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Histone demethylase KDM4C controls tumorigenesis of glioblastoma by epigenetically regulating p53 and c-Myc. Cell Death Dis 2021; 12:89. [PMID: 33462212 PMCID: PMC7814060 DOI: 10.1038/s41419-020-03380-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022]
Abstract
Glioblastoma is the most lethal brain tumor and its pathogenesis remains incompletely understood. KDM4C is a histone H3K9 demethylase that contributes to epigenetic regulation of both oncogene and tumor suppressor genes and is often overexpressed in human tumors, including glioblastoma. However, KDM4C’s roles in glioblastoma and the underlying molecular mechanisms remain unclear. Here, we show that KDM4C knockdown significantly represses proliferation and tumorigenesis of glioblastoma cells in vitro and in vivo that are rescued by overexpressing wild-type KDM4C but not a catalytic dead mutant. KDM4C protein expression is upregulated in glioblastoma, and its expression correlates with c-Myc expression. KDM4C also binds to the c-Myc promoter and induces c-Myc expression. Importantly, KDM4C suppresses the pro-apoptotic functions of p53 by demethylating p53K372me1, which is pivotal for the stability of chromatin-bound p53. Conversely, depletion or inhibition of KDM4C promotes p53 target gene expression and induces apoptosis in glioblastoma. KDM4C may serve as an oncogene through the dual functions of inactivation of p53 and activation of c-Myc in glioblastoma. Our study demonstrates KDM4C inhibition as a promising therapeutic strategy for targeting glioblastoma.
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102
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Genome-wide association study of problematic opioid prescription use in 132,113 23andMe research participants of European ancestry. Mol Psychiatry 2021; 26:6209-6217. [PMID: 34728798 PMCID: PMC8562028 DOI: 10.1038/s41380-021-01335-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/31/2022]
Abstract
The growing prevalence of opioid use disorder (OUD) constitutes an urgent health crisis. Ample evidence indicates that risk for OUD is heritable. As a surrogate (or proxy) for OUD, we explored the genetic basis of using prescription opioids 'not as prescribed'. We hypothesized that misuse of opiates might be a heritable risk factor for OUD. To test this hypothesis, we performed a genome-wide association study (GWAS) of problematic opioid use (POU) in 23andMe research participants of European ancestry (N = 132,113; 21% cases). We identified two genome-wide significant loci (rs3791033, an intronic variant of KDM4A; rs640561, an intergenic variant near LRRIQ3). POU showed positive genetic correlations with the two largest available GWAS of OUD and opioid dependence (rg = 0.64, 0.80, respectively). We also identified numerous additional genetic correlations with POU, including alcohol dependence (rg = 0.74), smoking initiation (rg = 0.63), pain relief medication intake (rg = 0.49), major depressive disorder (rg = 0.44), chronic pain (rg = 0.42), insomnia (rg = 0.39), and loneliness (rg = 0.28). Although POU was positively genetically correlated with risk-taking (rg = 0.38), conditioning POU on risk-taking did not substantially alter the magnitude or direction of these genetic correlations, suggesting that POU does not simply reflect a genetic tendency towards risky behavior. Lastly, we performed phenome- and lab-wide association analyses, which uncovered additional phenotypes that were associated with POU, including respiratory failure, insomnia, ischemic heart disease, and metabolic and blood-related biomarkers. We conclude that opioid misuse can be measured in population-based cohorts and provides a cost-effective complementary strategy for understanding the genetic basis of OUD.
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103
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The Crosstalk of Epigenetics and Metabolism in Herpesvirus Infection. Viruses 2020; 12:v12121377. [PMID: 33271926 PMCID: PMC7760534 DOI: 10.3390/v12121377] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Accepted: 11/29/2020] [Indexed: 01/31/2023] Open
Abstract
Epigenetics is a versatile player in manipulating viral infection and a potential therapeutic target for the treatment of viral-induced diseases. Both epigenetics and metabolism are crucial in establishing a highly specific transcriptional network, which may promote or suppress virus infection. Human herpesvirus infection can induce a broad range of human malignancies and is largely dependent on the status of cellular epigenetics as well as its related metabolism. However, the crosstalk between epigenetics and metabolism during herpesvirus infection has not been fully explored. Here, we describe how epigenetic regulation of cellular metabolism affects herpesvirus infection and induces viral diseases. This further highlights the importance of epigenetics and metabolism during viral infection and provides novel insights into the development of targeted therapies.
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104
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Kim JH, Jung DY, Kim HR, Jung MH. Histone H3K9 Demethylase JMJD2B Plays a Role in LXRα-Dependent Lipogenesis. Int J Mol Sci 2020; 21:ijms21218313. [PMID: 33167594 PMCID: PMC7664202 DOI: 10.3390/ijms21218313] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Ligand-activated liver X receptor α (LXRα) upregulates the expression of hepatic lipogenic genes, which leads to triglyceride (TG) accumulation, resulting in nonalcoholic fatty liver disease (NAFLD). Thus, LXRα regulation may provide a novel therapeutic target against NAFLD. However, histone methylation-mediated epigenetic regulation involved in LXRα-dependent lipogenesis is poorly understood. In this study, we investigated the functional role of the histone demethylase Jumonji domain-containing protein 2B (JMJD2B) in LXRα-dependent lipogenesis. JMJD2B expression level was upregulated in HepG2 cells treated with LXRα agonist T0901317 or palmitate and the liver of mice administered with T0901317 or fed a high-fat diet. Knockdown of JMJD2B using siRNA abrogated T0901317-induced LXRα-dependent lipogenic gene expression and lowered intracellular TG accumulation. Conversely, overexpression of JMJD2B in HepG2 cells upregulated the expression of LXRα-dependent lipogenic genes, in line with increased intracellular TG levels. JMJD2B overexpression or T0901317 treatment induced the recruitment of JMJD2B and LXRα to LXR response elements (LXRE) in the promoter region of LXRα-target gene and reduced the enrichment of H3K9me2 and H3K9me3 in the vicinity of the LXRE. Furthermore, JMJD2B enhanced T0901317 or LXRα-induced transcriptional activities of reporters containing LXRE. A co-immunoprecipitation assay revealed that JMJD2B interacted with activated LXRα. Moreover, overexpression of JMJD2B in mice resulted in upregulation of hepatic LXRα-dependent lipogenic genes, consistent with development of hepatic steatosis. Taken together, these results indicate that JMJD2B plays a role in LXRα-mediated lipogenesis via removing the repressive histone marks, H3K9me2 and H3K9me3, at LXRE, which might contribute to hepatic steatosis.
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105
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Gupta R, Janostiak R, Wajapeyee N. Transcriptional regulators and alterations that drive melanoma initiation and progression. Oncogene 2020; 39:7093-7105. [PMID: 33024276 PMCID: PMC7695596 DOI: 10.1038/s41388-020-01490-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/24/2020] [Indexed: 12/23/2022]
Abstract
Although melanoma is the least frequent type of skin cancer, it accounts for the majority of skin cancer-related deaths. Large-scale sequencing efforts have led to the classification of melanoma into four major subtypes (i.e., BRAF-mutant, NRAS-mutant, NF1-deficient, and triple wild-type). These sequencing studies have also revealed that melanoma genomes are some of the most mutated genomes of all cancers and therefore have a high neoantigen load. These findings have resulted in the development and clinical use of targeted therapies against the oncogenic BRAF→MEK→ERK pathway and immune checkpoint inhibitors for the treatment of metastatic melanoma. Although some patients with metastatic melanoma benefit immensely from these transformative therapies, others either become resistant or do not respond at all. These clinical challenges have intensified the search for new drug targets and drugs that can benefit patients who are either intrinsically resistant or have acquired resistance to targeted therapies and immunotherapies. Numerous signaling pathways and oncogenic drivers can cause changes in mRNA transcription that in turn drive melanoma initiation and progression. Transcriptional regulation of mRNA expression is necessary to maintain cell identity and cellular plasticity via the regulation of transcription factor expression and function, promoter/enhancer activities, chromatin regulators, and three-dimensional genome organization. Transcriptional deregulation can arise due to genetic and/or non-genetic alterations in the genome. Specifically, these deregulated transcriptional programs can become liabilities for melanoma cells due to their acquired dependencies on these programs for survival, which can be harnessed to develop new therapies for melanoma. In this article, we present an overview of the mechanisms that result in the transcriptional deregulation of mRNA expression in melanoma cells and assess how these changes facilitate melanoma initiation and progression. We also describe how these deregulated transcriptional pathways represent new opportunities for the development of unconventional and potentially impactful treatments for metastatic melanoma.
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Affiliation(s)
- Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Radoslav Janostiak
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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Moon Y, Kim I, Chang S, Park B, Lee S, Yoo S, Chae S, Hwang D, Park H. Hypoxia regulates allele-specific histone modification of the imprinted H19 gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194643. [DOI: 10.1016/j.bbagrm.2020.194643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/29/2020] [Accepted: 10/02/2020] [Indexed: 01/20/2023]
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107
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Radiation-induced H3K9 methylation on E-cadherin promoter mediated by ROS/Snail axis : Role of G9a signaling during lung epithelial-mesenchymal transition. Toxicol In Vitro 2020; 70:105037. [PMID: 33148527 DOI: 10.1016/j.tiv.2020.105037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/05/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Lung cancer patients who have undergone radiotherapy developed severe complications such as pneumonitis and fibrosis. Upon irradiation, epithelial cells acquire mesenchymal phenotype via a process called epithelial to mesenchymal transition (EMT), which plays a vital role in organ fibrosis. Several mechanisms have been studied on EMT, however, the correlation between radiation-induced EMT and epigenetic changes are not well known. In the present study, we investigated the role of histone methyltransferase G9a on radiation-induced EMT signaling. There was an increase in total global histone methylation level in irradiated epithelial cells. Western blot analysis on irradiated cells showed an increased expression of H3K9me2/3. The pre-treatment of G9a inhibitor enhanced E-cadherin expression and decreased the mesenchymal markers like N-cadherin, vimentin in the radiated group. Surprisingly, radiation-induced ROS generation and pERK1/2 levels were also inhibited by G9a inhibitor BIX01294, which is showing its antioxidant potential. The ChIP-qPCR analysis on the E-cadherin promoter suggested that G9a and Snail might have formed complex to enrich suppressive marker H3K9me2/3. On the whole, our present study suggested that 1] ROS could modify H3K9 methylation via G9a and promote radiation-induced lung EMT in Beas2B and A549 cells 2] E-cadherin promoter enrichment with heterochromatin mark H3K9me2 expression upon irradiation could be modified by regulating G9a methyltransferase.
