ribosomal protein gene and rRNA transcription, and blockade of newly synthesized proteins. QC6352 caused reduction of KDM4A-C levels by a proteasome-associated mechanism. The cellular phenotype caused by QC6352 treatment of reduced migration, proliferation, tumor spheroid growth, DNA damage, and S-phase cell-cycle arrest was most closely mirrored by knockdown of KDM4A as determined by siRNA knockdown of KDM4A-C. QC6352 sensitivity correlated with high basal levels of ribosomal gene transcription in more than 900 human cancer cell lines. Targeting KDM4A may be of future therapeutic interest in oncogenic cells of embryonic renal lineage or cells with high basal expression of ribosomal protein genes.
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Affiliation(s)
| | | | - Jie Fang
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Andrew M. Fleming
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hyea Jin Gil
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Matthew G. Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Melissa M. Ronan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Jennifer A. Roth
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Christopher L. Morton
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Gerard P. Zambetti
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Andrew M. Davidoff
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Andrew J. Murphy
- Department of Surgery, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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2
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Meng L. Chromatin-modifying enzymes as modulators of nuclear size during lineage differentiation. Cell Death Discov 2023; 9:384. [PMID: 37863956 PMCID: PMC10589317 DOI: 10.1038/s41420-023-01639-z] [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: 04/18/2023] [Revised: 08/17/2023] [Accepted: 08/31/2023] [Indexed: 10/22/2023] Open
Abstract
The mechanism of nuclear size determination and alteration during normal lineage development and cancer pathologies which is not fully understood. As recently reported, chromatin modification can change nuclear morphology. Therefore, we screened a range of pharmacological chemical compounds that impact the activity of chromatin-modifying enzymes, in order to get a clue of the specific types of chromatin-modifying enzymes that remarkably effect nuclear size and shape. We found that interrupted activity of chromatin-modifying enzymes is associated with nuclear shape abnormalities. Furthermore, the activity of chromatin-modifying enzymes perturbs cell fate determination in cellular maintenance and lineage commitment. Our results indicated that chromatin-modifying enzyme regulates cell fate decision during lineage differentiation and is associate with nuclear size alteration.
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Affiliation(s)
- Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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3
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Shelke V, Yelgonde V, Kale A, Lech M, Gaikwad AB. Epigenetic regulation of mitochondrial-endoplasmic reticulum dynamics in kidney diseases. J Cell Physiol 2023; 238:1716-1731. [PMID: 37357431 DOI: 10.1002/jcp.31058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/25/2023] [Accepted: 05/26/2023] [Indexed: 06/27/2023]
Abstract
Kidney diseases are serious health problems affecting >800 million individuals worldwide. The high number of affected individuals and the severe consequences of kidney dysfunction demand an intensified effort toward more effective prevention and treatment. The pathophysiology of kidney diseases is complex and comprises diverse organelle dysfunctions including mitochondria and endoplasmic reticulum (ER). The recent findings prove interactions between the ER membrane and nearly all cell compartments and give new insights into molecular events involved in cellular mechanisms in health and disease. Interactions between the ER and mitochondrial membranes, known as the mitochondria-ER contacts regulate kidney physiology by interacting with each other via membrane contact sites (MCS). ER controls mitochondrial dynamics through ER stress sensor proteins or by direct communication via mitochondria-associated ER membrane to activate signaling pathways such as apoptosis, calcium transport, and autophagy. More importantly, these organelle dynamics are found to be regulated by several epigenetic mechanisms such as DNA methylation, histone modifications, and noncoding RNAs and can be a potential therapeutic target against kidney diseases. However, a thorough understanding of the role of epigenetic regulation of organelle dynamics and their functions is not well understood. Therefore, this review will unveil the role of epigenetic mechanisms in regulating organelle dynamics during various types of kidney diseases. Moreover, we will also shed light on different stress origins in organelles leading to kidney disease. Henceforth, by understanding this we can target epigenetic mechanisms to maintain/control organelle dynamics and serve them as a novel therapeutic approach against kidney diseases.
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Affiliation(s)
- Vishwadeep Shelke
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Vinayak Yelgonde
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Ajinath Kale
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
| | - Maciej Lech
- Department of Internal Medicine IV, Division of Nephrology, Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Anil Bhanudas Gaikwad
- Laboratory of Molecular Pharmacology, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, Rajasthan, India
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4
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Abstract
Virtually all cell types have the same DNA, yet each type exhibits its own cell-specific pattern of gene expression. During the brief period of mitosis, the chromosomes exhibit changes in protein composition and modifications, a marked condensation, and a consequent reduction in transcription. Yet as cells exit mitosis, they reactivate their cell-specific programs with high fidelity. Initially, the field focused on the subset of transcription factors that are selectively retained in, and hence bookmark, chromatin in mitosis. However, recent studies show that many transcription factors can be retained in mitotic chromatin and that, surprisingly, such retention can be due to nonspecific chromatin binding. Here, we review the latest studies focusing on low-level transcription via promoters, rather than enhancers, as contributing to mitotic memory, as well as new insights into chromosome structure dynamics, histone modifications, cell cycle signaling, and nuclear envelope proteins that together ensure the fidelity of gene expression through a round of mitosis.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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5
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Wu Q, Young B, Wang Y, Davidoff AM, Rankovic Z, Yang J. Recent Advances with KDM4 Inhibitors and Potential Applications. J Med Chem 2022; 65:9564-9579. [PMID: 35838529 PMCID: PMC9531573 DOI: 10.1021/acs.jmedchem.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histone lysine demethylase 4 (KDM4) family plays an important role in regulating gene transcription, DNA repair, and metabolism. The dysregulation of KDM4 functions is associated with many human disorders, including cancer, obesity, and cardiovascular diseases. Selective and potent KDM4 inhibitors may help not only to understand the role of KDM4 in these disorders but also to provide potential therapeutic opportunities. Here, we provide an overview of the field and discuss current status, challenges, and opportunities lying ahead in the development of KDM4-based anticancer therapeutics.
