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Yang S, Xing J, Liu D, Song Y, Yu H, Xu S, Zuo Y. Review and new insights into the catalytic structural domains of the Fe(ll) and 2-Oxoglutarate families. Int J Biol Macromol 2024:134798. [PMID: 39153678 DOI: 10.1016/j.ijbiomac.2024.134798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
Histone lysine demethylase (KDM), AlkB homolog (ALKBH), and Ten-Eleven Translocation (TET) proteins are members of the 2-Oxoglutarate (2OG) and ferrous iron-dependent oxygenases, each of which harbors a catalytic domain centered on a double-stranded β-helix whose topology restricts the regions directly involved in substrate binding. However, they have different catalytic functions, and the deeply structural biological reasons are not yet clear. In this review, the catalytic domain features of the three protein families are summarized from both sequence and structural perspectives. The construction of the phylogenetic tree and comparison of the structure show ten relatively conserved β-sheets and three key regions with substantial structural differences. We summarize the relationship between three key regions of remarkable differences and the substrate compatibility of the three protein families. This review facilitates research into substrate-selective inhibition and bioengineering by providing new insights into the catalytic domains of KDM, ALKBH, and TET proteins.
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Affiliation(s)
- Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Jixiang Xing
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Dongyang Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yancheng Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Haoyu Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China
| | - Shuhua Xu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China; State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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2
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Ahmed F, Mishra NK, Alghamdi OA, Khan MI, Ahmad A, Khan N, Rehan M. Deciphering KDM8 dysregulation and CpG methylation in hepatocellular carcinoma using multi-omics and machine learning. Epigenomics 2024:1-23. [PMID: 39072393 DOI: 10.1080/17501911.2024.2374702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/25/2024] [Indexed: 07/30/2024] Open
Abstract
Aim: This study investigates the altered expression and CpG methylation patterns of histone demethylase KDM8 in hepatocellular carcinoma (HCC), aiming to uncover insights and promising diagnostics biomarkers. Materials & methods: Leveraging TCGA-LIHC multi-omics data, we employed R/Bioconductor libraries and Cytoscape to analyze and construct a gene correlation network, and LASSO regression to develop an HCC-predictive model. Results: In HCC, KDM8 downregulation is correlated with CpGs hypermethylation. Differential gene correlation analysis unveiled a liver carcinoma-associated network marked by increased cell division and compromised liver-specific functions. The LASSO regression identified a highly accurate HCC prediction signature, prominently featuring CpG methylation at cg02871891. Conclusion: Our study uncovers CpG hypermethylation at cg02871891, possibly influencing KDM8 downregulation in HCC, suggesting these as promising biomarkers and targets.
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Affiliation(s)
- Firoz Ahmed
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nitish Kumar Mishra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38015, USA
| | - Othman A Alghamdi
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammad Imran Khan
- Research Center, King Faisal Specialist Hospital & Research Centre, Jeddah, Saudi Arabia
- Department of Biochemistry & Molecular Medicine, College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Nargis Khan
- Snyder Institute of Chronic Diseases, Health Research & Innovation Center, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Mohammad Rehan
- Snyder Institute of Chronic Diseases, Health Research & Innovation Center, Cumming School of Medicine, University of Calgary, Alberta, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
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3
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Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A, de Mendoza A. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. SCIENCE ADVANCES 2024; 10:eado6406. [PMID: 38996012 PMCID: PMC11244446 DOI: 10.1126/sciadv.ado6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention and its genomic consequences are still poorly understood. Here, we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, hypermethylated genomic regions in Amoebidium derive from viral insertions, including hundreds of endogenized giant viruses, contributing 14% of the proteome. Using a combination of inhibitors and genomic assays, we demonstrate that 5mC silences these giant virus insertions. Moreover, alternative Amoebidium isolates show polymorphic giant virus insertions, highlighting a dynamic process of infection, endogenization, and purging. Our results indicate that 5mC is critical for the controlled coexistence of newly acquired viral DNA into eukaryotic genomes, making Amoebidium a unique model to understand the hybrid origins of eukaryotic DNA.
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Affiliation(s)
- Luke A. Sarre
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Iana V. Kim
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Vladimir Ovchinnikov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Marine Olivetta
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Omaya Dudin
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arnau Sebé-Pedrós
- CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- ICREA, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
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Yang T, Liu Y, Lin Z, Chen F, Zhu L, Zhang L, Zhou B, Li F, Sun H. Altered N6-methyladenosine methylation level in spermatozoa messenger RNA of the male partners is related to unexplained recurrent pregnancy loss. Andrology 2024. [PMID: 38979761 DOI: 10.1111/andr.13678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/17/2024] [Accepted: 05/30/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND Understanding the pathogenesis of unexplained recurrent pregnancy loss is paramount for advancing effective treatments. Various biological processes, including spermatogenesis and embryo development, are tightly regulated by N6-methyladenosine modifications. However, few studies have focused on the impact of sperm N6-methyladenosine modifications on embryonic development. Therefore, we aimed to study altered N6-methyladenosine-mediated messenger RNA methylation modifications in the spermatozoa of male partners from couples experiencing unexplained recurrent pregnancy loss, to identify potential diagnostic markers and explore their potential molecular mechanisms in pregnancy loss and embryogenesis. METHODS Methylated RNA immunoprecipitation (MeRIP) sequencing and RNA sequencing were conducted on the spermatozoa of men from couples in the 'unexplained recurrent pregnancy loss' group (n = 6), and the fertility control group (n = 6). To identify the role of the detected key genes, zebrafish model embryos were studied, and multi-omics (transcriptomics, proteomics, and metabolomics) analyses helped to explore the molecular mechanism of abnormal embryogenesis. FINDINGS Comparing unexplained recurrent pregnancy loss with the fertility control group, 217 N6-methyladenosine peaks were significantly upregulated, and 40 were downregulated in the spermatozoa. The combined analyses of spermatozoa-methylated RNA immunoprecipitation sequencing and RNA sequencing indicated that N6-methyladenosine methylation and the expression of SEMA5A, MT-ATP6, ZNF662, and KDM4C were significantly different. In zebrafish embryos, the altered expression of the four genes increased embryonic mortality and malformations by disturbing several key signaling pathways and zygotic genome activation. INTERPRETATION This study highlights the paternal epigenome, which could be one of the reasons for faulty embryogenesis leading to pregnancy loss. The N6-methyladenosine modification, the most prevalent RNA modification, contributes to the exploration and understanding of the paternal epigenome in the maintenance of pregnancy and fetal growth and development. The four genes identified in this study may serve as potential diagnostic markers and elucidate novel molecular mechanisms of embryogenesis.
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Affiliation(s)
- Tingting Yang
- Department of Andrology/Human Sperm Bank of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yanyan Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Medical Genetics, Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ziyuan Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Feng Chen
- Department of Andrology/Human Sperm Bank of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lin Zhu
- Department of Nephrology/Hemodialysis Center, West China Hospital, Sichuan University and West China School of Nursing, Sichuan University, Chengdu, China
| | - Lin Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Bin Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Fuping Li
- Department of Andrology/Human Sperm Bank of Sichuan Province, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
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Oh S, Janknecht R. Versatile JMJD proteins: juggling histones and much more. Trends Biochem Sci 2024:S0968-0004(24)00152-X. [PMID: 38926050 DOI: 10.1016/j.tibs.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Jumonji C domain-containing (JMJD) proteins are found in bacteria, fungi, animals, and plants. They belong to the 2-oxoglutarate-dependent oxygenase superfamily and are endowed with various enzymatic activities, including demethylation of histones and hydroxylation of non-histone proteins. Many JMJD proteins are involved in the epigenetic control of gene expression, yet they also modulate a myriad other cellular processes. In this review we focus on the 33 human JMJD proteins and their established and controversial catalytic properties, survey their epigenetic and non-epigenetic functions, emphasize their contribution to sex-specific disease differences, and highlight how they sense metabolic changes. All this underlines not only their key roles in development and homeostasis, but also that JMJD proteins are destined to become drug targets in multiple diseases.
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Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, 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; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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6
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Bush W, Bosart K, Bouley RA, Petreaca RC. KDM4B mutations in human cancers. Mutat Res 2024; 829:111866. [PMID: 38878505 DOI: 10.1016/j.mrfmmm.2024.111866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 07/17/2024]
Abstract
Homologous recombination (HR) is essential for repair of DNA double-strand breaks (DSBs) and restart of stalled or collapsed replication forks. Most cancers are characterized by mutations in components of the DSB repair pathways. Redundant DSB repair pathways exist in eukaryotes from yeast to humans and recent evidence has shown that complete loss of HR function appears to be lethal. Recent evidence has also shown that cancer cells with mutations in one DSB repair pathway can be killed by inhibiting one or more parallel pathways, a strategy that is currently aggressively explored as a cancer therapy. KDM4B is a histone demethylase with pleiotropic functions, which participates in preparing DSBs for repair by contributing to chromatin remodeling. In this report we carried out a pan-cancer analysis of KDM4B mutations with the goal of understanding their distribution and interaction with other DSB genes. We find that although KDM4B mutations co-occur with DSB repair genes, most KDM4B mutations are not drivers or pathogenic. A sequence conservation analysis from yeast to humans shows that highly conserved residues are resistant to mutation. Finally, all mutations occur in a heterozygous state. A single mutation, R986L, was predicted to significantly affect protein structure using computational modeling. This analysis suggests that KDM4B makes contributions to DSB repair but is not a key player.
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Affiliation(s)
- Wesley Bush
- Biology Program, The Ohio State University, Marion, OH 43302, USA
| | - Korey Bosart
- Biology Program, The Ohio State University, Marion, OH 43302, USA; Cancer Biology Program, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Renee A Bouley
- Department of Chemistry and Biochemistry, The Ohio State University, Marion, OH 43302, USA.
| | - Ruben C Petreaca
- Cancer Biology Program, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA.
