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Histone Methyltransferase SETDB1 Promotes Immune Evasion in Colorectal Cancer via FOSB-Mediated Downregulation of MicroRNA-22 through BATF3/PD-L1 Pathway. J Immunol Res 2022; 2022:4012920. [PMID: 35497876 PMCID: PMC9045983 DOI: 10.1155/2022/4012920] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/24/2022] [Indexed: 12/24/2022] Open
Abstract
Tumors may develop a variety of immune evasion mechanisms during the progression of colorectal cancer (CRC). Here, we intended to explore the mechanism of histone methyltransferase SETDB1 in immune evasion in CRC. The expression of SETDB1, microRNA-22 (miR-22), BATF3, PD-L1, and FOSB in CRC tissues and cells was determined with their interactions analyzed also. Gain-of-function and loss-of-function approaches were employed to evaluate the effects of the SETDB1/FOSB/miR-22/BATF3/PD-L1 axis on T cell function, immune cell infiltration, and tumorigenesis. Aberrant high SETDB1 expression in CRC was positively associated with PD-L1 expression. SETDB1 negatively regulated miR-22 expression by downregulating FOSB expression, while miR-22 downregulated PD-L1 expression via targeting BATF3. Furthermore, SETDB1 silencing promoted the T cell-mediated cytotoxicity to tumor cells via the FOSB/miR-22/BATF3/PD-L1 axis and hindered CRC tumor growth in mice while leading to decreased immune cell infiltration. Taken together, SETDB1 could activate the BATF3/PD-L1 axis by inhibiting FOSB-mediated miR-22 and promote immune evasion in CRC, which provides a better understanding of the mechanisms underlying immune evasion in CRC.
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Peng C, Jian X, Xie Y, Li L, Ouyang J, Tang L, Zhang X, Su J, Zhao S, Liu H, Yin M, Wu D, Wan M, Xie L, Chen X. Genomic alterations of dermatofibrosarcoma protuberans revealed by whole-genome sequencing. Br J Dermatol 2022; 186:997-1009. [PMID: 35441365 PMCID: PMC9325047 DOI: 10.1111/bjd.20976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 12/18/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022]
Abstract
Background Dermatofibrosarcoma protuberans (DFSP) is a rare and marginal cutaneous sarcoma of intermediate‐grade malignancy, for which the genomic landscape remains unclear. Understanding the landscape of DFSP will help to further classify the genomic pathway of malignant development in soft tissue. Objectives To identify the comprehensive molecular pathogenesis of DFSP. Methods In this study, the comprehensive genomic features, with 53 tumour‐normal pairs of DFSP, were revealed by whole‐genome sequencing. Results The mutational signature 1 (C > T mutation at CpG dinucleotides) is featured in DFSP, resulting in higher mutations in DNA replication. Interestingly, the recurrence of DFSP is correlated with low tumour mutation burden. Novel mutation genes in DFSP were identified, including MUC4/6, KMT2C and BRCA1, and subsequently, three molecular subtypes of DFSP were classified on the basis of MUC4 and MUC6 mutations. Various structural aberrations including genomic rearrangements were identified in DSFPs, particularly in 17q and 22q, which cause oncogene amplification (AKT1, SPHK1, COL1A1, PDGFβ) or tumour suppressor deletion (CDKN2A/B). In addition to gene fusion of COL1A1‐PDGFβ [t(17;22)], we identified gene fusion of SLC2A5‐BTBD7 [t(1;14)] in DFSP through whole‐genome sequencing, and verified it experimentally. Enrichment analysis of altered molecules revealed that DNA repair, cell cycle, phosphoinositide 3‐kinase and Janus kinase pathways were primarily involved in DFSP. Conclusions This is the first large‐scale whole‐genome sequencing for DFSP, and our findings describe the comprehensive genomic landscape, highlighting the molecular complexity and genomic aberrations of DFSP. Our findings also provide novel potential diagnostic and therapeutic targets for this disease. What is already known about this topic?Chromosomal translocation between chromosome 17 and chromosome 22 is the main feature in the pathogenesis of dermatofibrosarcoma protuberans (DFSP).
What does this study add?We describe the comprehensive genomic landscape of DFSP, highlighting the molecular complexity and genomic aberrations. Our findings provide novel potential diagnostic and therapeutic targets for this disease.
What is the translational message?Our study revealed novel molecular subtypes of DFSP based on genetic mutations, which benefits precision diagnosis. We also found oncogene amplification, including AKT1 and SPHK1, which provides novel potential target molecules for further DFSP treatment. In addition to gene fusion of COL1A1‐PDGFβ, we identified a novel gene fusion of SLC2A5‐BTBD7 in DFSP, which is a novel potential diagnostic and therapeutic target for this disease.
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Affiliation(s)
- Cong Peng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Xingxing Jian
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yang Xie
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lingfeng Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Jian Ouyang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Ling Tang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Xu Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Shuang Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Hong Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Mingzhu Yin
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Dan Wu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Miaojian Wan
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, Hunan, China.,Hunan Engineering Research Center of Skin Health and Disease, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
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Małecki JM, Davydova E, Falnes PØ. Protein methylation in mitochondria. J Biol Chem 2022; 298:101791. [PMID: 35247388 PMCID: PMC9006661 DOI: 10.1016/j.jbc.2022.101791] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Many proteins are modified by posttranslational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g., respiratory Complex I, citrate synthase, and the ATP synthase. In the present review, we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation and present an outlook for this emergent research field.
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
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Fear VS, Forbes CA, Anderson D, Rauschert S, Syn G, Shaw N, Jamieson S, Ward M, Baynam G, Lassmann T. CRISPR single base editing, neuronal disease modelling and functional genomics for genetic variant analysis: pipeline validation using Kleefstra syndrome EHMT1 haploinsufficiency. Stem Cell Res Ther 2022; 13:69. [PMID: 35139903 PMCID: PMC8827184 DOI: 10.1186/s13287-022-02740-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Background Over 400 million people worldwide are living with a rare disease. Next Generation Sequencing (NGS) identifies potential disease causative genetic variants. However, many are identified as variants of uncertain significance (VUS) and require functional laboratory validation to determine pathogenicity, and this creates major diagnostic delays. Methods In this study we test a rapid genetic variant assessment pipeline using CRISPR homology directed repair to introduce single nucleotide variants into inducible pluripotent stem cells (iPSCs), followed by neuronal disease modelling, and functional genomics on amplicon and RNA sequencing, to determine cellular changes to support patient diagnosis and identify disease mechanism. Results As proof-of-principle, we investigated an EHMT1 (Euchromatin histone methyltransferase 1; EHMT1 c.3430C > T; p.Gln1144*) genetic variant pathogenic for Kleefstra syndrome and determined changes in gene expression during neuronal progenitor cell differentiation. This pipeline rapidly identified Kleefstra syndrome in genetic variant cells compared to healthy cells, and revealed novel findings potentially implicating the key transcription factors REST and SP1 in disease pathogenesis. Conclusion The study pipeline is a rapid, robust method for genetic variant assessment that will support rare diseases patient diagnosis. The results also provide valuable information on genome wide perturbations key to disease mechanism that can be targeted for drug treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02740-3.
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Affiliation(s)
- Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
| | - Denise Anderson
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Sebastian Rauschert
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Genevieve Syn
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Nicole Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia
| | - Sarra Jamieson
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia.,Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, Australia
| | - Timo Lassmann
- Translational Genetics, Precision Health, Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, 6009, Australia.,Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
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Li X, Han M, Zhang H, Liu F, Pan Y, Zhu J, Liao Z, Chen X, Zhang B. Structures and biological functions of zinc finger proteins and their roles in hepatocellular carcinoma. Biomark Res 2022; 10:2. [PMID: 35000617 PMCID: PMC8744215 DOI: 10.1186/s40364-021-00345-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022] Open
Abstract
Zinc finger proteins are transcription factors with the finger domain, which plays a significant role in gene regulation. As the largest family of transcription factors in the human genome, zinc finger (ZNF) proteins are characterized by their different DNA binding motifs, such as C2H2 and Gag knuckle. Different kinds of zinc finger motifs exhibit a wide variety of biological functions. Zinc finger proteins have been reported in various diseases, especially in several cancers. Hepatocellular carcinoma (HCC) is the third leading cause of cancer-associated death worldwide, especially in China. Most of HCC patients have suffered from hepatitis B virus (HBV) and hepatitis C virus (HCV) injection for a long time. Although the surgical operation of HCC has been extremely developed, the prognosis of HCC is still very poor, and the underlying mechanisms in HCC tumorigenesis are still not completely understood. Here, we summarize multiple functions and recent research of zinc finger proteins in HCC tumorigenesis and progression. We also discuss the significance of zinc finger proteins in HCC diagnosis and prognostic evaluation.
