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Guan S, Tang J, Ma X, Miao R, Cheng B. CBX7C⋅PHC2 interaction facilitates PRC1 assembly and modulates its phase separation properties. iScience 2024; 27:109548. [PMID: 38600974 PMCID: PMC11004992 DOI: 10.1016/j.isci.2024.109548] [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: 08/06/2023] [Revised: 02/04/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
CBX7 is a key component of PRC1 complex. Cbx7C is an uncharacterized Cbx7 splicing isoform specifically expressed in mouse embryonic stem cells (mESCs). We demonstrate that CBX7C functions as an epigenetic repressor at the classic PRC1 targets in mESCs, and its preferential interaction to PHC2 facilitates PRC1 assembly. Both Cbx7C and Phc2 are significantly upregulated during cell differentiation, and knockdown of Cbx7C abolishes the differentiation of mESCs to embryoid bodies. Interestingly, CBX7C⋅PHC2 interaction at low levels efficiently undergoes the formation of functional Polycomb bodies with high mobility, whereas the coordination of the two factors at high doses results in the formation of large, low-mobility, chromatin-free aggregates. Overall, these findings uncover the unique roles and molecular basis of the CBX7C⋅PHC2 interaction in PRC1 assembly on chromatin and Pc body formation and open a new avenue of controlling PRC1 activities via modulation of its phase separation properties.
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Affiliation(s)
- Shanli Guan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Jiajia Tang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Ruidong Miao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Bo Cheng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
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Yi SJ, Lim J, Kim K. Exploring epigenetic strategies for the treatment of osteoporosis. Mol Biol Rep 2024; 51:398. [PMID: 38453825 DOI: 10.1007/s11033-024-09353-4] [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: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
The worldwide trend toward an aging population has resulted in a higher incidence of chronic conditions, such as osteoporosis. Osteoporosis, a prevalent skeletal disorder characterized by decreased bone mass and increased fracture risk, encompasses primary and secondary forms, each with distinct etiologies. Mechanistically, osteoporosis involves an imbalance between bone resorption by osteoclasts and bone formation by osteoblasts. Current pharmacological interventions for osteoporosis, such as bisphosphonates, denosumab, and teriparatide, aim to modulate bone turnover and preserve bone density. Hormone replacement therapy and lifestyle modifications are also recommended to manage the condition. While current medications offer therapeutic options, they are not devoid of limitations. Recent studies have highlighted the importance of epigenetic mechanisms, including DNA methylation and histone modifications, in regulating gene expression during bone remodeling. The use of epigenetic drugs, or epidrugs, to target these mechanisms offers a promising avenue for therapeutic intervention in osteoporosis. In this review, we comprehensively examine the recent advancements in the application of epidrugs for treating osteoporosis.
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Affiliation(s)
- Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jaeho Lim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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3
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Zhang S, Lin T, Xiong X, Chen C, Tan P, Wei Q. Targeting histone modifiers in bladder cancer therapy - preclinical and clinical evidence. Nat Rev Urol 2024:10.1038/s41585-024-00857-z. [PMID: 38374198 DOI: 10.1038/s41585-024-00857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/21/2024]
Abstract
Bladder cancer in the most advanced, muscle-invasive stage is lethal, and very limited therapeutic advances have been reported for decades. To date, cisplatin-based chemotherapy remains the first-line therapy for advanced bladder cancer. Late-line options have historically been limited. In the past few years, next-generation sequencing technology has enabled chromatin remodelling gene mutations to be characterized, showing that these alterations are more frequent in urothelial bladder carcinoma than in other cancer types. Histone modifiers have functional roles in tumour progression by modulating the expression of tumour suppressors and oncogenes and, therefore, have been considered as novel drug targets for cancer therapy. The roles of epigenetic reprogramming through histone modifications have been increasingly studied in bladder cancer, and the therapeutic efficacy of targeting those histone modifiers genetically or chemically is being assessed in preclinical studies. Results from preclinical studies in bladder cancer encouraged the investigation of some of these drugs in clinical trials, which yield mixed results. Further understanding of how alterations of histone modification mechanistically contribute to bladder cancer progression, drug resistance and tumour microenvironment remodelling will be required to facilitate clinical application of epigenetic drugs in bladder cancer.
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Affiliation(s)
- Shiyu Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xingyu Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Ping Tan
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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Park MJ, Sohn WM, Bae YA. Genome-wide identification of histone lysine methyltransferases and their implications in the epigenetic regulation of eggshell formation-related genes in a trematode parasite Clonorchis sinensis. PARASITES, HOSTS AND DISEASES 2024; 62:98-116. [PMID: 38443774 PMCID: PMC10915263 DOI: 10.3347/phd.23116] [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: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 03/07/2024]
Abstract
Epigenetic writers including DNA and histone lysine methyltransferases (DNMT and HKMT, respectively) play an initiative role in the differentiation and development of eukaryotic organisms through the spatiotemporal regulation of functional gene expressions. However, the epigenetic mechanisms have long been suspected in helminth parasites lacking the major DNA methyltransferases DNMT1 and DNMT3a/3b. Very little information on the evolutionary status of the epigenetic tools and their role in regulating chromosomal genes is currently available in the parasitic trematodes. We previously suggested the probable role of a DNMT2-like protein (CsDNMT2) as a genuine epigenetic writer in a trematode parasite Clonorchis sinensis. Here, we analyzed the phylogeny of HKMT subfamily members in the liver fluke and other platyhelminth species. The platyhelminth genomes examined conserved genes for the most of SET domain-containing HKMT and Disruptor of Telomeric Silencing 1 subfamilies, while some genes were expanded specifically in certain platyhelminth genomes. Related to the high gene dosages for HKMT activities covering differential but somewhat overlapping substrate specificities, variously methylated histones were recognized throughout the tissues/organs of C. sinensis adults. The temporal expressions of genes involved in eggshell formation were gradually decreased to their lowest levels proportionally to aging, whereas those of some epigenetic tool genes were re-boosted in the later adult stages of the parasite. Furthermore, these expression levels were significantly affected by treatment with DNMT and HKMT inhibitors. Our data strongly suggest that methylated histones are potent epigenetic markers that modulate the spatiotemporal expressions of C. sinensis genes, especially those involved in sexual reproduction.
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Affiliation(s)
- Min-Ji Park
- Department of Microbiology, College of Medicine and Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999,
Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999,
Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Young-An Bae
- Department of Microbiology, College of Medicine and Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999,
Korea
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Yao B, Xing M, Meng S, Li S, Zhou J, Zhang M, Yang C, Qu S, Jin Y, Yuan H, Zen K, Ma C. EBF2 Links KMT2D-Mediated H3K4me1 to Suppress Pancreatic Cancer Progression via Upregulating KLLN. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302037. [PMID: 38015024 PMCID: PMC10787067 DOI: 10.1002/advs.202302037] [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: 03/29/2023] [Revised: 10/09/2023] [Indexed: 11/29/2023]
Abstract
Mono-methylation of histone H3 on Lys 4 (H3K4me1), which is catalyzed by histone-lysine N-methyltransferase 2D (KMT2D), serves as an important epigenetic regulator in transcriptional control. In this study, the authors identify early B-cell factor 2 (EBF2) as a binding protein of H3K4me1. Combining analyses of RNA-seq and ChIP-seq data, the authors further identify killin (KLLN) as a transcriptional target of KMT2D and EBF2 in pancreatic ductal adenocarcinoma (PDAC) cells. KMT2D-dependent H3K4me1 and EBF2 are predominantly over-lapped proximal to the transcription start site (TSS) of KLLN gene. Comprehensive functional assays show that KMT2D and EBF2 cooperatively inhibit PDAC cells proliferation, migration, and invasion through upregulating KLLN. Such inhibition on PDAC progression is also achieved through increasing H3K4me1 level by GSK-LSD1, a selective inhibitor of lysine-specific demethylase 1 (LSD1). Taken together, these findings reveal a new mechanism underlying PDAC progression and provide potential therapeutic targets for PDAC treatment.
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Affiliation(s)
- Bing Yao
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Mengying Xing
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Shixin Meng
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Shang Li
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Jingwan Zhou
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Ming Zhang
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Chen Yang
- The State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing University163 Xianlin AvenueNanjing210023China
| | - Shuang Qu
- School of Life Science and TechnologyChina Pharmaceutical University639 Longmian AvenueNanjingJiangsu211198China
| | - Yucui Jin
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
| | - Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDC20007USA
| | - Ke Zen
- The State Key Laboratory of Pharmaceutical BiotechnologySchool of Life SciencesNanjing University163 Xianlin AvenueNanjing210023China
| | - Changyan Ma
- Department of Medical GeneticsNanjing Medical University101 Longmian AvenueNanjing211166China
- Jiangsu Key Laboratory of XenotransplantationNanjing Medical University101 Longmian AvenueNanjing211166China
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Tang D, Lu Y, Zuo N, Yan R, Wu C, Wu L, Liu S, He Y. The H3K27 demethylase controls the lateral line embryogenesis of zebrafish. Cell Biol Toxicol 2023; 39:1137-1152. [PMID: 34716527 PMCID: PMC10406677 DOI: 10.1007/s10565-021-09669-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/11/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Kdm6b, a specific histone 3 lysine 27 (H3K27) demethylase, has been reported to be implicated in a variety of developmental processes including cell differentiation and cell fate determination and multiple organogenesis. Here, we regulated the transcript level of kdm6bb to study the potential role in controlling the hearing organ development of zebrafish. METHODS A morpholino antisense oligonucleotide (MO) strategy was used to induce Kdm6b deficiency; immunohistochemical staining and in situ hybridization analysis were conducted to figure out the morphologic alterations and embryonic mechanisms. RESULTS Kdm6bb is expressed in the primordium and neuromasts at the early stage of zebrafish embryogenesis, suggesting a potential function of Kdm6b in the development of mechanosensory organs. Knockdown of kdm6bb severely influences the cell migration and proliferation in posterior lateral line primordium, abates the number of neuromasts along the trunk, and mRNA-mediated rescue test can partially renew the neuromasts. Loss of kdm6bb might be related to aberrant expressions of chemokine genes encompassing cxcl12a and cxcr4b/cxcr7b in the migrating primordium. Moreover, inhibition of kdm6bb reduces the expression of genes in Fgf signaling pathway, while it increases the axin2 and lef1 expression level of Wnt/β-catenin signaling during the migrating stage. CONCLUSIONS Collectively, our results revealed that Kdm6b plays an essential role in guiding the migration of primordium and in regulating the deposition of zebrafish neuromasts by mediating the gene expression of chemokines and Wnt and Fgf signaling pathway. Since histone methylation and demethylation are reversible, targeting Kdm6b may present as a novel therapeutic regimen for hearing disorders.