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Kovács H, Jakusch T, May NV, Tóth S, Szakács G, Enyedy ÉA. Complex formation of ML324, the histone demethylase inhibitor, with essential metal ions: Relationship between solution chemistry and anticancer activity. J Inorg Biochem 2024; 255:112540. [PMID: 38552361 DOI: 10.1016/j.jinorgbio.2024.112540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
N-(3-(dimethylamino)propyl-4-(8-hydroxyquinolin-6-yl)benzamide (ML324, HL) is a potent inhibitor of the iron-containing histone demethylase KDM4, a recognized potential target of cancer therapeutics. Herein, we report the proton dissociation and complex formation processes of ML324 with essential metal ions such as Fe(II), Fe(III), Cu(II) and Zn(II) using UV-visible, fluorescence, electron paramagnetic resonance and 1H NMR spectroscopic methods. The electrochemical behaviour of the copper and iron complexes was characterized by cyclic voltammetry and spectroelectrochemistry. The solid phase structure of ML324 analysed by X-ray crystallography is also provided. Based on the solution equilibrium data, ML324 is present in solution in H2L+ form with a protonated dimethylammonium moiety at pH 7.4, and this (N,O) donor bearing ligand forms mono and bis complexes with all the studied metal ions and the tris-ligand species is also observed with Fe(III). At pH 7.4 the metal binding ability of ML324 follows the order: Fe(II) < Zn(II) < Cu(II) < Fe(III). Complexation with iron resulted in a negative redox potential (E'1/2 = -145 mV vs. NHE), further suggesting that the ligand has a preference for Fe(III) over Fe(II). ML324 was tested for its anticancer activity in chemosensitive and resistant human cancer cells overexpressing the efflux pump P-glycoprotein. ML324 exerted similar activity in all tested cells (IC50 = 1.9-3.6 μM). Co-incubation and complexation of the compound with Cu(II) and Zn(II) had no impact on the cytotoxicity of ML324, whereas Fe(III) decreased the toxicity in a concentration-dependent manner, and this effect was more pronounced in the multidrug resistant cells.
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Affiliation(s)
- Hilda Kovács
- MTA-SZTE Lendület Functional Metal Complexes Research Group, Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary; Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary
| | - Tamás Jakusch
- Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary
| | - Nóra V May
- Centre for Structural Science, Research Centre for Natural Sciences, Hungarian Research Network (HUN-REN), Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Szilárd Tóth
- Drug Resistance Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network (HUN-REN), Magyar Tudósok krt. 2, H-1117 Budapest, Hungary; National Laboratory for Drug Research and Development, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary
| | - Gergely Szakács
- Drug Resistance Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network (HUN-REN), Magyar Tudósok krt. 2, H-1117 Budapest, Hungary; Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Éva A Enyedy
- MTA-SZTE Lendület Functional Metal Complexes Research Group, Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary; Department of Molecular and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7-8, H-6720 Szeged, Hungary.
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8
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Li L, Song Q, Zhou J, Ji Q. Controllers of histone methylation-modifying enzymes in gastrointestinal cancers. Biomed Pharmacother 2024; 174:116488. [PMID: 38520871 DOI: 10.1016/j.biopha.2024.116488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024] Open
Abstract
Gastrointestinal (GI) cancers have been considered primarily genetic malignancies, caused by a series of progressive genetic alterations. Accumulating evidence shows that histone methylation, an epigenetic modification program, plays an essential role in the different pathological stages of GI cancer progression, such as precancerous lesions, tumorigenesis, and tumor metastasis. Histone methylation-modifying enzymes, including histone methyltransferases (HMTs) and demethylases (HDMs), are the main executor of post-transcriptional modification. The abnormal expression of histone methylation-modifying enzymes characterizes GI cancers with complex pathogenesis and progression. Interactions between upstream controllers and histone methylation-modifying enzymes have recently been revealed, and have provided numerous opportunities to elucidate the pathogenesis of GI cancers in depth and clearly. Here we focus on the association between histone methylation-modifying enzymes and their controllers, aiming to provide a new perspective on the molecular research and clinical management of GI cancers.
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Affiliation(s)
- Ling Li
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qing Song
- Department of Medical Oncology, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, Jiangsu 215007, China
| | - Jing Zhou
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Liver Disease Department of Integrative Medicine, Ningbo No.2 Hospital, Ningbo, Zhejiang 315000, China.
| | - Qing Ji
- Department of Medical Oncology & Cancer Institute of Integrative Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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9
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Wang XY, Li HM, Xia R, Li X, Zhang X, Jin TZ, Zhang HS. KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner. Mol Cell Biochem 2024; 479:915-928. [PMID: 37249813 DOI: 10.1007/s11010-023-04777-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/21/2023] [Indexed: 05/31/2023]
Abstract
Despite recent advances have been made in clinical treatments of breast cancer, the general prognosis of patients remains poor. Therefore, it is imperative to develop a more effective therapeutic strategy. Lysine demethylase 4B (KDM4B) has been reported to participate in breast cancer development recently, but its exact biological role in breast cancer remains unclear. Here, we observed that KDM4B was down-regulated in human primary BRCA tissues and the low levels of KDM4B expression were correlated with poor survival. Gain- and loss-of-function experiments showed that KDM4B inhibited the proliferation and metastasis of breast cancer cells. Besides, knockdown of KDM4B promoted the epithelial-mesenchymal transition (EMT) and cell stemness in breast cancer cells. Mechanistically, KDM4B down-regulates PHGDH by decreasing the enrichment of H3K36me3 on the promoter region of PHGDH. Knockdown of PHGDH could significantly reversed proliferation, migration, EMT, and cell stemness induced by KDM4B silencing in breast cancer cells. Collectively, we propose a model for a KDM4B/PHGDH axis that provides novel insight into breast cancer development, which may serve as a potential factor for predicting prognosis and a therapeutic target for breast cancer.
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Affiliation(s)
- Xin-Yu Wang
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Hong-Ming Li
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Ran Xia
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Xiang Li
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Xing Zhang
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Tong-Zhao Jin
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China
| | - Hong-Sheng Zhang
- Faculty of Environment and Life, Beijing University of Technology, Pingleyuan 100#, District of Chaoyang, Beijing, 100124, China.
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10
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Zhu K, Zhang H, Luan Y, Hu B, Shen T, Ma B, Zhang Z, Zheng X. KDM4C promotes mouse hippocampal neural stem cell proliferation through modulating ApoE expression. FASEB J 2024; 38:e23511. [PMID: 38421303 DOI: 10.1096/fj.202302439r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
KDM4C is implicated in the regulation of cell proliferation, differentiation, and maintenance in various stem cell types. However, its function in neural stem cells (NSCs) remains poorly understood. Therefore, this study aims to investigate the role and regulatory mechanism of KDM4C in NSCs. Primary hippocampal NSCs were isolated from neonatal mice, and both in vivo and in vitro lentivirus-mediated overexpression of KDM4C were induced in these hippocampal NSCs. Staining results revealed a significant increase in BrdU- and Ki-67-positive cells, along with an elevated number of cells in S phases due to KDM4C overexpression. Subsequently, RNA-seq was employed to analyze gene expression changes following KDM4C upregulation. GO enrichment analysis, KEGG analysis, and GSEA highlighted KDM4C-regulated genes associated with development, cell cycle, and neurogenesis. Protein-protein interaction analysis uncovered that ApoE protein interacts with several genes (top 10 upregulated and downregulated) regulated by KDM4C. Notably, knocking down ApoE mitigated the proliferative effect induced by KDM4C overexpression in NSCs. Our study demonstrates that KDM4C overexpression significantly upregulates ApoE expression, ultimately promoting proliferation in mouse hippocampal NSCs. These findings provide valuable insights into the molecular mechanisms governing neurodevelopment, with potential implications for therapeutic strategies in neurological disorders.
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Affiliation(s)
- Kun Zhu
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hanyue Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Yan Luan
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Baoqi Hu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Tu Shen
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
- The Medical Services Section, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bo Ma
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhichao Zhang
- Institute of Neurobiology, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiaoyan Zheng
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Yang G, Li C, Tao F, Liu Y, Zhu M, Du Y, Fei C, She Q, Chen J. The emerging roles of lysine-specific demethylase 4A in cancer: Implications in tumorigenesis and therapeutic opportunities. Genes Dis 2024; 11:645-663. [PMID: 37692513 PMCID: PMC10491877 DOI: 10.1016/j.gendis.2022.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/28/2022] [Indexed: 09/12/2023] Open
Abstract
Lysine-specific demethylase 4 A (KDM4A, also named JMJD2A, KIA0677, or JHDM3A) is a demethylase that can remove methyl groups from histones H3K9me2/3, H3K36me2/3, and H1.4K26me2/me3. Accumulating evidence suggests that KDM4A is not only involved in body homeostasis (such as cell proliferation, migration and differentiation, and tissue development) but also associated with multiple human diseases, especially cancers. Recently, an increasing number of studies have shown that pharmacological inhibition of KDM4A significantly attenuates tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. Although there are several reviews on the roles of the KDM4 subfamily in cancer development and therapy, all of them only briefly introduce the roles of KDM4A in cancer without systematically summarizing the specific mechanisms of KDM4A in various physiological and pathological processes, especially in tumorigenesis, which greatly limits advances in the understanding of the roles of KDM4A in a variety of cancers, discovering targeted selective KDM4A inhibitors, and exploring the adaptive profiles of KDM4A antagonists. Herein, we present the structure and functions of KDM4A, simply outline the functions of KDM4A in homeostasis and non-cancer diseases, summarize the role of KDM4A and its distinct target genes in the development of a variety of cancers, systematically classify KDM4A inhibitors, summarize the difficulties encountered in the research of KDM4A and the discovery of related drugs, and provide the corresponding solutions, which would contribute to understanding the recent research trends on KDM4A and advancing the progression of KDM4A as a drug target in cancer therapy.
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Affiliation(s)
- Guanjun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Changyun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Fan Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yanjun Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Minghui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yu Du
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Fei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Qiusheng She
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan 467044, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, Zhejiang 315211, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, Ningbo, Zhejiang 315211, China
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Jayawickrama SM, Ranaweera PM, Pradeep RGGR, Jayasinghe YA, Senevirathna K, Hilmi AJ, Rajapakse RMG, Kanmodi KK, Jayasinghe RD. Developments and future prospects of personalized medicine in head and neck squamous cell carcinoma diagnoses and treatments. Cancer Rep (Hoboken) 2024; 7:e2045. [PMID: 38522008 PMCID: PMC10961052 DOI: 10.1002/cnr2.2045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Precision healthcare has entered a new era because of the developments in personalized medicine, especially in the diagnosis and treatment of head and neck squamous cell carcinoma (HNSCC). This paper explores the dynamic landscape of personalized medicine as applied to HNSCC, encompassing both current developments and future prospects. RECENT FINDINGS The integration of personalized medicine strategies into HNSCC diagnosis is driven by the utilization of genetic data and biomarkers. Epigenetic biomarkers, which reflect modifications to DNA that can influence gene expression, have emerged as valuable indicators for early detection and risk assessment. Treatment approaches within the personalized medicine framework are equally promising. Immunotherapy, gene silencing, and editing techniques, including RNA interference and CRISPR/Cas9, offer innovative means to modulate gene expression and correct genetic aberrations driving HNSCC. The integration of stem cell research with personalized medicine presents opportunities for tailored regenerative approaches. The synergy between personalized medicine and technological advancements is exemplified by artificial intelligence (AI) and machine learning (ML) applications. These tools empower clinicians to analyze vast datasets, predict patient responses, and optimize treatment strategies with unprecedented accuracy. CONCLUSION The developments and prospects of personalized medicine in HNSCC diagnosis and treatment offer a transformative approach to managing this complex malignancy. By harnessing genetic insights, biomarkers, immunotherapy, gene editing, stem cell therapies, and advanced technologies like AI and ML, personalized medicine holds the key to enhancing patient outcomes and ushering in a new era of precision oncology.