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Affiliation(s)
- Xinxin Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Mengzhen Han
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Hongwei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Yonglong Pan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Jinghan Zhu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
| | - Xiaoping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China. .,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, 430030, China.
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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57
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Goodman S, Chappell G, Guyton KZ, Pogribny IP, Rusyn I. Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: An update of a systematic literature review. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108408. [PMID: 35690411 PMCID: PMC9188653 DOI: 10.1016/j.mrrev.2021.108408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/28/2021] [Accepted: 12/07/2021] [Indexed: 01/03/2023]
Abstract
Epigenetic alterations, such as changes in DNA methylation, histones/chromatin structure, nucleosome positioning, and expression of non-coding RNAs, are recognized among key characteristics of carcinogens; they may occur independently or concomitantly with genotoxic effects. While data on genotoxicity are collected through standardized guideline tests, data collected on epigenetic effects is far less uniform. In 2016, we conducted a systematic review of published studies of genotoxic carcinogens that reported epigenetic endpoints to better understand the evidence for epigenetic alterations of human carcinogens, and the potential association with genotoxic endpoints. Since then, the number of studies of epigenetic effects of chemicals has nearly doubled. This review stands as an update on epigenetic alterations induced by occupational and environmental human carcinogens that were previously and recently classified as Group 1 by the International Agency for Research on Cancer. We found that the evidence of epigenetic effects remains uneven across agents. Studies of DNA methylation are most abundant, while reports concerning effects on non-coding RNA have increased over the past 5 years. By contrast, mechanistic toxicology studies of histone modifications and chromatin state alterations remain few. We found that most publications of epigenetic effects of carcinogens were studies in exposed humans or human cells. Studies in rodents represent the second most common species used for epigenetic studies in toxicology, in vivo exposures being the most predominant. Future studies should incorporate dose- and time-dependent study designs and also investigate the persistence of effects following cessation of exposure, considering the dynamic nature of most epigenetic alterations.
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Affiliation(s)
- Samantha Goodman
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | | | | | - Igor P Pogribny
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
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Li M, Qiu C, Bian Y, Shi D, Wang B, Ma Q, Wang X, Shi J, Zhang L, Ma Y, Zhu P, Cheng T, Chu Y, Yuan W. SETD5 modulates homeostasis of hematopoietic stem cells by mediating RNA Polymerase II pausing in cooperation with HCF-1. Leukemia 2022; 36:1111-1122. [PMID: 34853439 PMCID: PMC8979820 DOI: 10.1038/s41375-021-01481-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 12/23/2022]
Abstract
SETD5 mutations were identified as the genetic causes of neurodevelopmental disorders. While the whole-body knockout of Setd5 in mice leads to embryonic lethality, the role of SETD5 in adult stem cell remains unexplored. Here, a critical role of Setd5 in hematopoietic stem cells (HSCs) is identified. Specific deletion of Setd5 in hematopoietic system significantly increased the number of immunophenotypic HSCs by promoting HSC proliferation. Setd5-deficient HSCs exhibited impaired long-term self-renewal capacity and multiple-lineage differentiation potentials under transplantation pressure. Transcriptome analysis of Setd5-deficient HSCs revealed a disruption of quiescence state of long-term HSCs, a cause of the exhaustion of functional HSCs. Mechanistically, SETD5 was shown to regulate HSC quiescence by mediating the release of promoter-proximal paused RNA polymerase II (Pol II) on E2F targets in cooperation with HCF-1 and PAF1 complex. Taken together, these findings reveal an essential role of SETD5 in regulating Pol II pausing-mediated maintenance of adult stem cells.
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Affiliation(s)
- Mengke Li
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chen Qiu
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yujie Bian
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Deyang Shi
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Bichen Wang
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Qiuyi Ma
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaomin Wang
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jun Shi
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lianfeng Zhang
- grid.506261.60000 0001 0706 7839Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Yuanwu Ma
- grid.506261.60000 0001 0706 7839Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Peking Union Medicine College, Beijing, China
| | - Ping Zhu
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Tao Cheng
- grid.461843.cState Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yajing Chu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
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Wilson JR. Determination of Histone Methyltransferase Structure by Crystallography. Methods Mol Biol 2022; 2529:137-147. [PMID: 35733014 DOI: 10.1007/978-1-0716-2481-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As discussed in previous chapters, the methylation of specific arginine and lysine side chains is carried out by two families of histone methyltransferases, the Protein Arginine Methyltransferase (PRMT) family for arginine, and the SET domain family for lysine. The methylation of H3K79 by Dot1 is a notable outlier. In all cases, X-ray crystallography has been a powerful technique that has provided the framework for understanding the enzyme mechanism, kinetics, regulation and specificity of these enzymes and is now a platform for the design of compounds aimed to inhibit their activity either to further understand their function or in a therapeutic setting. Notably, in combination with the structures of the complementary recognition domains that recognize their products, these structures have provided an important insight into how integral the number of methyl groups added to the acceptor amine is to making histone methylation a key process in epigenetic regulation of gene transcription. Here the concepts applied to determine their structure by X-ray crystallography are outlined, with particular emphasis on lysine methylation by the SET domain.
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Structural Analysis of SMYD3 Lysine Methyltransferase for the Development of Competitive and Specific Enzyme Inhibitors. Diseases 2021; 10:diseases10010004. [PMID: 35076487 PMCID: PMC8788566 DOI: 10.3390/diseases10010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/03/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022] Open
Abstract
Lysine methylation is among the key posttranslational modifications to histones that contribute to epigenetic regulation. SMYD3 is a lysine methyltransferase that is essential for the proliferation of a range of tumorigenic cells. The findings that SMYD3 is significantly upregulated in most colorectal carcinomas, hepatocellular carcinomas, and breast cell carcinomas support a model in which its aberrant expression modifies established patterns of gene expression, ultimately driving unrestrained proliferation. Herein, we dissect the unique structural features of SMYD3 relative to other SET enzymes, with an emphasis on the implications for selective design of therapeutics for the clinical management of cancer. Further, we illustrate the ability of inhibitors targeting the SET domain of SMYD3 to reduce the viability of colorectal and lung carcinoma cells.
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Li M, Ning J, Wang J, Yan Q, Zhao K, Jia X. SETD7 regulates chondrocyte differentiation and glycolysis via the Hippo signaling pathway and HIF‑1α. Int J Mol Med 2021; 48:210. [PMID: 34617577 PMCID: PMC8510680 DOI: 10.3892/ijmm.2021.5043] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
Chondrocytes are well adapted to hypoxia and produce more functional extracellular matrix in low oxygen environments in vitro. In our previous study, methyltransferase SET domain containing (SETD)7 regulated chondrocyte activity in hypoxic conditions. However, the precise association between SETD7 and chondrocyte differentiation under low oxygen partial pressure remains unclear. The association between SETD7 and chondrocyte differentiation was studied by silencing SETD7 in chondrocytes in vitro. The results showed that the silencing of SETD7 in ATDC5 cells inhibited the Hippo signaling pathway, decreased Yes-associated protein (YAP) phosphorylation and increased the levels of YAP and hypoxia inducible factor-1α (HIF-1α) in the nucleus. YAP combined with HIF-1α to form a complex that promoted the expression of genes involved in chondrogenic differentiation and the glycolytic pathway. Thus, SETD7 inhibited chondrocyte differentiation and glycolysis via the Hippo signaling pathway. The present study demonstrated that SETD7 was a potential molecular target that maintained the chondrocyte phenotype during cartilage tissue engineering and cartilage-associated disease.