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108
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Oh S, Song H, Freeman WM, Shin S, Janknecht R. Cooperation between ETS transcription factor ETV1 and histone demethylase JMJD1A in colorectal cancer. Int J Oncol 2020; 57:1319-1332. [PMID: 33174020 PMCID: PMC7646594 DOI: 10.3892/ijo.2020.5133] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022] Open
Abstract
ETS variant 1 (ETV1) is an oncogenic transcription factor. However, its role in colorectal cancer has remained understudied. The present study demonstrated that ETV1 downregulation led to reduced HCT116 colorectal cancer cell growth and clonogenic activity. Furthermore, the ETV1 mRNA levels were enhanced in colorectal tumors and were associated with disease severity. In addition, ETV1 directly bound to Jumonji C domain-containing (JMJD) 1A, a histone demethylase known to promote colon cancer. ETV1 and JMJD1A, but not a catalytically inactive mutant thereof, cooperated in inducing the matrix metalloproteinase (MMP)1 gene promoter that was similar to the cooperation between ETV1 and another histone demethylase, JMJD2A. RNA-sequencing revealed multiple potential ETV1 target genes in HCT116 cells, including the FOXQ1 and TBX6 transcription factor genes. Moreover, JMJD1A co-regulated FOXQ1 and other ETV1 target genes, but not TBX6, whereas JMJD2A downregulation had no impact on FOXQ1 as well as TBX6 transcription. Accordingly, the FOXQ1 gene promoter was stimulated by ETV1 and JMJD1A in a cooperative manner, and both ETV1 and JMJD1A bound to the FOXQ1 promoter. Notably, the overexpression of FOXQ1 partially reversed the growth inhibitory effects of ETV1 ablation on HCT116 cells, whereas TBX6 impaired HCT116 cell growth and may thereby dampen the oncogenic activity of ETV1. The latter also revealed for the first time, to the best of our knowledge, a potential tumor suppressive function of TBX6. Taken together, the present study uncovered a ETV1/JMJD1A-FOXQ1 axis that may drive colorectal tumorigenesis.
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Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Hoogeun Song
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | | | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Abstract
![]()
Vitamin
C (ascorbic acid) is a water-soluble antioxidant and a
cofactor for a large number of enzymes. It is present in all tissues
and especially abundant in corneal epithelium, stem cells, and neurons.
Although similar to thiols in its ability to react with many reactive
oxygen species (ROS), ascorbate is much better (>100× faster)
than glutathione at scavenging of primary ROS (superoxide radical
and singlet oxygen). Ascorbate appears to be especially important
for elimination of O2•– in the
nucleus which contains little or no SOD activity. Cofactor functions
of ascorbate involve the maintenance of activity of Fe(II)/2-oxoglutarate-dependent
dioxygenases via reduction of Fe(III). The most prominent activity
of ascorbate-dependent dioxygenases in the cytoplasm is hydroxylation
of prolines in proteins involved in the formation of extracellular
matrix and regulation of metabolism and hypoxia responses. In the
nucleus, ascorbate is important for oxidative demethylation of 5-methylcytosine
in DNA (by TET proteins) and removal of methyl groups from histone
lysines (by JmjC demethylases). Differentiation and other cellular
reprograming processes involving DNA demethylation are especially
sensitive to ascorbate insufficiency. High doses of vitamin C alone
or in combinations with drugs produced cancer-suppressive effects
which involved redox, immune, and epigenetic mechanisms. Solutions
to vitamin C deficiency in cultured cells are discussed to improve
the physiological relevance of in vitro models. An
abundance of vitamin C in rodents limits their ability to fully recapitulate
human sensitivity to adverse health effects of malnutrition and xenobiotics,
including neurotoxicity, lung injury, and intergenerational and other
epigenetic effects.
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Affiliation(s)
- Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
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Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the JmjC histone demethylase KDM4A integrates substrate dynamics, correlated motions and molecular orbital control. Chem Sci 2020; 11:9950-9961. [PMID: 34094257 PMCID: PMC8162366 DOI: 10.1039/d0sc03713c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Nε-methyl lysine status of histones is important in the regulation of eukaryotic transcription. The Fe(ii) and 2-oxoglutarate (2OG) -dependent JmjC domain enzymes are the largest family of histone Nε-methyl lysine demethylases (KDMs). The human KDM4 subfamily of JmjC KDMs is linked with multiple cancers and some of its members are medicinal chemistry targets. We describe the use of combined molecular dynamics (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) methods to study the mechanism of KDM4A, which catalyzes demethylation of both tri- and di-methylated forms of histone H3 at K9 and K36. The results show that the oxygen activation at the active site of KDM4A is optimized towards the generation of the reactive Fe(iv)-oxo intermediate. Factors including the substrate binding mode, correlated motions of the protein and histone substrates, and molecular orbital control synergistically contribute to the reactivity of the Fe(iv)-oxo intermediate. In silico substitutions were performed to investigate the roles of residues (Lys241, Tyr177, and Asn290) in substrate orientation. The Lys241Ala substitution abolishes activity due to altered substrate orientation consistent with reported experimental studies. Calculations with a macrocyclic peptide substrate analogue reveal that induced conformational changes/correlated motions in KDM4A are sequence-specific in a manner that influences substrate binding affinity. Second sphere residues, such as Ser288 and Thr289, may contribute to KDM4A catalysis by correlated motions with active site residues. Residues that stabilize key intermediates, and which are predicted to be involved in correlated motions with other residues in the second sphere and beyond, are shown to be different in KDM4A compared to those in another JmjC KDM (PHF8), which acts on H3K9 di- and mono-methylated forms, suggesting that allosteric type inhibition is of interest from the perspective of developing selective JmjC KDM inhibitors. The second sphere residues and regions of the protein in histone demethylase enzymes that makes correlated motion with the active site contribute to efficient catalysis.![]()
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan Ann Arbor MI 48019 USA
| | | | | | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
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111
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Chen DB, Xie XW, Zhao YJ, Wang XY, Liao WJ, Chen P, Deng KJ, Fei R, Qin WY, Wang JH, Wu X, Shao QX, Wei L, Chen HS. RFX5 promotes the progression of hepatocellular carcinoma through transcriptional activation of KDM4A. Sci Rep 2020; 10:14538. [PMID: 32883983 PMCID: PMC7471945 DOI: 10.1038/s41598-020-71403-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Regulatory factor X-5 (RFX5) represents a key transcription regulator of MHCII gene expression in the immune system. This study aims to explore the molecular mechanisms and biological significance of RFX5. Firstly, by analyzing ENCODE chromatin immunoprecipitation (ChIP)-seq in HepG2 and TCGA RNA-seq data, we discovered lysine-specific demethylase 4A (KDM4A), also named JMJD2A, to be a major downstream target gene of RFX5. Moreover, RFX5 was verified to bind directly to the KDM4A's promoter region and sequentially promoted its transcription determined by the ChIP-PCR assay and luciferase assay. In addition, RFX5-dependent regulation of KDM4A was demonstrated in HCC. Compared with adjacent non-tumor tissues, the expression levels of KDM4A were significantly raised in HCC tumor tissues. Notably, elevated levels of KDM4A were strongly correlated with HCC patient prognosis. Functionally, KDM4A overexpression largely rescued the growth inhibitory effects of RFX5 deletion, highlighting KDM4A as a downstream effector of RFX5. Mechanistically, the RFX5-KDM4A pathway promoted the progression of the cell cycle from G0/G1 to S phase and was protective against cell apoptosis through regulation of p53 and its downstream genes in HCC. In conclusion, RFX5 could promote HCC progression via transcriptionally activating KDM4A expression.
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Affiliation(s)
- Dong-Bo Chen
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Xing-Wang Xie
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Yang-Jing Zhao
- Department of Immunology, and the Key Laboratory of Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xue-Yan Wang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Wei-Jia Liao
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Pu Chen
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Kang-Jian Deng
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Ran Fei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Wan-Ying Qin
- Laboratory of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jiang-Hua Wang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Xu Wu
- Center of Excellence, Becton Dickinson Biosciences, China Central Place, Beijing, 100176, China
| | - Qi-Xiang Shao
- Department of Immunology, and the Key Laboratory of Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Lai Wei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China
| | - Hong-Song Chen
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Disease, Beijing, 100044, China.