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Affiliation(s)
| | | | | | | | - Kalpani Senevirathna
- Centre for Research in Oral Cancer, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
| | | | | | - Kehinde Kazeem Kanmodi
- School of DentistryUniversity of RwandaKigaliRwanda
- Faculty of DentistryUniversity of PuthisastraPhnom PenhCambodia
- Cephas Health Research Initiative IncIbadanNigeria
- School of Health and Life SciencesTeesside UniversityMiddlesbroughUK
| | - Ruwan Duminda Jayasinghe
- Centre for Research in Oral Cancer, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
- Faculty of DentistryUniversity of PuthisastraPhnom PenhCambodia
- School of Health and Life SciencesTeesside UniversityMiddlesbroughUK
- Department of Oral Medicine and Periodontology, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
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13
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Chen H, Fang X, Shao J, Zhang Q, Xu L, Chen J, Mei Y, Jiang M, Wang Y, Li Z, Chen Z, Chen Y, Yu C, Ma L, Zhang P, Zhang T, Liao Y, Lv Y, Wang X, Yang L, Fu Y, Chen D, Jiang L, Yan F, Lu W, Chen G, Shen H, Wang J, Wang C, Liang T, Han X, Wang Y, Guo G. Pan-Cancer Single-Nucleus Total RNA Sequencing Using snHH-Seq. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304755. [PMID: 38010945 PMCID: PMC10837386 DOI: 10.1002/advs.202304755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Indexed: 11/29/2023]
Abstract
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis.Therefore, a high-throughput and high-sensitivity method called snHH-seq is developed, which combines random primers and a preindex strategy in the droplet microfluidic platform. This innovative method allows for the detection of total RNA in single nuclei from clinically frozen samples. A robust pipeline to facilitate the analysis of full-length RNA-seq data is also established. snHH-seq is applied to more than 730 000 single nuclei from 32 patients with various tumor types. The pan-cancer study enables it to comprehensively profile data on the tumor transcriptome, including expression levels, mutations, splicing patterns, clone dynamics, etc. New malignant cell subclusters and exploring their specific function across cancers are identified. Furthermore, the malignant status of epithelial cells is investigated among different cancer types with respect to mutation and splicing patterns. The ability to detect full-length RNA at the single-nucleus level provides a powerful tool for studying complex biological systems and has broad implications for understanding tumor pathology.
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Affiliation(s)
- Haide Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- M20 Genomics, Hangzhou, 311121, China
| | - Xiunan Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Jikai Shao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Xu
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | | | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Yuting Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhouyang Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Yang Chen
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
- The Second Clinical Medical College of Zhejiang Chinese Medical University Hangzhou, Hangzhou, 310053, China
| | - Chengxuan Yu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
| | | | - Yuan Liao
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- M20 Genomics, Hangzhou, 311121, China
| | | | - Xueyi Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Daobao Chen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Liming Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Wei Lu
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, Zhejiang Provincial Clinical Research Center for Cancer, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, 310009, China
| | - Huahao Shen
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
| | - Changchun Wang
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology, Hangzhou, 310022, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310006, China
- The Innovation Center for the Study of Pancreatic Diseases of Zhejiang Province, Hangzhou, 310006, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongcheng Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310006, China
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14
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Ni F, Tang H, Cheng S, Yu Y, Yuan Z, Chen Y, Zhang E, Wang X. KDM4B: A promising oncology therapeutic target. Cancer Sci 2024; 115:8-16. [PMID: 37923555 PMCID: PMC10823266 DOI: 10.1111/cas.16005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
Epigenetic modifications are significant in tumor pathogenesis, wherein the process of histone demethylation is indispensable for regulating gene transcription, apoptosis, DNA replication, and repair of damaged DNA. The lysine demethylases (KDMs) serve an essential role in the aforementioned processes, with particular emphasis on the KDM4 family, also referred to as JMJD2. Multiple studies have underscored the significance of the KDM4 family in the regulation of various biological processes including, but not limited to, the cell cycle, DNA repair mechanisms, signaling pathways, and the progression of tumor formation. Nevertheless, it is imperative to elucidate the underlying mechanism of KDM4B, which belongs to the KDM4 gene family. This review presents a comprehensive examination of the structure, mechanism, and function of KDM4B, as well as a critical analysis of the current body of research pertaining to its involvement in tumorigenesis and development. Furthermore, this review explores the potential therapeutic strategies that specifically target KDM4B.
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Affiliation(s)
- Fangjing Ni
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Heting Tang
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Siteng Cheng
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Yaoyu Yu
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Zhihao Yuan
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Yingfei Chen
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Encheng Zhang
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
| | - Xiang Wang
- Department of Urology, School of Medicine, Shanghai General HospitalShanghai Jiao Tong UniversityShanghaiChina
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15
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Lombino J, Vallone R, Cimino M, Gulotta MR, De Simone G, Morando MA, Sabbatella R, Di Martino S, Fogazza M, Sarno F, Coronnello C, De Rosa M, Cipollina C, Altucci L, Perricone U, Alfano C. In-silico guided chemical exploration of KDM4A fragments hits. Clin Epigenetics 2023; 15:197. [PMID: 38129913 PMCID: PMC10740270 DOI: 10.1186/s13148-023-01613-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Lysine demethylase enzymes (KDMs) are an emerging class of therapeutic targets, that catalyse the removal of methyl marks from histone lysine residues regulating chromatin structure and gene expression. KDM4A isoform plays an important role in the epigenetic dysregulation in various cancers and is linked to aggressive disease and poor clinical outcomes. Despite several efforts, the KDM4 family lacks successful specific molecular inhibitors. RESULTS Herein, starting from a structure-based fragments virtual screening campaign we developed a synergic framework as a guide to rationally design efficient KDM4A inhibitors. Commercial libraries were used to create a fragments collection and perform a virtual screening campaign combining docking and pharmacophore approaches. The most promising compounds were tested in-vitro by a Homogeneous Time-Resolved Fluorescence-based assay developed for identifying selective substrate-competitive inhibitors by means of inhibition of H3K9me3 peptide demethylation. 2-(methylcarbamoyl)isonicotinic acid was identified as a preliminary active fragment, displaying inhibition of KDM4A enzymatic activity. Its chemical exploration was deeply investigated by computational and experimental approaches which allowed a rational fragment growing process. The in-silico studies guided the development of derivatives designed as expansion of the primary fragment hit and provided further knowledge on the structure-activity relationship. CONCLUSIONS Our study describes useful insights into key ligand-KDM4A protein interaction and provides structural features for the development of successful selective KDM4A inhibitors.
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Affiliation(s)
- Jessica Lombino
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy
- C4T S.r.l., Colosseum Combinatorial Chemistry Center, 00133, Rome, Italy
| | - Rosario Vallone
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Maura Cimino
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | | | - Giada De Simone
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Maria Agnese Morando
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Raffaele Sabbatella
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy
| | | | - Mario Fogazza
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
- Axxam SpA, 20091, Bresso, MI, Italy
| | - Federica Sarno
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli", 80100, Naples, Italy
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713, Groningen, GZ, The Netherlands
| | | | - Maria De Rosa
- Medicinal Chemistry Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Chiara Cipollina
- Target Identification and Screening Group, Fondazione Ri.MED, 90100, Palermo, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli", 80100, Naples, Italy
- BIOGEM, 83031, Ariano Irpino, AV, Italy
- IEOS-CNR, 80100, Naples, Italy
| | - Ugo Perricone
- Molecular Informatics Group, Fondazione Ri.MED, 90100, Palermo, Italy.
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, 90100, Palermo, Italy.
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16
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Feliciello I, Ugarković Đ. Alpha Satellite DNA in Targeted Drug Therapy for Prostate Cancer. Int J Mol Sci 2023; 24:15585. [PMID: 37958565 PMCID: PMC10648476 DOI: 10.3390/ijms242115585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Prostate cancer is the most common solid cancer in men and, despite the development of many new therapies, metastatic castration-resistant prostate cancer still remains a deadly disease. Therefore, novel concepts for the treatment of metastatic prostate cancer are needed. In our opinion, the role of the non-coding part of the genome, satellite DNA in particular, has been underestimated in relation to diseases such as cancer. Here, we hypothesise that this part of the genome should be considered as a potential target for the development of new drugs. Specifically, we propose a novel concept directed at the possible treatment of metastatic prostate cancer that is mostly based on epigenetics. Namely, metastatic prostate cancer is characterized by the strongly induced transcription of alpha satellite DNA located in pericentromeric heterochromatin and, according to our hypothesis, the stable controlled transcription of satellite DNA might be important in terms of the control of disease development. This can be primarily achieved through the epigenetic regulation of pericentromeric heterochromatin by using specific enzymes as well as their activators/inhibitors that could act as potential anti-prostate cancer drugs. We believe that our concept is innovative and should be considered in the potential treatment of prostate cancer in combination with other more conventional therapies.
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Affiliation(s)
- Isidoro Feliciello
- Medical School, Department of Clinical Medicine and Surgery, Universiy of Naples Federico II, 80131 Naples, Italy
| | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
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17
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Gu R, Kim TD, Song H, Sui Y, Shin S, Oh S, Janknecht R. SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A. JCI Insight 2023; 8:e164990. [PMID: 37870957 PMCID: PMC10619491 DOI: 10.1172/jci.insight.164990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2023] [Indexed: 10/25/2023] Open
Abstract
The histone demethylase JMJD2A/KDM4A facilitates prostate cancer development, yet how JMJD2A function is regulated has remained elusive. Here, we demonstrate that SET7/9-mediated methylation on 6 lysine residues modulated JMJD2A. Joint mutation of these lysine residues suppressed JMJD2A's ability to stimulate the MMP1 matrix metallopeptidase promoter upon recruitment by the ETV1 transcription factor. Mutation of just 3 methylation sites (K505, K506, and K507) to arginine residues (3xR mutation) was sufficient to maximally reduce JMJD2A transcriptional activity and also decreased its binding to ETV1. Introduction of the 3xR mutation into DU145 prostate cancer cells reduced in vitro growth and invasion and also severely compromised tumorigenesis. Consistently, the 3xR genotype caused transcriptome changes related to cell proliferation and invasion pathways, including downregulation of MMP1 and the NPM3 nucleophosmin/nucleoplasmin gene. NPM3 downregulation phenocopied and its overexpression rescued, to a large degree, the 3xR mutation in DU145 cells, suggesting that NPM3 was a seminal downstream effector of methylated JMJD2A. Moreover, we found that NPM3 was overexpressed in prostate cancer and might be indicative of disease aggressiveness. SET7/9-mediated lysine methylation of JMJD2A may aggravate prostate tumorigenesis in a manner dependent on NPM3, implying that the SET7/9→JMJD2A→NPM3 axis could be targeted for therapy.