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Affiliation(s)
- Maoquan Li
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Jinqiu Ning
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Jiwei Wang
- Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510140, P.R. China
| | - Qiqian Yan
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Ke Zhao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Xiaoshi Jia
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
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62
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Witecka A, Kwiatkowski S, Ishikawa T, Drozak J. The Structure, Activity, and Function of the SETD3 Protein Histidine Methyltransferase. Life (Basel) 2021; 11:1040. [PMID: 34685411 PMCID: PMC8537074 DOI: 10.3390/life11101040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 12/03/2022] Open
Abstract
SETD3 has been recently identified as a long sought, actin specific histidine methyltransferase that catalyzes the Nτ-methylation reaction of histidine 73 (H73) residue in human actin or its equivalent in other metazoans. Its homologs are widespread among multicellular eukaryotes and expressed in most mammalian tissues. SETD3 consists of a catalytic SET domain responsible for transferring the methyl group from S-adenosyl-L-methionine (AdoMet) to a protein substrate and a RuBisCO LSMT domain that recognizes and binds the methyl-accepting protein(s). The enzyme was initially identified as a methyltransferase that catalyzes the modification of histone H3 at K4 and K36 residues, but later studies revealed that the only bona fide substrate of SETD3 is H73, in the actin protein. The methylation of actin at H73 contributes to maintaining cytoskeleton integrity, which remains the only well characterized biological effect of SETD3. However, the discovery of numerous novel methyltransferase interactors suggests that SETD3 may regulate various biological processes, including cell cycle and apoptosis, carcinogenesis, response to hypoxic conditions, and enterovirus pathogenesis. This review summarizes the current advances in research on the SETD3 protein, its biological importance, and role in various diseases.
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Affiliation(s)
- Apolonia Witecka
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (A.W.); (S.K.)
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (A.W.); (S.K.)
| | - Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (A.W.); (S.K.)
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63
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Yang C, Wang K, Liang Q, Tian TT, Zhong Z. Role of NSD1 as potential therapeutic target in tumor. Pharmacol Res 2021; 173:105888. [PMID: 34536546 DOI: 10.1016/j.phrs.2021.105888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/29/2022]
Abstract
Nuclear receptor binding SET Domain Protein 1 (NSD1) is a bifunctional transcriptional regulatory protein that encodes histone methyltransferase. Mono- and di-methylation of H3K36 by NSD1 is mainly primarily involved in the regulation of gene expression, DNA repair, alternative splicing, and other important biological processes. Many types of cancers, including acute myelogenous leukemia (AML), liver cancer, lung cancer, endometrial carcinoma, colorectal cancer, and pancreatic cancer, are associated with NSD1 fusion, missense mutation, nonsense mutation, silent mutation, deletion, and insertion of frameshift, and deletion in a frame. Therefore, targeting NSD1 may be a potential strategy for tumor therapy. An in-depth study of the structure and biological activities of NSD1 sets the groundwork for improving tumor therapy and creating NSD1 inhibitors. This article emphasizes the role of NSD1 in tumorigenesis and the development of NSD1 targeted small-molecule inhibitors.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Qilian Liang
- Oncology Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province 524001, China
| | - Tian-Tian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province 519087, China.
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
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64
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Reyes DA, Sarría VMS, Salazar-Viedma M, D'Afonseca V. Histone Methyltransferases Useful in Gastric Cancer Research. Cancer Inform 2021; 20:11769351211039862. [PMID: 34413625 PMCID: PMC8369960 DOI: 10.1177/11769351211039862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
Gastric cancer (GC) is one of the most frequent tumors in the world. Stomach adenocarcinoma is a heterogeneous tumor, turning the prognosis prediction and patients’ clinical management difficult. Some diagnosis tests for GC are been development using knowledge based in polymorphisms, somatic copy number alteration (SCNA) and aberrant histone methylation. This last event, a posttranslational modification that occurs at the chromatin level, is an important epigenetic alteration seen in several tumors including stomach adenocarcinoma. Histone methyltransferases (HMT) are the proteins responsible for the methylation in specific amino acids residues of histones tails. Here, were presented several HMTs that could be relating to GC process. We use public data from 440 patients with stomach adenocarcinoma. We evaluated the alterations as SCNAs, mutations, and genes expression level of HMTs in these aforementioned samples. As results, it was identified the 10 HMTs most altered (up to 30%) in stomach adenocarcinoma samples, which are the PRDM14, PRDM9, SUV39H2, NSD2, SMYD5, SETDB1, PRDM12, SUV39H1, NSD3, and EHMT2 genes. The PRDM9 gene is among most mutated and amplified HMTs within the data set studied. PRDM14 is downregulated in 79% of the samples and the SUV39H2 gene is down expressed in patients with recurred/progressed disease. Several HMTs are altered in many cancers. It is important to generate a genetic atlas of alterations of cancer-related genes to improve the understanding of tumorigenesis events and to propose novel tools of diagnosis and prognosis for the cancer control.
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Affiliation(s)
- Dafne Alejandra Reyes
- Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | | | - Marcela Salazar-Viedma
- Laboratorio de Genética y Microevolución, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, Chile
| | - Vívian D'Afonseca
- Centro de Investigación y Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Posgrado, Universidad Católica del Maule, Talca, Chile
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65
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Pickering OJ, Breininger SP, Underwood TJ, Walters ZS. Histone Modifying Enzymes as Targets for Therapeutic Intervention in Oesophageal Adenocarcinoma. Cancers (Basel) 2021; 13:4084. [PMID: 34439236 PMCID: PMC8392153 DOI: 10.3390/cancers13164084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 12/24/2022] Open
Abstract
Oesophageal adenocarcinoma (OAC) has a dismal prognosis, where curable disease occurs in less than 40% of patients, and many of those with incurable disease survive for less than a year from diagnosis. Despite the widespread use of systematic chemotherapy in OAC treatment, many patients receive no benefit. New treatments are urgently needed for OAC patients. There is an emerging interest in epigenetic regulators in cancer pathogenesis, which are now translating into novel cancer therapeutic strategies. Histone-modifying enzymes (HMEs) are key epigenetic regulators responsible for dynamic covalent histone modifications that play roles in both normal and dysregulated cellular processes including tumorigenesis. Several HME inhibitors are in clinical use for haematological malignancies and sarcomas, with numerous on-going clinical trials for their use in solid tumours. This review discusses the current literature surrounding HMEs in OAC pathogenesis and their potential use in targeted therapies for this disease.
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Affiliation(s)
| | | | | | - Zoë S. Walters
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK; (O.J.P.); (S.P.B.); (T.J.U.)
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66
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Klonou A, Chlamydas S, Piperi C. Structure, Activity and Function of the MLL2 (KMT2B) Protein Lysine Methyltransferase. Life (Basel) 2021; 11:823. [PMID: 34440566 PMCID: PMC8401916 DOI: 10.3390/life11080823] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022] Open
Abstract
The Mixed Lineage Leukemia 2 (MLL2) protein, also known as KMT2B, belongs to the family of mammalian histone H3 lysine 4 (H3K4) methyltransferases. It is a large protein of 2715 amino acids, widely expressed in adult human tissues and a paralog of the MLL1 protein. MLL2 contains a characteristic C-terminal SET domain responsible for methyltransferase activity and forms a protein complex with WRAD (WDR5, RbBP5, ASH2L and DPY30), host cell factors 1/2 (HCF 1/2) and Menin. The MLL2 complex is responsible for H3K4 trimethylation (H3K4me3) on specific gene promoters and nearby cis-regulatory sites, regulating bivalent developmental genes as well as stem cell and germinal cell differentiation gene sets. Moreover, MLL2 plays a critical role in development and germ line deletions of Mll2 have been associated with early growth retardation, neural tube defects and apoptosis that leads to embryonic death. It has also been involved in the control of voluntary movement and the pathogenesis of early stage childhood dystonia. Additionally, tumor-promoting functions of MLL2 have been detected in several cancer types, including colorectal, hepatocellular, follicular cancer and gliomas. In this review, we discuss the main structural and functional aspects of the MLL2 methyltransferase with particular emphasis on transcriptional mechanisms, gene regulation and association with diseases.
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Affiliation(s)
- Alexia Klonou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
| | - Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
- Research and Development Department, Active Motif, Inc., Carlsbad, CA 92008, USA
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.K.); (S.C.)