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Affiliation(s)
- Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yan Wang
- Department of Geriatrics and Occupational Disease, Qingdao Central Hospital, Qingdao 266044, China
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163, United States
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6
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Sasaki K, Suzuki M, Sonoda T, Schneider-Poetsch T, Ito A, Takagi M, Fujishiro S, Sohtome Y, Dodo K, Umehara T, Aburatani H, Shin-Ya K, Nakao Y, Sodeoka M, Yoshida M. Visualization of the dynamic interaction between nucleosomal histone H3K9 tri-methylation and HP1α chromodomain in living cells. Cell Chem Biol 2022; 29:1153-1161.e5. [PMID: 35728598 DOI: 10.1016/j.chembiol.2022.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/05/2022] [Accepted: 05/23/2022] [Indexed: 11/26/2022]
Abstract
Histone lysine methylation is an epigenetic mark that can control gene expression. In particular, H3K9me3 contributes to transcriptional repression by regulating chromatin structure. Successful mitotic progression requires correct timing of chromatin structure changes, including epigenetic marks. However, spatiotemporal information on histone modifications in living cells remains limited. In this study, we created an FRET-based probe for live-cell imaging based on the HP1α chromodomain (HP1αCD), which binds to H3K9me3. The probe was incorporated into chromatin and the emission ratio decreased after treatment with histone methyltransferase inhibitors, indicating that it successfully traced dynamic changes in H3K9me3. Upon entry into mitosis, the probe's emission ratio transiently increased with a concomitant increase in H3K9me3, then exhibited a stepwise decrease, probably due to loss of HP1αCD binding caused by phosphorylation of H3S10 and demethylation of H3K9me3. This probe will be a useful tool for detecting dynamic changes in chromatin structure associated with HP1α.
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Affiliation(s)
- Kazuki Sasaki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
| | - Michihiro Suzuki
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Sonoda
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Motoki Takagi
- Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, 135-0064, Japan
| | - Shinya Fujishiro
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Aburatani
- Genome Science & Medicine Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan; Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoichi Nakao
- Department of Chemistry and Biochemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Catalysis and Integrated Research Group, RIKEN Center for Sustainable Research Science, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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7
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RNA Molecular Signature Profiling in PBMCs of Sporadic ALS Patients: HSP70 Overexpression Is Associated with Nuclear SOD1. Cells 2022; 11:cells11020293. [PMID: 35053410 PMCID: PMC8774074 DOI: 10.3390/cells11020293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Superoxide dismutase 1 (SOD1) is one of the causative genes associated with amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder. SOD1 aggregation contributes to ALS pathogenesis. A fraction of the protein is localized in the nucleus (nSOD1), where it seems to be involved in the regulation of genes participating in the oxidative stress response and DNA repair. Peripheral blood mononuclear cells (PBMCs) were collected from sporadic ALS (sALS) patients (n = 18) and healthy controls (n = 12) to perform RNA-sequencing experiments and differential expression analysis. Patients were stratified into groups with “high” and “low” levels of nSOD1. We obtained different gene expression patterns for high- and low-nSOD1 patients. Differentially expressed genes in high nSOD1 form a cluster similar to controls compared to the low-nSOD1 group. The pathways activated in high-nSOD1 patients are related to the upregulation of HSP70 molecular chaperones. We demonstrated that, in this condition, the DNA damage is reduced, even under oxidative stress conditions. Our findings highlight the importance of the nuclear localization of SOD1 as a protective mechanism in sALS patients.
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8
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Herlihy CP, Hahn S, Hermance NM, Crowley EA, Manning AL. Suv420 enrichment at the centromere limits Aurora B localization and function. J Cell Sci 2021; 134:jcs249763. [PMID: 34342353 PMCID: PMC8353524 DOI: 10.1242/jcs.249763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Centromere structure and function are defined by the epigenetic modification of histones at centromeric and pericentromeric chromatin. The constitutive heterochromatin found at pericentromeric regions is highly enriched for H3K9me3 and H4K20me3. Although mis-expression of the methyltransferase enzymes that regulate these marks, Suv39 and Suv420, is common in disease, the consequences of such changes are not well understood. Our data show that increased centromere localization of Suv39 and Suv420 suppresses centromere transcription and compromises localization of the mitotic kinase Aurora B, decreasing microtubule dynamics and compromising chromosome alignment and segregation. We find that inhibition of Suv420 methyltransferase activity partially restores Aurora B localization to centromeres and that restoration of the Aurora B-containing chromosomal passenger complex to the centromere is sufficient to suppress mitotic errors that result when Suv420 and H4K20me3 is enriched at centromeres. Consistent with a role for Suv39 and Suv420 in negatively regulating Aurora B, high expression of these enzymes corresponds with increased sensitivity to Aurora kinase inhibition in human cancer cells, suggesting that increased H3K9 and H4K20 methylation may be an underappreciated source of chromosome mis-segregation in cancer. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | | | | | | | - Amity L. Manning
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609USA
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9
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Gao Y, Liu Y, Liu Y, Peng Y, Yuan B, Fu Y, Qi X, Zhu Q, Cao T, Zhang S, Yin L, Li X. UHRF1 promotes androgen receptor-regulated CDC6 transcription and anti-androgen receptor drug resistance in prostate cancer through KDM4C-Mediated chromatin modifications. Cancer Lett 2021; 520:172-183. [PMID: 34265399 DOI: 10.1016/j.canlet.2021.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/26/2021] [Accepted: 07/08/2021] [Indexed: 12/30/2022]
Abstract
The UHRF1 and CDC6, oncogenes play critical roles in therapeutic resistance. In the present study, we found that UHRF1 mediates androgen receptor (AR)-regulated CDC6 transcription in prostate cancer cells. In prostate cancer tissues and cell lines, levels of UHRF1 and CDC6 were simultaneously upregulated, and this was associated with worse survival. UHRF1 silencing significantly promoted the cytotoxicity and anti-prostate cancer efficacy of bicalutamide in mouse xenografts by inhibiting CDC6 gene expression. UHRF1 promoted AR-regulated CDC6 transcription by binding to the CCAAT motif near the androgen response element (ARE) in the CDC6 promoter. We further found that UHRF1 promoted androgen-dependent chromatin occupancy of AR protein by recruiting the H3K9me2/3-specific demethyltransferase KDM4C and modifying the intense heterochromatin status. Altogether, we found for the first time that UHRF1 promotes AR-regulated CDC6 transcription through a novel chromatin modification mechanism and contributes to anti-AR drug resistance in prostate cancer. Targeting AR and UHRF1 simultaneously may be a novel and promising therapeutic modality for prostate cancer.