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Su Y, Wang X, Guo Z, Wang J. Aberrant JmjC domain-containing protein 8 (JMJD8) expression promotes activation of AKT and tumor epithelial-mesenchymal transition. Oncogene 2020; 39:6451-6467. [PMID: 32879443 DOI: 10.1038/s41388-020-01446-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/23/2022]
Abstract
Posttranslational modifications of histone and nonhistone proteins greatly influence numerous molecular events in multiple diseases. Jumonji domain-containing proteins are a family functioning as histone demethylase. Jumonji domain-containing protein 8 (JMJD8) is Jumonji C (JmjC) domain-only member of this family, and its physiological functions remain largely unknown. In this study, we investigated the mechanism by which aberrant JMJD8 stimulates phosphorylation of AKT and activate AKT/GSK3β/β-catenin signaling pathway thereby promotes tumor cell epithelial-mesenchymal transition (EMT). We demonstrated that knockdown of JMJD8 increased the interaction of SETDB1 and phosphoinositide-dependent kinase 1 (PDK1) with AKT1 and resulted in enhanced trimethylation of AKT1 at lysine 142 (K142), which is crucial for cell membrane recruitment, phosphorylation, and activation of AKT. Moreover, the mutation of histidine 200 of JMJD8 (JMJD8-H200Q) disrupted its binding with AKT1 and increased interaction of SETDB1 and PDK1 with AKT1. Furthermore, histone demethylase jumonji domain-containing protein 2B functioned as an adapter to recruit β-catenin to the methylated AKT1 upon JMJD8 depression, which facilitated the phosphorylation of β-catenin at Ser552 and its accumulation in cell nucleus where the activated β-catenin transcriptionally stimulated the expression of genes involved in EMT. In conclusion, our data unraveled a novel role of JMJD8 in regulating the migration and invasion of tumor via modulating AKT methylation and activation. In addition, this study showed that JMJD8 is a potential biomarker and drug design target for tumor EMT.
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Affiliation(s)
- Yao Su
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, HFIPS, Chinese Academy of Sciences, Hefei, 230031, PR China
| | - Xueying Wang
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Zhen Guo
- Anhui Key Laboratory for Cellular Dynamics and Chemical Biology, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Jun Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, HFIPS, Chinese Academy of Sciences, Hefei, 230031, PR China.
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113
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Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress. Semin Cancer Biol 2020; 83:452-471. [PMID: 32814115 DOI: 10.1016/j.semcancer.2020.07.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.
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Affiliation(s)
- Margarita E Neganova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Sergey G Klochkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Gjumrakch Aliev
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation.,I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russian Federation.,Laboratory of Cellular Pathology, Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation.,GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA.
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Van Rechem C, Ji F, Mishra S, Chakraborty D, Murphy SE, Dillingham ME, Sadreyev RI, Whetstine JR. The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194624. [PMID: 32798738 DOI: 10.1016/j.bbagrm.2020.194624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/22/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022]
Abstract
Chromatin modulation provides a key checkpoint for controlling cell cycle regulated gene networks. The replicative canonical histone genes are one such gene family under tight regulation during cell division. These genes are most highly expressed during S phase when histones are needed to chromatinize the new DNA template. While this fact has been known for a while, limited knowledge exists about the specific chromatin regulators controlling their temporal expression during cell cycle. Since histones and their associated mutations are emerging as major players in diseases such as cancer, identifying the chromatin factors modulating their expression is critical. The histone lysine tri-demethylase KDM4A is regulated over cell cycle and plays a direct role in DNA replication timing, site-specific rereplication, and DNA amplifications during S phase. Here, we establish an unappreciated role for the catalytically active KDM4A in directly regulating canonical replicative histone gene networks during cell cycle. Of interest, we further demonstrate that KDM4A interacts with proteins controlling histone expression and RNA processing (i.e., hnRNPUL1 and FUS/TLS). Together, this study provides a new function for KDM4A in modulating canonical histone gene expression.
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Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Fei Ji
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America
| | - Sweta Mishra
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Damayanti Chakraborty
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Sedona E Murphy
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Megan E Dillingham
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America
| | - Ruslan I Sadreyev
- Massachusetts General Hospital, Department of Molecular Biology, Simches Research Center, Boston, MA 02114, United States of America; Massachusetts General Hospital, Department of Pathology and Harvard Medical School, Simches Research Center, Boston, MA 02114, United States of America.
| | - Johnathan R Whetstine
- Massachusetts General Hospital, Cancer Center and Harvard Medical School, Department of Medicine, 13th street bldg. 149, Charlestown, MA 02129, United States of America; Fox Chase Cancer Center, 333 Cottman Avenue West 260, Philadelphia, PA 19111, United States of America.
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115
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Xiang Y, Guo J, Li F, Xiong J. Tudor domain of histone demethylase KDM4B is a reader of H4K20me3. Acta Biochim Biophys Sin (Shanghai) 2020; 52:901-906. [PMID: 32537648 DOI: 10.1093/abbs/gmaa064] [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: 01/02/2020] [Revised: 11/05/2019] [Accepted: 01/20/2020] [Indexed: 01/07/2023] Open
Abstract
The lysine histone demethylase KDM4B is overexpressed in several types of cancers and plays dual roles in genome stability maintenance. Although KDM4B is able to recognize several histone methylations, the underlying molecular mechanism is still unknown. In this study, we purified the KDM4B chromatin-associated hybrid tudor domains (HTDs) and plant home domains (PHDs) and performed the pull-down assay to screen the tri-methyl modified histone peptides that could be efficiently recognized by KDM4B. Our results showed that both HTD alone and the combination of HTD and PHD were able to specifically bind to H3K4me3 and H4K20me3. Because H4K20me3 is essential for KDM4B's rapid recruitment to DNA damage site, we further aligned the multiple tudor peptide sequence and identified two conserved residues Y993 and W987 that are critical for KDM4B-H4K20me3 interaction. The surface plasmon resonance analysis revealed that HTD displayed a rapid H4K20me3 bind-dissociate pattern. These findings therefore provided mechanistic insights into the binding of tudor domain of KDM4B protein with H4K20me3.
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Affiliation(s)
- Ying Xiang
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jing Guo
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Feng Li
- Department of Medical Genetics, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy and Immune-related Diseases, Wuhan University School of Medicine, Wuhan 430071, China
| | - Jie Xiong
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
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116
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Li Z, Jiang G, Liu X, Ding X, Zhang D, Wang X, Zhou Y, Yan H, Li T, Wu K, Jiang Y, Duan X. Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato. THE NEW PHYTOLOGIST 2020; 227:1138-1156. [PMID: 32255501 DOI: 10.1111/nph.16590] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/27/2020] [Indexed: 05/22/2023]
Abstract
Fruit ripening is governed by a complex regulatory network. Reversible histone methylation and demethylation regulate chromatin structure and gene expression. However, little is known about the involvement of histone demethylases in regulating fruit ripening. Here, we found that the tomato (Solanum lycopersicum) SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerates tomato fruit ripening, which is associated with the upregulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and chromatin immunoprecipitation followed by sequencing identified 32 genes directly targeted by SlJMJ6 and transcriptionally upregulated with decreased H3K27m3 in SlJMJ6-overexpressed fruit. Numerous SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation and hormone signaling. Eleven ripening-related genes including RIPENING INHIBITOR (RIN), 1-aminocyclopropane 1-carboxylate synthase-4 (ACS4), 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1), pectate lyase (PL) and beta-galactosidase 4 (TBG4), and a DNA demethylase DML2, were confirmed to be regulated directly by SlJMJ6 through removing H3K27me3. Our results demonstrate that SlJMJ6 is a ripening-prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating tomato fruit ripening. Our work also reveals a novel link between histone demethylation and DNA demethylation in regulating fruit ripening. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.
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Affiliation(s)
- Zhiwei Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoxiang Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Science, Guangzhou, 510650, China
| | - Xiaochun Ding
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Dandan Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xiaowan Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yijie Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiling Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Taotao Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 106, Taiwan
| | - Yueming Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Science, Guangzhou, 510650, China
| | - Xuewu Duan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Science, Guangzhou, 510650, China
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117
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Abstract
As a unique subpopulation of cancer cells, cancer stem cells (CSCs) acquire the resistance to conventional therapies and appear to be the prime cause of cancer recurrence. Like their normal counterparts, CSCs can renew themselves and generate differentiated progenies. Cancer stem cells are distinguished among heterogenous cancer cells by molecular markers and their capacity of efficiently forming new tumors composed of diverse and heterogenous cancer cells. Tumor heterogeneity can be inter- or intra-tumor, molecularly resulting from the accumulation of genetic and non-genetic alterations. Non-genetic alterations are mainly changes on epigenetic modifications of DNA and histone, and chromatin remodeling. As tumor-initiating cells and contributing to the tumor heterogeneity in the brain, glioblastoma stem cells (GSCs) attract extensive research interests. Epigenetic modifications confer on tumor cells including CSCs reversible and inheritable genomic changes and affect gene expression without alteration in DNA sequence. Here, we will review recent advances in histone demethylation, DNA methylation, RNA methylation and ubiquitination in glioblastomas and their impacts on tumorigenesis with a focus on CSCs.
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Affiliation(s)
- Kezhou Zhu
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Victoria Xie
- M.D. Program, Baylor College of Medicine, Houston, TX, United States
| | - Suyun Huang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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118
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Wang J, Yu C, Zhang S, Ye J, Dai H, Wang H, Huang J, Cao X, Ma J, Ma H, Wang Y. Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis. NATURE PLANTS 2020; 6:823-837. [PMID: 32572214 DOI: 10.1038/s41477-020-0697-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 05/17/2020] [Indexed: 05/25/2023]
Abstract
Histone demethylation is crucial for proper chromatin structure and to ensure normal development, and requires the large family of Jumonji C (JmjC)-containing demethylases; however, the molecular mechanisms that regulate the substrate specificity of these JmjC-containing demethylases remain largely unknown. Here, we show that the substrate specificity of the Arabidopsis histone demethylase JMJ16 is broadened from Lys 4 of histone H3 (H3K4) alone in somatic cells to both H3K4 and H3K9 when it binds to the meiocyte-specific histone reader MMD1. Consistent with this, the JMJ16 catalytic domain exhibits both H3K4 and H3K9 demethylation activities. Moreover, the JMJ16 C-terminal FYR domain interacts with the JMJ16 catalytic domain and probably restricts its substrate specificity. By contrast, MMD1 can compete with the N-terminal catalytic domain of JMJ16 for binding to the FYR-C domain, thereby expanding the substrate specificity of JMJ16 by preventing the FYR domain from binding to the catalytic domain. We propose that MMD1 and JMJ16 together in male meiocytes promote gene expression in an H3K9me3-dependent manner and thereby contribute to meiotic chromosome condensation.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chaoyi Yu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuaibin Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Juanying Ye
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hang Dai
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Hongkuan Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiyue Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Hong Ma
- Department of Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China.