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67
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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68
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Psychostimulants and opioids differentially influence the epigenetic modification of histone acetyltransferase and histone deacetylase in astrocytes. PLoS One 2021; 16:e0252895. [PMID: 34115777 PMCID: PMC8195369 DOI: 10.1371/journal.pone.0252895] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
Illicit drugs are known to affect central nervous system (CNS). Majorly psychostimulants such as cocaine, methamphetamine (METH) and opioids such as morphine are known to induce epigenetic changes of histone modifications and chromatin remodeling which are mediated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). Aberrant changes in histone acetylation-deacetylation process further exacerbate dysregulation of gene expression and protein modification which has been linked with neuronal impairments including memory formation and synaptic plasticity. In CNS, astrocytes play a pivotal role in cellular homeostasis. However, the impact of psychostimulants and opioid mediated epigenetic changes of HAT/HADCs in astrocytes has not yet been fully elucidated. Therefore, we have investigated the effects of the psychostimulants and opioid on the acetylation-regulating enzymes- HAT and HDACs role in astrocytes. In this study, Class I and II HDACs and HATs gene expression, protein changes and global level changes of acetylation of H3 histones at specific lysines were analyzed. In addition, we have explored the neuroprotective “nootropic” drug piracetam were exposed with or without psychostimulants and opioid in the human primary astrocytes. Results revealed that psychostimulants and opioid upregulated HDAC1, HDAC4 and p300 expression, while HDAC5 and GCN5 expression were downregulated. These effects were reversed by piracetam coexposure. Psychostimulants and opioid exposure upregulated global acetylation levels of all H3Ks, except H3K14. These results suggest that psychostimulants and opioids differentially influence HATs and HDACs.
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69
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Mei YC, Feng J, He F, Li YM, Liu Y, Li F, Chen Y, Du HN. Set2-mediated H3K36 methylation states redundantly repress the production of antisense transcripts: role in transcription regulation. FEBS Open Bio 2021. [PMID: 34115924 PMCID: PMC8329787 DOI: 10.1002/2211-5463.13226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/30/2021] [Accepted: 06/10/2021] [Indexed: 01/04/2023] Open
Abstract
Methyltransferase Set2‐mediated methylation of histone H3 lysine 36 (H3K36), which involves the addition of up to three methyl groups at this site, has been demonstrated to function in many chromatin‐coupled events. The methylation of H3K36 is known to recruit different chromatin effector proteins, affecting transcription, mRNA splicing and DNA repair. In this study, we engineered two yeast set2 mutants that lack H3K36 mono/dimethylation (H3K36me1/2) and trimethylation (H3K36me3), respectively, and characterized their roles in the production of antisense transcripts under nutrient‐rich conditions. Using our new bioinformatics identification pipeline analysis, we are able to identify a larger number of antisense transcripts in set2∆ cells than has been published previously. We further show that H3K36me1/2 or H3K36me3 redundantly repressed the production of antisense transcripts. Moreover, gene ontology (GO) analysis implies that H3K36me3‐mediated antisense transcription might play a role in DNA replication and DNA damage repair, which is independent of regulation of the corresponding sense gene expression. Overall, our results validate a coregulatory mechanism of different H3K36 methylation states, particularly in the repression of antisense transcription.
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Affiliation(s)
- Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, RNA Institute, Wuhan University, China
| | - Jiangpeng Feng
- State Key Laboratory of Virology, College of Life Sciences, RNA Institute, Wuhan University, China
| | - Fei He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, RNA Institute, Wuhan University, China
| | - Yafei Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, RNA Institute, Wuhan University, China
| | - Feng Li
- School of Basic Medical Sciences, Wuhan University, China
| | - Yu Chen
- State Key Laboratory of Virology, College of Life Sciences, RNA Institute, Wuhan University, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, RNA Institute, Wuhan University, China
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70
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Zhai X, Brownell JE. Biochemical perspectives on targeting KMT2 methyltransferases in cancer. Trends Pharmacol Sci 2021; 42:688-699. [PMID: 34074527 DOI: 10.1016/j.tips.2021.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/20/2021] [Accepted: 05/05/2021] [Indexed: 02/05/2023]
Abstract
KMT2 methyltransferases are important regulators of gene transcription through the methylation of histone H3 lysine 4 at promoter and enhancer regions. They reside in large, multisubunit protein complexes, which not only regulate their catalytic activities but also mediate their interactions with chromatin. The KMT2 family was initially associated with cancer due to the discovery of KMT2A translocations in mixed-lineage leukemia (MLL). However, emerging evidences suggest that the methyltransferase activity of KMT2 enzymes can also be important in cancer, raising the prospect of targeting the catalytic domain of KMT2 as a therapeutic strategy. In this review, we summarize recent advances in our understanding of KMT2 enzyme mechanisms and their regulation on nucleosomes, which will provide mechanistic insights into therapeutic discoveries targeting their methyltransferase activities.
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Affiliation(s)
- Xiang Zhai
- Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Waltham, MA 02451, USA.
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71
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Małecki JM, Odonohue MF, Kim Y, Jakobsson ME, Gessa L, Pinto R, Wu J, Davydova E, Moen A, Olsen JV, Thiede B, Gleizes PE, Leidel SA, Falnes PØ. Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function. Nucleic Acids Res 2021; 49:3185-3203. [PMID: 33693809 PMCID: PMC8034639 DOI: 10.1093/nar/gkab088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
Protein methylation occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knockout (KO) cells, identified as 60S ribosomal protein L3 (RPL3). We also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. We found that His-245 in RPL3 carries a 3-methylhistidine (3MH; τ-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be automethylated at His-154, thus further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysome formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.
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Affiliation(s)
- Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Marie-Francoise Odonohue
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Yeji Kim
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation, Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Luca Gessa
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jie Wu
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation, Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Bernd Thiede
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sebastian A Leidel
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
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Yang Y, Wang Y. Role of Epigenetic Regulation in Plasticity of Tumor Immune Microenvironment. Front Immunol 2021; 12:640369. [PMID: 33868269 PMCID: PMC8051582 DOI: 10.3389/fimmu.2021.640369] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/15/2021] [Indexed: 12/24/2022] Open
Abstract
The tumor immune microenvironment (TIME), an immunosuppressive niche, plays a pivotal role in contributing to the development, progression, and immune escape of various types of cancer. Compelling evidence highlights the feasibility of cancer therapy targeting the plasticity of TIME as a strategy to retrain the immunosuppressive immune cells, including innate immune cells and T cells. Epigenetic alterations, such as DNA methylation, histone post-translational modifications, and noncoding RNA-mediated regulation, regulate the expression of many human genes and have been reported to be accurate in the reprogramming of TIME according to vast majority of published results. Recently, mounting evidence has shown that the gut microbiome can also influence the colorectal cancer and even extraintestinal tumors via metabolites or microbiota-derived molecules. A tumor is a kind of heterogeneous disease with specificity in time and space, which is not only dependent on genetic regulation, but also regulated by epigenetics. This review summarizes the reprogramming of immune cells by epigenetic modifications in TIME and surveys the recent progress in epigenetic-based cancer clinical therapeutic approaches. We also discuss the ongoing studies and future areas of research that benefits to cancer eradication.
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Affiliation(s)
- Yunkai Yang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Xing J, Jie W. Methyltransferase SET domain family and its relationship with cardiovascular development and diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 51:251-260. [PMID: 35462466 DOI: 10.3724/zdxbyxb-2021-0192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Abnormal epigenetic modification is closely related to the occurrence and development of cardiovascular diseases. The SET domain (SETD) family is an important epigenetic modifying enzyme containing SETD. They mainly affect gene expression by methylating H3K4, H3K9, H3K36 and H4K20. Additionally, the SETD family catalyzes the methylation of non-histone proteins, thereby affects the signal transduction of signal transduction and activator of transcription (STAT) 1, Wnt/β-catenin, hypoxia-inducible factor (HIF)-1α and Hippo/YAP pathways. The SETD family has the following regulatory effects on cardiovascular development and diseases: regulating coronary artery formation and cardiac development; protecting cardiac tissue from ischemia reperfusion injury; regulating inflammation, oxidative stress and apoptosis in cardiovascular complications of diabetes; participating in the formation of pulmonary hypertension; regulating thrombosis, cardiac hypertrophy and arrhythmia. This article summarizes the basic structures, expression regulation mechanisms and the role of existing SETD family members in cardiovascular development and diseases, in order to provide a basis for understanding the molecular mechanism of cardiovascular disease and exploring the therapeutic targets.