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Affiliation(s)
- Yingxue Gao
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Yijun Liu
- School of Basic Medicine, Changsha Medical University, China
| | - Youhong Liu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Yuchong Peng
- Center for Clinical Precision Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, China
| | - Bowen Yuan
- Department of Pathology, The Third Xiangya Hospital, Central South University, China
| | - Yuxin Fu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Xuli Qi
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Qianling Zhu
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Tuoyu Cao
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Songwei Zhang
- Department of Oncology, Center for Molecular Medicine, Xiangya Hospital, Central South University, China; Hunan Key Laboratory of Molecular Radiation Oncology, Xiangya Hospital, Central South University, China
| | - Linglong Yin
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, China
| | - Xiong Li
- Center for Clinical Precision Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, China; School of Clinical Pharmacy, Guangdong Pharmaceutical University, China; NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, China.
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10
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Xiao Z, Yang X, Liu Z, Shao Z, Song C, Zhang K, Wang X, Li Z. GASC1 promotes glioma progression by enhancing NOTCH1 signaling. Mol Med Rep 2021; 23:310. [PMID: 33649841 PMCID: PMC7974312 DOI: 10.3892/mmr.2021.11949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/21/2021] [Indexed: 12/21/2022] Open
Abstract
Recent studies have reported that gene amplified in squamous cell carcinoma 1 (GASC1) is involved in the progression of several types of cancer. However, whether GASC1 promotes glioma progression remains unknown. Therefore, the present study aimed to investigate the effect of GASC1 exposure on glioma tumorigenesis. The western blot demonstrated that grade III and IV glioma tissues exhibited a higher mRNA and protein expression of GASC1. Moreover, CD133+ U87 or U251 cells from magnetic cell separation exhibited a higher GASC1 expression. Invasion Transwell assay, clonogenic assay and wound healing assay have shown that GASC1 inhibition using a pharmacological inhibitor and specific short hairpin (sh)RNA suppressed the invasive, migratory and tumorsphere forming abilities of primary culture human glioma cells. Furthermore, GASC1‑knockdown decreased notch receptor (Notch) responsive protein hes family bHLH transcription factor 1 (Hes1) signaling. GASC1 inhibition reduced notch receptor 1 (NOTCH1) expression, and a NOTCH1 inhibitor enhanced the effects of GASC1 inhibition on the CD133+ U87 or U251 cell tumorsphere forming ability, while NOTCH1 overexpression abrogated these effects. In addition, the GASC1 inhibitor caffeic acid and/or the NOTCH1 inhibitor DAPT (a γ‑Secretase Inhibitor), efficiently suppressed the human glioma xenograft tumors. Thus, the present results demonstrated the importance of GASC1 in the progression of glioma and identified that GASC1 promotes glioma progression, at least in part, by enhancing NOTCH signaling, suggesting that GASC1/NOTCH1 signaling may be a potential therapeutic target for glioma treatment.
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Affiliation(s)
- Zhengzheng Xiao
- Department of Neurosurgery, Henan Key Laboratory of Cancer Epigenetics, Cancer Institute, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Xiaoli Yang
- Department of General Practice, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Zebin Liu
- Department of Neurosurgery, Henan Key Laboratory of Cancer Epigenetics, Cancer Institute, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Zheng Shao
- Department of Neurosurgery, Henan Key Laboratory of Cancer Epigenetics, Cancer Institute, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Chaojun Song
- Department of Neurosurgery, Henan Key Laboratory of Cancer Epigenetics, Cancer Institute, The First Affiliated Hospital and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, Henan 471003, P.R. China
| | - Kun Zhang
- Spine Tumor Center, Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai 210011, P.R. China
| | - Xiaobin Wang
- Department of Urology, Carson International Cancer Centre, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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11
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Shao N, Cheng J, Huang H, Gong X, Lu Y, Idris M, Peng X, Ong BX, Zhang Q, Xu F, Liu C. GASC1 promotes hepatocellular carcinoma progression by inhibiting the degradation of ROCK2. Cell Death Dis 2021; 12:253. [PMID: 33692332 PMCID: PMC7946911 DOI: 10.1038/s41419-021-03550-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 12/27/2022]
Abstract
Hepatocellular carcinoma (HCC) is a devastating malignancy without targeted therapeutic options. Our results indicated that the histone demethylase GASC1 signature is associated with later tumor stage and poorer survival in HCC patients. GASC1 depletion led to diminished HCC proliferation and tumor growth. A distinct heterogeneity in GASC1 levels was observed among HCC cell populations, predicting their inherent high or low tumor-initiating capacity. Mechanistically, GASC1 is involved in the regulation of several components of the Rho-GTPase signaling pathway including its downstream target ROCK2. GASC1 demethylase activity ensured the transcriptional repression of FBXO42, a ROCK2 protein-ubiquitin ligase, thereby inhibiting ROCK2 degradation via K63-linked poly-ubiquitination. Treatment with the GASC1 inhibitor SD70 impaired the growth of both HCC cell lines and xenografts in mice, sensitizing them to standard-of-care chemotherapy. This work identifies GASC1 as a malignant-cell-selective target in HCC, and GASC1-specific therapeutics represent promising candidates for new treatment options to control this malignancy.
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Affiliation(s)
- Na Shao
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, 400038, Chongqing, PR China
- Department of Biomedical Materials Science, School of Biomedical Engineering, Army Medical University, 400038, Chongqing, PR China
| | - Jiamin Cheng
- Comprehensive Liver Cancer Center, The Fifth Medical Center of Chinese PLA General Hospital, 100000, Beijing, PR China
| | - Hong Huang
- Clinical Medical Research Center, Southwest Hospital, Army Medical University, 400038, Chongqing, PR China
| | - Xiaoshan Gong
- Department of Biomedical Materials Science, School of Biomedical Engineering, Army Medical University, 400038, Chongqing, PR China
| | - Yongling Lu
- Clinical Medical Research Center, Southwest Hospital, Army Medical University, 400038, Chongqing, PR China
| | - Muhammad Idris
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
| | - Xu Peng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
| | - Belinda X Ong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Republic of Singapore
| | - Qiongyi Zhang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
| | - Feng Xu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Republic of Singapore.
| | - Chungang Liu
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, 400038, Chongqing, PR China.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore.