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Affiliation(s)
- Dongmei Tang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
| | - Yitong Lu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Na Zuo
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Renchun Yan
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Cheng Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Lijuan Wu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China
| | - Shaofeng Liu
- Department of Otolaryngology-Head and Neck Surgery, Yijishan Hospital of Wannan Medical College, 2 Zheshanwest Road, Wuhu, 241001, Anhui, China.
| | - Yingzi He
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, NHC Key Laboratory of Hearing Medicine, Fudan University, 83 Fenyang Road, Shanghai, 200031, China.
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7
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Chen Y, Sun Y, Xue X, Ma H. Comprehensive analysis of epigenetics mechanisms in osteoporosis. Front Genet 2023; 14:1153585. [PMID: 37056287 PMCID: PMC10087084 DOI: 10.3389/fgene.2023.1153585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Epigenetic modification pertains to the alteration of genetic-expression, which could be transferred to the next generations, without any alteration in the fundamental DNA sequence. Epigenetic modification could include various processes such as DNA methylation, histone alteration, non-coding RNAs (ncRNAs), and chromatin adjustment are among its primary operations. Osteoporosis is a metabolic disorder that bones become more fragile due to the decrease in mineral density, which could result in a higher risk of fracturing. Recently, as the investigation of the causal pathology of osteoporosis has been progressed, remarkable improvement has been made in epigenetic research. Recent literatures have illustrated that epigenetics is estimated to be one of the most contributing factors to the emergence and progression of osteoporosis. This dissertation primarily focuses on indicating the research progresses of epigenetic mechanisms and also the regulation of bone metabolism and the pathogenesis of osteoporosis in light of the significance of epigenetic mechanisms. In addition, it aims to provide new intelligence for the treatment of diseases related to bone metabolism.
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Affiliation(s)
- Yuzhu Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yumiao Sun
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiangyu Xue
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Huanzhi Ma
- Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Huanzhi Ma,
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Behura A, Naik L, Patel S, Das M, Kumar A, Mishra A, Nayak DK, Manna D, Mishra A, Dhiman R. Involvement of epigenetics in affecting host immunity during SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166634. [PMID: 36577469 PMCID: PMC9790847 DOI: 10.1016/j.bbadis.2022.166634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Coronavirus disease 19 (COVID-19) is caused by a highly contagious RNA virus Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2), originated in December 2019 in Wuhan, China. Since then, it has become a global public health concern and leads the disease table with the highest mortality rate, highlighting the necessity for a thorough understanding of its biological properties. The intricate interaction between the virus and the host immune system gives rise to diverse implications of COVID-19. RNA viruses are known to hijack the host epigenetic mechanisms of immune cells to regulate antiviral defence. Epigenetics involves processes that alter gene expression without changing the DNA sequence, leading to heritable phenotypic changes. The epigenetic landscape consists of reversible modifications like chromatin remodelling, DNA/RNA methylation, and histone methylation/acetylation that regulates gene expression. The epigenetic machinery contributes to many aspects of SARS-CoV-2 pathogenesis, like global DNA methylation and receptor angiotensin-converting enzyme 2 (ACE2) methylation determines the viral entry inside the host, viral replication, and infection efficiency. Further, it is also reported to epigenetically regulate the expression of different host cytokines affecting antiviral response. The viral proteins of SARS-CoV-2 interact with various host epigenetic enzymes like histone deacetylases (HDACs) and bromodomain-containing proteins to antagonize cellular signalling. The central role of epigenetic factors in SARS-CoV-2 pathogenesis is now exploited as promising biomarkers and therapeutic targets against COVID-19. This review article highlights the ability of SARS-CoV-2 in regulating the host epigenetic landscape during infection leading to immune evasion. It also discusses the ongoing therapeutic approaches to curtail and control the viral outbreak.
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Affiliation(s)
- Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Salina Patel
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Mousumi Das
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ashish Kumar
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Dev Kiran Nayak
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Debraj Manna
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342011, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Rocha MA, de Campos Vidal B, Mello MLS. Sodium Valproate Modulates the Methylation Status of Lysine Residues 4, 9 and 27 in Histone H3 of HeLa Cells. Curr Mol Pharmacol 2023; 16:197-210. [PMID: 35297358 DOI: 10.2174/1874467215666220316110405] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Valproic acid/sodium valproate (VPA), a well-known anti-epileptic agent, inhibits histone deacetylases, induces histone hyperacetylation, promotes DNA demethylation, and affects the histone methylation status in some cell models. Histone methylation profiles have been described as potential markers for cervical cancer prognosis. However, histone methylation markers that can be studied in a cervical cancer cell line, like HeLa cells, have not been investigated following treatment with VPA. METHODS In this study, the effect of 0.5 mM and 2.0 mM VPA for 24 h on H3K4me2/me3, H3K9me/me2 and H3K27me/me3 signals as well as on KMT2D, EZH2, and KDM3A gene expression was investigated using confocal microscopy, Western blotting, and RT-PCR. Histone methylation changes were also investigated by Fourier-transform infrared spectroscopy (FTIR). RESULTS We found that VPA induces increased levels of H3K4me2/me3 and H3K9me, which are indicative of chromatin activation. Particularly, H3K4me2 markers appeared intensified close to the nuclear periphery, which may suggest their implication in increased transcriptional memory. The abundance of H3K4me2/me3 in the presence of VPA was associated with increased methyltransferase KMT2D gene expression. VPA induced hypomethylation of H3K9me2, which is associated with gene silencing, and concomitant with the demethylase KDM3A, it increased gene expression. Although VPA induces increased H3K27me/me3 levels, it is suggested that the role of the methyltransferase EZH2 in this context could be affected by interactions with this drug. CONCLUSION Histone FTIR spectra were not affected by VPA under present experimental conditions. Whether our epigenetic results are consistent with VPA affecting the aggressive tumorous state of HeLa cells, further investigation is required.
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Affiliation(s)
- Marina Amorim Rocha
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), 13083-862 Campinas, SP, Brazil
| | - Benedicto de Campos Vidal
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), 13083-862 Campinas, SP, Brazil
| | - Maria Luiza Silveira Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), 13083-862 Campinas, SP, Brazil
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Micale V, Di Bartolomeo M, Di Martino S, Stark T, Dell'Osso B, Drago F, D'Addario C. Are the epigenetic changes predictive of therapeutic efficacy for psychiatric disorders? A translational approach towards novel drug targets. Pharmacol Ther 2023; 241:108279. [PMID: 36103902 DOI: 10.1016/j.pharmthera.2022.108279] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 02/06/2023]
Abstract
The etiopathogenesis of mental disorders is not fully understood and accumulating evidence support that clinical symptomatology cannot be assigned to a single gene mutation, but it involves several genetic factors. More specifically, a tight association between genes and environmental risk factors, which could be mediated by epigenetic mechanisms, may play a role in the development of mental disorders. Several data suggest that epigenetic modifications such as DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA) may modify the severity of the disease and the outcome of the therapy. Indeed, the study of these mechanisms may help to identify patients particularly vulnerable to mental disorders and may have potential utility as biomarkers to facilitate diagnosis and treatment of psychiatric disorders. This article summarizes the most relevant preclinical and human data showing how epigenetic modifications can be central to the therapeutic efficacy of antidepressant and/or antipsychotic agents, as possible predictor of drugs response.
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Affiliation(s)
- Vincenzo Micale
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | - Tibor Stark
- Department of Pharmacology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; Scientific Core Unit Neuroimaging, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences 'Luigi Sacco', University of Milan, Milan, Italy, Department of Mental Health, ASST Fatebenefratelli-Sacco, Milan, Italy; "Aldo Ravelli" Research Center for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan Medical School, Milan, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA
| | - Filippo Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy.
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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11
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JMJD family proteins in cancer and inflammation. Signal Transduct Target Ther 2022; 7:304. [PMID: 36050314 PMCID: PMC9434538 DOI: 10.1038/s41392-022-01145-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
The occurrence of cancer entails a series of genetic mutations that favor uncontrollable tumor growth. It is believed that various factors collectively contribute to cancer, and there is no one single explanation for tumorigenesis. Epigenetic changes such as the dysregulation of enzymes modifying DNA or histones are actively involved in oncogenesis and inflammatory response. The methylation of lysine residues on histone proteins represents a class of post-translational modifications. The human Jumonji C domain-containing (JMJD) protein family consists of more than 30 members. The JMJD proteins have long been identified with histone lysine demethylases (KDM) and histone arginine demethylases activities and thus could function as epigenetic modulators in physiological processes and diseases. Importantly, growing evidence has demonstrated the aberrant expression of JMJD proteins in cancer and inflammatory diseases, which might serve as an underlying mechanism for the initiation and progression of such diseases. Here, we discuss the role of key JMJD proteins in cancer and inflammation, including the intensively studied histone lysine demethylases, as well as the understudied group of JMJD members. In particular, we focused on epigenetic changes induced by each JMJD member and summarized recent research progress evaluating their therapeutic potential for the treatment of cancer and inflammatory diseases.
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Habash NW, Sehrawat TS, Shah VH, Cao S. Epigenetics of alcohol-related liver diseases. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2022; 4:100466. [PMID: 35462859 PMCID: PMC9018389 DOI: 10.1016/j.jhepr.2022.100466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.