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Affiliation(s)
- Jingci Xing
- 1. Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang 524023, Guangdong Province, China
| | - Wei Jie
- 1. Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang 524023, Guangdong Province, China.,Medical University, Key Laboratory of Emergency and Trauma, Ministry of Education, Hainan Provincial Key Laboratory of Tropical Cardiovascular Diseases Research, Haikou 571199, China
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74
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Cosby RL, Judd J, Zhang R, Zhong A, Garry N, Pritham EJ, Feschotte C. Recurrent evolution of vertebrate transcription factors by transposase capture. Science 2021; 371:eabc6405. [PMID: 33602827 PMCID: PMC8186458 DOI: 10.1126/science.abc6405] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022]
Abstract
Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured-primarily via alternative splicing-to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.
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Affiliation(s)
- Rachel L Cosby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ruiling Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Alan Zhong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Nathaniel Garry
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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75
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Davydova E, Shimazu T, Schuhmacher MK, Jakobsson ME, Willemen HLDM, Liu T, Moen A, Ho AYY, Małecki J, Schroer L, Pinto R, Suzuki T, Grønsberg IA, Sohtome Y, Akakabe M, Weirich S, Kikuchi M, Olsen JV, Dohmae N, Umehara T, Sodeoka M, Siino V, McDonough MA, Eijkelkamp N, Schofield CJ, Jeltsch A, Shinkai Y, Falnes PØ. The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Nat Commun 2021; 12:891. [PMID: 33563959 PMCID: PMC7873184 DOI: 10.1038/s41467-020-20670-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
Post-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where "x" is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.
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Affiliation(s)
- Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Tadahiro Shimazu
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Maren Kirstin Schuhmacher
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Medicon Village, 22100, Lund, Sweden
| | - Hanneke L D M Willemen
- Center for Translational Immunology (CTI), University Medical Center Utrecht, Utrecht University, 3584, Utrecht, EA, The Netherlands
| | - Tongri Liu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Jędrzej Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Lisa Schroer
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Ida A Grønsberg
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Mai Akakabe
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Medicon Village, 22100, Lund, Sweden
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Niels Eijkelkamp
- Center for Translational Immunology (CTI), University Medical Center Utrecht, Utrecht University, 3584, Utrecht, EA, The Netherlands
| | | | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway.
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76
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Lukinović V, Casanova AG, Roth GS, Chuffart F, Reynoird N. Lysine Methyltransferases Signaling: Histones are Just the Tip of the Iceberg. Curr Protein Pept Sci 2021; 21:655-674. [PMID: 31894745 DOI: 10.2174/1871527319666200102101608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022]
Abstract
Protein lysine methylation is a functionally diverse post-translational modification involved in various major cellular processes. Lysine methylation can modulate proteins activity, stability, localization, and/or interaction, resulting in specific downstream signaling and biological outcomes. Lysine methylation is a dynamic and fine-tuned process, deregulation of which often leads to human pathologies. In particular, the lysine methylome and its associated signaling network can be linked to carcinogenesis and cancer progression. Histone modifications and chromatin regulation is a major aspect of lysine methylation importance, but increasing evidence suggests that a high relevance and impact of non-histone lysine methylation signaling has emerged in recent years. In this review, we draw an updated picture of the current scientific knowledge regarding non-histone lysine methylation signaling and its implication in physiological and pathological processes. We aim to demonstrate the significance of lysine methylation as a major and yet underestimated posttranslational modification, and to raise the importance of this modification in both epigenetic and cellular signaling by focusing on the observed activities of SET- and 7β-strandcontaining human lysine methyltransferases. Recent evidence suggests that what has been observed so far regarding lysine methylation's implication in human pathologies is only the tip of the iceberg. Therefore, the exploration of the "methylome network" raises the possibility to use these enzymes and their substrates as promising new therapeutic targets for the development of future epigenetic and methyllysine signaling cancer treatments.
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Affiliation(s)
- Valentina Lukinović
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Alexandre G Casanova
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Gael S Roth
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Florent Chuffart
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
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77
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Kwiatkowski S, Drozak J. Protein Histidine Methylation. Curr Protein Pept Sci 2021; 21:675-689. [PMID: 32188384 DOI: 10.2174/1389203721666200318161330] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 01/14/2023]
Abstract
Protein histidine methylation is a rarely studied posttranslational modification in eukaryotes. Although the presence of N-methylhistidine was demonstrated in actin in the early 1960s, so far, only a limited number of proteins containing N-methylhistidine have been reported, including S100A9, myosin, skeletal muscle myosin light chain kinase (MLCK 2), and ribosomal protein Rpl3. Furthermore, the role of histidine methylation in the functioning of the protein and in cell physiology remains unclear due to a shortage of studies focusing on this topic. However, the molecular identification of the first two distinct histidine-specific protein methyltransferases has been established in yeast (Hpm1) and in metazoan species (actin-histidine N-methyltransferase), giving new insights into the phenomenon of protein methylation at histidine sites. As a result, we are now beginning to recognize protein histidine methylation as an important regulatory mechanism of protein functioning whose loss may have deleterious consequences in both cells and in organisms. In this review, we aim to summarize the recent advances in the understanding of the chemical, enzymological, and physiological aspects of protein histidine methylation.
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Affiliation(s)
- Sebastian Kwiatkowski
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
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78
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Farhangdoost N, Horth C, Hu B, Bareke E, Chen X, Li Y, Coradin M, Garcia BA, Lu C, Majewski J. Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma. Cell Rep 2021; 34:108769. [PMID: 33626351 PMCID: PMC8006058 DOI: 10.1016/j.celrep.2021.108769] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/12/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin dysregulation has emerged as an important mechanism of oncogenesis. To develop targeted treatments, it is important to understand the transcriptomic consequences of mutations in chromatin modifier genes. Recently, mutations in the histone methyltransferase gene nuclear receptor binding SET domain protein 1 (NSD1) have been identified in a subset of common and deadly head and neck squamous cell carcinomas (HNSCCs). Here, we use genome-wide approaches and genome editing to dissect the downstream effects of loss of NSD1 in HNSCC. We demonstrate that NSD1 mutations are responsible for loss of intergenic H3K36me2 domains, followed by loss of DNA methylation and gain of H3K27me3 in the affected genomic regions. In addition, those regions are enriched in cis-regulatory elements, and subsequent loss of H3K27ac correlates with reduced expression of their target genes. Our analysis identifies genes and pathways affected by the loss of NSD1 and paves the way to further understanding the interplay among chromatin modifications in cancer. Farhangdoost et al. use genome editing and TCGA primary tumor data to provide a link between NSD1 loss, chromatin and regulatory landscape, gene expression, and molecular characteristics of this tumor subtype. Their study extends the understanding of tumorigenic mechanisms underlying head and neck cancers with mutations in NSD1.
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Affiliation(s)
- Nargess Farhangdoost
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada.
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79
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Macchia PE, Nettore IC, Franchini F, Santana-Viera L, Ungaro P. Epigenetic regulation of adipogenesis by histone-modifying enzymes. Epigenomics 2021; 13:235-251. [PMID: 33502245 DOI: 10.2217/epi-2020-0304] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many studies investigating the transcriptional control of adipogenesis have been published so far; recently the research is focusing on the role of epigenetic mechanisms in regulating the process of adipocyte development. Histone-modifying enzymes and the histone tails post-transcriptional modifications catalyzed by them, are fundamentally involved in the epigenetic regulation of adipogenesis. In our review, we will discuss recent advances in epigenomic regulation of adipogenesis with a focus on histone-modifying enzymes implicated in the various phases of adipocytes differentiation process from mesenchymal stem cells to mature adipocytes. Understanding adipogenesis, may provide new ways to treat obesity and related metabolic diseases.
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Affiliation(s)
- Paolo E Macchia
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Immacolata C Nettore
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Fabiana Franchini
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Napoli, Italy
| | - Laura Santana-Viera
- National Research Council - Institute for Experimental Endocrinology & Oncology 'Gaetano Salvatore', 80145 Napoli, Italy
| | - Paola Ungaro
- National Research Council - Institute for Experimental Endocrinology & Oncology 'Gaetano Salvatore', 80145 Napoli, Italy
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80
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Maksimenko OG, Fursenko DV, Belova EV, Georgiev PG. CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers. Acta Naturae 2021; 13:31-46. [PMID: 33959385 PMCID: PMC8084297 DOI: 10.32607/actanaturae.11206] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. The class of transcription factors that carry a cluster of C2H2-type zinc fingers consisting of five or more domains (C2H2 proteins) is widely represented in all groups of animals. The functions of most C2H2 proteins still remain unknown. This review presents data on the structure and possible functions of these proteins, using the example of the vertebrate CTCF protein and several well- characterized C2H2 proteins in Drosophila and mammals.