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12
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Yin Y, Guan B, Zhao Y, Li Y. SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5610658. [PMID: 32908899 PMCID: PMC7468611 DOI: 10.1155/2020/5610658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]
Abstract
Detecting SNP-SNP interactions associated with disease is significant in genome-wide association study (GWAS). Owing to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power and long running time. To tackle these drawbacks, a fast self-adaptive memetic algorithm (SAMA) is proposed in this paper. In this method, the crossover, mutation, and selection of standard memetic algorithm are improved to make SAMA adapt to the detection of SNP-SNP interactions associated with disease. Furthermore, a self-adaptive local search algorithm is introduced to enhance the detecting power of the proposed method. SAMA is evaluated on a variety of simulated datasets and a real-world biological dataset, and a comparative study between it and the other four methods (FHSA-SED, AntEpiSeeker, IEACO, and DESeeker) that have been developed recently based on evolutionary algorithms is performed. The results of extensive experiments show that SAMA outperforms the other four compared methods in terms of detection power and running time.
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Affiliation(s)
- Ying Yin
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Boxin Guan
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yuhai Zhao
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yuan Li
- School of Information Science and Technology, North China University of Technology, Beijing 100144, China
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13
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Meng F, Stamms K, Bennewitz R, Green A, Oback F, Turner P, Wei J, Oback B. Targeted histone demethylation improves somatic cell reprogramming into cloned blastocysts but not postimplantation bovine concepti†. Biol Reprod 2020; 103:114-125. [PMID: 32318688 DOI: 10.1093/biolre/ioaa053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/16/2020] [Accepted: 04/20/2020] [Indexed: 11/12/2022] Open
Abstract
Correct reprogramming of epigenetic marks in the donor nucleus is a prerequisite for successful cloning by somatic cell transfer (SCT). In several mammalian species, repressive histone (H) lysine (K) trimethylation (me3) marks, in particular H3K9me3, form a major barrier to somatic cell reprogramming into pluripotency and totipotency. We engineered bovine embryonic fibroblasts (BEFs) for the doxycycline-inducible expression of a biologically active, truncated form of murine Kdm4b, a demethylase that removes H3K9me3 and H3K36me3 marks. Upon inducing Kdm4b, H3K9me3 and H3K36me3 levels were reduced about 3-fold and 5-fold, respectively, compared with noninduced controls. Donor cell quiescence has been previously associated with reduced somatic trimethylation levels and increased cloning efficiency in cattle. Simultaneously inducing Kdm4b expression (via doxycycline) and quiescence (via serum starvation) further reduced global H3K9me3 and H3K36me3 levels by a total of 18-fold and 35-fold, respectively, compared with noninduced, nonstarved control fibroblasts. Following SCT, Kdm4b-BEFs reprogrammed significantly better into cloned blastocysts than noninduced donor cells. However, detrimethylated donors and sustained Kdm4b-induction during embryo culture did not increase the rates of postblastocyst development from implantation to survival into adulthood. In summary, overexpressing Kdm4b in donor cells only improved their reprogramming into early preimplantation stages, highlighting the need for alternative experimental approaches to reliably improve somatic cloning efficiency in cattle.
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Affiliation(s)
- Fanli Meng
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Kathrin Stamms
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,Institute of Nutrition, University Jena, Jena, Germany
| | - Romina Bennewitz
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,Institute of Neurology, University Hospital Frankfurt, Frankfurt, Germany
| | - Andria Green
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Fleur Oback
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Pavla Turner
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Jingwei Wei
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,Animal Science Institute, Guangxi University, Nanning, China
| | - Björn Oback
- AgResearch Ruakura Research Centre, Hamilton, New Zealand.,School of Medical Sciences, University of Auckland, Auckland, New Zealand
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14
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15
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Chen Y, Fang R, Yue C, Chang G, Li P, Guo Q, Wang J, Zhou A, Zhang S, Fuller GN, Shi X, Huang S. Wnt-Induced Stabilization of KDM4C Is Required for Wnt/β-Catenin Target Gene Expression and Glioblastoma Tumorigenesis. Cancer Res 2019; 80:1049-1063. [PMID: 31888886 DOI: 10.1158/0008-5472.can-19-1229] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Abstract
Wnt/β-catenin signaling activates the transcription of target genes to regulate stem cells and cancer development. However, the contribution of epigenetic regulation to this process is unknown. Here, we report that Wnt activation stabilizes the epigenetic regulator KDM4C that promotes tumorigenesis and survival of human glioblastoma cells by epigenetically activating the transcription of Wnt target genes. KDM4C protein expression was upregulated in human glioblastomas, and its expression directly correlated with Wnt activity and Wnt target gene expression. KDM4C was essential for Wnt-induced gene expression and tumorigenesis of glioblastoma cells. In the absence of Wnt3a, protein kinase R phosphorylated KDM4C at Ser918, inducing KDM4C ubiquitination and degradation. Wnt3a stabilized KDM4C through inhibition of GSK3-dependent protein kinase R activity. Stabilized KDM4C accumulated in the nucleus and bound to and demethylated TCF4-associated histone H3K9 by interacting with β-catenin, promoting HP1γ removal and transcriptional activation. These findings reveal that Wnt-KDM4C-β-catenin signaling represents a novel mechanism for the transcription of Wnt target genes and regulation of tumorigenesis, with important clinical implications. SIGNIFICANCE: These findings identify the Wnt-KDM4C-β-catenin signaling axis as a critical mechanism for glioma tumorigenesis that may serve as a new therapeutic target in glioblastoma.