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Key Words
- 3C, chromosome conformation capture
- 4C, chromosome conformation capture-on-chip
- AH, alcohol-related hepatitis
- ARLD, alcohol-related liver disease
- ASH, alcohol-related steatohepatitis
- ATAC, assay for transposase-accessible chromatin
- Acetylation
- Alcohol liver disease
- BET, bromodomain and extraterminal motif
- BETi, BET inhibitor
- BRD, bromodomain
- CCL2, C-C motif chemokine ligand 2
- CTCF, CCCTC-binding factor
- CXCL, C-X-C motif chemokine ligand
- Chromatin architecture
- Computational biology
- DNA methylation
- DNMT, DNA methyltransferase
- E-P, enhancer-promoter
- Epidrugs
- Epigenetics
- FKBP5, FK506-binding protein 5
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HIF1α, hypoxia inducible factor-1α
- HMGB1, high-mobility group box protein 1
- HNF4α, hepatocyte nuclear factor 4α
- HSC, hepatic stellate cell
- Hi-C, chromosome capture followed by high-throughput sequencing
- Histones
- IL, interleukin
- LPS, lipopolysaccharide
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MECP2, methyl-CpG binding protein 2
- NAFLD, non-alcohol-related fatty liver disease
- PPARG, peroxisome proliferator activated receptor-γ
- SAA, salvianolic acid A
- SIRT, sirtuin
- SREBPs, sterol regulatory element-binding proteins
- Single cell epigenome
- TAD, topologically associating domain
- TEAD, TEA domain transcription factor
- TLR, Toll-like receptor
- TNF, tumour necrosis factor
- YAP, Yes-associated protein
- lncRNA, long non-coding RNA
- miRNA, microRNA
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Affiliation(s)
| | | | - Vijay H. Shah
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
| | - Sheng Cao
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
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RIOX1-demethylated cGAS regulates ionizing radiation-elicited DNA repair. Bone Res 2022; 10:19. [PMID: 35210392 PMCID: PMC8873214 DOI: 10.1038/s41413-022-00194-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/10/2021] [Indexed: 02/05/2023] Open
Abstract
Exposure to radiation causes DNA damage; hence, continuous surveillance and timely DNA repair are important for genome stability. Epigenetic modifications alter the chromatin architecture, thereby affecting the efficiency of DNA repair. However, how epigenetic modifiers coordinate with the DNA repair machinery to modulate cellular radiosensitivity is relatively unknown. Here, we report that loss of the demethylase ribosomal oxygenase 1 (RIOX1) restores cell proliferation and reduces cell death after exposure to ionizing radiation. Furthermore, RIOX1 depletion enhances homologous recombination (HR) repair but not nonhomologous end-joining (NHEJ) repair in irradiated bone marrow cells and oral mucosal epithelial cells. Mechanistic study demonstrates that RIOX1 removes monomethylation at K491 of cyclic GMP-AMP synthase (cGAS) to release cGAS from its interaction with the methyl-lysine reader protein SAGA complex-associated factor 29 (SGF29), which subsequently enables cGAS to interact with poly(ADP-ribosyl)ated poly(ADP-ribose) polymerase 1 (PARP1) at DNA break sites, thereby blocking PARP1-mediated recruitment of Timeless. High expression of RIOX1 maintains cGAS K491me at a low level, which impedes HR repair and reduces cellular tolerance to ionizing radiation. This study highlights a novel RIOX1-dependent mechanism involved in the non-immune function of cGAS that is essential for the regulation of ionizing radiation-elicited HR repair.
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Yang Y, Luan Y, Feng Q, Chen X, Qin B, Ren KD, Luan Y. Epigenetics and Beyond: Targeting Histone Methylation to Treat Type 2 Diabetes Mellitus. Front Pharmacol 2022; 12:807413. [PMID: 35087408 PMCID: PMC8788853 DOI: 10.3389/fphar.2021.807413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/24/2021] [Indexed: 12/30/2022] Open
Abstract
Diabetes mellitus is a global public health challenge with high morbidity. Type 2 diabetes mellitus (T2DM) accounts for 90% of the global prevalence of diabetes. T2DM is featured by a combination of defective insulin secretion by pancreatic β-cells and the inability of insulin-sensitive tissues to respond appropriately to insulin. However, the pathogenesis of this disease is complicated by genetic and environmental factors, which needs further study. Numerous studies have demonstrated an epigenetic influence on the course of this disease via altering the expression of downstream diabetes-related proteins. Further studies in the field of epigenetics can help to elucidate the mechanisms and identify appropriate treatments. Histone methylation is defined as a common histone mark by adding a methyl group (-CH3) onto a lysine or arginine residue, which can alter the expression of downstream proteins and affect cellular processes. Thus, in tthis study will discuss types and functions of histone methylation and its role in T2DM wilsed. We will review the involvement of histone methyltransferases and histone demethylases in the progression of T2DM and analyze epigenetic-based therapies. We will also discuss the potential application of histone methylation modification as targets for the treatment of T2DM.
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Affiliation(s)
- Yang Yang
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Luan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qi Feng
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Xing Chen
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Qin
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kai-Di Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Yi Luan
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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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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Singh S, Jain K, Sharma R, Singh J, Paul D. Epigenetic Modifications in Myeloma: Focused Review of Current Data and Potential Therapeutic Applications. Indian J Med Paediatr Oncol 2021. [DOI: 10.1055/s-0041-1732861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
AbstractMultiple myeloma is a common hematologic malignancy with an incidence of 1 per 100,000 population and is characterized by a nearly 100% risk of relapse, necessitating treatment with newer therapeutic agents at each instance of progression. However, use of newer agents is often precluded by cost and accessibility in a resource-constrained setting. Description of newer pathways of disease pathogenesis potentially provides opportunities for identification of therapeutic targets and a better understanding of disease biology. Identification of epigenetic changes in myeloma is an emerging premise, with several pathways contributing to pathogenesis and progression of disease. Greater understanding of epigenetic alterations provides opportunities to detect several targetable enzymes or pathways that can be of clinical use.
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Affiliation(s)
- Suvir Singh
- Department of Clinical Hematology and Stem Cell Transplantation, Dayanand Medical College, Ludhiana, Punjab, India
| | - Kunal Jain
- Department of Medical Oncology, Dayanand Medical College, Ludhiana, Punjab, India
| | - Rintu Sharma
- Department of Clinical Hematology and Stem Cell Transplantation, Dayanand Medical College, Ludhiana, Punjab, India
| | - Jagdeep Singh
- Department of Medical Oncology, Dayanand Medical College, Ludhiana, Punjab, India
| | - Davinder Paul
- Department of Medical Oncology, Dayanand Medical College, Ludhiana, Punjab, India
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17
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Hoekstra M, Biggar KK. Identification of in vitro JMJD lysine demethylase candidate substrates via systematic determination of substrate preference. Anal Biochem 2021; 633:114429. [PMID: 34678252 DOI: 10.1016/j.ab.2021.114429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 01/25/2023]
Abstract
A major regulatory influence over gene expression is the dynamic post translational methylation of histone proteins, with major implications from both lysine methylation and demethylation. The KDM5/JARID1 sub-family of Fe(II)/2-oxoglutarate dependent lysine-specific demethylases is, in part, responsible for the removal of tri/dimethyl modifications from lysine 4 of histone H3 (i.e., H3K4me3/2), a mark associated with active gene expression. Although the relevance of KDM5 activity to disease progression has been primarily established through its ability to regulate gene expression via histone methylation, there is evidence that these enzymes may also target non-histone proteins. To aid in the identification of new non-histone substrates, we examined KDM5A in vitro activity towards a library of 180 permutated peptide substrates derived from the H3K4me3 sequence. From this data, a recognition motif was identified and used to predict candidate KDM5A substrates from the methyllysine proteome. High-ranking candidate substrates were then validated for in vitro KDM5A activity using representative trimethylated peptides. Our approach correctly identified activity towards 90% of high-ranked substrates. Here, we have demonstrated the usefulness of our method in identifying candidate substrates that is applicable to any Fe(II)- and 2-oxoglutarate dependent demethylase.
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
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18
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Deng D, Yang X, An J, Zhang K, Lin S, Dong X. Sulfonated calix[4]arene functionalized SiO 2@TiO 2 for recognition of lysine methylation. Talanta 2021; 224:121819. [PMID: 33379044 DOI: 10.1016/j.talanta.2020.121819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 11/18/2022]
Abstract
Lysine methylations are common protein post-translational modifications (PTMs), that play significant roles in regulating gene activities. Studies of their functions and connections with diseases have important values. However, due to the small variations from their native structures and very low component proportions, it is very difficult to extract methylated peptides from biological mixtures. In this research, a new material that utilizes sulfonated calix[4]arene (SC4A) as the recognition unit and silica coated with TiO2 as carrier, denoted as SiO2@TiO2@SC4A, was synthesized. The equilibrium binding experiments demonstrated that SiO2@TiO2@SC4A can identify lysine and arginine methylation and peptides with these methylated residues. The maximum isotherm binding capacities are 70.0, 55.9, 31.4 and 24.8 μmol g-1 for Lys(Me3), Lys(Me)2, Lys(Me) and Lys, respectively. It demonstrated that the higher the degree of methylation, the stronger the interactions. In addition, the analyses of high performance liquid chromatography (HPLC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) demonstrated that peptides with methylated lysine or arginine can be selectively extracted from spiked histone trypsin digestion. The recoveries for the spiked GGAK(Me)R, GGAKR(Me)2 and GGAK(Me)3R are 83%, 78%, and 84% respectively. The experiments from the nuclear extracts of HeLa cells also illustrated that SiO2@TiO2@SC4A holds a potential in the enrichment and identification of lysine methylations.
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Affiliation(s)
- Dandan Deng
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Xu Yang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Jinying An
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China; Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, 251 Fukang Road, Tianjin, 300384, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Shen Lin
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
| | - XiangChao Dong
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China.
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19
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Mondal P, Natesh J, Penta D, Meeran SM. Progress and promises of epigenetic drugs and epigenetic diets in cancer prevention and therapy: A clinical update. Semin Cancer Biol 2020; 83:503-522. [PMID: 33309850 DOI: 10.1016/j.semcancer.2020.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic modifications are heritable yet reversible, essential for normal physiological functions and biological development. Aberrant epigenetic modifications, including DNA methylation, histone modification, and non-coding RNA (ncRNA)-mediated gene regulation play a crucial role in cancer progression. In cellular reprogramming, irregular epigenomic modulations alter cell signaling pathways and the expression of tumor suppressor genes and oncogenes, resulting in cancer growth and metastasis. Therefore, alteration of epigenetic-status in cancer cells can be used as a potential target for cancer therapy. Several synthetic epigenetic inhibitors (epi-drugs) and natural epigenetic modulatory bioactives (epi-diets) have been shown to have the potential to alter the aberrant epigenetic status and inhibit cancer progression. Further, the use of combinatorial approaches with epigenetic drugs and diets has brought promising outcomes in cancer prevention and therapy. In this article, we have summarized the epigenetic modulatory activities of epi-drugs, epi-diets, and their combination against various cancers. We have also compiled the preclinical and clinical status of these epigenetic modulators in different cancers.