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Affiliation(s)
- O. G. Maksimenko
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
| | | | - E. V. Belova
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
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81
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Hwang S, Kim S, Kim K, Yeom J, Park S, Kim I. Euchromatin histone methyltransferase II (EHMT2) regulates the expression of ras-related GTP binding C (RRAGC) protein. BMB Rep 2020. [PMID: 32684241 PMCID: PMC7704221 DOI: 10.5483/bmbrep.2020.53.11.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Dimethylation of the histone H3 protein at lysine residue 9 (H3K9) is mediated by euchromatin histone methyltransferase II (EHMT2) and results in transcriptional repression of target genes. Recently, chemical inhibition of EHMT2 was shown to induce various physiological outcomes, including endoplasmic reticulum stress-associated genes transcription in cancer cells. To identify genes that are transcriptionally repressed by EHMT2 during apoptosis, and cell stress responses, we screened genes that are upregulated by BIX-01294, a chemical inhibitor of EHMT2. RNA sequencing analyses revealed 77 genes that were upregulated by BIX-01294 in all four hepatic cell carcinoma (HCC) cell lines. These included genes that have been impli-cated in apoptosis, the unfolded protein response (UPR), and others. Among these genes, the one encoding the stress-response protein Ras-related GTPase C (RRAGC) was upregulated in all BIX-01294-treated HCC cell lines. We confirmed the regulatory roles of EHMT2 in RRAGC expression in HCC cell lines using proteomic analyses, chromatin immune precipitation (ChIP) assay, and small guide RNA-mediated loss-of-function experiments. Upregulation of RRAGC was limited by the reactive oxygen species (ROS) scavenger N-acetyl cysteine (NAC), suggesting that ROS are involved in EHMT2-mediated transcriptional regulation of stress-response genes in HCC cells. Finally, combined treatment of cells with BIX-01294 and 5-Aza-cytidine induced greater upregulation of RRAGC protein expression. These findings suggest that EHMT2 suppresses expression of the RRAGC gene in a ROS-dependent manner and imply that EHMT2 is a key regulator of stress-responsive gene expression in liver cancer cells.
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Affiliation(s)
- Supyong Hwang
- Biomedical Research Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
| | - Soyoung Kim
- Biomedical Research Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
| | - Kyungkon Kim
- Biomedical Research Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
- Convergence Medicine Research Center (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Jeonghun Yeom
- Convergence Medicine Research Center (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
| | - Sojung Park
- Biomedical Research Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
| | - Inki Kim
- Biomedical Research Center, ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
- Convergence Medicine Research Center (CREDIT), ASAN Institute for Life Sciences, ASAN Medical Center, Seoul 05505, Korea
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
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82
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Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat Genet 2020; 52:1271-1281. [PMID: 33257899 DOI: 10.1038/s41588-020-00736-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022]
Abstract
Histone-modifying enzymes are implicated in the control of diverse DNA-templated processes including gene expression. Here, we outline historical and current thinking regarding the functions of histone modifications and their associated enzymes. One current viewpoint, based largely on correlative evidence, posits that histone modifications are instructive for transcriptional regulation and represent an epigenetic 'code'. Recent studies have challenged this model and suggest that histone marks previously associated with active genes do not directly cause transcriptional activation. Additionally, many histone-modifying proteins possess non-catalytic functions that overshadow their enzymatic activities. Given that much remains unknown regarding the functions of these proteins, the field should be cautious in interpreting loss-of-function phenotypes and must consider both cellular and developmental context. In this Perspective, we focus on recent progress relating to the catalytic and non-catalytic functions of the Trithorax-COMPASS complexes, Polycomb repressive complexes and Clr4/Suv39 histone-modifying machineries.
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83
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Shu WJ, Du HN. The methyltransferase SETD3-mediated histidine methylation: Biological functions and potential implications in cancers. Biochim Biophys Acta Rev Cancer 2020; 1875:188465. [PMID: 33157163 DOI: 10.1016/j.bbcan.2020.188465] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/16/2022]
Abstract
SETD3 belongs to a family of SET-domain containing proteins. Recently, SETD3 was found as the first and so-far the only known metazoan histidine methyltransferase that catalyzes actin histidine 73 (His73) methylation, a pervasive modification which was discovered more than 50 years ago. In this review, we summarize some recent advances in SETD3 research, focusing on structural properties, substrate-recognition features, and physiological functions. We particularly highlight potential pathological relevance of SETD3 in human cancers and raise some questions to promote discussion about this novel histidine methyltransferase.
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Affiliation(s)
- Wen-Jie Shu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Cancer Center of Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Cancer Center of Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.
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84
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Yao Z, Chen Y, Cao W, Shyh‐Chang N. Chromatin-modifying drugs and metabolites in cell fate control. Cell Prolif 2020; 53:e12898. [PMID: 32979011 PMCID: PMC7653270 DOI: 10.1111/cpr.12898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
For multicellular organisms, it is essential to produce a variety of specialized cells to perform a dazzling panoply of functions. Chromatin plays a vital role in determining cellular identities, and it dynamically regulates gene expression in response to changing nutrient metabolism and environmental conditions. Intermediates produced by cellular metabolic pathways are used as cofactors or substrates for chromatin modification. Drug analogues of metabolites that regulate chromatin-modifying enzyme reactions can also regulate cell fate by adjusting chromatin organization. In recent years, there have been many studies about how chromatin-modifying drug molecules or metabolites can interact with chromatin to regulate cell fate. In this review, we systematically discuss how DNA and histone-modifying molecules alter cell fate by regulating chromatin conformation and propose a mechanistic model that explains the process of cell fate transitions in a concise and qualitative manner.
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Affiliation(s)
- Ziyue Yao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Chen
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wenhua Cao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ng Shyh‐Chang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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85
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From 1957 to Nowadays: A Brief History of Epigenetics. Int J Mol Sci 2020; 21:ijms21207571. [PMID: 33066397 PMCID: PMC7588895 DOI: 10.3390/ijms21207571] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 01/01/2023] Open
Abstract
Due to the spectacular number of studies focusing on epigenetics in the last few decades, and particularly for the last few years, the availability of a chronology of epigenetics appears essential. Indeed, our review places epigenetic events and the identification of the main epigenetic writers, readers and erasers on a historic scale. This review helps to understand the increasing knowledge in molecular and cellular biology, the development of new biochemical techniques and advances in epigenetics and, more importantly, the roles played by epigenetics in many physiological and pathological situations.
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86
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Sugeedha J, Gautam J, Tyagi S. SET1/MLL family of proteins: functions beyond histone methylation. Epigenetics 2020; 16:469-487. [PMID: 32795105 PMCID: PMC8078731 DOI: 10.1080/15592294.2020.1809873] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SET1 family of enzymes are well known for their involvement in the histone 3 lysine 4 (H3K4) methylation, a conserved trait of euchromatin associated with transcriptional activation. These methyltransferases are distinct, and involved in various biological functions in the cell. Impairment in the function of SET1 family members leads to a number of abnormalities such as skeletal and neurological defects, leukaemogenesis and even lethality. Tremendous progress has been made in understanding the unique biological roles and the mechanism of SET1 enzymes in context with H3K4 methylation/canonical functions. However, in recent years, several studies have indicated the novel role of SET1 family proteins, other than H3K4 methylation, which are equally important for cellular functions. In this review, we focus on these non-canonical function of SET1 family members.