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Affiliation(s)
- Yaohui Chen
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Runping Fang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Chen Yue
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guoqiang Chang
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Peng Li
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Qing Guo
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aidong Zhou
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sicong Zhang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Xiaobing Shi
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
- Department of Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan
| | - Suyun Huang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
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16
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Kim JE. Bookmarking by histone methylation ensures chromosomal integrity during mitosis. Arch Pharm Res 2019; 42:466-480. [PMID: 31020544 DOI: 10.1007/s12272-019-01156-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/19/2019] [Indexed: 12/22/2022]
Abstract
The cell cycle is an orchestrated process that replicates DNA and transmits genetic information to daughter cells. Cell cycle progression is governed by diverse histone modifications that control gene transcription in a timely fashion. Histone modifications also regulate cell cycle progression by marking specific chromatic regions. While many reviews have covered histone phosphorylation and acetylation as regulators of the cell cycle, little attention has been paid to the roles of histone methylation in the faithful progression of mitosis. Indeed, specific histone methylations occurring before, during, or after mitosis affect kinetochore assembly and chromosome condensation and segregation. In addition to timing, histone methylations specify the chromatin regions such as chromosome arms, pericentromere, and centromere. Therefore, spatiotemporal programming of histone methylations ensures epigenetic inheritance through mitosis. This review mainly discusses histone methylations and their relevance to mitotic progression.
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Affiliation(s)
- Ja-Eun Kim
- Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, 02447, Republic of Korea.
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17
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Emerging roles of H3K9me3, SETDB1 and SETDB2 in therapy-induced cellular reprogramming. Clin Epigenetics 2019; 11:43. [PMID: 30850015 PMCID: PMC6408861 DOI: 10.1186/s13148-019-0644-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/28/2019] [Indexed: 12/21/2022] Open
Abstract
Background A multitude of recent studies has observed common epigenetic changes develop in tumour cells of multiple lineages following exposure to stresses such as hypoxia, chemotherapeutics, immunotherapy or targeted therapies. A significant increase in the transcriptionally repressive mark trimethylated H3K9 (H3K9me3) is becoming associated with treatment-resistant phenotypes suggesting upstream mechanisms may be a good target for therapy. We have reported that the increase in H3K9me3 is derived from the methyltransferases SETDB1 and SETDB2 following treatment in melanoma, lung, breast and colorectal cancer cell lines, as well as melanoma patient data. Other groups have observed a number of characteristics such as epigenetic remodelling, increased interferon signalling, cell cycle inhibition and apoptotic resistance that have also been reported by us suggesting these independent studies are investigating similar or identical phenomena. Main body Firstly, this review introduces reports of therapy-induced reprogramming in cancer populations with highly similar slow-cycling phenotypes that suggest a role for both IFN signalling and epigenetic remodelling in the acquisition of drug tolerance. We then describe plausible connections between the type 1 IFN pathway, slow-cycling phenotypes and these epigenetic mechanisms before reviewing recent evidence on the roles of SETDB1 and SETDB2, alongside their product H3K9me3, in treatment-induced reprogramming and promotion of drug resistance. The potential mechanisms for the activation of SETDB1 and SETDB2 and how they might arise in treatment is also discussed mechanistically, with a focus on their putative induction by inflammatory signalling. Moreover, we theorise their timely role in attenuating inflammation after their activation in order to promote a more resilient phenotype through homeostatic coordination of H3K9me3. We also examine the relatively uncharacterized functions of SETDB2 with some comparison to the more well-known qualities of SETDB1. Finally, an emerging overall mechanism for the epigenetic maintenance of this transient phenotype is outlined by summarising the collective literature herein. Conclusion A number of converging phenotypes outline a stress-responsive mechanism for SETDB1 and SETDB2 activation and subsequent increased survival, providing novel insights into epigenetic biology. A clearer understanding of how SETDB1/2-mediated transcriptional reprogramming can subvert treatment responses will be invaluable in improving length and efficacy of modern therapies.
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18
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Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proc Natl Acad Sci U S A 2018; 115:E11681-E11690. [PMID: 30478057 DOI: 10.1073/pnas.1811818115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The dramatic reorganization of chromatin during mitosis is perhaps one of the most fundamental of all cell processes. It remains unclear how epigenetic histone modifications, despite their crucial roles in regulating chromatin architectures, are dynamically coordinated with chromatin reorganization in controlling this process. We have developed and characterized biosensors with high sensitivity and specificity based on fluorescence resonance energy transfer (FRET). These biosensors were incorporated into nucleosomes to visualize histone H3 Lys-9 trimethylation (H3K9me3) and histone H3 Ser-10 phosphorylation (H3S10p) simultaneously in the same live cell. We observed an anticorrelated coupling in time between H3K9me3 and H3S10p in a single live cell during mitosis. A transient increase of H3S10p during mitosis is accompanied by a decrease of H3K9me3 that recovers before the restoration of H3S10p upon mitotic exit. We further showed that H3S10p is causatively critical for the decrease of H3K9me3 and the consequent reduction of heterochromatin structure, leading to the subsequent global chromatin reorganization and nuclear envelope dissolution as a cell enters mitosis. These results suggest a tight coupling of H3S10p and H3K9me3 dynamics in the regulation of heterochromatin dissolution before a global chromatin reorganization during mitosis.
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19
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Garcia J, Lizcano F. Kdm4c is Recruited to Mitotic Chromosomes and Is Relevant for Chromosomal Stability, Cell Migration and Invasion of Triple Negative Breast Cancer Cells. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2018; 12:1178223418773075. [PMID: 30083054 PMCID: PMC6073829 DOI: 10.1177/1178223418773075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/04/2018] [Indexed: 01/23/2023]
Abstract
Members of the jumonji-containing lysine demethylase protein family have been associated with cancer development, although their specific roles in the evolution of tumor cells remain unknown. This work examines the effects of lysine demethylase 4C (KDM4C) knockdown on the behavior of a triple-negative breast cancer cell line. KDM4C expression was knocked-down by siRNA and analyzed by Western blot and immunofluorescence. HCC38 cell proliferation was examined by MTT assay, while breast cancer cells’ migration and invasion were tested in Transwell format by chemotaxis. Immunofluorescence assays showed that KDM4C, which is a key protein for modulating histone demethylation and chromosome stability through the distribution of genetic information, is located at the chromosomes during mitosis. Proliferation assays demonstrated that KDM4C is important for cell survival, while Transwell migration and invasion assays indicated that this protein is relevant for cancer progression. These data indicate that KDM4C is relevant for breast cancer progression and highlight its importance as a potential therapeutic target.