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Affiliation(s)
- Priya Mondal
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagadish Natesh
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Dhanamjai Penta
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Syed Musthapa Meeran
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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20
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Prados MB, Sica MP, Miranda S. Inflammatory conditions promote a switch of oligosaccharyltransferase (OST) catalytic subunit isoform expression. Arch Biochem Biophys 2020; 693:108538. [PMID: 32810478 DOI: 10.1016/j.abb.2020.108538] [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: 05/19/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Oligosaccharyltransferase (OST) complex catalyzes the N-glycosylation of nascent polypeptides in the endoplasmic reticulum. Glycoproteins are critical for normal cell-cell interactions, especially during an immune response. Abnormal glycosylation is an insignia of several inflammatory diseases. However, the mechanisms that regulate the differential N-glycosylation are not fully understood. The OST complex can be assembled with one out of two catalytic subunits, STT3A or STT3B, which have different enzymatic properties. In this work, we investigated the expression of STT3A and STT3B in several mouse models such as a crossbreeding of normal and abortion-prone mice and an intestinal inflammation model. These animals were either exposed or not to acoustic stress (acute or chronic). The expression of the isoforms was analysed by immunohistochemistry and protein immunoblot. Finally, we investigated the gene regulatory elements employing public databases. Results demonstrated that inflammation alters the balance between the expression of both isoforms in the affected tissues. In homoeostatic conditions, STT3A expression predominates over STT3B, especially in epithelial cells. This relation is reversed as a consequence of inflammation. An increase in STT3B activity was associated to the generation of mannose-rich N-glycans. Accordingly, this type of N-glycans were found to decorate diverse inflamed tissues. The STT3A and STT3B genes are differentially regulated, which could account for the differences in the expression levels observed here. Our results support the idea that these isoforms could play different roles in cellular physiology. This study opens the possibility of studying the STT3A/STT3B expression ratio as a biomarker in acute inflammation or chronic diseases.
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Affiliation(s)
- María Belén Prados
- Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Universidad de Buenos Aires. CONICET, Marcelo T. de Alvear 2270, C1122AAJ, Buenos Aires, Argentina.
| | - Mauricio Pablo Sica
- Instituto de Energía y Desarrollo Sustentable, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica, CONICET, Av. E. Bustillo 9500, 8400 S. C. de Bariloche, Río Negro, Argentina; Instituto Balseiro, Universidad Nacional de Cuyo, Centro Atómico Bariloche, Av. E. Bustillo 9500, 8400 S. C. de Bariloche, Río Negro, Argentina.
| | - Silvia Miranda
- Instituto Alberto C. Taquini de Investigaciones en Medicina Traslacional (IATIMET), Universidad de Buenos Aires. CONICET, Marcelo T. de Alvear 2270, C1122AAJ, Buenos Aires, Argentina.
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21
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Rahman MM, Kim IS, Ahn D, Tae HJ, Park BY. PR domaincontaining protein 12 (prdm12) is a downstream target of the transcription factor zic1 during cellular differentiation in the central nervous system: PR domain containing protein is the right form. Int J Dev Neurosci 2020; 80:528-537. [PMID: 32640092 DOI: 10.1002/jdn.10048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/05/2022] Open
Abstract
Transcription factor zic1 is an important regulator of neural plate patterning, formation of neural crest and cerebellar development, where its main function is neuronal cell differentiation. Among the genes identified, PR domain-containing 12 (prdm12) is a member of the prdm family and is expressed in the placode domain in the neurula stage. prdm12 is distinctly expressed in the dorsal part of the midbrain, trigeminal ganglion, and the motor neuron in the spinal cord. prdm12 knockdown results in the ventralization of the neural tube. zic1 knockdown results in the reduction of prdm12 expression in the midbrain, motor neuron and trigeminal ganglion, and overexpression of zic1 results in the expansion of prdm12 expression in the midbrain. zic1-activated wnt signaling is also a regulator of prdm12 expression in the midbrain. We propose that prdm12 is the downstream of zic1 and a novel player in the gene regulatory network controlling brain cell differentiation, along with some ganglions in Xenopus.
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Affiliation(s)
- Md Mahfujur Rahman
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Medicine, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - In-Shik Kim
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Dongchoon Ahn
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Hyun-Jin Tae
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Byung-Yong Park
- College of Veterinary Medicine and Biosafety Research Institute, Jeonbuk National University, Iksan, Republic of Korea
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22
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Wamucho A, Heffley A, Tsyusko OV. Epigenetic effects induced by silver nanoparticles in Caenorhabditis elegans after multigenerational exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 725:138523. [PMID: 32305644 DOI: 10.1016/j.scitotenv.2020.138523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/02/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
Multigenerational effects of silver nanoparticles (Ag-NPs) on reproduction of the soil nematode Caenorhabditis elegans have been observed previously. However, mechanisms of this reproductive sensitivity are unknown. Here we examine whether epigenetic changes occur as a result of multigenerational exposure to Ag-NPs and whether such modifications can be inherited by unexposed generations. Changes at histone methylation markers, histone 3 lysine 4 dimethylation (H3K4me2) and histone 3 lysine 9 trimethylation (H3K9me3), known to affect reproduction, as well as changes in the expression of the genes encoding demethylases and methyltransferases associated with the selected markers, were investigated. We exposed C. elegans at EC30 to AgNO3, pristine Ag-NPs, and its environmentally transformed product, sulfidized Ag-NPs (sAg-NPs). Histone methylation levels at H3K4me2 increase in response to pristine Ag-NP exposure and did not recover after rescue from the exposure, suggesting transgenerational inheritance. Compared to pristine Ag-NPs, exposure to transformed sAg-NPs significantly decreased H3K4me2 and H3K9me3 levels. These changes in the histone methylation were also supported by expression of spr-5 and jmjd-2 (H3K4me2 and H3K9me3 demethylases, respectively) and set-30 (H3K4me2 methyltransferase). Our study demonstrates that multigenerational exposure to Ag-NPs induces epigenetic changes that are inherited by unexposed offspring. However, environmental transformations of Ag-NPs may also reduce toxicity via epigenetic mechanisms, such as changes at histone methylation.
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Affiliation(s)
- Anye Wamucho
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Department of Toxicology and Cancer Biology, University of Kentucky, 1095 V.A. Drive, Lexington, KY 40536, USA
| | - Allison Heffley
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Miami University, 501 E. High St., Oxford, OH 45056, USA
| | - Olga V Tsyusko
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone St., Lexington, KY 40546, USA; Department of Toxicology and Cancer Biology, University of Kentucky, 1095 V.A. Drive, Lexington, KY 40536, USA.
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23
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Raby L, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model. Genes (Basel) 2020; 11:genes11040362. [PMID: 32230868 PMCID: PMC7230241 DOI: 10.3390/genes11040362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 01/25/2023] Open
Abstract
The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. Furthermore, since zebrafish is a widely used vertebrate model for studying development, we report on the expression of the cbx family members during zebrafish development and in adult tissues. We showed that all cbx genes are ubiquitously expressed with some variations during early development.
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24
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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25
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Cheng Y, He C, Wang M, Ma X, Mo F, Yang S, Han J, Wei X. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials. Signal Transduct Target Ther 2019; 4:62. [PMID: 31871779 PMCID: PMC6915746 DOI: 10.1038/s41392-019-0095-0] [Citation(s) in RCA: 519] [Impact Index Per Article: 103.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 02/05/2023] Open
Abstract
Epigenetic alternations concern heritable yet reversible changes in histone or DNA modifications that regulate gene activity beyond the underlying sequence. Epigenetic dysregulation is often linked to human disease, notably cancer. With the development of various drugs targeting epigenetic regulators, epigenetic-targeted therapy has been applied in the treatment of hematological malignancies and has exhibited viable therapeutic potential for solid tumors in preclinical and clinical trials. In this review, we summarize the aberrant functions of enzymes in DNA methylation, histone acetylation and histone methylation during tumor progression and highlight the development of inhibitors of or drugs targeted at epigenetic enzymes.
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Affiliation(s)
- Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Cai He
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Manni Wang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelei Ma
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Fei Mo
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyong Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Junhong Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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Ngwa CJ, Kiesow MJ, Orchard LM, Farrukh A, Llinás M, Pradel G. The G9a Histone Methyltransferase Inhibitor BIX-01294 Modulates Gene Expression during Plasmodium falciparum Gametocyte Development and Transmission. Int J Mol Sci 2019; 20:ijms20205087. [PMID: 31615031 PMCID: PMC6829282 DOI: 10.3390/ijms20205087] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/01/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022] Open
Abstract
Transmission of the malaria parasite Plasmodium falciparum from the human to the mosquito is initiated by specialized sexual cells, the gametocytes. In the human, gametocytes are formed in response to stress signals and following uptake by a blood-feeding Anopheles mosquito initiate sexual reproduction. Gametocytes need to fine-tune their gene expression in order to develop inside the mosquito to continue life-cycle progression. Previously, we showed that post-translational histone acetylation controls gene expression during gametocyte development and transmission. However, the role of histone methylation remains poorly understood. We here use the histone G9a methyltransferase inhibitor BIX-01294 to investigate the role of histone methylation in regulating gene expression in gametocytes. In vitro assays demonstrated that BIX-01294 inhibits intraerythrocytic replication with a half maximal inhibitory concentration (IC50) of 13.0 nM. Furthermore, BIX-01294 significantly impairs gametocyte maturation and reduces the formation of gametes and zygotes. Comparative transcriptomics between BIX-01294-treated and untreated immature, mature and activated gametocytes demonstrated greater than 1.5-fold deregulation of approximately 359 genes. The majority of these genes are transcriptionally downregulated in the activated gametocytes and could be assigned to transcription, translation, and signaling, indicating a contribution of histone methylations in mediating gametogenesis. Our combined data show that inhibitors of histone methylation may serve as a multi-stage antimalarial.
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Affiliation(s)
- Che Julius Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Meike Jutta Kiesow
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Lindsey Marie Orchard
- Department of Biochemistry and Molecular Biology & Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Afia Farrukh
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology & Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany.
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27
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Bone Remodeling: Histone Modifications as Fate Determinants of Bone Cell Differentiation. Int J Mol Sci 2019; 20:ijms20133147. [PMID: 31252653 PMCID: PMC6651527 DOI: 10.3390/ijms20133147] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
The bone tissue is a dynamic complex that constitutes of several interdependent systems and is continuously remodeled through the concerted actions of bone cells. Osteoblasts are mononucleated cells, derived from mesenchymal stem cells, responsible for bone formation. Osteoclasts are large multinucleated cells that differentiate from hematopoietic progenitors of the myeloid lineage and are responsible for bone resorption. The lineage-specific differentiation of bone cells requires an epigenetic regulation of gene expressions involving chromatin dynamics. The key step for understanding gene regulatory networks during bone cell development lies in characterizing the chromatin modifying enzymes responsible for reorganizing and potentiating particular chromatin structure. This review covers the histone-modifying enzymes involved in bone development, discusses the impact of enzymes on gene expression, and provides future directions and clinical significance in this area.