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119
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Jeon HY, Hussain A, Qi J. Role of H3K9 demethylases in DNA double-strand break repair. JOURNAL OF CANCER BIOLOGY 2020; 1:10-15. [PMID: 32696030 DOI: 10.46439/cancerbiology.1.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
H3K9 demethylases can remove the repressive H3K9 methylation marks on histones to alter chromatin structure, gene transcription and epigenetic state of cells. By counteracting the function of H3K9 methyltransferases, H3K9 demethylases have been shown to play an important role in numerous biological processes, including diseases such as cancer. Recent evidence points to a key role for some H3K9 demethylases in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) and/or non-homologous end joining (NHEJ) pathways. Mechanistically, H3K9 demethylases can upregulate the expression of DNA repair factors. They can also be recruited to the DNA damage sites and regulate the recruitment or function of DNA repair factors. Here, we will discuss the role and mechanisms of H3K9 demethylases in the regulation of DSB repair.
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Affiliation(s)
- Hee-Young Jeon
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Arif Hussain
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.,Baltimore VA Medical Center, Baltimore, MD, USA
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
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120
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Wang P, Deng Y, Yan X, Zhu J, Yin Y, Shu Y, Bai D, Zhang S, Xu H, Lu X. The Role of ARID5B in Acute Lymphoblastic Leukemia and Beyond. Front Genet 2020; 11:598. [PMID: 32595701 PMCID: PMC7303299 DOI: 10.3389/fgene.2020.00598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/18/2020] [Indexed: 02/05/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common malignancy in children with distinct characteristics among different subtypes. Although the etiology of ALL has not been fully unveiled, initiation of ALL has been demonstrated to partly depend on genetic factors. As indicated by several genome wide association studies (GWASs) and candidate gene analyses, ARID5B, a member of AT-rich interactive domain (ARID) protein family, is associated with the occurrence and prognosis of ALL. However, the mechanisms by which ARID5B genotype impact on the susceptibility and treatment outcome remain vague. In this review, we outline developments in the understanding of ARID5B in the susceptibility of ALL and its therapeutic perspectives, and summarize the underlying mechanisms based on the limited functional studies, hoping to illustrate the possible mechanisms of ARID5B impact and highlight the potential treatment regimens.
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Affiliation(s)
- Peiqi Wang
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yun Deng
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyu Yan
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jianhui Zhu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shouyue Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Precision Medicine Center, State Key Laboratory of Biotherapy and Precision Medicine, Key Laboratory of Sichuan Province, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaoxi Lu
- Department of Pediatric Hematology/Oncology, West China Second University Hospital, Sichuan University, Chengdu, China
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121
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Deng L, Liu Q, Lei C, Zhang Y, Huang Y, Nie Z, Yao S. Fluorometric and Colorimetric Dual-Readout Assay for Histone Demethylase Activity Based on Formaldehyde Inhibition of Ag+-Triggered Oxidation of O-Phenylenediamine. Anal Chem 2020; 92:9421-9428. [DOI: 10.1021/acs.analchem.0c01927] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lu Deng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Qingqing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Youyu Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, P.R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, P.R. China
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122
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Sulkowski PL, Oeck S, Dow J, Economos NG, Mirfakhraie L, Liu Y, Noronha K, Bao X, Li J, Shuch BM, King MC, Bindra RS, Glazer PM. Oncometabolites suppress DNA repair by disrupting local chromatin signalling. Nature 2020; 582:586-591. [PMID: 32494005 PMCID: PMC7319896 DOI: 10.1038/s41586-020-2363-0] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/28/2020] [Indexed: 01/06/2023]
Abstract
Deregulation of metabolism and disruption of genome integrity are hallmarks of cancer1. Increased levels of the metabolites 2-hydroxyglutarate, succinate and fumarate occur in human malignancies owing to somatic mutations in the isocitrate dehydrogenase-1 or -2 (IDH1 or IDH2) genes, or germline mutations in the fumarate hydratase (FH) and succinate dehydrogenase genes (SDHA, SDHB, SDHC and SDHD), respectively2-4. Recent work has made an unexpected connection between these metabolites and DNA repair by showing that they suppress the pathway of homology-dependent repair (HDR)5,6 and confer an exquisite sensitivity to inhibitors of poly (ADP-ribose) polymerase (PARP) that are being tested in clinical trials. However, the mechanism by which these oncometabolites inhibit HDR remains poorly understood. Here we determine the pathway by which these metabolites disrupt DNA repair. We show that oncometabolite-induced inhibition of the lysine demethylase KDM4B results in aberrant hypermethylation of histone 3 lysine 9 (H3K9) at loci surrounding DNA breaks, masking a local H3K9 trimethylation signal that is essential for the proper execution of HDR. Consequently, recruitment of TIP60 and ATM, two key proximal HDR factors, is substantially impaired at DNA breaks, with reduced end resection and diminished recruitment of downstream repair factors. These findings provide a mechanistic basis for oncometabolite-induced HDR suppression and may guide effective strategies to exploit these defects for therapeutic gain.
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Affiliation(s)
- Parker L Sulkowski
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sebastian Oeck
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Medical Oncology, University of Duisburg-Essen, Essen, Germany
| | - Jonathan Dow
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Nicholas G Economos
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lily Mirfakhraie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yanfeng Liu
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Katelyn Noronha
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Xun Bao
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Jing Li
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Brian M Shuch
- Department of Urology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Megan C King
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
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123
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Qi Q, Wang Y, Wang X, Yang J, Xie Y, Zhou J, Li X, Wang B. Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling. Cell Mol Life Sci 2020; 77:2407-2421. [PMID: 31515577 PMCID: PMC11105029 DOI: 10.1007/s00018-019-03289-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/08/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
Abstract
Epigenetic modifications play a central role in cell differentiation and development. In the current study, we have recognized lysine demethylase 4A (KDM4A) as a novel epigenetic regulator of osteoblast and adipocyte differentiation. Kdm4a expression was upregulated during osteogenesis and adipogenesis of primary marrow stromal cells and established stromal ST2 line. Overexpression of wild-type Kdm4a promoted adipogenic differentiation and blocked osteogenic differentiation of the progenitor cells. This effect was largely alleviated when the catalytically dead mutation was made. Conversely, depletion or inactivation of Kdm4a in undifferentiated progenitor cells inhibited the formation of adipocytes and promoted the differentiation of osteoblasts. Mechanism explorations showed that overexpression of Kdm4a upregulated the expression of secreted frizzled-related protein 4 (Sfrp4) and CCAAT/enhancer-binding protein α (C/ebpα). Chromatin immunoprecipitation assay demonstrated that KDM4A directly bound the promoters of Sfrp4 and C/ebpα, removed the histone methylation mark H3K9me3, and reduced DNA methylation levels of CpG in promoter regions of C/ebpα and Sfrp4. Furthermore, overexpression of Kdm4a inactivated canonical Wnt signaling. Moreover, activation of canonical Wnt signaling through silencing of Sfrp4 in ST2 attenuated the inhibition of osteogenic differentiation and the enhancement of adipogenic differentiation by KDM4A. These data have identified KDM4A as a novel regulator of osteoblast and adipocyte differentiation and suggest KDM4A inhibition as a potential therapeutic target for treating metabolic disorders such as osteoporosis.
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Affiliation(s)
- Qi Qi
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China
| | - Yi Wang
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China
| | - Xiaochen Wang
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China
| | - Junying Yang
- College of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yan Xie
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China
| | - Jie Zhou
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China
| | - Xiaoxia Li
- College of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Baoli Wang
- NHC Key Lab of Hormones and Development, Tianjin Key Lab of Metabolic Diseases, Chu Hsien-I Memorial Hospital and Institute of Endocrinology, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Box 126, Tianjin, 300070, China.
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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125
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Yoo J, Jeon YH, Cho HY, Lee SW, Kim GW, Lee DH, Kwon SH. Advances in Histone Demethylase KDM3A as a Cancer Therapeutic Target. Cancers (Basel) 2020; 12:cancers12051098. [PMID: 32354028 PMCID: PMC7280979 DOI: 10.3390/cancers12051098] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Lysine-specific histone demethylase 3 (KDM3) subfamily proteins are H3K9me2/me1 histone demethylases that promote gene expression. The KDM3 subfamily primarily consists of four proteins (KDM3A−D). All four proteins contain the catalytic Jumonji C domain (JmjC) at their C-termini, but whether KDM3C has demethylase activity is under debate. In addition, KDM3 proteins contain a zinc-finger domain for DNA binding and an LXXLL motif for interacting with nuclear receptors. Of the KDM3 proteins, KDM3A is especially deregulated or overexpressed in multiple cancers, making it a potential cancer therapeutic target. However, no KDM3A-selective inhibitors have been identified to date because of the lack of structural information. Uncovering the distinct physiological and pathological functions of KDM3A and their structure will give insight into the development of novel selective inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM3A in cancer. We also discuss existing KDM3A-related inhibitors and review their potential as therapeutic agents for overcoming cancer.