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Affiliation(s)
| | | | | | | | - Sook Shin
- Department of Cell Biology
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Sangphil Oh
- Department of Cell Biology
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Ralf Janknecht
- Department of Cell Biology
- Department of Pathology, and
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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18
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He Y, Liu T. Oxidized low-density lipoprotein regulates macrophage polarization in atherosclerosis. Int Immunopharmacol 2023; 120:110338. [PMID: 37210916 DOI: 10.1016/j.intimp.2023.110338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Atherosclerosis is the pathological basis of acute cardiovascular and cerebrovascular diseases. Oxidized LDL has been recognized as a major atherogenic factor in the vessel wall for decades. A growing body of evidence suggests that oxidized LDL modulates macrophage phenotypes in atherosclerosis. This article reviews the research progress on the regulation of macrophage polarization by oxidized LDL. Mechanistically, oxidized LDL induces macrophage polarization via cell signaling, metabolic reprogramming, epigenetic regulation, and intercellular regulation. This review is expected to provide new targets for the treatment of atherosclerosis.
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Affiliation(s)
- Yonghang He
- The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808, China
| | - Tingting Liu
- The First Dongguan Affiliated Hospital, Guangdong Medical University, No. 42 Jiaoping Road, Tangxia Town, Dongguan City, Guangdong Province 523710, China; The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808, China.
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19
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Bonnici J, Oueini R, Salah E, Johansson C, Schofield CJ, Kawamura A. The catalytic domains of all human KDM5 JmjC demethylases catalyse N-methyl arginine demethylation. FEBS Lett 2023; 597:933-946. [PMID: 36700827 PMCID: PMC10952680 DOI: 10.1002/1873-3468.14586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023]
Abstract
The demethylation of Nε -methyllysine residues on histones by Jumonji-C lysine demethylases (JmjC-KDMs) has been established. A subset of JmjC-KDMs has also been reported to have Nω -methylarginine residue demethylase (RDM) activity. Here, we describe biochemical screening studies, showing that the catalytic domains of all human KDM5s (KDM5A-KDM5D), KDM4E and, to a lesser extent, KDM4A/D, have both KDM and RDM activities with histone peptides. Ras GTPase-activating protein-binding protein 1 peptides were shown to be RDM substrates for KDM5C/D. No RDM activity was observed with KDM1A and the other JmjC-KDMs tested. The results highlight the potential of JmjC-KDMs to catalyse reactions other than Nε -methyllysine demethylation. Although our study is limited to peptide fragments, the results should help guide biological studies investigating JmjC functions.
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Affiliation(s)
- Joanna Bonnici
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
| | - Razanne Oueini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Catrine Johansson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Botnar Research Centre, NIHR Oxford Biomedical Research UnitUniversity of OxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
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20
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Lee YT, Tan YJ, Oon CE. Benzimidazole and its derivatives as cancer therapeutics: The potential role from traditional to precision medicine. Acta Pharm Sin B 2023; 13:478-497. [PMID: 36873180 PMCID: PMC9978992 DOI: 10.1016/j.apsb.2022.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/11/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Cancer is the second leading cause of mortality globally which remains a continuing threat to human health today. Drug insensitivity and resistance are critical hurdles in cancer treatment; therefore, the development of new entities targeting malignant cells is considered a high priority. Targeted therapy is the cornerstone of precision medicine. The synthesis of benzimidazole has garnered the attention of medicinal chemists and biologists due to its remarkable medicinal and pharmacological properties. Benzimidazole has a heterocyclic pharmacophore, which is an essential scaffold in drug and pharmaceutical development. Multiple studies have demonstrated the bioactivities of benzimidazole and its derivatives as potential anticancer therapeutics, either through targeting specific molecules or non-gene-specific strategies. This review provides an update on the mechanism of actions of various benzimidazole derivatives and the structure‒activity relationship from conventional anticancer to precision healthcare and from bench to clinics.
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21
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Liao C, Liu X, Zhang C, Zhang Q. Tumor hypoxia: From basic knowledge to therapeutic implications. Semin Cancer Biol 2023; 88:172-186. [PMID: 36603793 PMCID: PMC9929926 DOI: 10.1016/j.semcancer.2022.12.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/07/2022] [Accepted: 12/31/2022] [Indexed: 01/04/2023]
Abstract
Diminished oxygen availability, termed hypoxia, within solid tumors is one of the most common characteristics of cancer. Hypoxia shapes the landscape of the tumor microenvironment (TME) into a pro-tumorigenic and pro-metastatic niche through arrays of pathological alterations such as abnormal vasculature, altered metabolism, immune-suppressive phenotype, etc. In addition, emerging evidence suggests that limited efficacy or the development of resistance towards antitumor therapy may be largely due to the hypoxic TME. This review will focus on summarizing the knowledge about the molecular machinery that mediates the hypoxic cellular responses and adaptations, as well as highlighting the effects and consequences of hypoxia, especially for angiogenesis regulation, cellular metabolism alteration, and immunosuppressive response within the TME. We also outline the current advances in novel therapeutic implications through targeting hypoxia in TME. A deep understanding of the basics and the role of hypoxia in the tumor will help develop better therapeutic avenues in cancer treatment.
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Affiliation(s)
- Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599, USA
| | - Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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22
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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23
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Jiang Y, Liu L, Yang ZQ. KDM4 Demethylases: Structure, Function, and Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:87-111. [PMID: 37751137 DOI: 10.1007/978-3-031-38176-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
KDM4 histone demethylases mainly catalyze the removal of methyl marks from H3K9 and H3K36 to epigenetically regulate chromatin structure and gene expression. KDM4 expression is strictly regulated to ensure proper function in a myriad of biological processes, including transcription, cellular proliferation and differentiation, DNA damage repair, immune response, and stem cell self-renewal. Aberrant expression of KDM4 demethylase has been documented in many types of blood and solid tumors, and thus, KDM4s represent promising therapeutic targets. In this chapter, we summarize the current knowledge of the structures and regulatory mechanisms of KDM4 proteins and our understanding of their alterations in human pathological processes with a focus on development and cancer. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Lanxin Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA.
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24
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Kumar A, Emdad L, Fisher PB, Das SK. Targeting epigenetic regulation for cancer therapy using small molecule inhibitors. Adv Cancer Res 2023; 158:73-161. [PMID: 36990539 DOI: 10.1016/bs.acr.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Cancer cells display pervasive changes in DNA methylation, disrupted patterns of histone posttranslational modification, chromatin composition or organization and regulatory element activities that alter normal programs of gene expression. It is becoming increasingly clear that disturbances in the epigenome are hallmarks of cancer, which are targetable and represent attractive starting points for drug creation. Remarkable progress has been made in the past decades in discovering and developing epigenetic-based small molecule inhibitors. Recently, epigenetic-targeted agents in hematologic malignancies and solid tumors have been identified and these agents are either in current clinical trials or approved for treatment. However, epigenetic drug applications face many challenges, including low selectivity, poor bioavailability, instability and acquired drug resistance. New multidisciplinary approaches are being designed to overcome these limitations, e.g., applications of machine learning, drug repurposing, high throughput virtual screening technologies, to identify selective compounds with improved stability and better bioavailability. We provide an overview of the key proteins that mediate epigenetic regulation that encompass histone and DNA modifications and discuss effector proteins that affect the organization of chromatin structure and function as well as presently available inhibitors as potential drugs. Current anticancer small-molecule inhibitors targeting epigenetic modified enzymes that have been approved by therapeutic regulatory authorities across the world are highlighted. Many of these are in different stages of clinical evaluation. We also assess emerging strategies for combinatorial approaches of epigenetic drugs with immunotherapy, standard chemotherapy or other classes of agents and advances in the design of novel epigenetic therapies.
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25
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Sui Y, Jiang H, Kellogg CM, Oh S, Janknecht R. Promotion of colorectal cancer by transcription factor BHLHE40 involves upregulation of ADAM19 and KLF7. Front Oncol 2023; 13:1122238. [PMID: 36890812 PMCID: PMC9986587 DOI: 10.3389/fonc.2023.1122238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
BHLHE40 is a transcription factor, whose role in colorectal cancer has remained elusive. We demonstrate that the BHLHE40 gene is upregulated in colorectal tumors. Transcription of BHLHE40 was jointly stimulated by the DNA-binding ETV1 protein and two associated histone demethylases, JMJD1A/KDM3A and JMJD2A/KDM4A, which were shown to also form complexes on their own and whose enzymatic activity was required for BHLHE40 upregulation. Chromatin immunoprecipitation assays revealed that ETV1, JMJD1A and JMJD2A interacted with several regions within the BHLHE40 gene promoter, suggesting that these three factors directly control BHLHE40 transcription. BHLHE40 downregulation suppressed both growth and clonogenic activity of human HCT116 colorectal cancer cells, strongly hinting at a pro-tumorigenic role of BHLHE40. Through RNA sequencing, the transcription factor KLF7 and the metalloproteinase ADAM19 were identified as putative BHLHE40 downstream effectors. Bioinformatic analyses showed that both KLF7 and ADAM19 are upregulated in colorectal tumors as well as associated with worse survival and their downregulation impaired HCT116 clonogenic activity. In addition, ADAM19, but not KLF7, downregulation reduced HCT116 cell growth. Overall, these data have revealed a ETV1/JMJD1A/JMJD2A→BHLHE40 axis that may stimulate colorectal tumorigenesis through upregulation of genes such as KLF7 and ADAM19, suggesting that targeting this axis represents a potential novel therapeutic avenue.