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Affiliation(s)
- Jeison Garcia
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
| | - Fernando Lizcano
- Doctorate in Biociences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
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20
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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21
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Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity. Dev Cell 2017; 42:156-169.e5. [PMID: 28743002 DOI: 10.1016/j.devcel.2017.06.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 03/21/2017] [Accepted: 06/16/2017] [Indexed: 11/23/2022]
Abstract
Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair. We demonstrate that dKDM4A demethylase activity is dispensable for PEV. In contrast, dKDM4A enzymatic activity is required to relocate heterochromatic double-strand breaks outside the domain, as well as for organismal survival when DNA repair is compromised. Finally, DNA damage triggers dKDM4A-dependent changes in the levels of H3K56me3, suggesting that dKDM4A demethylates this heterochromatic mark to facilitate repair. We conclude that dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.
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22
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Chen YK, Bonaldi T, Cuomo A, Del Rosario JR, Hosfield DJ, Kanouni T, Kao SC, Lai C, Lobo NA, Matuszkiewicz J, McGeehan A, O’Connell SM, Shi L, Stafford JA, Stansfield RK, Veal JM, Weiss MS, Yuen NY, Wallace MB. Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS Med Chem Lett 2017; 8:869-874. [PMID: 28835804 DOI: 10.1021/acsmedchemlett.7b00220] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in the regulation of chromatin-related processes. Herein, we describe our discovery of a series of potent KDM4 inhibitors that are both cell permeable and antiproliferative in cancer models. The modulation of histone H3K9me3 and H3K36me3 upon compound treatment was verified by homogeneous time-resolved fluorescence assay and by mass spectroscopy detection. Optimization of the series using structure-based drug design led to compound 6 (QC6352), a potent KDM4 family inhibitor that is efficacious in breast and colon cancer PDX models.
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Affiliation(s)
- Young K. Chen
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Tiziana Bonaldi
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Alessandro Cuomo
- Department
of Experimental Oncology, European Institute of Oncology, Via Adamello
16, 20139 Milano, Italy
| | - Joselyn R. Del Rosario
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - David J. Hosfield
- Ben
May Department for Cancer Research, University of Chicago, 929 East
57th Street, Chicago, Illinois 60637, United States
| | - Toufike Kanouni
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Shih-chu Kao
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Chon Lai
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Neethan A. Lobo
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Jennifer Matuszkiewicz
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Andrew McGeehan
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Shawn M. O’Connell
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Lihong Shi
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Jeffrey A. Stafford
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Ryan K. Stansfield
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - James M. Veal
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
| | - Michael S. Weiss
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Natalie Y. Yuen
- Celgene Quanticel Research, 1500
Owens Street, Suite 500, San Francisco, California 94158, United States
| | - Michael B. Wallace
- Celgene Quanticel Research, 10300
Campus Point Drive, Suite 100, San Diego, California 92121, United States
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Histone demethylase JMJD2C: epigenetic regulators in tumors. Oncotarget 2017; 8:91723-91733. [PMID: 29207681 PMCID: PMC5710961 DOI: 10.18632/oncotarget.19176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022] Open
Abstract
Histone methylation is one of the major epigenetic modifications, and various histone methylases and demethylases participate in the epigenetic regulating. JMJD2C has been recently identified as one of the histone lysine demethylases. As one member of the Jumonji-C histone demethylase family, JMJD2C has the ability to demethylate tri- or di-methylated histone 3 and 2 in either K9 (lysine residue 9) or K36 (lysine residue 36) sites by an oxidative reaction, thereby affecting heterochromatin formation, genomic imprinting, X-chromosome inactivation, and transcriptional regulation of genes. JMJD2C was firstly found to involve in embryonic development and stem cell regulation. Afterwards, aberrant status of JMJD2C histone methylation was observed during the formation and development of various tumors, and it has been reported to play crucial roles in the progression of breast cancer, prostate carcinomas, osteosarcoma, blood neoplasms and so on, indicating that JMJD2C represents a promising anti-cancer target. In this review, we will focus on the research progress and prospect of JMJD2C in tumors, and provide abundant evidence for the functional application and therapeutic potential of targeting JMJD2C in tumors.
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24
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Budczies J, Mechtersheimer G, Denkert C, Klauschen F, Mughal SS, Chudasama P, Bockmayr M, Jöhrens K, Endris V, Lier A, Lasitschka F, Penzel R, Dietel M, Brors B, Gröschel S, Glimm H, Schirmacher P, Renner M, Fröhling S, Stenzinger A. PD-L1 (CD274) copy number gain, expression, and immune cell infiltration as candidate predictors for response to immune checkpoint inhibitors in soft-tissue sarcoma. Oncoimmunology 2017; 6:e1279777. [PMID: 28405504 DOI: 10.1080/2162402x.2017.1279777] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 12/25/2022] Open
Abstract
Soft-tissue sarcomas (STS) are rare malignancies that account for 1% of adult cancers and comprise more than 50 entities. Current therapeutic options for advanced-stage STS are limited. Immune checkpoint inhibitors targeting the PD-1/PD-L1 signaling axis are being explored as new treatment modality in STS; however, the determinants of response to these agents are largely unknown. Using the sarcoma data set of The Cancer Genome Altas (TCGA) and an independent cohort of untreated high-grade STS, we analyzed DNA copy number status and mRNA expression of PD-L1 in a total of 335 STS cases. Copy number gains (CNG) were detected in 54 TCGA cases (21.1%), of which 21 (8.2%) harbored focal PD-L1 CNG and that were most prevalent in myxofibrosarcoma (35%) and undifferentiated pleomorphic sarcoma (34%). In the untreated high-grade STS cohort, we detected CNG in six cases (7.6%). Analysis of co-amplified genes identified a 5.6-Mb core region comprising 27 genes, including JAK2. Patients with PD-L1 CNG had higher PD-L1 expression compared with STS without CNG (fold change, 1.8; p = 0.02), an effect that was most pronounced in the setting of focal PD-L1 CNG (fold change, 3.0; p = 0.0027). STS with PD-L1 CNG showed a significantly higher mutational load compared with tumors with a diploid PD-L1 locus (median number of mutated genes; 58 vs. 40; p = 3.6E-06), and PD-L1 CNG were associated with inferior survival (HR = 1.82; p = 0.025). In contrast, T-cell infiltrates quantified by mRNA expression of CD3Z were associated with improved survival (HR = 0.88; p = 0.024) and consequently influenced the prognostic power of PD-L1 CNG, with low CD3Z levels conferring poor survival in cases with PD-L1 CNG (HR = 1.8; p = 0.049). These data demonstrate that PD-L1 GNG and elevated expression of PD-L1 occur in a substantial proportion of STS, have prognostic impact that is modulated by T-cell infiltrates, and thus warrant investigation as response predictors for immune checkpoint inhibition.