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Affiliation(s)
- Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Ha Young Cho
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-32-749-4513
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126
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Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K. The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. iScience 2020; 23:101030. [PMID: 32299058 PMCID: PMC7160574 DOI: 10.1016/j.isci.2020.101030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/29/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Haploinsufficiency of SETD5 is implicated in syndromic autism spectrum disorder (ASD), but the molecular mechanism underlying the pathological role of this protein has remained unclear. We have now shown that Setd5+/– mice manifest ASD-related behavioral phenotypes and that the expression of ribosomal protein genes and rDNA is disturbed in the brain of these mice. SETD5 recruited the HDAC3 complex to the rDNA promoter, resulting in removal of the histone mark H4K16ac and its reader protein TIP5, a repressor of rDNA expression. Depletion of SETD5 attenuated rDNA expression, translational activity, and neural cell proliferation, whereas ablation of TIP5 in SETD5-deficient cells rescued these effects. Translation of cyclin D1 mRNA was specifically down-regulated in SETD5-insufficient cells. Our results thus suggest that SETD5 positively regulates rDNA expression via an HDAC3-mediated epigenetic mechanism and that such regulation is essential for translation of cyclin D1 mRNA and neural cell proliferation. Setd5+/– mice manifest syndromic autism-related phenotypes SETD5 recruits the HDAC3 complex to the rDNA promoter SETD5 deficiency reduces rRNA abundance and attenuates translational activity SETD5 deficiency inhibits cyclin D1 mRNA translation and neural cell proliferation
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Affiliation(s)
- Tadashi Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Satoko Hattori
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Risa Nobuta
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryuichi Kimura
- Division of Developmental Neuroscience, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Makiko Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuko Nagasawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Noriko Osumi
- Division of Developmental Neuroscience, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan.
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127
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Ordway B, Swietach P, Gillies RJ, Damaghi M. Causes and Consequences of Variable Tumor Cell Metabolism on Heritable Modifications and Tumor Evolution. Front Oncol 2020; 10:373. [PMID: 32292719 PMCID: PMC7119341 DOI: 10.3389/fonc.2020.00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/03/2020] [Indexed: 01/02/2023] Open
Abstract
When cancer research advanced into the post-genomic era, it was widely anticipated that the sought-after cure will be delivered promptly. Instead, it became apparent that an understanding of cancer genomics, alone, is unable to translate the wealth of information into successful cures. While gene sequencing has significantly improved our understanding of the natural history of cancer and identified candidates for therapeutic targets, it cannot predict the impact of the biological response to therapies. Hence, patients with a common mutational profile may respond differently to the same therapy, due in part to different microenvironments impacting on gene regulation. This complexity arises from a feedback circuit involving epigenetic modifications made to genes by the metabolic byproducts of cancer cells. New insights into epigenetic mechanisms, activated early in the process of carcinogenesis, have been able to describe phenotypes which cannot be inferred from mutational analyses per se. Epigenetic changes can propagate throughout a tumor via heritable modifications that have long-lasting consequences on ensuing phenotypes. Such heritable epigenetic changes can be evoked profoundly by cancer cell metabolites, which then exercise a broad remit of actions across all stages of carcinogenesis, culminating with a meaningful impact on the tumor's response to therapy. This review outlines some of the cross-talk between heritable epigenetic changes and tumor cell metabolism, and the consequences of such changes on tumor progression.
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Affiliation(s)
- Bryce Ordway
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Robert J Gillies
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Mehdi Damaghi
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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128
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Heme, A Metabolic Sensor, Directly Regulates the Activity of the KDM4 Histone Demethylase Family and Their Interactions with Partner Proteins. Cells 2020; 9:cells9030773. [PMID: 32235736 PMCID: PMC7140707 DOI: 10.3390/cells9030773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/10/2023] Open
Abstract
The KDM4 histone demethylase subfamily is constituted of yeast JmjC domain-containing proteins, such as Gis1, and human Gis1 orthologues, such as KDM4A/B/C. KDM4 proteins have important functions in regulating chromatin structure and gene expression in response to metabolic and nutritional stimuli. Heme acts as a versatile signaling molecule to regulate important cellular functions in diverse organisms ranging from bacteria to humans. Here, using purified KDM4 proteins containing the JmjN/C domain, we showed that heme stimulates the histone demethylase activity of the JmjN/C domains of KDM4A and Cas well as full-length Gis1. Furthermore, we found that the C-terminal regions of KDM4 proteins, like that of Gis1, can confer heme regulation when fused to an unrelated transcriptional activator. Interestingly, biochemical pull-down of Gis1-interacting proteins followed by mass spectrometry identified 147 unique proteins associated with Gis1 under heme-sufficient and/or heme-deficient conditions. These 147 proteins included a significant number of heterocyclic compound-binding proteins, Ubl-conjugated proteins, metabolic enzymes/proteins, and acetylated proteins. These results suggested that KDM4s interact with diverse cellular proteins to form a complex network to sense metabolic and nutritional conditions like heme levels and respond by altering their interactions with other proteins and functional activities, such as histone demethylation.
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129
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Raiymbek G, An S, Khurana N, Gopinath S, Larkin A, Biswas S, Trievel RC, Cho US, Ragunathan K. An H3K9 methylation-dependent protein interaction regulates the non-enzymatic functions of a putative histone demethylase. eLife 2020; 9:53155. [PMID: 32195666 PMCID: PMC7192584 DOI: 10.7554/elife.53155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
H3K9 methylation (H3K9me) specifies the establishment and maintenance of transcriptionally silent epigenetic states or heterochromatin. The enzymatic erasure of histone modifications is widely assumed to be the primary mechanism that reverses epigenetic silencing. Here, we reveal an inversion of this paradigm where a putative histone demethylase Epe1 in fission yeast, has a non-enzymatic function that opposes heterochromatin assembly. Mutations within the putative catalytic JmjC domain of Epe1 disrupt its interaction with Swi6HP1 suggesting that this domain might have other functions besides enzymatic activity. The C-terminus of Epe1 directly interacts with Swi6HP1, and H3K9 methylation stimulates this protein-protein interaction in vitro and in vivo. Expressing the Epe1 C-terminus is sufficient to disrupt heterochromatin by outcompeting the histone deacetylase, Clr3 from sites of heterochromatin formation. Our results underscore how histone modifying proteins that resemble enzymes have non-catalytic functions that regulate the assembly of epigenetic complexes in cells. A cell’s identity depends on which of its genes are active. One way for cells to control this process is to change how accessible their genes are to the molecular machinery that switches them on and off. Special proteins called histones determine how accessible genes are by altering how loosely or tightly DNA is packed together. Histones can be modified by enzymes, which are proteins that add or remove specific chemical ‘tags’. These tags regulate how accessible genes are and provide cells with a memory of gene activity. For example, a protein found in yeast called Epe1 helps reactivate large groups of genes after cell division, effectively ‘re-setting’ the yeast’s genome and eliminating past memories of the genes being inactive. For a long time, Epe1 was thought to do this by removing methyl groups, a ‘tag’ that indicates a gene is inactive, from histones – that is, by acting like an enzyme. However, no direct evidence to support this hypothesis has been found. Raiymbek et al. therefore set out to determine exactly how Epe1 worked, and whether or not it did indeed behave like an enzyme. Initial experiments testing mutant versions of Epe1 in yeast cells showed that the changes expected to stop Epe1 from removing methyl groups instead prevented the protein from ‘homing’ to the sections of DNA it normally activates. Detailed microscope imaging, using live yeast cells engineered to produce proteins with fluorescent markers, revealed that this inability to ‘home’ was due to a loss of interaction with Epe1’s main partner, a protein called Swi6. This protein recognizes and binds histones that have methyl tags. Swi6 also acts as a docking site for proteins involved in deactivating genes in close proximity to these histones. Further biochemical studies revealed how the interaction between Epe1 and Swi6 can help in gene reactivation. The methyl tag on histones in inactive regions of the genome inadvertently helps Epe1 interact more efficiently with Swi6. Then, Epe1 can simply block every other protein that binds to Swi6 from participating in gene deactivation. This observation contrasts with the prevailing view where the active removal of methyl tags by proteins such as Epe1 switches genes from an inactive to an active state. This work shows for the first time that Epe1 influences the state of the genome through a process that does not involve enzyme activity. In other words, although the protein may ‘moonlight’ as an enzyme, its main job uses a completely different mechanism. More broadly, these results increase the understanding of the many different ways that gene activity, and ultimately cell identity, can be controlled.
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Affiliation(s)
- Gulzhan Raiymbek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Sojin An
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Nidhi Khurana
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Saarang Gopinath
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Ajay Larkin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.,Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.,Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Kaushik Ragunathan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, United States
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130
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Mohammed SA, Ambrosini S, Lüscher T, Paneni F, Costantino S. Epigenetic Control of Mitochondrial Function in the Vasculature. Front Cardiovasc Med 2020; 7:28. [PMID: 32195271 PMCID: PMC7064473 DOI: 10.3389/fcvm.2020.00028] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/24/2022] Open
Abstract
The molecular signatures of epigenetic regulation and chromatin architecture are emerging as pivotal regulators of mitochondrial function. Recent studies unveiled a complex intersection among environmental factors, epigenetic signals, and mitochondrial metabolism, ultimately leading to alterations of vascular phenotype and increased cardiovascular risk. Changing environmental conditions over the lifetime induce covalent and post-translational chemical modification of the chromatin template which sensitize the genome to establish new transcriptional programs and, hence, diverse functional states. On the other hand, metabolic alterations occurring in mitochondria affect the availability of substrates for chromatin-modifying enzymes, thus leading to maladaptive epigenetic signatures altering chromatin accessibility and gene transcription. Indeed, several components of the epigenetic machinery require intermediates of cellular metabolism (ATP, AcCoA, NADH, α-ketoglutarate) for enzymatic function. In the present review, we describe the emerging role of epigenetic modifications as fine tuners of gene transcription in mitochondrial dysfunction and vascular disease. Specifically, the following aspects are described in detail: (i) mitochondria and vascular function, (ii) mitochondrial ROS, (iii) epigenetic regulation of mitochondrial function; (iv) the role of mitochondrial metabolites as key effectors for chromatin-modifying enzymes; (v) epigenetic therapies. Understanding epigenetic routes may pave the way for new approaches to develop personalized therapies to prevent mitochondrial insufficiency and its complications.