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Affiliation(s)
- Yuan Sui
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Hanlin Jiang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Collyn M Kellogg
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Ralf Janknecht
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Stephenson Cancer Center, Oklahoma City, OK, United States
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26
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Sogutlu F, Pekerbas M, Biray Avci C. Epigenetic signatures in gastric cancer: current knowledge and future perspectives. Expert Rev Mol Diagn 2022; 22:1063-1075. [PMID: 36522183 DOI: 10.1080/14737159.2022.2159381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Gastric cancer (GC) is the fifth most common malignancy in the world and accounts for 7.7% of all cancer-related deaths. Early diagnosis of GC is critical in terms of prognosis, and aberrations at the molecular level, especially epigenetic alterations, manifest much earlier than histological findings. In recent years, there has been a great deal of research on the epigenomic profile of GC, and epigenetic alterations seem to play a more important role than genetic factors. With the introduction of epigenetic drugs into clinical use in the last decade, the importance of the epigenetic background of GC has increased considerably. AREAS COVERED In this review, we summarize the role of methylation changes, histone modifications, and non-coding RNAs in the pathogenesis of GC and how these signatures can be used as diagnostic and therapeutic targets in clinical management. EXPERT OPINION Epigenetic alterations take place before most genetic aberrations observed in GC and may have an initiating role in the pathogenesis of GC. They can be used as biomarkers in risk calculation, early diagnosis, and evaluation of prognosis of GC, as well as treatment targets.
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Affiliation(s)
- Fatma Sogutlu
- Department of Medical Biology, Faculty of Medicine, Ege University, Bornova, 35100, Izmir, Turkey
| | - Mert Pekerbas
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, 35100, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Bornova, 35100, Izmir, Turkey
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27
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Reader J, Opperman DFL, van der Watt ME, Theron A, Leshabane M, da Rocha S, Turner J, Garrabrant K, Piña I, Mills C, Woster PM, Birkholtz L. New Transmission-Selective Antimalarial Agents through Hit-to-Lead Optimization of 2-([1,1'-Biphenyl]-4-carboxamido)benzoic Acid Derivatives. Chembiochem 2022; 23:e202200427. [PMID: 36106425 PMCID: PMC10946866 DOI: 10.1002/cbic.202200427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/14/2022] [Indexed: 11/12/2022]
Abstract
Malaria elimination requires multipronged approaches, including the application of antimalarial drugs able to block human-to-mosquito transmission of malaria parasites. The transmissible gametocytes of Plasmodium falciparum seem to be highly sensitive towards epidrugs, particularly those targeting demethylation of histone post-translational marks. Here, we report exploration of compounds from a chemical library generated during hit-to-lead optimization of inhibitors of the human histone lysine demethylase, KDM4B. Derivatives of 2-([1,1'-biphenyl]-4-carboxamido) benzoic acid, around either the amide or a sulfonamide linker backbone (2-(arylcarboxamido)benzoic acid, 2-carboxamide (arylsulfonamido)benzoic acid and N-(2-(1H-tetrazol-5-yl)phenyl)-arylcarboxamide), showed potent activity towards late-stage gametocytes (stage IV/V) of P. falciparum, with the most potent compound reaching single digit nanomolar activity. Structure-activity relationship trends were evident and frontrunner compounds also displayed microsomal stability and favourable solubility profiles. Simplified synthetic routes support further derivatization of these compounds for further development of these series as malaria transmission-blocking agents.
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Affiliation(s)
- Janette Reader
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Daniel F. L. Opperman
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Mariëtte E. van der Watt
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
- School of Health Systems and Public HealthUniversity of Pretoria, HatfieldPretoria0028South Africa
| | - Anjo Theron
- Next Generation HealthCouncil for Scientific and Industrial ResearchPretoria0001South Africa
| | - Meta Leshabane
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Shanté da Rocha
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
| | - Jonathan Turner
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Kathleen Garrabrant
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Ivett Piña
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Catherine Mills
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Patrick M. Woster
- Department of Drug Discovery and Biomedical SciencesMedical University of South CarolinaCharlestonSC 29425USA
| | - Lyn‐Marié Birkholtz
- Department of BiochemistryGenetics and MicrobiologyInstitute for Sustainable Malaria ControlUniversity of PretoriaLynnwood RoadPretoria0028South Africa
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28
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Yang Y, Feng K, Yuan L, Liu Y, Zhang M, Guo K, Yin Z, Wang W, Zhou S, Sun H, Yan K, Yan X, Wang X, Duan Y, Hu Y, Han J. Compound Danshen Dripping Pill inhibits hypercholesterolemia/atherosclerosis-induced heart failure in ApoE and LDLR dual deficient mice via multiple mechanisms. Acta Pharm Sin B 2022; 13:1036-1052. [PMID: 36970211 PMCID: PMC10031343 DOI: 10.1016/j.apsb.2022.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/19/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Heart failure is the leading cause of death worldwide. Compound Danshen Dripping Pill (CDDP) or CDDP combined with simvastatin has been widely used to treat patients with myocardial infarction and other cardiovascular diseases in China. However, the effect of CDDP on hypercholesterolemia/atherosclerosis-induced heart failure is unknown. We constructed a new model of heart failure induced by hypercholesterolemia/atherosclerosis in apolipoprotein E (ApoE) and LDL receptor (LDLR) dual deficient (ApoE-/-LDLR-/-) mice and investigated the effect of CDDP or CDDP plus a low dose of simvastatin on the heart failure. CDDP or CDDP plus a low dose of simvastatin inhibited heart injury by multiple actions including anti-myocardial dysfunction and anti-fibrosis. Mechanistically, both Wnt and lysine-specific demethylase 4A (KDM4A) pathways were significantly activated in mice with heart injury. Conversely, CDDP or CDDP plus a low dose of simvastatin inhibited Wnt pathway by markedly up-regulating expression of Wnt inhibitors. While the anti-inflammation and anti-oxidative stress by CDDP were achieved by inhibiting KDM4A expression and activity. In addition, CDDP attenuated simvastatin-induced myolysis in skeletal muscle. Taken together, our study suggests that CDDP or CDDP plus a low dose of simvastatin can be an effective therapy to reduce hypercholesterolemia/atherosclerosis-induced heart failure.
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Affiliation(s)
- Yanfang Yang
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin 300071, China
| | - Ke Feng
- Department of Physiology, Binzhou Medical University, Yantai 264003, China
| | - Liying Yuan
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin 300071, China
| | - Yuxin Liu
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin 300071, China
| | - Mengying Zhang
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
| | - Kaimin Guo
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
| | - Zequn Yin
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, China
| | - Wenjia Wang
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
| | - Shuiping Zhou
- The State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tasly Academy, Tasly Holding Group Co., Ltd., Tianjin 300410, China
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300410, China
| | - He Sun
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
- The State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tasly Academy, Tasly Holding Group Co., Ltd., Tianjin 300410, China
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300410, China
| | - Kaijing Yan
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
- The State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tasly Academy, Tasly Holding Group Co., Ltd., Tianjin 300410, China
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300410, China
| | - Xijun Yan
- The State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tasly Academy, Tasly Holding Group Co., Ltd., Tianjin 300410, China
- Tasly Pharmaceutical Group Co., Ltd., Tianjin 300410, China
| | - Xuerui Wang
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, China
| | - Yajun Duan
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, China
- Department of Cardiology, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, China
- Corresponding authors. Tel.: +86 17352916451 (Yajun Duan); +86 18522755110 (Yunhui Hu); +86 13920545670 (Jihong Han).
| | - Yunhui Hu
- Cloudphar Pharmaceuticals Co., Ltd., Shenzhen 518000, China
- Corresponding authors. Tel.: +86 17352916451 (Yajun Duan); +86 18522755110 (Yunhui Hu); +86 13920545670 (Jihong Han).
| | - Jihong Han
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials of Ministry of Education, Nankai University, Tianjin 300071, China
- Key Laboratory of Metabolism and Regulation for Major Diseases of Anhui Higher Education Institutes, Hefei University of Technology, Hefei 230009, China
- Corresponding authors. Tel.: +86 17352916451 (Yajun Duan); +86 18522755110 (Yunhui Hu); +86 13920545670 (Jihong Han).
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29
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Proteomic and phosphoproteomic landscapes of acute myeloid leukemia. Blood 2022; 140:1533-1548. [PMID: 35895896 PMCID: PMC9523374 DOI: 10.1182/blood.2022016033] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023] Open
Abstract
We have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow-derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate-dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA-initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.
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30
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Diao W, Zheng J, Li Y, Wang J, Xu S. Targeting histone demethylases as a potential cancer therapy (Review). Int J Oncol 2022; 61:103. [PMID: 35801593 DOI: 10.3892/ijo.2022.5393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/15/2022] [Indexed: 11/06/2022] Open
Abstract
Post‑translational modifications of histones by histone demethylases have an important role in the regulation of gene transcription and are implicated in cancers. Recently, the family of lysine (K)‑specific demethylase (KDM) proteins, referring to histone demethylases that dynamically regulate histone methylation, were indicated to be involved in various pathways related to cancer development. To date, numerous studies have been conducted to explore the effects of KDMs on cancer growth, metastasis and drug resistance, and a majority of KDMs have been indicated to be oncogenes in both leukemia and solid tumors. In addition, certain KDM inhibitors have been developed and have become the subject of clinical trials to explore their safety and efficacy in cancer therapy. However, most of them focus on hematopoietic malignancy. This review summarizes the effects of KDMs on tumor growth, drug resistance and the current status of KDM inhibitors in clinical trials.
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Affiliation(s)
- Wenfei Diao
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Jiabin Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Yong Li
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Junjiang Wang
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Songhui Xu
- Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
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31
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Ma X, Lu J, Yang P, Zhang Z, Huang B, Li R, Ye R. 8-Hydroxyquinoline-modified ruthenium(II) polypyridyl complexes for JMJD inhibition and photodynamic antitumor therapy. Dalton Trans 2022; 51:13902-13909. [PMID: 36040403 DOI: 10.1039/d2dt01765b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As an ideal scaffold for metal ion chelation, 8-hydroxyquinoline (8HQ) can chelate different metal ions, such as Fe2+, Cu2+, Zn2+, etc. Here, by integrating 8HQ with a ruthenium(II) polypyridyl moiety, two Ru(II)-8HQ complexes (Ru1 and Ru2), [Ru(N-N)2L](PF6)2 (L = 2-(1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)quinolin-8-ol; N-N: 2,2'-bipyridine (bpy, in Ru1), 1,10-phenanthroline (phen, in Ru2)) were designed and synthesized. In both complexes, ligand L is an 8HQ derivative designed to chelate the cofactor Fe2+ of jumonji C domain-containing demethylase (JMJD). As expected, Ru1 and Ru2 could inhibit the activity of JMJD by chelating the key cofactor Fe2+ of JMJD, resulting in the upregulation of histone-methylation levels in human lung cancer (A549) cells, and the upregulation was more pronounced under light conditions. In addition, MTT data showed that Ru1 and Ru2 exhibited lower dark toxicity, and light irradiation could significantly enhance their antitumor activity. The marked photodynamic activities of Ru1 and Ru2 could induce the elevation of reactive oxygen species (ROS), depolarization of mitochondrial membrane potential (MMP), and activation of caspases. These mechanistic studies indicated that Ru1 and Ru2 could induce apoptosis through the combination of JMJD inhibitory and PDT activities, thereby achieving dual antitumor effects.