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Affiliation(s)
- Jan Budczies
- Institute of Pathology, Charité University Hospital, Berlin, Germany; German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Carsten Denkert
- Institute of Pathology, Charité University Hospital, Berlin, Germany; German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Sadaf S Mughal
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Disease (NCT) Heidelberg , Heidelberg, Germany
| | - Priya Chudasama
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ) , Heidelberg, Germany
| | - Michael Bockmayr
- Institute of Pathology, Charité University Hospital , Berlin, Germany
| | - Korinna Jöhrens
- Institute of Pathology, Charité University Hospital , Berlin, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg , Heidelberg, Germany
| | - Amelie Lier
- Institute of Pathology, University Hospital Heidelberg , Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University Hospital Heidelberg , Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg , Heidelberg, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital, Berlin, Germany; German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt Brors
- German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Disease (NCT) Heidelberg, Heidelberg, Germany
| | - Stefan Gröschel
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hanno Glimm
- German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schirmacher
- German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcus Renner
- Institute of Pathology, University Hospital Heidelberg , Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany; Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), partner sites Heidelberg and Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
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25
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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun 2016; 7:13387. [PMID: 27841353 PMCID: PMC5114558 DOI: 10.1038/ncomms13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
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Affiliation(s)
- Zhangli Su
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
| | - Jin-Hee Lee
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Kimberly A. Krautkramer
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy J. Thorpe
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Melissa D. Boersma
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Vyacheslav I. Kuznetsov
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | | | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - George N. Phillips
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
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26
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Garcia J, Lizcano F. KDM4C Activity Modulates Cell Proliferation and Chromosome Segregation in Triple-Negative Breast Cancer. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2016; 10:169-175. [PMID: 27840577 PMCID: PMC5094578 DOI: 10.4137/bcbcr.s40182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/14/2016] [Accepted: 08/20/2016] [Indexed: 12/23/2022]
Abstract
The Jumonji-containing domain protein, KDM4C, is a histone demethylase associated with the development of several forms of human cancer. However, its specific function in the viability of tumoral lineages is yet to be determined. This work investigates the importance of KDM4C activity in cell proliferation and chromosome segregation of three triple-negative breast cancer cell lines using a specific demethylase inhibitor. Immunofluorescence assays show that KDM4C is recruited to mitotic chromosomes and that the modulation of its activity increases the number of mitotic segregation errors. However, 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) cell proliferation assays demonstrate that the demethylase activity is required for cell viability. These results suggest that the histone demethylase activity of KDM4C is essential for breast cancer progression given its role in the maintenance of chromosomal stability and cell growth, thus highlighting it as a potential therapeutic target.
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Affiliation(s)
- Jeison Garcia
- Doctorate in Biosciences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
| | - Fernando Lizcano
- Doctorate in Biosciences, Center of Biomedical Research Universidad de La Sabana-CIBUS, School of Medicine, Universidad de La Sabana, Chía, Colombia
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27
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Pedersen MT, Kooistra SM, Radzisheuskaya A, Laugesen A, Johansen JV, Hayward DG, Nilsson J, Agger K, Helin K. Continual removal of H3K9 promoter methylation by Jmjd2 demethylases is vital for ESC self-renewal and early development. EMBO J 2016; 35:1550-64. [PMID: 27266524 DOI: 10.15252/embj.201593317] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/06/2016] [Indexed: 12/12/2022] Open
Abstract
Chromatin-associated proteins are essential for the specification and maintenance of cell identity. They exert these functions through modulating and maintaining transcriptional patterns. To elucidate the functions of the Jmjd2 family of H3K9/H3K36 histone demethylases, we generated conditional Jmjd2a/Kdm4a, Jmjd2b/Kdm4b and Jmjd2c/Kdm4c/Gasc1 single, double and triple knockout mouse embryonic stem cells (ESCs). We report that while individual Jmjd2 family members are dispensable for ESC maintenance and embryogenesis, combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired ESC self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions. We further show that Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3. Jmjd2 catalytic activity is required for ESC maintenance, and increased H3K9me3 levels in knockout ESCs compromise the expression of several Jmjd2a/c targets, including genes that are important for ESC self-renewal. Thus, continual removal of H3K9 promoter methylation by Jmjd2 demethylases represents a novel mechanism ensuring transcriptional competence and stability of the pluripotent cell identity.
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Affiliation(s)
- Marianne Terndrup Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Marije Kooistra
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Aliaksandra Radzisheuskaya
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Daniel Geoffrey Hayward
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karl Agger
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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28
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Zhao E, Ding J, Xia Y, Liu M, Ye B, Choi JH, Yan C, Dong Z, Huang S, Zha Y, Yang L, Cui H, Ding HF. KDM4C and ATF4 Cooperate in Transcriptional Control of Amino Acid Metabolism. Cell Rep 2016; 14:506-519. [PMID: 26774480 DOI: 10.1016/j.celrep.2015.12.053] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 11/10/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022] Open
Abstract
The histone lysine demethylase KDM4C is often overexpressed in cancers primarily through gene amplification. The molecular mechanisms of KDM4C action in tumorigenesis are not well defined. Here, we report that KDM4C transcriptionally activates amino acid biosynthesis and transport, leading to a significant increase in intracellular amino acid levels. Examination of the serine-glycine synthesis pathway reveals that KDM4C epigenetically activates the pathway genes under steady-state and serine deprivation conditions by removing the repressive histone modification H3 lysine 9 (H3K9) trimethylation. This action of KDM4C requires ATF4, a transcriptional master regulator of amino acid metabolism and stress responses. KDM4C activates ATF4 transcription and interacts with ATF4 to target serine pathway genes for transcriptional activation. We further present evidence for KDM4C in transcriptional coordination of amino acid metabolism and cell proliferation. These findings suggest a molecular mechanism linking KDM4C-mediated H3K9 demethylation and ATF4-mediated transactivation in reprogramming amino acid metabolism for cancer cell proliferation.