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Affiliation(s)
- Jeyapal Sugeedha
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Jyoti Gautam
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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87
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Horn RL, Kamphaus C, Murdoch K, Narum SR. Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01307-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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88
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Neganova ME, Klochkov SG, Aleksandrova YR, Aliev G. Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress. Semin Cancer Biol 2020; 83:452-471. [PMID: 32814115 DOI: 10.1016/j.semcancer.2020.07.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic changes associated with histone modifications play an important role in the emergence and maintenance of the phenotype of various cancer types. In contrast to direct mutations in the main DNA sequence, these changes are reversible, which makes the development of inhibitors of enzymes of post-translational histone modifications one of the most promising strategies for the creation of anticancer drugs. To date, a wide variety of histone modifications have been found that play an important role in the regulation of chromatin state, gene expression, and other nuclear events. This review examines the main features of the most common and studied epigenetic histone modifications with a proven role in the pathogenesis of a wide range of malignant neoplasms: acetylation / deacetylation and methylation / demethylation of histone proteins, as well as the role of enzymes of the HAT / HDAC and HMT / HDMT families in the development of oncological pathologies. The data on the relationship between histone modifications and certain types of cancer are presented and discussed. Special attention is devoted to the consideration of various strategies for the development of epigenetic inhibitors. The main directions of the development of inhibitors of histone modifications are analyzed and effective strategies for their creation are identified and discussed. The most promising strategy is the use of multitarget drugs, which will affect multiple molecular targets of cancer. A critical analysis of the current status of approved epigenetic anticancer drugs has also been performed.
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Affiliation(s)
- Margarita E Neganova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Sergey G Klochkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Yulia R Aleksandrova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation
| | - Gjumrakch Aliev
- Institute of Physiologically Active Compounds Russian Academy of Sciences, 1, Severnii pr., Chernogolovka, 142432, Russian Federation.,I. M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Str., Moscow, 119991, Russian Federation.,Laboratory of Cellular Pathology, Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation.,GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA.
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89
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Nemoto M, Iwaki S, Moriya H, Monden Y, Tamura T, Inagaki K, Mayama S, Obuse K. Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:551-563. [PMID: 32488507 DOI: 10.1007/s10126-020-09976-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms.
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Affiliation(s)
- Michiko Nemoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
| | - Sayako Iwaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Kenji Inagaki
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Shigeki Mayama
- Department of Biology, Tokyo Gakugei University, Tokyo, 184-8511, Japan
| | - Kiori Obuse
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
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90
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Saleh R, Toor SM, Sasidharan Nair V, Elkord E. Role of Epigenetic Modifications in Inhibitory Immune Checkpoints in Cancer Development and Progression. Front Immunol 2020; 11:1469. [PMID: 32760400 PMCID: PMC7371937 DOI: 10.3389/fimmu.2020.01469] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/05/2020] [Indexed: 12/16/2022] Open
Abstract
A balance between co-inhibitory and co-stimulatory signals in the tumor microenvironment (TME) is critical to suppress tumor development and progression, primarily via maintaining effective immunosurveillance. Aberrant expression of immune checkpoints (ICs), including programmed cell death protein 1 (PD-1), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), lymphocyte-activation gene 3 (LAG-3) and T cell immunoreceptor with Ig and ITIM domains (TIGIT), can create an immune-subversive environment, which helps tumor cells to evade immune destruction. Recent studies showed that epigenetic modifications play critical roles in regulating the expression of ICs and their ligands in the TME. Reports showed that the promoter regions of genes encoding ICs/IC ligands can undergo inherent epigenetic alterations, such as DNA methylation and histone modifications (acetylation and methylation). These epigenetic aberrations can significantly contribute to the transcriptomic upregulation of ICs and their ligands. Epigenetic therapeutics, including DNA methyltransferase and histone deacetylase inhibitors, can be used to revert these epigenetic anomalies acquired during the progression of disease. These discoveries have established a promising therapeutic modality utilizing the combination of epigenetic and immunotherapeutic agents to restore the physiological epigenetic profile and to re-establish potent host immunosurveillance mechanisms. In this review, we highlight the roles of epigenetic modifications on the upregulation of ICs, focusing on tumor development, and progression. We discuss therapeutic approaches of epigenetic modifiers, including clinical trials in various cancer settings and their impact on current and future anti-cancer therapies.
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Affiliation(s)
- Reem Saleh
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Salman M Toor
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, United Kingdom
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91
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Sampaio RV, Sangalli JR, De Bem THC, Ambrizi DR, Del Collado M, Bridi A, de Ávila ACFCM, Macabelli CH, de Jesus Oliveira L, da Silveira JC, Chiaratti MR, Perecin F, Bressan FF, Smith LC, Ross PJ, Meirelles FV. Catalytic inhibition of H3K9me2 writers disturbs epigenetic marks during bovine nuclear reprogramming. Sci Rep 2020; 10:11493. [PMID: 32661262 PMCID: PMC7359371 DOI: 10.1038/s41598-020-67733-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/28/2020] [Indexed: 01/28/2023] Open
Abstract
Orchestrated events, including extensive changes in epigenetic marks, allow a somatic nucleus to become totipotent after transfer into an oocyte, a process termed nuclear reprogramming. Recently, several strategies have been applied in order to improve reprogramming efficiency, mainly focused on removing repressive epigenetic marks such as histone methylation from the somatic nucleus. Herein we used the specific and non-toxic chemical probe UNC0638 to inhibit the catalytic activity of the histone methyltransferases EHMT1 and EHMT2. Either the donor cell (before reconstruction) or the early embryo was exposed to the probe to assess its effect on developmental rates and epigenetic marks. First, we showed that the treatment of bovine fibroblasts with UNC0638 did mitigate the levels of H3K9me2. Moreover, H3K9me2 levels were decreased in cloned embryos regardless of treating either donor cells or early embryos with UNC0638. Additional epigenetic marks such as H3K9me3, 5mC, and 5hmC were also affected by the UNC0638 treatment. Therefore, the use of UNC0638 did diminish the levels of H3K9me2 and H3K9me3 in SCNT-derived blastocysts, but this was unable to improve their preimplantation development. These results indicate that the specific reduction of H3K9me2 by inhibiting EHMT1/2 during nuclear reprogramming impacts the levels of H3K9me3, 5mC, and 5hmC in preimplantation bovine embryos.
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Affiliation(s)
- Rafael Vilar Sampaio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil.
- Centre de Recherche en Reproduction et Fértilité, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada.
- Department of Animal Science, University of California Davis, Davis, USA.
| | - Juliano Rodrigues Sangalli
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
- Department of Animal Science, University of California Davis, Davis, USA
| | - Tiago Henrique Camara De Bem
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Dewison Ricardo Ambrizi
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Maite Del Collado
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Alessandra Bridi
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | | | | | - Lilian de Jesus Oliveira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Juliano Coelho da Silveira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | | | - Felipe Perecin
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Fabiana Fernandes Bressan
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Lawrence Charles Smith
- Centre de Recherche en Reproduction et Fértilité, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, USA
| | - Flávio Vieira Meirelles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil.
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92
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Cheng L, Zhang X, Wang Y, Gan H, Xu X, Lv X, Hua X, Que J, Ordog T, Zhang Z. Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit. Nucleic Acids Res 2020; 47:11114-11131. [PMID: 31586391 PMCID: PMC6868363 DOI: 10.1093/nar/gkz858] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Establishment and subsequent maintenance of distinct chromatin domains during embryonic stem cell (ESC) differentiation are crucial for lineage specification and cell fate determination. Here we show that the histone chaperone Chromatin Assembly Factor 1 (CAF-1), which is recruited to DNA replication forks through its interaction with proliferating cell nuclear antigen (PCNA) for nucleosome assembly, participates in the establishment of H3K27me3-mediated silencing during differentiation. Deletion of CAF-1 p150 subunit impairs the silencing of many genes including Oct4, Sox2 and Nanog as well as the establishment of H3K27me3 at these gene promoters during ESC differentiation. Mutations of PCNA residues involved in recruiting CAF-1 to the chromatin also result in defects in differentiation in vitro and impair early embryonic development as p150 deletion. Together, these results reveal that the CAF-1-PCNA nucleosome assembly pathway plays an important role in the establishment of H3K27me3-mediated silencing during cell fate determination.