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Affiliation(s)
- Xiurong Ma
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
| | - Junjian Lu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
| | - Peixin Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
| | - Zheng Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
| | - Bo Huang
- Faculty of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650500, P. R. China.
| | - Rongtao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
| | - Ruirong Ye
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P. R. China.
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32
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Papadakos SP, Tsagkaris C, Papadakis M, Papazoglou AS, Moysidis DV, Zografos CG, Theocharis S. Angiogenesis in gastrointestinal stromal tumors: From bench to bedside. World J Gastrointest Oncol 2022; 14:1469-1477. [PMID: 36160752 PMCID: PMC9412926 DOI: 10.4251/wjgo.v14.i8.1469] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/15/2022] [Accepted: 07/17/2022] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are rare neoplasms with an estimated incidence from 0.78 to 1-1.5 patients per 100000. They most commonly occur in the elderly during the eighth decade of life affecting predominantly the stomach, but also the small intestine, the omentum, mesentery and rectosigmoid. The available treatments for GIST are associated with a significant rate of recurrent disease and adverse events. Thorough understanding of GIST’s pathophysiology and translation of this knowledge into novel regimens or drug repurposing is essential to counter this challenge. The present review summarizes the existing evidence about the role of angiogenesis in GIST’s development and progression and discusses its clinical underpinnings.
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Affiliation(s)
- Stavros P Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, Athens 10679, Greece
| | | | - Marios Papadakis
- University Hospital Witten-Herdecke, University of Witten-Herdecke, Wuppertal 42283, Germany
| | - Andreas S Papazoglou
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki 54636, Greece
| | - Dimitrios V Moysidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki 54636, Greece
| | - Constantinos G Zografos
- First Department of Surgery, Athens Medical School, National and Kapodistrian University of Athens, Laikon General Hospital, Athens 11527, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, University of Athens, Athens 11527, Greece
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33
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SUMO Modification of Histone Demethylase KDM4A in Kaposi's Sarcoma-Associated Herpesvirus-Induced Primary Effusion Lymphoma. J Virol 2022; 96:e0075522. [PMID: 35914074 PMCID: PMC9400493 DOI: 10.1128/jvi.00755-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Primary effusion lymphoma (PEL) is a fatal B-cell lymphoma caused by Kaposi’s sarcoma-associated herpesvirus (KSHV) infection. Inducing KSHV lytic replication that causes the death of host cells is an attractive treatment approach for PE; however, combination therapy inhibiting viral production is frequently needed to improve its outcomes. We have previously shown that the KSHV lytic protein K-bZIP can SUMOylate histone lysine demethylase 4A (KDM4A) at lysine 471 (K471) and this SUMOylation is required for virus production upon KSHV reactivation. Here, we demonstrate that SUMOylation of KDM4A orchestrates PEL cell survival, a major challenge for the success of PEL treatment; and cell movement and angiogenesis, the cell functions contributing to PEL cell extravasation and dissemination. Furthermore, integrated ChIP-seq and RNA-seq analyses identified interleukin-10 (IL-10), an immunosuppressive cytokine, as a novel downstream target of KDM4A. We demonstrate that PEL-induced angiogenesis is dependent on IL-10. More importantly, single-cell RNA sequencing (scRNA-seq) analysis demonstrated that, at the late stage of KSHV reactivation, KDM4A determines the fates of PEL cells, as evidenced by two distinct cell populations; one with less apoptotic signaling expresses high levels of viral genes and the other is exactly opposite, while KDM4A-K417R-expressing cells contain only the apoptotic population with less viral gene expression. Consistently, KDM4A knockout significantly reduced cell viability and virus production in KSHV-reactivated PEL cells. Since inhibiting PEL extravasation and eradicating KSHV-infected PEL cells without increasing viral load provide a strong rationale for treating PEL, this study indicates targeting KDM4A as a promising therapeutic option for treating PEL. IMPORTANCE PEL is an aggressive and untreatable B-cell lymphoma caused by KSHV infection. Therefore, new therapeutic approaches for PEL need to be investigated. Since simultaneous induction of KSHV reactivation and apoptosis can directly kill PEL cells, they have been applied in the treatment of this hematologic malignancy and have made progress. Epigenetic therapy with histone deacetylase (HDAC) inhibitors has been proved to treat PEL. However, the antitumor efficacies of HDAC inhibitors are modest and new approaches are needed. Following our previous report showing that the histone lysine demethylase KDM4A and its SUMOylation are required for lytic reactivation of KSHV in PEL cells, we further investigated its cellular function. Here, we found that SUMOylation of KDM4A is required for the survival, movement, and angiogenesis of lytic KSHV-infected PEL cells. Together with our previous finding showing the importance of KDM4A SUMOylation in viral production, KDM4A can be a potential therapeutic target for PEL.
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34
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Wu Q, Young B, Wang Y, Davidoff AM, Rankovic Z, Yang J. Recent Advances with KDM4 Inhibitors and Potential Applications. J Med Chem 2022; 65:9564-9579. [PMID: 35838529 PMCID: PMC9531573 DOI: 10.1021/acs.jmedchem.2c00680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histone lysine demethylase 4 (KDM4) family plays an important role in regulating gene transcription, DNA repair, and metabolism. The dysregulation of KDM4 functions is associated with many human disorders, including cancer, obesity, and cardiovascular diseases. Selective and potent KDM4 inhibitors may help not only to understand the role of KDM4 in these disorders but also to provide potential therapeutic opportunities. Here, we provide an overview of the field and discuss current status, challenges, and opportunities lying ahead in the development of KDM4-based anticancer therapeutics.
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Affiliation(s)
- Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yan Wang
- Department of Geriatrics and Occupational Disease, Qingdao Central Hospital, Qingdao 266044, China
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163, United States
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35
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Singh S, Abu-Zaid A, Jin H, Fang J, Wu Q, Wang T, Feng H, Quarni W, Shao Y, Maxham L, Abdolvahabi A, Yun MK, Vaithiyalingam S, Tan H, Bowling J, Honnell V, Young B, Guo Y, Bajpai R, Pruett-Miller SM, Grosveld GC, Hatley M, Xu B, Fan Y, Wu G, Chen EY, Chen T, Lewis PW, Rankovic Z, Li Y, Murphy AJ, Easton J, Peng J, Chen X, Wang R, White SW, Davidoff AM, Yang J. Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma. Sci Transl Med 2022; 14:eabq2096. [PMID: 35857643 PMCID: PMC9548378 DOI: 10.1126/scitranslmed.abq2096] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3-Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1+ RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1-governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1+ RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1-related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.
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Affiliation(s)
- Shivendra Singh
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jie Fang
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Tingting Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Helin Feng
- Department of Orthopedics, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Waise Quarni
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ying Shao
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lily Maxham
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Alireza Abdolvahabi
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Protein Technologies Center, Molecular Interaction Analysis, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Haiyan Tan
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Center for Proteomics and Metabolomics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Bowling
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Victoria Honnell
- Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yian Guo
- Department of Biostatistics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richa Bajpai
- Center for Advanced Genome Engineering, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gerard C Grosveld
- Department of Genetics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mark Hatley
- Department of Oncology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Eleanor Y. Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yimei Li
- Department of Biostatistics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew J. Murphy
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - John Easton
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Center for Proteomics and Metabolomics, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Stephen W. White
- Department of Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Andrew M. Davidoff
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Graduate School of Biomedical Sciences, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.,Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave, Suite 500, Memphis, TN 38163, USA
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Li Y, Wang C, Gao H, Gu J, Zhang Y, Zhang Y, Xie M, Cheng X, Yang M, Zhang W, Li Y, He M, Xu H, Zhang H, Ji Q, Ma T, Ding S, Zhao Y, Gao Y. KDM4 inhibitor SD49-7 attenuates leukemia stem cell via KDM4A/MDM2/p21 CIP1 axis. Theranostics 2022; 12:4922-4934. [PMID: 35836814 PMCID: PMC9274755 DOI: 10.7150/thno.71460] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/04/2022] [Indexed: 01/12/2023] Open
Abstract
Rationale: Traditional treatments for leukemia fail to address stem cell drug resistance characterized by epigenetic mediators such as histone lysine-specific demethylase 4 (KDM4). The KDM4 family, which acts as epigenetic regulators inducing histone demethylation during the development and progression of leukemia, lacks specific molecular inhibitors. Methods: The KDM4 inhibitor, SD49-7, was synthesized and purified based on acyl hydrazone Schiff base. The interaction between SD49-7 and KDM4s was monitored in vitro by surface plasma resonance (SPR). In vitro and in vivo biological function experiments were performed to analyze apoptosis, colony-formation, proliferation, differentiation, and cell cycle in cell sub-lines and mice. Molecular mechanisms were demonstrated by RNA-seq, ChIP-seq, RT-qPCR and Western blotting. Results: We found significantly high KDM4A expression levels in several human leukemia subtypes. The knockdown of KDM4s inhibited leukemogenesis in the MLL-AF9 leukemia mouse model but did not affect the survival of normal human hematopoietic cells. We identified SD49-7 as a selective KDM4 inhibitor that impaired the progression of leukemia stem cells (LSCs) in vitro. SD49-7 suppressed leukemia development in the mouse model and patient-derived xenograft model of leukemia. Depletion of KDM4s activated the apoptosis signaling pathway by suppressing MDM2 expression via modulating H3K9me3 levels on the MDM2 promoter region. Conclusion: Our study demonstrates a unique KDM4 inhibitor for LSCs to overcome the resistance to traditional treatment and offers KDM4 inhibition as a promising strategy for resistant leukemia therapy.