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Affiliation(s)
- Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China; Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Jane Ding
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Yingfeng Xia
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Mengling Liu
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Bingwei Ye
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Jeong-Hyeon Choi
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Chunhong Yan
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Zheng Dong
- Department of Cell Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Shuang Huang
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL 32611, USA
| | - Yunhong Zha
- Insititute of Translational Neuroscience and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, Yichang 443000, China
| | - Liqun Yang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and System Biology, Southwest University, Chongqing 400715, China.
| | - Han-Fei Ding
- Cancer Center, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA; Department of Pathology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA.
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29
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Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
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Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
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30
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Ye Q, Holowatyj A, Wu J, Liu H, Zhang L, Suzuki T, Yang ZQ. Genetic alterations of KDM4 subfamily and therapeutic effect of novel demethylase inhibitor in breast cancer. Am J Cancer Res 2015; 5:1519-1530. [PMID: 26101715 PMCID: PMC4473328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 03/10/2015] [Indexed: 06/04/2023] Open
Abstract
The histone lysine demethylase KDM4 subfamily, comprised of four members (A, B, C, and D), play critical roles in controlling transcription, chromatin architecture and cellular differentiation. We previously demonstrated that KDM4C is significantly amplified and overexpressed in aggressive basal-like breast cancers and functions as a transforming oncogene. However, information regarding the genomic and transcriptomic alterations of the KDM4 subfamily in different subtypes of breast cancer remains largely incomplete. Here, we conducted a meta-analysis of KDM4A, B, C and D in breast cancer and identified associations among recurrent copy number alterations, gene expression and breast cancer subtypes. We demonstrated that KDM4A and D are also significantly overexpressed in basal-like breast cancer, whereas KDM4B overexpression is more dominant in estrogen-receptor-positive, luminal breast cancer. Next, we investigated the therapeutic potential of a novel histone demethylase inhibitor, NCDM-32B, in breast cancer. The treatment of basal breast cancer cell lines with NCDM-32B resulted in the decrease of cell viability and anchorage independent growth in soft agar. Furthermore, we found that NCDM-32B impaired several critical pathways that drive cellular proliferation and transformation in breast cancer. Our findings demonstrate genetic amplification and overexpression of the KDM4 demethylases in different subtypes of breast cancer. Furthermore, histone methylation is reversible and KDM4 demethylases are druggable targets. Thus, KDM4 inhibitors may serve as a novel therapeutic approach for a subset of aggressive breast cancer.
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Affiliation(s)
- Qin Ye
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- School of Life Science, Jiangsu Normal UniversityJiangsu 221116, China
| | - Andreana Holowatyj
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Jack Wu
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Hui Liu
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
| | - Lihong Zhang
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- Shandong Provincial Research Institute for Family PlanningJinan, Shandong 250002, China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of MedicineKyoto, 606-0823, Japan
| | - Zeng-Quan Yang
- Department of Oncology, Wayne State University School of MedicineDetroit, MI 48201, USA
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer InstituteDetroit, MI 48201, USA
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31
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Awwad SW, Ayoub N. Overexpression of KDM4 lysine demethylases disrupts the integrity of the DNA mismatch repair pathway. Biol Open 2015; 4:498-504. [PMID: 25770186 PMCID: PMC4400592 DOI: 10.1242/bio.201410991] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The KDM4 family of lysine demethylases consists of five members, KDM4A, -B and -C that demethylate H3K9me2/3 and H3K36me2/3 marks, while KDM4D and -E demethylate only H3K9me2/3. Recent studies implicated KDM4 proteins in regulating genomic instability and carcinogenesis. Here, we describe a previously unrecognized pathway by which hyperactivity of KDM4 demethylases promotes genomic instability. We show that overexpression of KDM4A-C, but not KDM4D, disrupts MSH6 foci formation during S phase by demethylating its binding site, H3K36me3. Consequently, we demonstrate that cells overexpressing KDM4 members are defective in DNA mismatch repair (MMR), as evident by the instability of four microsatellite markers and the remarkable increase in the spontaneous mutations frequency at the HPRT locus. Furthermore, we show that the defective MMR in cells overexpressing KDM4C is mainly due to the increase in its demethylase activity and can be mended by KDM4C downregulation. Altogether, our data suggest that cells overexpressing KDM4A-C are defective in DNA MMR and this may contribute to genomic instability and tumorigenesis.
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Affiliation(s)
- Samah W Awwad
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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32
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Khoury-Haddad H, Nadar-Ponniah PT, Awwad S, Ayoub N. The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites. Cell Cycle 2015; 14:950-8. [PMID: 25714495 PMCID: PMC4614868 DOI: 10.1080/15384101.2015.1014147] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
KDM4D is a lysine demethylase that removes tri- and di- methylated residues from H3K9 and is involved in transcriptional regulation and carcinogenesis. We recently showed that KDM4D is recruited to DNA damage sites in a PARP1-dependent manner and facilitates double-strand break repair in human cells. Moreover, we demonstrated that KDM4D is an RNA binding protein and mapped its RNA-binding motifs. Interestingly, KDM4D-RNA interaction is essential for its localization on chromatin and subsequently for efficient demethylation of its histone substrate H3K9me3. Here, we provide new data that shed mechanistic insights into KDM4D accumulation at DNA damage sites. We show for the first time that KDM4D binds poly(ADP-ribose) (PAR) in vitro via its C-terminal region. In addition, we demonstrate that KDM4D-RNA interaction is required for KDM4D accumulation at DNA breakage sites. Finally, we discuss the recruitment mode and the biological functions of additional lysine demethylases including KDM4B, KDM5B, JMJD1C, and LSD1 in DNA damage response.
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Affiliation(s)
| | | | - Samah Awwad
- Department of Biology; Israel Institute of Technology; Haifa, Israel
| | - Nabieh Ayoub
- Department of Biology; Israel Institute of Technology; Haifa, Israel
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