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28
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Chuang SM, Lu JH, Lin KL, Long CY, Lee YC, Hsiao HP, Tsai CC, Wu WJ, Yang HJ, Juan YS. Epigenetic regulation of COX‑2 expression by DNA hypomethylation via NF‑κB activation in ketamine‑induced ulcerative cystitis. Int J Mol Med 2019; 44:797-812. [PMID: 31257475 PMCID: PMC6657979 DOI: 10.3892/ijmm.2019.4252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/05/2019] [Indexed: 01/03/2023] Open
Abstract
The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)-2 promoter via nuclear factor (NF)-κB transcriptional regulation and elucidated its effect on the COX-2 transcriptional expression in a ketamine-induced ulcerative cystitis (KIC) animal model. The results of the present study revealed that ketamine treatment induced NF-κB p65 translocation to nuclei and activated COX-2 expression and prostaglandin (PGE)2 production in bladder tissue, whereas COX-2 inhibitor suppressed the inflammatory effect. Moreover, DNA hypomethylation of the COX-2 promoter region located from -1,522 to -829 bp might contribute to transcriptional regulation of COX-2 expression and induce a pro-inflammatory response in KIC. Ketamine treatment increased the binding of NF-κB and permissive histone H3 lysine-4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX-2 promoter ranging from -1,522 to -1,331 bp as determined by a chromatin immunoprecipitation assay. Moreover, in the ketamine group, the level of Ten-Eleven-Translocation methylcytosine dioxygenase for demethylation as determined by reverse transcription-quantitative PCR assay was increased in comparison with the control group, but that was not the case for the level of DNA methyltransferases for methylation. The present findings revealed that there was a hypomethylation pattern of the COX-2 promoter in association with the level of COX-2 transcription in KIC.
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Affiliation(s)
- Shu-Mien Chuang
- Translational Research Center, Cancer Center, Department of Medical Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Jian-He Lu
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Kun-Ling Lin
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C
| | - Cheng-Yu Long
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C
| | - Yung-Chin Lee
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Hui-Pin Hsiao
- Division of Genetics, Endocrinology and Metabolism, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan, R.O.C
| | - Chia-Chun Tsai
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Wen-Jeng Wu
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Hui-Jun Yang
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
| | - Yung-Shun Juan
- Department of Urology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan, R.O.C
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Qadi SA, Hassan MA, Sheikh RA, Baothman OA, Zamzami MA, Choudhry H, Al-Malki AL, Albukhari A, Alhosin M. Thymoquinone-Induced Reactivation of Tumor Suppressor Genes in Cancer Cells Involves Epigenetic Mechanisms. Epigenet Insights 2019; 12:2516865719839011. [PMID: 31058255 PMCID: PMC6452588 DOI: 10.1177/2516865719839011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 02/26/2019] [Indexed: 02/06/2023] Open
Abstract
The epigenetic silencing of tumor suppressor genes (TSGs) is a common finding in several solid and hematological tumors involving various epigenetic readers and writers leading to enhanced cell proliferation and defective apoptosis. Thymoquinone (TQ), the major biologically active compound of black seed oil, has demonstrated anticancer activities in various tumors by targeting several pathways. However, its effects on the epigenetic code of cancer cells are largely unknown. In the present study, we performed RNA sequencing to investigate the anticancer mechanisms of TQ-treated T-cell acute lymphoblastic leukemia cell line (Jurkat cells) and examined gene expression using different tools. We found that many key epigenetic players, including ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1), DNMT1,3A,3B, G9A, HDAC1,4,9, KDM1B, and KMT2A,B,C,D,E, were downregulated in TQ-treated Jurkat cells. Interestingly, several TSGs, such as DLC1, PPARG, ST7, FOXO6, TET2, CYP1B1, SALL4, and DDIT3, known to be epigenetically silenced in various tumors, including acute leukemia, were upregulated, along with the upregulation of several downstream pro-apoptotic genes, such as RASL11B, RASD1, GNG3, BAD, and BIK. Data obtained from RNA sequencing were confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) in Jurkat cells, as well as in a human breast cancer cell line (MDA-MB-468 cells). We found that the decrease in cell proliferation and in the expression of UHRF1, DNMT1, G9a, and HDAC1 genes in both cancer cell (Jurkat cells and MDA-MB-468 cells) lines depends on the TQ dose. Our results indicate that the use of TQ as an epigenetic drug represents a promising strategy for epigenetic therapy for both solid and blood tumors by targeting both DNA methylation and histone post-translational modifications.
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Affiliation(s)
- Shahad A Qadi
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed A Hassan
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Basic Medical Sciences, College of Medicine and Health Sciences, Hadhramout University, Mukalla, Yemen
| | - Ryan A Sheikh
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman As Baothman
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ashwag Albukhari
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmoud Alhosin
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
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30
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Ezh1 arises from Ezh2 gene duplication but its function is not required for zebrafish development. Sci Rep 2019; 9:4319. [PMID: 30867490 PMCID: PMC6416316 DOI: 10.1038/s41598-019-40738-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/18/2019] [Indexed: 02/07/2023] Open
Abstract
Trimethylation on H3K27 mediated by Polycomb Repressive Complex 2 (PRC2) is required to control gene repression programs involved in development, regulation of tissue homeostasis or maintenance and lineage specification of stem cells. In Drosophila, the PRC2 catalytic subunit is the single protein E(z), while in mammals this function is fulfilled by two proteins, Ezh1 and Ezh2. Based on database searches, we propose that Ezh1 arose from an Ezh2 gene duplication that has occurred in the common ancestor to elasmobranchs and bony vertebrates. Expression studies in zebrafish using in situ hybridization and RT-PCR followed by the sequencing of the amplicon revealed that ezh1 mRNAs are maternally deposited. Then, ezh1 transcripts are ubiquitously distributed in the entire embryo at 24 hpf and become more restricted to anterior part of the embryo at later developmental stages. To unveil the function of ezh1 in zebrafish, a mutant line was generated using the TALEN technology. Ezh1-deficient mutant fish are viable and fertile, but the loss of ezh1 function is responsible for the earlier death of ezh2 mutant larvae indicating that ezh1 contributes to zebrafish development in absence of zygotic ezh2 gene function. Furthermore, we show that presence of ezh1 transcripts from the maternal origin accounts for the delayed lethality of ezh2-deficient larvae.
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31
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Shafabakhsh R, Aghadavod E, Ghayour‐Mobarhan M, Ferns G, Asemi Z. Role of histone modification and DNA methylation in signaling pathways involved in diabetic retinopathy. J Cell Physiol 2018; 234:7839-7846. [DOI: 10.1002/jcp.27844] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Esmat Aghadavod
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Majid Ghayour‐Mobarhan
- Metabolic Syndrome Research Center School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton UK
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
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32
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Cheng H, Wang Y, Zhang J, Zhang S, Ma X, An X, Man X, Zhang X, Li Z, Tang B. Effects of PRDM14 Silencing on Parthenogenetically Activated Porcine Embryos. Cell Reprogram 2018; 20:382-388. [PMID: 30325654 DOI: 10.1089/cell.2018.0029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Hui Cheng
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yutian Wang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jian Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Sheng Zhang
- Academy of Translational Medicine, First Hospital, Jilin University, Changchun, China
| | - Xiaoling Ma
- Academy of Translational Medicine, First Hospital, Jilin University, Changchun, China
| | - Xinglan An
- Academy of Translational Medicine, First Hospital, Jilin University, Changchun, China
| | - Xiaxia Man
- Academy of Translational Medicine, First Hospital, Jilin University, Changchun, China
| | - Xueming Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ziyi Li
- Academy of Translational Medicine, First Hospital, Jilin University, Changchun, China
| | - Bo Tang
- College of Veterinary Medicine, Jilin University, Changchun, China
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33
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Ge S, Zhao P, Liu X, Zhao Z, Liu M. Necessity to Evaluate Epigenetic Quality of the Sperm for Assisted Reproductive Technology. Reprod Sci 2018; 26:315-322. [DOI: 10.1177/1933719118808907] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shaoqin Ge
- Hebei University Health Science Center, Baoding, China
- The Institute for Reproductive Medicine of Hebei University, Baoding, China
- The Center for Reproductive Medicine of Affiliated Hospital of Hebei University, Baoding, China
| | - Penghui Zhao
- Hebei University Health Science Center, Baoding, China
| | - Xuanchen Liu
- Hebei University Health Science Center, Baoding, China
| | - Zhenghui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meiyun Liu
- The Center for Reproductive Medicine of Affiliated Hospital of Hebei University, Baoding, China
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34
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Ramya Chandar Charles M, Hsieh HP, Selvaraj Coumar M. Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study. J Biomol Struct Dyn 2018; 37:2581-2592. [PMID: 30047835 DOI: 10.1080/07391102.2018.1491422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mono- and di-methylation of the H3K9 residue in the histone tail by G9a lysine methyltransferase is associated with transcriptional suppression of genes. Here, we use molecular dynamics simulation and free energy calculations of five different modified/mutated G9a substrate peptides to elucidate the rationale behind the substrate binding to G9a. We also investigated the binding energy contribution based architecture of the active site of G9a to understand substrate and inhibitor binding. Wild-type peptide (H3K9) shows better binding affinity than mono- and di-methylated lysine (K9) and other modified peptides (K9A and R8A). Arg8 of the substrate peptide is crucial for determining the degree of conformational freedom/stability of the wild-type substrate peptide, as well as binding to G9a. Our results also suggest that the G9a active site is segregated into energy rich and low regions, and the energy rich region alone is used by the inhibitors for binding. These insights into the active site architecture should be taken into consideration in virtual screening experiments designed to discover novel inhibitors for G9a. In particular, compounds that could interact with the six residues of G9a - Asp1074, Asp1083, Leu1086, Asp1088, Tyr1154 and Phe1158 - should be preferentially tested in G9a inhibition biological assays. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Hsing-Pang Hsieh
- b Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan , Taiwan , ROC
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35
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Luna RCP, de Oliveira Y, Lisboa JVC, Chaves TR, de Araújo TAM, de Sousa EE, Miranda Neto M, Pirola L, Braga VA, de Brito Alves JL. Insights on the epigenetic mechanisms underlying pulmonary arterial hypertension. ACTA ACUST UNITED AC 2018; 51:e7437. [PMID: 30365723 PMCID: PMC6207290 DOI: 10.1590/1414-431x20187437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022]
Abstract
Pulmonary arterial hypertension (PAH), characterized by localized increased
arterial blood pressure in the lungs, is a slow developing long-term disease
that can be fatal. PAH is characterized by inflammation, vascular tone
imbalance, pathological pulmonary vascular remodeling, and right-sided heart
failure. Current treatments for PAH are palliative and development of new
therapies is necessary. Recent and relevant studies have demonstrated that
epigenetic processes may exert key influences on the pathogenesis of PAH and may
be promising therapeutic targets in the prevention and/or cure of this
condition. The aim of the present mini-review is to summarize the occurrence of
epigenetic-based mechanisms in the context of PAH physiopathology, focusing on
the roles of DNA methylation, histone post-translational modifications and
non-coding RNAs. We also discuss the potential of epigenetic-based therapies for
PAH.