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Affiliation(s)
- Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Thomas Lüscher
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Research, Education and Development, Royal Brompton and Harefield Hospital Trust and Imperial College, London, United Kingdom
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
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131
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ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020; 38:728-736. [PMID: 32123383 PMCID: PMC7289633 DOI: 10.1038/s41587-020-0434-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023]
Abstract
Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications remains to be fully characterized. Here, we use natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 a H3K27 residues. We first demonstrate their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone modification–binding preference. By fusing eCRs to the biotin ligase BASU, we establish ChromID, a method for identifying the chromatin-dependent protein interactome based on proximity biotinylation, and apply it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.
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132
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Urulangodi M, Mohanty A. DNA damage response and repair pathway modulation by non-histone protein methylation: implications in neurodegeneration. J Cell Commun Signal 2020; 14:31-45. [PMID: 31749026 PMCID: PMC7176765 DOI: 10.1007/s12079-019-00538-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Protein post-translational modifications (PTMs) have emerged to be combinatorial, essential mechanisms used by eukaryotic cells to regulate local chromatin structure, diversify and extend their protein functions and dynamically coordinate complex intracellular signalling processes. Most common types of PTMs include enzymatic addition of small chemical groups resulting in phosphorylation, glycosylation, poly(ADP-ribosyl)ation, nitrosylation, methylation, acetylation or covalent attachment of complete proteins such as ubiquitin and SUMO. Protein arginine methyltransferases (PRMTs) and protein lysine methyltransferases (PKMTs) enzymes catalyse the methylation of arginine and lysine residues in target proteins, respectively. Rapid progress in quantitative proteomic analysis and functional assays have not only documented the methylation of histone proteins post-translationally but also identified their occurrence in non-histone proteins which dynamically regulate a plethora of cellular functions including DNA damage response and repair. Emerging advances have now revealed the role of both histone and non-histone methylations in the regulating the DNA damage response (DDR) proteins, thereby modulating the DNA repair pathways both in proliferating and post-mitotic neuronal cells. Defects in many cellular DNA repair processes have been found primarily manifested in neuronal tissues. Moreover, fine tuning of the dynamicity of methylation of non-histone proteins as well as the perturbations in this dynamic methylation processes have recently been implicated in neuronal genomic stability maintenance. Considering the impact of methylation on chromatin associated pathways, in this review we attempt to link the evidences in non-histone protein methylation and DDR with neurodegenerative research.
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Affiliation(s)
- Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, PIN-695011, India.
| | - Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, PIN-110085, India.
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133
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Inflammation-induced JMJD2D promotes colitis recovery and colon tumorigenesis by activating Hedgehog signaling. Oncogene 2020; 39:3336-3353. [PMID: 32094404 DOI: 10.1038/s41388-020-1219-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/11/2022]
Abstract
Histone demethylase JMJD2D can promote gene expression by specifically demethylating H3K9me2/3. The role of JMJD2D in colitis and colitis-associated colorectal cancer (CRC) progression remains unclear. Here, we show that colonic JMJD2D is induced by TNFα during dextran sulfate sodium-induced colitis. JMJD2D-deficient mice exhibit more severe colon damage and defective colon regeneration due to impaired Hedgehog signaling activation after colitis. JMJD2D knockdown in CRC cells suppresses Hedgehog signaling, resulting in reduced CRC growth and metastasis. Mechanistically, JMJD2D promotes Hedgehog target gene expression through interacting with Gli2 to reduce H3K9me3 levels at the promoter. Clinically, JMJD2D expression is upregulated and positively correlated with Gli2 expression in human inflammatory bowel disease specimens and CRC specimens. The JMJD2D inhibitor 5-c-8HQ or aspirin synergizes with Hedgehog inhibitor vismodegib to inhibit CRC cell proliferation and tumorigenesis. Collectively, our findings unveil an essential role of JMJD2D in activating the processes of colonic protection, regeneration, and tumorigenesis.
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134
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Histone demethylase KDM4D cooperates with NFIB and MLL1 complex to regulate adipogenic differentiation of C3H10T1/2 mesenchymal stem cells. Sci Rep 2020; 10:3050. [PMID: 32080306 PMCID: PMC7033117 DOI: 10.1038/s41598-020-60049-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/06/2020] [Indexed: 11/09/2022] Open
Abstract
The coordinated and sequential actions of lineage-specific transcription factors and epigenetic regulators are essential for the initiation and maintenance of cellular differentiation. We here report KDM4D histone demethylase as a key regulator of adipogenesis in C3H10T1/2 mesenchymal stem cells. The depletion of KDM4D results in impaired differentiation, which can be rescued by exogenous KDM4D, PPARγ, and C/EBPα, but not by C/EBPβ. In addition, KDM4D interacts physically and functionally with both NFIB and MLL1 complex to regulate C/EBPα and PPARγ expression upon adipogenic hormonal induction. Although KDM4D is dispensable for the binding of both NFIB and MLL1 complex to the target promoters, the demethylation of tri-methylated H3K9 by KDM4D is required for NFIB and MLL1 complex to deposit tri-methylated H3K4 and activate PPARγ and C/EBPα expression. Taken together, our data provide a molecular framework for lineage-specific transcription factor and histone modifiers to cooperate in adipogenic differentiation, in which KDM4D removes repressive histone marks at genes with a bivalent chromatin domain and allows NFIB and MLL1 complex to promote the expression of key adipogenic regulators.
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135
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Lee S, Liu H, Hill R, Chen C, Hong X, Crawford F, Kingsley M, Zhang Q, Liu X, Chen Z, Lengeling A, Bernt KM, Marrack P, Kappler J, Zhou Q, Li CY, Xue Y, Hansen K, Zhang G. JMJD6 cleaves MePCE to release positive transcription elongation factor b (P-TEFb) in higher eukaryotes. eLife 2020; 9:53930. [PMID: 32048991 PMCID: PMC7064345 DOI: 10.7554/elife.53930] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/11/2020] [Indexed: 12/19/2022] Open
Abstract
More than 30% of genes in higher eukaryotes are regulated by promoter-proximal pausing of RNA polymerase II (Pol II). Phosphorylation of Pol II CTD by positive transcription elongation factor b (P-TEFb) is a necessary precursor event that enables productive transcription elongation. The exact mechanism on how the sequestered P-TEFb is released from the 7SK snRNP complex and recruited to Pol II CTD remains unknown. In this report, we utilize mouse and human models to reveal methylphosphate capping enzyme (MePCE), a core component of the 7SK snRNP complex, as the cognate substrate for Jumonji domain-containing 6 (JMJD6)’s novel proteolytic function. Our evidences consist of a crystal structure of JMJD6 bound to methyl-arginine, enzymatic assays of JMJD6 cleaving MePCE in vivo and in vitro, binding assays, and downstream effects of Jmjd6 knockout and overexpression on Pol II CTD phosphorylation. We propose that JMJD6 assists bromodomain containing 4 (BRD4) to recruit P-TEFb to Pol II CTD by disrupting the 7SK snRNP complex. In animals, an enzyme known as RNA polymerase II (Pol II for short) is a key element of the transcription process, whereby the genetic information contained in DNA is turned into messenger RNA molecules in the cells, which can then be translated to proteins. To perform this task, Pol II needs to be activated by a complex of proteins called P-TEFb; however, P-TEFb is usually found in an inactive form held by another group of proteins. Yet, it is unclear how P-TEFb is released and allowed to activate Pol II. Scientists have speculated that another protein called JMJD6 (Jumonji domain-containing 6) is important for P-TEFb to activate Pol II. Various roles for JMJD6 have been proposed, but its exact purpose remains unclear. Recently, two enzymes closely related to JMJD6 were found to be able to make precise cuts in other proteins; Lee, Liu et al. therefore wanted to test whether this is also true of JMJD6. Experiments using purified JMJD6 showed that it could make a cut in an enzyme called MePCE, which belongs to the group of proteins that hold P-TEFb in its inactive form. Lee, Liu et al. then tested the relationships between these proteins in living human and mouse cells. The levels of activated Pol II were lower in cells without JMJD6 and higher in those without MePCE. Together, the results suggest that JMJD6 cuts MePCE to release P-TEFb, which then activates Pol II. JMJD6 appears to know where to cut by following a specific pattern of elements in the structure of MePCE. When MePCE was mutated so that the pattern changed, JMJD6 was unable to cut it. These results suggest that JMJD6 and related enzymes belong to a new family of proteases, the molecular scissors that can cleave other proteins. The molecules that regulate transcription often are major drug targets, for example in the fight against cancer. Ultimately, understanding the role of JMJD6 might help to identify new avenues for cancer drug development.