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Affiliation(s)
- Yinghui Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Chaoqun Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Huier Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.,Department of Pharmacy, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300192, China
| | - Jiali Gu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yiran Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55901, USA
| | - Min Xie
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Ming Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wenshan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yafang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mei He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Hui Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Hexiao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Qing Ji
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Tianhua Ma
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.,✉ Corresponding authors: Yingdai Gao, E-mail: , +86-022-23909416; Yu Zhao, E-mail: ; Sheng Ding, E-mail:
| | - Yu Zhao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China.,✉ Corresponding authors: Yingdai Gao, E-mail: , +86-022-23909416; Yu Zhao, E-mail: ; Sheng Ding, E-mail:
| | - Yingdai Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.,✉ Corresponding authors: Yingdai Gao, E-mail: , +86-022-23909416; Yu Zhao, E-mail: ; Sheng Ding, E-mail:
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37
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Liu C, Zhou X, Jin J, Zhu Q, Li L, Yin Q, Xu T, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of CD160, ISYNA1 and RAD51B in the Chinese Population. Front Genet 2022; 13:927519. [PMID: 35812748 PMCID: PMC9261985 DOI: 10.3389/fgene.2022.927519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 12/25/2022] Open
Abstract
Recent studies have identified DNA methylation signatures in the white blood cells as potential biomarkers for breast cancer (BC) in the European population. Here, we investigated the association between BC and blood-based methylation of cluster of differentiation 160 (CD160), inositol-3-phosphate synthase 1 (ISYNA1) and RAD51 paralog B (RAD51B) genes in the Chinese population. Peripheral blood samples were collected from two independent case-control studies with a total of 272 sporadic early-stage BC cases (76.5% at stage I&II) and 272 cancer-free female controls. Mass spectrometry was applied to quantitatively measure the levels of DNA methylation. The logistic regression and non-parametric tests were used for the statistical analyses. In contrast to the protective effects reported in European women, we reported the blood-based hypomethylation in CD160, ISYNA1 and RAD51B as risk factors for BC in the Chinese population (CD160_CpG_3, CD160_CpG_4/cg20975414, ISYNA1_CpG_2, RAD51B_CpG_3 and RAD51B_CpG_4; odds ratios (ORs) per -10% methylation ranging from 1.08 to 1.67, p < 0.05 for all). Moreover, hypomethylation of CD160, ISYNA1 and RAD51B was significantly correlated with age, BC subtypes including estrogen receptor (ER)-negative BC tumors, triple negative tumors, BC cases with larger size, advanced stages and more lymph node involvement. Our results supported the report in European women that BC is associated with altered methylation of CD160, ISYNA1 and RAD51B in the peripheral blood, although the effects are opposite in the Chinese population. The difference between the two populations may be due to variant genetic background or life styles, implicating that the validations of epigenetic biomarkers in variant ethnic groups are warranted.
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Affiliation(s)
- Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiajie Zhou
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jialie Jin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiming Yin
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Rongxi Yang,
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Histone Demethylase JMJD2D: A Novel Player in Colorectal and Hepatocellular Cancers. Cancers (Basel) 2022; 14:cancers14122841. [PMID: 35740507 PMCID: PMC9221006 DOI: 10.3390/cancers14122841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Histone demethylase JMJD2D is a multifunctional epigenetic factor coordinating androgen receptor activation, DNA damage repair, DNA replication, cell cycle regulation, and inflammation modulation. JMJD2D is also a well-established epigenetic facilitator in the progression of multiple malignant tumors, especially in colorectal cancer (CRC) and hepatocellular cancer (HCC). This review aims to summarize the mechanisms of JMJD2D in promoting CRC and HCC progression, which provides novel ideas for targeting JMJD2D in oncotherapy. JMJD2D promotes gene transcription by reducing H3K9 methylation and serves as a coactivator to enhance the activities of multiple carcinogenic pathways, including Wnt/β-catenin, Hedgehog, HIF1, JAK-STAT3, and Notch signaling; or acts as an antagonist of the tumor suppressor p53. Abstract Posttranslational modifications (PTMs) of histones are well-established contributors in a variety of biological functions, especially tumorigenesis. Histone demethylase JMJD2D (also known as KDM4D), a member of the JMJD2 subfamily, promotes gene transcription by antagonizing H3K9 methylation. JMJD2D is an epigenetic factor coordinating androgen receptor activation, DNA damage repair, DNA replication, and cell cycle regulation. Recently, the oncogenic role of JMJD2D in colorectal cancer (CRC) and hepatocellular cancer (HCC) has been recognized. JMJD2D serves as a coactivator of β-catenin, Gli1/2, HIF1α, STAT3, IRF1, TCF4, and NICD or an antagonist of p53 to promote the progression of CRC and HCC. In this review, we summarize the molecular mechanisms of JMJD2D in promoting the progression of CRC and HCC as well as the constructive role of its targeting inhibitors in suppressing tumorigenesis and synergistically enhancing the efficacy of anti-PD-1/PD-L1 immunotherapy.
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Molenaar TM, van Leeuwen F. SETD2: from chromatin modifier to multipronged regulator of the genome and beyond. Cell Mol Life Sci 2022; 79:346. [PMID: 35661267 PMCID: PMC9167812 DOI: 10.1007/s00018-022-04352-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022]
Abstract
Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.
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Niu F, Xu J, Yan Y. Histone demethylase KDM5A regulates the functions of human periodontal ligament stem cells during periodontitis via the miR-495-3p/HOXC8 axis. Regen Ther 2022; 20:95-106. [PMID: 35509266 PMCID: PMC9046131 DOI: 10.1016/j.reth.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fang Niu
- Department of Oral Implantology and Prosthodontics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, 450000, PR China
- Corresponding author. Department of Oral Implantology and Prosthodontics, The First Affiliated Hospital of Zhengzhou University, No.1 Jianshe East Road, Erqi District, Zhengzhou, Henan Province, 450000, China.
| | - Jing Xu
- Department of Oral Orthodontics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, 450000, PR China
| | - Yujuan Yan
- Department of Oral Prosthodontics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, 450000, PR China
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López C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, González Sánchez JC, Apic G, Hübschmann D, Janz M, Kreuz M, Mottok A, Müller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schüle R, Trümper L, Klapper W, Radlwimmer B, Lichter P, Küppers R, Schlesner M, Mathas S, Siebert R. Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas. Haematologica 2022; 108:543-554. [PMID: 35522148 PMCID: PMC9890021 DOI: 10.3324/haematol.2021.280005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 02/03/2023] Open
Abstract
Histone methylation-modifiers, such as EZH2 and KMT2D, are recurrently altered in B-cell lymphomas. To comprehensively describe the landscape of alterations affecting genes encoding histone methylation-modifiers in lymphomagenesis we investigated whole genome and transcriptome data of 186 mature B-cell lymphomas sequenced in the ICGC MMML-Seq project. Besides confirming common alterations of KMT2D (47% of cases), EZH2 (17%), SETD1B (5%), PRDM9 (4%), KMT2C (4%), and SETD2 (4%), also identified by prior exome or RNA-sequencing studies, we here found recurrent alterations to KDM4C in chromosome 9p24, encoding a histone demethylase. Focal structural variation was the main mechanism of KDM4C alterations, and was independent from 9p24 amplification. We also identified KDM4C alterations in lymphoma cell lines including a focal homozygous deletion in a classical Hodgkin lymphoma cell line. By integrating RNA-sequencing and genome sequencing data we predict that KDM4C structural variants result in loss-offunction. By functional reconstitution studies in cell lines, we provide evidence that KDM4C can act as a tumor suppressor. Thus, we show that identification of structural variants in whole genome sequencing data adds to the comprehensive description of the mutational landscape of lymphomas and, moreover, establish KDM4C as a putative tumor suppressive gene recurrently altered in subsets of B-cell derived lymphomas.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,*CL and NS contributed equally as co-first authors
| | - Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,*CL and NS contributed equally as co-first authors
| | - Stephan H. Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kortine Kleinheinz
- Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany
| | | | - Henrike L. Sczakiel
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Umut H. Toprak
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany,Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Division of Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Gordana Apic
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany,Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Judith M. Müller
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Leibniz Institute on Ageing-Fritz Lipmann Institute (FLI), Computational Biology, Jena, Germany
| | - Jan O. Korbel
- EMBL Heidelberg, Genome Biology Unit, Heidelberg,, Germany
| | - Robert B. Russell
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Roland Schüle
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany,BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany, and German Cancer Consortium (DKTK)
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,SM and RS contributed equally as co-senior authors
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,SM and RS contributed equally as co-senior authors
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del Moral-Morales A, Salgado-Albarrán M, Ortiz-Gutiérrez E, Pérez-Hernández G, Soto-Reyes E. Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer. Front Genet 2022; 13:860924. [PMID: 35480330 PMCID: PMC9036480 DOI: 10.3389/fgene.2022.860924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
KDM4 proteins are a subfamily of histone demethylases that target the trimethylation of lysines 9 and 36 of histone H3, which are associated with transcriptional repression and elongation respectively. Their deregulation in cancer may lead to chromatin structure alteration and transcriptional defects that could promote malignancy. Despite that KDM4 proteins are promising drug targets in cancer therapy, only a few drugs have been described as inhibitors of these enzymes, while studies on natural compounds as possible inhibitors are still needed. Natural compounds are a major source of biologically active substances and many are known to target epigenetic processes such as DNA methylation and histone deacetylation, making them a rich source for the discovery of new histone demethylase inhibitors. Here, using transcriptomic analyses we determined that the KDM4 family is deregulated and associated with a poor prognosis in multiple neoplastic tissues. Also, by molecular docking and molecular dynamics approaches, we screened the COCONUT database to search for inhibitors of natural origin compared to FDA-approved drugs and DrugBank databases. We found that molecules from natural products presented the best scores in the FRED docking analysis. Molecules with sugars, aromatic rings, and the presence of OH or O- groups favor the interaction with the active site of KDM4 subfamily proteins. Finally, we integrated a protein-protein interaction network to correlate data from transcriptomic analysis and docking screenings to propose FDA-approved drugs that could be used as multitarget therapies or in combination with the potential natural inhibitors of KDM4 enzymes. This study highlights the relevance of the KDM4 family in cancer and proposes natural compounds that could be used as potential therapies.