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Affiliation(s)
- R C P Luna
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - Y de Oliveira
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - J V C Lisboa
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - T R Chaves
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - T A M de Araújo
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - E E de Sousa
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - M Miranda Neto
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - L Pirola
- INSERM U1060, Lyon 1 University, Oullins, France
| | - V A Braga
- Departamento de Biotecnologia, Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
| | - J L de Brito Alves
- Departamento de Nutrição, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, PB, Brasil.,Departamento de Biotecnologia, Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, PB, Brasil
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36
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Chen Y, Liu X, Li Y, Quan C, Zheng L, Huang K. Lung Cancer Therapy Targeting Histone Methylation: Opportunities and Challenges. Comput Struct Biotechnol J 2018; 16:211-223. [PMID: 30002791 PMCID: PMC6039709 DOI: 10.1016/j.csbj.2018.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Lung cancer is one of the most common malignancies. In spite of the progress made in past decades, further studies to improve current therapy for lung cancer are required. Dynamically controlled by methyltransferases and demethylases, methylation of lysine and arginine residues on histone proteins regulates chromatin organization and thereby gene transcription. Aberrant alterations of histone methylation have been demonstrated to be associated with the progress of multiple cancers including lung cancer. Inhibitors of methyltransferases and demethylases have exhibited anti-tumor activities in lung cancer, and multiple lead candidates are under clinical trials. Here, we summarize how histone methylation functions in lung cancer, highlighting most recent progresses in small molecular inhibitors for lung cancer treatment.
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Key Words
- ALK, anaplastic lymphoma kinase
- DUSP3, dual-specificity phosphatase 3
- EMT, epithelial-to-mesenchymal transition
- Elk1, ETS-domain containing protein
- HDAC, histone deacetylase
- Histone demethylase
- Histone demethylation
- Histone methylation
- Histone methyltransferase
- IHC, immunohistochemistry
- Inhibitors
- KDMs, lysine demethylases
- KLF2, Kruppel-like factor 2
- KMTs, lysine methyltransferases
- LSDs, lysine specific demethylases
- Lung cancer
- MEP50, methylosome protein 50
- NSCLC, non-small cell lung cancer
- PAD4, peptidylarginine deiminase 4
- PCNA, proliferating cell nuclear antigen
- PDX, patient-derived xenografts
- PRC2, polycomb repressive complex 2
- PRMTs, protein arginine methyltrasferases
- PTMs, posttranslational modifications
- SAH, S-adenosyl-L-homocysteine
- SAM, S-adenosyl-L-methionine
- SCLC, small cell lung cancer
- TIMP3, tissue inhibitor of metalloproteinase 3
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Affiliation(s)
- Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Xinran Liu
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Yangkai Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Chuntao Quan
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Ling Zheng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
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Tran M, Liu Y, Huang W, Wang L. Nuclear receptors and liver disease: Summary of the 2017 basic research symposium. Hepatol Commun 2018; 2:765-777. [PMID: 30129636 PMCID: PMC6049066 DOI: 10.1002/hep4.1203] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/03/2018] [Accepted: 05/10/2018] [Indexed: 12/11/2022] Open
Abstract
The nuclear receptor superfamily contains important transcriptional regulators that play pleiotropic roles in cell differentiation, development, proliferation, and metabolic processes to govern liver physiology and pathology. Many nuclear receptors are ligand-activated transcription factors that regulate the expression of their target genes by modulating transcriptional activities and epigenetic changes. Additionally, the protein complex associated with nuclear receptors consists of a multitude of coregulators, corepressors, and noncoding RNAs. Therefore, acquiring new information on nuclear receptors may provide invaluable insight into novel therapies and shed light on new interventions to reduce the burden and incidence of liver diseases. (Hepatology Communications 2018;2:765-777).
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Affiliation(s)
- Melanie Tran
- Department of Physiology and Neurobiology and Institute for Systems Genomics, University of Connecticut, Storrs, CT
| | - Yanjun Liu
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope National Medical Center Duarte CA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute City of Hope National Medical Center Duarte CA
| | - Li Wang
- Department of Physiology and Neurobiology and Institute for Systems Genomics, University of Connecticut, Storrs, CT.,Veterans Affairs Connecticut Healthcare System West Haven CT.,Department of Internal Medicine, Section of Digestive Diseases Yale University New Haven CT
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Powis Z, Farwell Hagman K, Mroske C, McWalter K, Cohen J, Colombo R, Serretti A, Fatemi A, David K, Reynolds J, Immken L, Nagakura H, Cunniff C, Payne K, Barbaro-Dieber T, Gripp K, Baker L, Stamper T, Aleck K, Jordan E, Hersh J, Burton J, Wentzensen I, Guillen Sacoto M, Willaert R, Cho M, Petrik I, Huether R, Tang S. Expansion and further delineation of the SETD5
phenotype leading to global developmental delay, variable dysmorphic features, and reduced penetrance. Clin Genet 2018; 93:752-761. [DOI: 10.1111/cge.13132] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Z. Powis
- Division of Emerging Genetics Medicine; Ambry Genetics; Aliso Viejo California
| | | | - C. Mroske
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | | | - J.S. Cohen
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
| | - R. Colombo
- Faculty of Medicine, Institute of Clinical Biochemistry; Catholic University and Policlinico Agostino Gemelli; Rome Italy
- Center for the Study of Rare Hereditary Disease; Niguarda Ca’ Granda Metropolitan Hospital; Milan Italy
| | - A. Serretti
- Department of Biomedical and NeuroMotor Sciences; University of Bologna; Bologna Italy
| | - A. Fatemi
- Division of Neurogenetics, Hugo W. Moser Research Institute; Kennedy Krieger Institute; Baltimore Maryland
- Department of Neurology and Pediatrics; The Johns Hopkins Hospital; Baltimore Maryland
| | - K.L. David
- Department of Medicine, Division of Genetics, New York Methodist Hospital; Brooklyn New York
| | - J. Reynolds
- Department of Medical Genetics, Shodair Children's Hospital; Helena Montana
| | - L. Immken
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - H. Nagakura
- Department of Genetics Specially for Children Genetics; Austin Texas
| | - C.M. Cunniff
- Department of Pediatrics, Weill Cornell Medicine; New York New York
| | - K. Payne
- Child Neurology; Riley Hospital for Children; Indianapolis Indiana
| | - T. Barbaro-Dieber
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - K.W. Gripp
- Department of Genetics, Cook Children's Medical Center; Fort Worth Texas
| | - L. Baker
- Division of Medical Genetics; A.I. duPont Hospital for Children; Wilmington Delaware
| | - T. Stamper
- Department of Pediatrics, Section on Medical Genetics; Wake Forest Baptist Medical Center; Winston-Salem North Carolina
| | - K.A. Aleck
- Department of Genetics and Metabolism, Phoenix Children's Hospital; Phoenix Arizona
| | - E.S. Jordan
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J.H. Hersh
- Weisskopf Center, University of Louisville Clinical Genetics Unit; Louisville Kentucky
| | - J. Burton
- Department of Genetics, University of Illinois College of Medicine at Peoria; Peoria Illinois
| | | | | | | | | | - I. Petrik
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - R. Huether
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
| | - S. Tang
- Division of Clinical Genomics; Ambry Genetics; Aliso Viejo California
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Satish M, Nivya MA, Abhishek S, Nakarakanti NK, Shivani D, Vani MV, Rajakumara E. Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize. Proteins 2017; 86:21-34. [PMID: 29024026 DOI: 10.1002/prot.25399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/21/2017] [Accepted: 10/08/2017] [Indexed: 12/15/2022]
Abstract
Histone lysine methylation by histone lysine methyltransferases (HKMTs) has been implicated in regulation of gene expression. While significant progress has been made to understand the roles and mechanisms of animal HKMT functions, only a few plant HKMTs are functionally characterized. To unravel histone substrate specificity, degree of methylation and catalytic activity, we analyzed Arabidopsis Trithorax-like protein (ATX), Su(var)3-9 homologs protein (SUVH), Su(var)3-9 related protein (SUVR), ATXR5, ATXR6, and E(Z) HKMTs of Arabidopsis, maize and rice through sequence and structure comparison. We show that ATXs may exhibit methyltransferase specificity toward histone 3 lysine 4 (H3K4) and might catalyse the trimethylation. Our analyses also indicate that most SUVH proteins of Arabidopsis may bind histone H3 lysine 9 (H3K9). We also predict that SUVH7, SUVH8, SUVR1, SUVR3, ZmSET20 and ZmSET22 catalyse monomethylation or dimethylation of H3K9. Except for SDG728, which may trimethylate H3K9, all SUVH paralogs in rice may catalyse monomethylation or dimethylation. ZmSET11, ZmSET31, SDG713, SDG715, and SDG726 proteins are predicted to be catalytically inactive because of an incomplete S-adenosylmethionine (SAM) binding pocket and a post-SET domain. E(Z) homologs can trimethylate H3K27 substrate, which is similar to the Enhancer of Zeste homolog 2 of humans. Our comparative sequence analyses reveal that ATXR5 and ATXR6 lack motifs/domains required for protein-protein interaction and polycomb repressive complex 2 complex formation. We propose that subtle variations of key residues at substrate or SAM binding pocket, around the catalytic pocket, or presence of pre-SET and post-SET domains in HKMTs of the aforementioned plant species lead to variations in class-specific HKMT functions and further determine their substrate specificity, the degree of methylation and catalytic activity.