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Affiliation(s)
- Schuyler Lee
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
| | - Haolin Liu
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
| | - Ryan Hill
- Department of Genetics and Biochemistry, School of Medicine, University of Colorado, Aurora, United States
| | - Chunjing Chen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Xia Hong
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
| | - Fran Crawford
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Molly Kingsley
- Department of Pediatrics, Children Hospital, University of Colorado, Aurora, United States.,Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Qianqian Zhang
- State Key Laboratory of Agrobiotechnology, China Agriculture University, Beijing, China
| | - Xinjian Liu
- Department of Dermatology, Duke University, Durham, United States
| | - Zhongzhou Chen
- State Key Laboratory of Agrobiotechnology, China Agriculture University, Beijing, China
| | | | - Kathrin Maria Bernt
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Philippa Marrack
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
| | - John Kappler
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
| | - Qiang Zhou
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Chuan-Yuan Li
- Department of Dermatology, Duke University, Durham, United States
| | - Yuhua Xue
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Kirk Hansen
- Department of Genetics and Biochemistry, School of Medicine, University of Colorado, Aurora, United States
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, United States
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136
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Cornett EM, Ferry L, Defossez PA, Rothbart SB. Lysine Methylation Regulators Moonlighting outside the Epigenome. Mol Cell 2020; 75:1092-1101. [PMID: 31539507 DOI: 10.1016/j.molcel.2019.08.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
Abstract
Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
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Affiliation(s)
- Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Laure Ferry
- Université de Paris, Epigenetics and Cell Fate, CNRS, 75013 Paris, France
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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137
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Lee DH, Kim GW, Jeon YH, Yoo J, Lee SW, Kwon SH. Advances in histone demethylase KDM4 as cancer therapeutic targets. FASEB J 2020; 34:3461-3484. [PMID: 31961018 DOI: 10.1096/fj.201902584r] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 12/26/2022]
Abstract
The KDM4 subfamily H3K9 histone demethylases are epigenetic regulators that control chromatin structure and gene expression by demethylating histone H3K9, H3K36, and H1.4K26. The KDM4 subfamily mainly consists of four proteins (KDM4A-D), all harboring the Jumonji C domain (JmjC) but with differential substrate specificities. KDM4A-C proteins also possess the double PHD and Tudor domains, whereas KDM4D lacks these domains. KDM4 proteins are overexpressed or deregulated in multiple cancers, cardiovascular diseases, and mental retardation and are thus potential therapeutic targets. Despite extensive efforts, however, there are very few KDM4-selective inhibitors. Defining the exact physiological and oncogenic functions of KDM4 demethylase will provide the foundation for the discovery of novel potent inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM4s and the interplay between KDM4-mediated epigenetic and metabolic pathways in cancer. We also review currently available KDM4 inhibitors and discuss their potential as therapeutic agents for cancer treatment.
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Affiliation(s)
- Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Republic of Korea
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138
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Nawaz M, Malik I, Hameed M, Hussain Kuthu Z, Zhou J. Modifications of histones in parasites as drug targets. Vet Parasitol 2020; 278:109029. [PMID: 31978703 DOI: 10.1016/j.vetpar.2020.109029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
Abstract
Post-translational modifications of histones and histone modifying enzymes play important roles in gene regulations and other physiological processes in parasites. Inhibitors of such modifying enzymes could be useful as novel therapeutics against parasitic diseases or as chemical probes for investigation of epigenetics. Development of parasitic histone modulators has got rapid expansion in the last few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Some of these compounds have been widely used in humans targeting cancer and are found non-toxic. This review summarizes the antiparasitic activities of histone and histone modifying enzymes inhibitors evaluated in last few years. As the current chemotherapy against parasites is still not satisfactory, therefore, such compounds represents good starting points for the discovery of effective antiparasitic drugs.
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Affiliation(s)
- Mohsin Nawaz
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Irfan Malik
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Mudassar Hameed
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zulfiqar Hussain Kuthu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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139
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Zaghi M, Broccoli V, Sessa A. H3K36 Methylation in Neural Development and Associated Diseases. Front Genet 2020; 10:1291. [PMID: 31998360 PMCID: PMC6962298 DOI: 10.3389/fgene.2019.01291] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022] Open
Abstract
Post-translational methylation of H3 lysine 36 (H3K36) is an important epigenetic marker that majorly contributes to the functionality of the chromatin. This mark is interpreted by the cell in several crucial biological processes including gene transcription and DNA methylation. The homeostasis of H3K36 methylation is finely regulated by different enzyme classes which, when impaired, lead to a plethora of diseases; ranging from multi-organ syndromes to cancer, to pure neurological diseases often associated with brain development. This mini-review summarizes current knowledge on these important epigenetic signals with emphasis on the molecular mechanisms that (i) regulate their abundance, (ii) are influenced by H3K36 methylation, and (iii) the associated diseases.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Concilio Nazionale Delle Ricerche (CNR), Instituto di Neuroscienze, Milan, Italy
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
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140
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Letfus V, Jelić D, Bokulić A, Petrinić Grba A, Koštrun S. Rational design, synthesis and biological profiling of new KDM4C inhibitors. Bioorg Med Chem 2020; 28:115128. [DOI: 10.1016/j.bmc.2019.115128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022]
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141
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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142
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Turberfield AH, Kondo T, Nakayama M, Koseki Y, King HW, Koseki H, Klose RJ. KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity. Nucleic Acids Res 2019; 47:9005-9023. [PMID: 31363749 PMCID: PMC6753492 DOI: 10.1093/nar/gkz607] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
CpG islands (CGIs) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. Instead, we discover that KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CGI-associated gene promoters. We further show that KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters. Together this reveals a demethylase-independent role for KDM2 proteins in transcriptional repression and uncovers a new function for CGIs in constraining gene expression.
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Affiliation(s)
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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143
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Marquez J, Flores J, Kim AH, Nyamaa B, Nguyen ATT, Park N, Han J. Rescue of TCA Cycle Dysfunction for Cancer Therapy. J Clin Med 2019; 8:jcm8122161. [PMID: 31817761 PMCID: PMC6947145 DOI: 10.3390/jcm8122161] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/30/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Mitochondrion, a maternally hereditary, subcellular organelle, is the site of the tricarboxylic acid (TCA) cycle, electron transport chain (ETC), and oxidative phosphorylation (OXPHOS)—the basic processes of ATP production. Mitochondrial function plays a pivotal role in the development and pathology of different cancers. Disruption in its activity, like mutations in its TCA cycle enzymes, leads to physiological imbalances and metabolic shifts of the cell, which contributes to the progression of cancer. In this review, we explored the different significant mutations in the mitochondrial enzymes participating in the TCA cycle and the diseases, especially cancer types, that these malfunctions are closely associated with. In addition, this paper also discussed the different therapeutic approaches which are currently being developed to address these diseases caused by mitochondrial enzyme malfunction.
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Affiliation(s)
- Jubert Marquez
- Department of Health Science and Technology, College of Medicine, Inje University, Busan 47392, Korea; (J.M.); (A.H.K.)
| | - Jessa Flores
- Department of Physiology, College of Medicine, Inje University, Busan 47392, Korea; (J.F.); (B.N.); (A.T.T.N.)
| | - Amy Hyein Kim
- Department of Health Science and Technology, College of Medicine, Inje University, Busan 47392, Korea; (J.M.); (A.H.K.)
| | - Bayalagmaa Nyamaa
- Department of Physiology, College of Medicine, Inje University, Busan 47392, Korea; (J.F.); (B.N.); (A.T.T.N.)
- Department of Hematology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia
| | - Anh Thi Tuyet Nguyen
- Department of Physiology, College of Medicine, Inje University, Busan 47392, Korea; (J.F.); (B.N.); (A.T.T.N.)
| | - Nammi Park
- Cardiovascular and Metabolic Disease Center, Paik Hospital, Inje University, Busan 47392, Korea;
| | - Jin Han
- Department of Health Science and Technology, College of Medicine, Inje University, Busan 47392, Korea; (J.M.); (A.H.K.)
- Department of Physiology, College of Medicine, Inje University, Busan 47392, Korea; (J.F.); (B.N.); (A.T.T.N.)
- Cardiovascular and Metabolic Disease Center, Paik Hospital, Inje University, Busan 47392, Korea;
- Correspondence: ; Tel.: +8251-890-8748
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144
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Camacho J, Truong L, Kurt Z, Chen YW, Morselli M, Gutierrez G, Pellegrini M, Yang X, Allard P. The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1. Cell Rep 2019; 23:2392-2404. [PMID: 29791850 PMCID: PMC6003705 DOI: 10.1016/j.celrep.2018.04.078] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/15/2018] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
How artificial environmental cues are biologically integrated and transgenerationally inherited is still poorly understood. Here, we investigate the mechanisms of inheritance of reproductive outcomes elicited by the model environmental chemical Bisphenol A in C. elegans. We show that Bisphenol A (BPA) exposure causes the derepression of an epigenomically silenced transgene in the germline for 5 generations, regardless of ancestral response. Chromatin immunoprecipitation sequencing (ChIP-seq), histone modification quantitation, and immunofluorescence assays revealed that this effect is associated with a reduction of the repressive marks H3K9me3 and H3K27me3 in whole worms and in germline nuclei in the F3, as well as with reproductive dysfunctions, including germline apoptosis and embryonic lethality. Furthermore, targeting of the Jumonji demethylases JMJD-2 and JMJD-3/UTX-1 restores H3K9me3 and H3K27me3 levels, respectively, and it fully alleviates the BPA-induced transgenerational effects. Together, our results demonstrate the central role of repressive histone modifications in the inheritance of reproductive defects elicited by a common environmental chemical exposure.