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Affiliation(s)
- Aylin del Moral-Morales
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Marisol Salgado-Albarrán
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Elizabeth Ortiz-Gutiérrez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- *Correspondence: Ernesto Soto-Reyes, ; Gerardo Pérez-Hernández,
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
- *Correspondence: Ernesto Soto-Reyes, ; Gerardo Pérez-Hernández,
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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The Emerging Significance of Histone Lysine Demethylases as Prognostic Markers and Therapeutic Targets in Head and Neck Cancers. Cells 2022; 11:cells11061023. [PMID: 35326475 PMCID: PMC8946939 DOI: 10.3390/cells11061023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic aberrations, associated with altered DNA methylation profiles and global changes in the level of histone modifications, are commonly detected in head and neck squamous cell carcinomas (HNSCC). Recently, histone lysine demethylases have been implicated in the pathogenesis of HNSCC and emerged as potential molecular targets. Histone lysine demethylases (KDMs) catalyze the removal of methyl groups from lysine residues in histones. By affecting the methylation of H3K4, H3K9, H3K27, or H3K36, these enzymes take part in transcriptional regulation, which may result in changes in the level of expression of tumor suppressor genes and protooncogenes. KDMs are involved in many biological processes, including cell cycle control, senescence, DNA damage response, and heterochromatin formation. They are also important regulators of pluripotency. The overexpression of most KDMs has been observed in HNSCC, and their inhibition affects cell proliferation, apoptosis, cell motility, invasiveness, and stemness. Of all KDMs, KDM1, KDM4, KDM5, and KDM6 proteins are currently regarded as the most promising prognostic and therapeutic targets in head and neck cancers. The aim of this review is to present up-to-date knowledge on the significance of histone lysine demethylases in head and neck carcinogenesis and to discuss the possibility of using them as prognostic markers and pharmacological targets in patients’ treatment.
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Wang Z, Cai H, Zhao E, Cui H. The Diverse Roles of Histone Demethylase KDM4B in Normal and Cancer Development and Progression. Front Cell Dev Biol 2022; 9:790129. [PMID: 35186950 PMCID: PMC8849108 DOI: 10.3389/fcell.2021.790129] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/31/2021] [Indexed: 01/05/2023] Open
Abstract
Histone methylation status is an important process associated with cell growth, survival, differentiation and gene expression in human diseases. As a member of the KDM4 family, KDM4B specifically targets H1.4K26, H3K9, H3K36, and H4K20, which affects both histone methylation and gene expression. Therefore, KDM4B is often regarded as a key intermediate protein in cellular pathways that plays an important role in growth and development as well as organ differentiation. However, KDM4B is broadly defined as an oncoprotein that plays key roles in processes related to tumorigenesis, including cell proliferation, cell survival, metastasis and so on. In this review, we discuss the diverse roles of KDM4B in contributing to cancer progression and normal developmental processes. Furthermore, we focus on recent studies highlighting the oncogenic functions of KDM4B in various kinds of cancers, which may be a novel therapeutic target for cancer treatment. We also provide a relatively complete report of the progress of research related to KDM4B inhibitors and discuss their potential as therapeutic agents for overcoming cancer.
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Affiliation(s)
- Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
| | - Huarui Cai
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
| | - Erhu Zhao
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
- *Correspondence: Erhu Zhao, ; Hongjuan Cui,
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Medical Research Institute, Southwest University, Chongqing, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China
- *Correspondence: Erhu Zhao, ; Hongjuan Cui,
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Malbeteau L, Pham HT, Eve L, Stallcup MR, Poulard C, Le Romancer M. How Protein Methylation Regulates Steroid Receptor Function. Endocr Rev 2022; 43:160-197. [PMID: 33955470 PMCID: PMC8755998 DOI: 10.1210/endrev/bnab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 02/06/2023]
Abstract
Steroid receptors (SRs) are members of the nuclear hormonal receptor family, many of which are transcription factors regulated by ligand binding. SRs regulate various human physiological functions essential for maintenance of vital biological pathways, including development, reproduction, and metabolic homeostasis. In addition, aberrant expression of SRs or dysregulation of their signaling has been observed in a wide variety of pathologies. SR activity is tightly and finely controlled by post-translational modifications (PTMs) targeting the receptors and/or their coregulators. Whereas major attention has been focused on phosphorylation, growing evidence shows that methylation is also an important regulator of SRs. Interestingly, the protein methyltransferases depositing methyl marks are involved in many functions, from development to adult life. They have also been associated with pathologies such as inflammation, as well as cardiovascular and neuronal disorders, and cancer. This article provides an overview of SR methylation/demethylation events, along with their functional effects and biological consequences. An in-depth understanding of the landscape of these methylation events could provide new information on SR regulation in physiology, as well as promising perspectives for the development of new therapeutic strategies, illustrated by the specific inhibitors of protein methyltransferases that are currently available.
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Affiliation(s)
- Lucie Malbeteau
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Ha Thuy Pham
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Louisane Eve
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Coralie Poulard
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Muriel Le Romancer
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
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Inhibition of histone demethylase KDM4 by ML324 induces apoptosis through the unfolded protein response and Bim upregulation in hepatocellular carcinoma cells. Chem Biol Interact 2022; 353:109806. [PMID: 34999051 DOI: 10.1016/j.cbi.2022.109806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is an extremely aggressive malignancy that ranks as the sixth-leading cause of cancer-associated death worldwide. Recently, various epigenetic mechanisms including gene methylation were reported to be potential next era HCC therapeutics and biomarkers. Although inhibition of epigenetic enzymes including histone lysine demethylase 4 (KDM4) enhanced cell death in HCC cells, the detailed mechanism of cell death machinery is poorly understood. In this study, we found that ML324, a small molecule KDM4-specific inhibitor, induced the death of HCC cells in a general cell culture system and 3D spheroid culture with increased cleavage of caspase-3. Mechanistically, we identified that unfolded protein responses (UPR) were involved in ML324-induced HCC cell death. Incubation of HCC cells with ML324 upregulated death receptor 5 (DR5) expression through the activation transcription factor 3 (ATF3)-C/EBP homologous protein (CHOP)-dependent pathway. Moreover, we identified BIM protein as a mediator of ML324-induced apoptosis using CRISPR/Cas9 knockout analysis. We showed that the loss of Bim suppressed ML324-induced apoptosis by flow cytometry analysis, colony formation assay, and caspase-3 activation assay. Interestingly, BIM protein expression by ML324 was regulated by ATF3, CHOP, and DR5 which are factors involved in UPR. Specifically, we confirmed the regulating roles of KDM4E in Bim and CHOP expression using a chromatin immune precipitation (ChIP) assay. Physical binding of KDM4E to Bim and CHOP promoters decreased the response to ML324. Our findings suggest that KDM4 inhibition is a potent anti-tumor therapeutic strategy for human HCC, and further studies of UPR-induced apoptosis and the associated epigenetic functional mechanisms may lead to the discovery of novel target for future cancer therapy.
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Roggero CM, Esser V, Duan L, Rice AM, Ma S, Raj GV, Rosen MK, Liu ZP, Rizo J. Poly-glutamine-dependent self-association as a potential mechanism for regulation of androgen receptor activity. PLoS One 2022; 17:e0258876. [PMID: 34986150 PMCID: PMC8730435 DOI: 10.1371/journal.pone.0258876] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/13/2021] [Indexed: 01/01/2023] Open
Abstract
The androgen receptor (AR) plays a central role in prostate cancer. Development of castration resistant prostate cancer (CRPC) requires androgen-independent activation of AR, which involves its large N-terminal domain (NTD) and entails extensive epigenetic changes depending in part on histone lysine demethylases (KDMs) that interact with AR. The AR-NTD is rich in low-complexity sequences, including a polyQ repeat. Longer polyQ sequences were reported to decrease transcriptional activity and to protect against prostate cancer, although they can lead to muscular atrophy. However, the molecular mechanisms underlying these observations are unclear. Using NMR spectroscopy, here we identify weak interactions between the AR-NTD and the KDM4A catalytic domain, and between the AR ligand-binding domain and a central KDM4A region that also contains low-complexity sequences. We also show that the AR-NTD can undergo liquid-liquid phase separation in vitro, with longer polyQ sequences phase separating more readily. Moreover, longer polyQ sequences hinder nuclear localization in the absence of hormone and increase the propensity for formation of AR-containing puncta in the nucleus of cells treated with dihydrotestosterone. These results lead us to hypothesize that polyQ-dependent liquid-liquid phase separation may provide a mechanism to decrease the transcriptional activity of AR, potentially opening new opportunities to design effective therapies against CRPC and muscular atrophy.
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Affiliation(s)
- Carlos M. Roggero
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Victoria Esser
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Lingling Duan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Allyson M. Rice
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Shihong Ma
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ganesh V. Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michael K. Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Zhi-Ping Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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Igarashi K, Nishizawa H, Matsumoto M. Iron in Cancer Progression: Does BACH1 Promote Metastasis by Altering Iron Homeostasis? Subcell Biochem 2022; 100:67-80. [PMID: 36301491 DOI: 10.1007/978-3-031-07634-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The transcription factor BACH1, which is regulated by direct binding of prosthetic group heme, promotes epithelial-mesenchymal transition (EMT) and drives metastasis of diverse types of cancer cells. De-regulated target genes of BACH1 in cancer cells include those for glycolysis, oxidative phosphorylation, epithelial cell adhesion, and mesodermal cell motility. In addition, the canonical target genes of BACH1 include genes for the regulation of iron homeostasis. Importantly, cancer cells are addicted to iron. We summarize known functions of BACH1 in cancer and discuss how BACH1 may affect iron homeostasis in cancer cells to support their progression by increasing mobile iron within cells. The dependency on BACH1 for cancer progression may also confer upon cancer cells susceptibility to iron-dependent cell death ferroptosis. Finally, we discuss that the human transcription factors provide research opportunities for better understanding of cancer cell properties.
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Affiliation(s)
- Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
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Zhang M, Liu Y, Hou S, Wang Y, Wang C, Yin Y, Chen X. KDM4B, a potential prognostic biomarker revealed by large-scale of public databases and clinical samples in uterine corpus endometrial carcinoma. Mol Omics 2022; 18:506-519. [PMID: 35485290 DOI: 10.1039/d1mo00287b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract Background: Uterine corpus endometrial carcinoma (UCEC) is the fourth most common cancer among women worldwide. Lysine-specific demethylase 4B (KDM4B) is overexpressed or dysregulated in various cancers and is associated...
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Affiliation(s)
- Mengjun Zhang
- Harbin Medical University Cancer Hospital, Harbin, China.
| | - Yuan Liu
- Harbin Medical University Cancer Hospital, Harbin, China.
| | - Siyu Hou
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yiru Wang
- Harbin Medical University Cancer Hospital, Harbin, China.
| | - Can Wang
- Harbin Medical University Cancer Hospital, Harbin, China.
| | - Yue Yin
- Harbin Medical University Cancer Hospital, Harbin, China.
| | - Xiuwei Chen
- Harbin Medical University Cancer Hospital, Harbin, China.
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