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Affiliation(s)
- Mutyala Satish
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - M Angel Nivya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Suman Abhishek
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Naveen Kumar Nakarakanti
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Dixit Shivani
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Madishetti Vinuthna Vani
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana, 502285, India
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Yokoyama M, Chiba T, Zen Y, Oshima M, Kusakabe Y, Noguchi Y, Yuki K, Koide S, Tara S, Saraya A, Aoyama K, Mimura N, Miyagi S, Inoue M, Wakamatsu T, Saito T, Ogasawara S, Suzuki E, Ooka Y, Tawada A, Otsuka M, Miyazaki M, Yokosuka O, Iwama A. Histone lysine methyltransferase G9a is a novel epigenetic target for the treatment of hepatocellular carcinoma. Oncotarget 2017; 8:21315-21326. [PMID: 28423509 PMCID: PMC5400586 DOI: 10.18632/oncotarget.15528] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 01/27/2017] [Indexed: 12/31/2022] Open
Abstract
Histone H3 lysine 9 dimethylation (H3K9me2) is mainly regulated by the histone lysine methyltransferase G9a and is associated with the repression of transcription. However, both the role of G9a and the significance of H3K9me2 in hepatocellular carcinoma (HCC) cells remain unclear. In this study, we conducted loss-of-function assay of G9a using short-hairpin RNA and pharmacological interference. Knockdown of G9a reduced H3K9me2 levels and impaired both HCC cell growth and sphere formation. However, transforming growth factor β1-induced epithelial mesenchymal transition (EMT) was not suppressed by G9a knockdown. Combined analyses of chromatin immunoprecipitation followed by sequencing and RNA-sequencing led to successful identification of 96 candidate epigenetic targets of G9a. Pharmacological inhibition of G9a by BIX-01294 resulted in both cell growth inhibition and induction of apoptosis in HCC cells. Intraperitoneal administration of BIX-01294 suppressed the growth of xenograft tumors generated by implantation of HCC cells in non-obese diabetic/severe combined immunodeficient mice. Immunohistochemical analyses revealed high levels of G9a and H3K9me2 in 36 (66.7%) and 35 (64.8%) primary HCC tissues, respectively. G9a expression levels were significantly positively correlated with H3K9me2 levels in tumor tissues. In contrast, in non-tumor tissues, G9a and H3K9me2 were only observed in biliary epithelial cells and periportal hepatocytes. In conclusion, G9a inhibition impairs anchorage-dependent and -independent cell growth, but not EMT in HCC cells. Our data indicate that pharmacological interference of G9a might be a novel epigenetic approach for the treatment of HCC.
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Affiliation(s)
- Masayuki Yokoyama
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoh Zen
- Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Motohiko Oshima
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuko Kusakabe
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiko Noguchi
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kaori Yuki
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shuhei Koide
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Shiro Tara
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsunori Saraya
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazumasa Aoyama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoya Mimura
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoru Miyagi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masanori Inoue
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toru Wakamatsu
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoko Saito
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sadahisa Ogasawara
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Eiichiro Suzuki
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshihiko Ooka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akinobu Tawada
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masayuki Otsuka
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaru Miyazaki
- Department of General Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
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42
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In Silico Data Mining of Single Nucleotide Polymorphisms in EZH2 and Their Role in Cancer. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2017. [DOI: 10.5812/ijcm.5430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Luo Y, You S, Wang J, Fan S, Shi J, Peng A, Yu T. Association between Sumoylation-Related Gene rs77447679 Polymorphism and Risk of Gastric Cancer (GC) in a Chinese Population. J Cancer 2017; 8:3226-3231. [PMID: 29158794 PMCID: PMC5665038 DOI: 10.7150/jca.20587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 08/14/2017] [Indexed: 12/12/2022] Open
Abstract
Purpose: Sumoylation plays a critical role in gene regulation and tumorigenesis, and is hypothesized to correlate with the development of various cancers. So far, there has been no reported association between sumoylation-related genes and the risk of gastric cancer (GC). Methods: A total of 17 tagging single-nucleotide polymorphisms (tag-SNPs) in 5 sumoylation-related genes were selected and genotyped by SNaPshot in a case-control study, including 1021 GC patients and 1304 controls. Odds ratio (OR) and 95% confidential interval (CI) were computed to evaluate the genetic association of the onset of GC. Results: We demonstrated that CBX4 rs77447679 polymorphism was significantly associated with GC risk (P= 0.017; adjusted OR: 1.71; 95% CI: 1.10-2.66). The patients with CC genotype had a lower risk of GC (CC vs. CA+AA, P= 0.017; adjusted OR: 1.24; 95% CI: 1.04-1.49). Conclusion: This study revealed that CBX4 rs77447679 polymorphism was positively associated with GC, and individuals with CC genotype had less risk of GC. The risky effects and functional effect of this polymorphism in GC require further investigation.
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Affiliation(s)
- Ying Luo
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Sihong You
- Department of gastroenterology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China.,Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China
| | - Jirong Wang
- Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China.,Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Shuling Fan
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jie Shi
- Nanjing Red Cross Blood Center, Nanjing 210003, China
| | - Ai Peng
- Department of Nephrology & Rheumatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Tingting Yu
- Department of Developmental Genetics, Nanjing Medical University, Nanjing 211166, China
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In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level. J Comput Aided Mol Des 2017; 31:877-889. [PMID: 28879500 DOI: 10.1007/s10822-017-0052-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/22/2017] [Indexed: 10/18/2022]
Abstract
ERG-associated protein with the SET domain (ESET/SET domain bifurcated 1/SETDB1/KMT1E) is a histone lysine methyltransferase (HKMT) and it preferentially tri-methylates lysine 9 of histone H3 (H3K9me3). SETDB1/ESET leads to heterochromatin condensation and epigenetic gene silencing. These functional changes are reported to correlate with Huntington's disease (HD) progression and mood-related disorders which make SETDB1/ESET a viable drug target. In this context, the present investigation was performed to identify novel peptide-competitive small molecule inhibitors of the SETDB1/ESET by a combined in silico-in vitro approach. A ligand-based pharmacophore model was built and employed for the virtual screening of ChemDiv and Asinex database. Also, a human SETDB1/ESET homology model was constructed to supplement the data further. Biological evaluation of the selected 21 candidates singled out 5 compounds exhibiting a notable reduction of the H3K9me3 level via inhibitory potential of SETDB1/ESET activity in SETDB1/ESET-inducible cell line and HD striatal cells. Later on, we identified two compounds as final hits that appear to have neuronal effects without cytotoxicity based on the result from MTT assay. These compounds hold the calibre to become the future lead compounds and can provide structural insights into more SETDB1/ESET-focused drug discovery research. Moreover, these SETDB1/ESET inhibitors may be applicable for the preclinical study to ameliorate neurodegenerative disorders via epigenetic regulation.
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He Y, Bao B, Li H. Using zebrafish as a model to study the role of epigenetics in hearing loss. Expert Opin Drug Discov 2017; 12:967-975. [PMID: 28682135 DOI: 10.1080/17460441.2017.1340270] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The rapid progress of bioinformatics and high-throughput screening techniques in recent years has led to the identification of many candidate genes and small-molecule drugs that have the potential to make significant contributions to our understanding of the developmental and pathological processes of hearing, but it remains unclear how these genes and regulatory factors are coordinated. Increasing evidence suggests that epigenetic mechanisms are essential for establishing gene expression profiles and likely play an important role in the development of inner ear and in the pathology of hearing-associated diseases. Zebrafish are a valuable and tractable in vivo model organism for monitoring changes in the epigenome and for identifying new epigenetic processes and drug molecules that can influence vertebrate development. Areas covered: In this review, the authors focus on zebrafish as a model to summarize recent findings concerning the roles of epigenetics in the development, regeneration, and protection of hair cells. Expert opinion: Using the zebrafish model in combination with high-throughput screening and genome-editing technologies to investigate the function of epigenetics in hearing is crucial to help us better understand the molecular and genetic mechanisms of auditory development and function. It will also contribute to the development of new strategies to restore hearing loss.
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Affiliation(s)
- Yingzi He
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China
| | - Beier Bao
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China
| | - Huawei Li
- a ENT Institute and Otorhinolaryngology Department of Affiliated Eye and ENT Hospital, State Key Laboratory of Medical Neurobiology , Fudan University , Shanghai , China.,b Institutes of Biomedical Sciences , Fudan University , Shanghai , China.,c Key Laboratory of Hearing Medicine of NHFPC , Shanghai , China.,d Shanghai Engineering Research Centre of Cochlear Implant , Shanghai , China.,e The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science , Fudan University , Shanghai , China
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A Tox21 Approach to Altered Epigenetic Landscapes: Assessing Epigenetic Toxicity Pathways Leading to Altered Gene Expression and Oncogenic Transformation In Vitro. Int J Mol Sci 2017; 18:ijms18061179. [PMID: 28587163 PMCID: PMC5486002 DOI: 10.3390/ijms18061179] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 02/07/2023] Open
Abstract
An emerging vision for toxicity testing in the 21st century foresees in vitro assays assuming the leading role in testing for chemical hazards, including testing for carcinogenicity. Toxicity will be determined by monitoring key steps in functionally validated molecular pathways, using tests designed to reveal chemically-induced perturbations that lead to adverse phenotypic endpoints in cultured human cells. Risk assessments would subsequently be derived from the causal in vitro endpoints and concentration vs. effect data extrapolated to human in vivo concentrations. Much direct experimental evidence now shows that disruption of epigenetic processes by chemicals is a carcinogenic mode of action that leads to altered gene functions playing causal roles in cancer initiation and progression. In assessing chemical safety, it would therefore be advantageous to consider an emerging class of carcinogens, the epigenotoxicants, with the ability to change chromatin and/or DNA marks by direct or indirect effects on the activities of enzymes (writers, erasers/editors, remodelers and readers) that convey the epigenetic information. Evidence is reviewed supporting a strategy for in vitro hazard identification of carcinogens that induce toxicity through disturbance of functional epigenetic pathways in human somatic cells, leading to inactivated tumour suppressor genes and carcinogenesis. In the context of human cell transformation models, these in vitro pathway measurements ensure high biological relevance to the apical endpoint of cancer. Four causal mechanisms participating in pathways to persistent epigenetic gene silencing were considered: covalent histone modification, nucleosome remodeling, non-coding RNA interaction and DNA methylation. Within these four interacting mechanisms, 25 epigenetic toxicity pathway components (SET1, MLL1, KDM5, G9A, SUV39H1, SETDB1, EZH2, JMJD3, CBX7, CBX8, BMI, SUZ12, HP1, MPP8, DNMT1, DNMT3A, DNMT3B, TET1, MeCP2, SETDB2, BAZ2A, UHRF1, CTCF, HOTAIR and ANRIL) were found to have experimental evidence showing that functional perturbations played “driver” roles in human cellular transformation. Measurement of epigenotoxicants presents challenges for short-term carcinogenicity testing, especially in the high-throughput modes emphasized in the Tox21 chemicals testing approach. There is need to develop and validate in vitro tests to detect both, locus-specific, and genome-wide, epigenetic alterations with causal links to oncogenic cellular phenotypes. Some recent examples of cell-based high throughput chemical screening assays are presented that have been applied or have shown potential for application to epigenetic endpoints.