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Affiliation(s)
- Jessica Camacho
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lisa Truong
- Human Genetics and Genomic Analysis Training Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zeyneb Kurt
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Molecular, Cell and Developmental Biology Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gerardo Gutierrez
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Environmental and Occupational Health, California State University, Northridge, CA 91330, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology Department, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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145
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Huang H, Kong W, Jean M, Fiches G, Zhou D, Hayashi T, Que J, Santoso N, Zhu J. A CRISPR/Cas9 screen identifies the histone demethylase MINA53 as a novel HIV-1 latency-promoting gene (LPG). Nucleic Acids Res 2019; 47:7333-7347. [PMID: 31165872 PMCID: PMC6698651 DOI: 10.1093/nar/gkz493] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022] Open
Abstract
Although combination antiretroviral therapy is potent to block active replication of HIV-1 in AIDS patients, HIV-1 persists as transcriptionally inactive proviruses in infected cells. These HIV-1 latent reservoirs remain a major obstacle for clearance of HIV-1. Investigation of host factors regulating HIV-1 latency is critical for developing novel antiretroviral reagents to eliminate HIV-1 latent reservoirs. From our recently accomplished CRISPR/Cas9 sgRNA screens, we identified that the histone demethylase, MINA53, is potentially a novel HIV-1 latency-promoting gene (LPG). We next validated MINA53’s function in maintenance of HIV-1 latency by depleting MINA53 using the alternative RNAi approach. We further identified that in vitro MINA53 preferentially demethylates the histone substrate, H3K36me3 and that in cells MINA53 depletion by RNAi also increases the local level of H3K36me3 at LTR. The effort to map the downstream effectors unraveled that H3K36me3 has the cross-talk with another epigenetic mark H4K16ac, mediated by KAT8 that recognizes the methylated H3K36 and acetylated H4K16. Removing the MINA53-mediated latency mechanisms could benefit the reversal of post-integrated latent HIV-1 proviruses for purging of reservoir cells. We further demonstrated that a pan jumonji histone demethylase inhibitor, JIB-04, inhibits MINA53-mediated demethylation of H3K36me3, and JIB-04 synergizes with other latency-reversing agents (LRAs) to reactivate latent HIV-1.
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Affiliation(s)
- Huachao Huang
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Weili Kong
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Maxime Jean
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Guillaume Fiches
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Dawei Zhou
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Tsuyoshi Hayashi
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Netty Santoso
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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146
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Clarke TL, Tang R, Chakraborty D, Van Rechem C, Ji F, Mishra S, Ma A, Kaniskan HÜ, Jin J, Lawrence MS, Sadreyev RI, Whetstine JR. Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification. Cancer Discov 2019; 10:306-325. [PMID: 31776131 DOI: 10.1158/2159-8290.cd-19-0463] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022]
Abstract
Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplification are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMT) and demethylases (KDM) in regulating transient site-specific DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplification of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specific KMTs and KDMs are able to promote or block extrachromosomal EGFR amplification, which identifies potential therapeutic strategies for controlling EGFR copy-number heterogeneity in cancer, and, in turn, drug response. SIGNIFICANCE: This study identifies a network of epigenetic factors and cellular signals that directly control EGFR DNA amplification. We demonstrate that chemical inhibitors targeting enzymes controlling this amplification can be used to rheostat EGFR copy number, which uncovers therapeutic opportunities for controlling EGFR DNA amplification heterogeneity and the associated drug response.This article is highlighted in the In This Issue feature, p. 161.
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Affiliation(s)
- Thomas L Clarke
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.,School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Capucine Van Rechem
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sweta Mishra
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Anqi Ma
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, Charlestown, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
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147
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Sun P, Zhang SJ, Maksim S, Yao YF, Liu HM, Du J. Epigenetic Modification in Macrophages: A Promising Target for Tumor and Inflammation-associated Disease Therapy. Curr Top Med Chem 2019; 19:1350-1362. [PMID: 31215380 DOI: 10.2174/1568026619666190619143706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/25/2019] [Accepted: 05/09/2019] [Indexed: 01/13/2023]
Abstract
Macrophages are essential for supporting tissue homeostasis, regulating immune response, and promoting tumor progression. Due to its heterogeneity, macrophages have different phenotypes and functions in various tissues and diseases. It is becoming clear that epigenetic modification playing an essential role in determining the biological behavior of cells. In particular, changes of DNA methylation, histone methylation and acetylation regulated by the corresponding epigenetic enzymes, can directly control macrophages differentiation and change their functions under different conditions. In addition, epigenetic enzymes also have become anti-tumor targets, such as HDAC, LSD1, DNMT, and so on. In this review, we presented an overview of the latest progress in the study of macrophages phenotype and function regulated by epigenetic modifications, including DNA methylation and histone modifications, to better understand how epigenetic modification controls macrophages phenotype and function in inflammation-associated diseases, and the application prospect in anti-tumor.
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Affiliation(s)
- Pei Sun
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Co-Innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education of China, Zhengzhou, China
| | - Shu-Jing Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Co-Innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education of China, Zhengzhou, China
| | - Semenov Maksim
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Co-Innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education of China, Zhengzhou, China
| | - Yong-Fang Yao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Co-Innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education of China, Zhengzhou, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Co-Innovation Center of Henan Province for New Drug R & D and Preclinical Safety, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies (Zhengzhou University), Ministry of Education of China, Zhengzhou, China
| | - Juan Du
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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148
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KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis. Mol Cell 2019; 76:885-895.e7. [PMID: 31629659 DOI: 10.1016/j.molcel.2019.09.019] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 07/22/2019] [Accepted: 09/12/2019] [Indexed: 12/19/2022]
Abstract
Hypoxia, which occurs during tumor growth, triggers complex adaptive responses in which peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) plays a critical role in mitochondrial biogenesis and oxidative metabolism. However, how PGC-1α is regulated in response to oxygen availability remains unclear. We demonstrated that lysine demethylase 3A (KDM3A) binds to PGC-1α and demethylates monomethylated lysine (K) 224 of PGC-1α under normoxic conditions. Hypoxic stimulation inhibits KDM3A, which has a high KM of oxygen for its activity, and enhances PGC-1α K224 monomethylation. This modification decreases PGC-1α's activity required for NRF1- and NRF2-dependent transcriptional regulation of TFAM, TFB1M, and TFB2M, resulting in reduced mitochondrial biogenesis. Expression of PGC-1α K224R mutant significantly increases mitochondrial biogenesis, reactive oxygen species (ROS) production, and tumor cell apoptosis under hypoxia and inhibits brain tumor growth in mice. This study revealed that PGC-1α monomethylation, which is dependent on oxygen availability-regulated KDM3A, plays a critical role in the regulation of mitochondrial biogenesis.
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149
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Mutlu B, Chen HM, Gutnik S, Hall DH, Keppler-Ross S, Mango SE. Distinct functions and temporal regulation of methylated histone H3 during early embryogenesis. Development 2019; 146:dev174516. [PMID: 31540912 PMCID: PMC6803369 DOI: 10.1242/dev.174516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 09/09/2019] [Indexed: 01/25/2023]
Abstract
During the first hours of embryogenesis, formation of higher-order heterochromatin coincides with the loss of developmental potential. Here, we examine the relationship between these two events, and we probe the processes that contribute to the timing of their onset. Mutations that disrupt histone H3 lysine 9 (H3K9) methyltransferases reveal that the methyltransferase MET-2 helps terminate developmental plasticity, through mono- and di-methylation of H3K9 (me1/me2), and promotes heterochromatin formation, through H3K9me3. Although loss of H3K9me3 perturbs formation of higher-order heterochromatin, embryos are still able to terminate plasticity, indicating that the two processes can be uncoupled. Methylated H3K9 appears gradually in developing C. elegans embryos and depends on nuclear localization of MET-2. We find that the timing of H3K9me2 and nuclear MET-2 is sensitive to rapid cell cycles, but not to zygotic genome activation or cell counting. These data reveal distinct roles for different H3K9 methylation states in the generation of heterochromatin and loss of developmental plasticity by MET-2, and identify the cell cycle as a crucial parameter of MET-2 regulation.
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Affiliation(s)
- Beste Mutlu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Huei-Mei Chen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Silvia Gutnik
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Susan E Mango
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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150
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Tsurumi A, Xue S, Zhang L, Li J, Li WX. Genome-wide Kdm4 histone demethylase transcriptional regulation in Drosophila. Mol Genet Genomics 2019; 294:1107-1121. [PMID: 31020413 PMCID: PMC6813854 DOI: 10.1007/s00438-019-01561-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 04/03/2019] [Indexed: 12/23/2022]
Abstract
The histone lysine demethylase 4 (Kdm4/Jmjd2/Jhdm3) family is highly conserved across species and reverses di- and tri-methylation of histone H3 lysine 9 (H3K9) and lysine 36 (H3K36) at the N-terminal tail of the core histone H3 in various metazoan species including Drosophila, C.elegans, zebrafish, mice and humans. Previous studies have shown that the Kdm4 family plays a wide variety of important biological roles in different species, including development, oncogenesis and longevity by regulating transcription, DNA damage response and apoptosis. Only two functional Kdm4 family members have been identified in Drosophila, compared to five in mammals, thus providing a simple model system. Drosophila Kdm4 loss-of-function mutants do not survive past the early 2nd instar larvae stage and display a molting defect phenotype associated with deregulated ecdysone hormone receptor signaling. To further characterize and identify additional targets of Kdm4, we employed a genome-wide approach to investigate transcriptome alterations in Kdm4 mutants versus wild-type during early development. We found evidence of increased deregulated transcripts, presumably associated with a progressive accumulation of H3K9 and H3K36 methylation through development. Gene ontology analyses found significant enrichment of terms related to the ecdysteroid hormone signaling pathway important in development, as expected, and additionally previously unidentified potential targets that warrant further investigation. Since Kdm4 is highly conserved across species, our results may be applicable more widely to other organisms and our genome-wide dataset may serve as a useful resource for further studies.
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Affiliation(s)
- Amy Tsurumi
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, 50 Blossom St., Their 340, Boston, MA, 02114, USA.
- Department of Microbiology and Immunology, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
- Shriners Hospitals for Children-Boston®, 51 Blossom St., Boston, MA, 02114, USA.
| | - Shuang Xue
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Lin Zhang
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Jinghong Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Willis X Li
- Department of Medicine, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
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