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47
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Weirich S, Kudithipudi S, Jeltsch A. Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex. Mol Oncol 2017; 11:373-387. [PMID: 28182322 PMCID: PMC5527479 DOI: 10.1002/1878-0261.12041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/28/2017] [Accepted: 02/02/2017] [Indexed: 12/19/2022] Open
Abstract
Somatic missense mutations in the mixed lineage leukemia 1 (MLL1) histone H3K4 methyltransferase are often observed in cancers. MLL1 forms a complex with WDR5, RBBP5, and ASH2L (WRA) which stimulates its activity. The MM‐102 compound prevents the interaction between MLL1 and WDR5 and functions as an MLL1 inhibitor. We have studied the effects of four cancer mutations in the catalytic SET domain of MLL1 on the enzymatic activity of MLL1 and MLL1–WRA complexes. In addition, we studied the interaction of the MLL1 mutants with the WRA proteins and inhibition of MLL1–WRA complexes by MM‐102. All four investigated mutations had strong effects on the activity of MLL1. R3903H was inactive and S3865F showed reduced activity both alone and in complex with WRA, but its activity was stimulated by the WRA complex. By contrast, R3864C and R3841W were both more active than wild‐type MLL1, but still less active than the wild‐type MLL1–WRA complex. Both mutants were not stimulated by complex formation with WRA, although no differences in the interaction with the complex proteins were observed. These results indicate that both mutants are in an active conformation even in the absence of the WRA complex and their normal control of activity by the WRA complex is altered. In agreement with this observation, the activity of R3864C and R3841W was not reduced by addition of the MM‐102 inhibitor. We show that different cancer mutations in MLL1 lead to a loss or increase in activity, illustrating the complex and tumor‐specific role of MLL1 in carcinogenesis. Our data exemplify that biochemical investigations of somatic tumor mutations are required to decipher their pathological role. Moreover, our data indicate that MM‐102 may not be used as an MLL1 inhibitor if the R3864C and R3841W mutations are present. More generally, the efficacy of any enzyme inhibitor must be experimentally confirmed for mutant enzymes before an application can be considered.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Germany
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48
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Rutherford EL, Lowery LA. Exploring the developmental mechanisms underlying Wolf-Hirschhorn Syndrome: Evidence for defects in neural crest cell migration. Dev Biol 2016; 420:1-10. [PMID: 27777068 PMCID: PMC5193094 DOI: 10.1016/j.ydbio.2016.10.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/03/2016] [Accepted: 10/18/2016] [Indexed: 01/20/2023]
Abstract
Wolf-Hirschhorn Syndrome (WHS) is a neurodevelopmental disorder characterized by mental retardation, craniofacial malformation, and defects in skeletal and heart development. The syndrome is associated with irregularities on the short arm of chromosome 4, including deletions of varying sizes and microduplications. Many of these genotypic aberrations in humans have been correlated with the classic WHS phenotype, and animal models have provided a context for mapping these genetic irregularities to specific phenotypes; however, there remains a significant knowledge gap concerning the cell biological mechanisms underlying these phenotypes. This review summarizes literature that has made recent contributions to this topic, drawing from the vast body of knowledge detailing the genetic particularities of the disorder and the more limited pool of information on its cell biology. Finally, we propose a novel characterization for WHS as a pathophysiology owing in part to defects in neural crest cell motility and migration during development.
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Affiliation(s)
- Erin L Rutherford
- Boston College, Department of Biology, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, United States
| | - Laura Anne Lowery
- Boston College, Department of Biology, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, United States.
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Sanpaolo E, Miroballo M, Corbetta S, Verdelli C, Baorda F, Balsamo T, Graziano P, Fabrizio FP, Cinque L, Scillitani A, Muscarella LA, Guarnieri V. EZH2 and ZFX oncogenes in malignant behaviour of parathyroid neoplasms. Endocrine 2016; 54:55-59. [PMID: 26876532 DOI: 10.1007/s12020-016-0892-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/03/2016] [Indexed: 12/23/2022]
Abstract
Several studies reported somatic mutations of many genes (MEN1, CTNNB1, CDKIs and others) in parathyroid adenoma, although with different prevalence. Recently, activating mutations of the EZH2 and ZFX oncogenes were identified in benign parathyroid adenoma by whole exome sequencing. The same mutations had been found in blood and ovary malignant tumours. On one hand, this result raised the hypothesis that these oncogenes may play a role in the onset of parathyroid tumour, but it would also suggest they may be involved in malignant, rather benign, parathyroid neoplasm. Our aim was to verify the occurrence of selected mutations of the EZH2 and ZFX genes in an Italian cohort of 23 sporadic parathyroid carcinomas, 12 atypical and 45 typical adenomas. DNA was extracted from paraffin-embedded tissues, PCR amplified and directly sequenced. No mutations were detected in the coding sequence and boundaries of both genes in any of the samples. Two polymorphisms of the EZH2 gene were identified with different prevalence: the rs2072407 variant was present in the 30 % of the samples, in keeping with the overall frequency in larger populations, while the rs78589034 variant, located close to the 5' end of the exon 16, was detected in only one proband with familial isolated hyperparathyroidism; we investigated the possible outcome on the splicing process. EZH2 and ZFX genes do not seem to have an impact on the onset of most parathyroid tumours, both benign and malignant, though further studies on larger cohorts of different ethnicity are needed.
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Affiliation(s)
- E Sanpaolo
- Medical Genetics, Poliambulatorio Giovanni Paolo II, IRCCS Casa Sollievo della Sofferenza Hospital, 71013, San Giovanni Rotondo, FG, Italy
| | - M Miroballo
- Medical Genetics, Poliambulatorio Giovanni Paolo II, IRCCS Casa Sollievo della Sofferenza Hospital, 71013, San Giovanni Rotondo, FG, Italy
| | - S Corbetta
- Endocrinology Unit, Department of Biomedical Sciences for Health, University of Milan, IRCCS Policlinico San Donato, San Donato Milanese, MI, Italy
| | - C Verdelli
- Laboratory of Molecular Biology, IRCCS Policlinico San Donato, San Donato Milanese, MI, Italy
| | - F Baorda
- Medical Genetics, Poliambulatorio Giovanni Paolo II, IRCCS Casa Sollievo della Sofferenza Hospital, 71013, San Giovanni Rotondo, FG, Italy
| | - T Balsamo
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - P Graziano
- Pathology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - F P Fabrizio
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - L Cinque
- Medical Genetics, Poliambulatorio Giovanni Paolo II, IRCCS Casa Sollievo della Sofferenza Hospital, 71013, San Giovanni Rotondo, FG, Italy
| | - A Scillitani
- Endocrinology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - L A Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Vito Guarnieri
- Medical Genetics, Poliambulatorio Giovanni Paolo II, IRCCS Casa Sollievo della Sofferenza Hospital, 71013, San Giovanni Rotondo, FG, Italy.
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50
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Samuelsson JK, Dumbovic G, Polo C, Moreta C, Alibés A, Ruiz-Larroya T, Giménez-Bonafé P, Alonso S, Forcales SV, Manuel P. Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage. EPIGENOMES 2016; 1. [PMID: 31867127 PMCID: PMC6924650 DOI: 10.3390/epigenomes1010002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA hypomethylation at repetitive elements accounts for the genome-wide DNA hypomethylation common in cancer, including colorectal cancer (CRC). We identified a pericentromeric repeat element called SST1 frequently hypomethylated (>5% demethylation compared with matched normal tissue) in several cancers, including 28 of 128 (22%) CRCs. SST1 somatic demethylation associated with genome damage, especially in tumors with wild-type TP53. Seven percent of the 128 CRCs exhibited a higher (“severe”) level of demethylation (≥10%) that co-occurred with TP53 mutations. SST1 demethylation correlated with distinct histone marks in CRC cell lines and primary tumors: demethylated SST1 associated with high levels of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark and lower levels of histone 3 lysine 9 trimethylation (H3K9me3). Furthermore, induced demethylation of SST1 by 5-aza-dC led to increased H3K27me3 and reduced H3K9me3. Thus, in some CRCs, SST1 demethylation reflects an epigenetic reprogramming associated with changes in chromatin structure that may affect chromosomal integrity. The chromatin remodeler factor, the helicase lymphoid-specific (HELLS) enzyme, called the “epigenetic guardian of repetitive elements”, interacted with SST1 as shown by chromatin immunoprecipitation, and down-regulation of HELLS by shRNA resulted in demethylation of SST1 in vitro. Altogether these results suggest that HELLS contributes to SST1 methylation maintenance. Alterations in HELLS recruitment and function could contribute to the somatic demethylation of SST1 repeat elements undergone before and/or during CRC pathogenesis.
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Affiliation(s)
- Johanna K. Samuelsson
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Active Motif, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
| | - Gabrijela Dumbovic
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Cristian Polo
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Cristina Moreta
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Andreu Alibés
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | | | - Pepita Giménez-Bonafé
- Departament de Ciències Fisiòlogiques, Facultat de Medicina i Ciències de la Salut, Campus Ciències de la Salut, Bellvitge, Universitat de Barcelona, Hospitalet del Llobregat 08916, Barcelona, Spain
| | - Sergio Alonso
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Sonia-V. Forcales
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
- Correspondence: (S.-V.F.); (M.P.)
| | - Perucho Manuel
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
- Correspondence: (S.-V.F.); (M.P.)
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