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Affiliation(s)
- Liang Cheng
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Xu Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Yan Wang
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiangdong Lv
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Jianwen Que
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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93
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Treviño LS, Dong J, Kaushal A, Katz TA, Jangid RK, Robertson MJ, Grimm SL, Ambati CSR, Putluri V, Cox AR, Kim KH, May TD, Gallo MR, Moore DD, Hartig SM, Foulds CE, Putluri N, Coarfa C, Walker CL. Epigenome environment interactions accelerate epigenomic aging and unlock metabolically restricted epigenetic reprogramming in adulthood. Nat Commun 2020; 11:2316. [PMID: 32385268 PMCID: PMC7210260 DOI: 10.1038/s41467-020-15847-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Our early-life environment has a profound influence on developing organs that impacts metabolic function and determines disease susceptibility across the life-course. Using a rat model for exposure to an endocrine disrupting chemical (EDC), we show that early-life chemical exposure causes metabolic dysfunction in adulthood and reprograms histone marks in the developing liver to accelerate acquisition of an adult epigenomic signature. This epigenomic reprogramming persists long after the initial exposure, but many reprogrammed genes remain transcriptionally silent with their impact on metabolism not revealed until a later life exposure to a Western-style diet. Diet-dependent metabolic disruption was largely driven by reprogramming of the Early Growth Response 1 (EGR1) transcriptome and production of metabolites in pathways linked to cholesterol, lipid and one-carbon metabolism. These findings demonstrate the importance of epigenome:environment interactions, which early in life accelerate epigenomic aging, and later in adulthood unlock metabolically restricted epigenetic reprogramming to drive metabolic dysfunction. Early life exposure to environmental stressors, including endocrine disrupting chemicals (EDCs), can impact health later in life. Here, the authors show that neonatal EDC exposure in rats causes epigenetic reprogramming in the liver, which is transcriptionally silent until animals are placed on a Western-style diet.
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Affiliation(s)
- Lindsey S Treviño
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Division of Health Equities, Department of Population Sciences, City of Hope, Duarte, CA, 91010, USA
| | - Jianrong Dong
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ahkilesh Kaushal
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tiffany A Katz
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rahul Kumar Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew J Robertson
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chandra Shekar R Ambati
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vasanta Putluri
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Aaron R Cox
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kang Ho Kim
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thaddeus D May
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Morgan R Gallo
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David D Moore
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sean M Hartig
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Charles E Foulds
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nagireddy Putluri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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94
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Hou Z, Min W, Zhang R, Niu A, Li Y, Cao L, Han J, Luo C, Yang P, Ding H. Lead discovery, chemical optimization, and biological evaluation studies of novel histone methyltransferase SET7 small-molecule inhibitors. Bioorg Med Chem Lett 2020; 30:127061. [PMID: 32173197 DOI: 10.1016/j.bmcl.2020.127061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/14/2020] [Accepted: 02/22/2020] [Indexed: 10/24/2022]
Abstract
The post-translational modifications of histones, including histone methylation and demethylation, control the expression switch of multiple genes. SET domain-containing lysine methyltransferase 7 (SET7) is the only methyltransferase, which can specifically monomethylate lysine-4 of histone H3 (H3K4me1) and play critical roles in various diseases, including breast cancer, hepatitis C virus (HCV), atherosclerotic vascular disease, diabetes, prostate cancer, hepatocellular carcinoma, and obesity. However, several known SET7 inhibitors exhibit weak activity or poor selectivity. Therefore, the development of novel SET7 inhibitors is highly desirable and of great clinical value. In this study, we identified 2-79 as a new hit compound by structure-based virtual screening and further AlphaLISA-based biochemical evaluation. Via chemical optimization, the synthesized compound DC21 was confirmed as a potent SET7 inhibitor with an IC50 value of 15.93 μM. The interaction between DC21 and SET7 was also validated through SPR experiment. Especially, DC21 retarded proliferation of MCF7 cells with an IC50 value of 25.84 μM in cellular level. In addition, DC21 has good selectivity for several other epigenetic targets, such as SUV39H1, G9a, NSD1, DOT1L and MOF. DC21 can serve as a lead compound to develop more potential SET7 inhibitors and as a chemical probe for SET7 biological function studies.
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Affiliation(s)
- Zeng Hou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Rukang Zhang
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ao Niu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Yuanqing Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liyuan Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jie Han
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.
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95
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Zhao LN, Kaldis P. Cascading proton transfers are a hallmark of the catalytic mechanism of SAM-dependent methyltransferases. FEBS Lett 2020; 594:2128-2139. [PMID: 32353165 DOI: 10.1002/1873-3468.13799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 11/10/2022]
Abstract
The S-adenosyl methionine (SAM)-dependent methyltransferases attach a methyl group to the deprotonated methyl lysine using SAM as a donor. An intriguing, yet unanswered, question is how the deprotonation takes place. PRDM9 with well-defined enzyme activity is a good representative of the methyltransferase family to study the deprotonation and subsequently the methyl transfer. Our study has found that the pKa of Tyr357 is low enough to make it an ideal candidate for proton abstraction from the methyl lysine. The partially deprontonated Tyr357 is able to change its H-bond pattern thus bridging two proton tunneling states and providing a cascading proton transfer. We have uncovered a new catalytic mechanism for the deprotonation of the methyl lysine in methyltransferases.
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Affiliation(s)
- Li Na Zhao
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Clinical Sciences, Lund University, Clinical Research Center (CRC), Malmö, Sweden
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96
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Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K. The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression. iScience 2020; 23:101030. [PMID: 32299058 PMCID: PMC7160574 DOI: 10.1016/j.isci.2020.101030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/29/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Haploinsufficiency of SETD5 is implicated in syndromic autism spectrum disorder (ASD), but the molecular mechanism underlying the pathological role of this protein has remained unclear. We have now shown that Setd5+/– mice manifest ASD-related behavioral phenotypes and that the expression of ribosomal protein genes and rDNA is disturbed in the brain of these mice. SETD5 recruited the HDAC3 complex to the rDNA promoter, resulting in removal of the histone mark H4K16ac and its reader protein TIP5, a repressor of rDNA expression. Depletion of SETD5 attenuated rDNA expression, translational activity, and neural cell proliferation, whereas ablation of TIP5 in SETD5-deficient cells rescued these effects. Translation of cyclin D1 mRNA was specifically down-regulated in SETD5-insufficient cells. Our results thus suggest that SETD5 positively regulates rDNA expression via an HDAC3-mediated epigenetic mechanism and that such regulation is essential for translation of cyclin D1 mRNA and neural cell proliferation. Setd5+/– mice manifest syndromic autism-related phenotypes SETD5 recruits the HDAC3 complex to the rDNA promoter SETD5 deficiency reduces rRNA abundance and attenuates translational activity SETD5 deficiency inhibits cyclin D1 mRNA translation and neural cell proliferation
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Affiliation(s)
- Tadashi Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Satoko Hattori
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Risa Nobuta
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryuichi Kimura
- Division of Developmental Neuroscience, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Makiko Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuko Nagasawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Ryo Funayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Noriko Osumi
- Division of Developmental Neuroscience, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan.
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97
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Forkhead box M1 transcription factor: a novel target for pulmonary arterial hypertension therapy. World J Pediatr 2020; 16:113-119. [PMID: 31190319 DOI: 10.1007/s12519-019-00271-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Forkhead box M1 (FoxM1), a member of forkhead family, plays a key role in carcinogenesis, progression, invasion, metastasis and drug resistance. Based on the similarities between cancer and pulmonary arterial hypertension, studies on the roles and mechanisms of FoxM1 in pulmonary arterial hypertension have been increasing. This article aims to review recent advances in the mechanisms of signal transduction associated with FoxM1 in pulmonary arterial hypertension. DATA SOURCES Articles were retrieved from PubMed and MEDLINE published after 1990, including-but not limited to-FoxM1 and pulmonary arterial hypertension. RESULTS FoxM1 is overexpressed in pulmonary artery smooth muscle cells in both pulmonary arterial hypertension patients and animal models, and promotes pulmonary artery smooth muscle cell proliferation and inhibits cell apoptosis via regulating cell cycle progression. Multiple signaling molecules and pathways, including hypoxia-inducible factors, transforming growth factor-β/Smad, SET domain-containing 3/vascular endothelial growth factor, survivin, cell cycle regulatory genes and DNA damage response network, are reported to cross talk with FoxM1 in pulmonary arterial hypertension. Proteasome inhibitors are effective in the prevention and treatment of pulmonary arterial hypertension by inhibiting the expression and transcriptional activity of FoxM1. CONCLUSIONS FoxM1 has a crucial role in the pathogenesis of pulmonary arterial hypertension and may represent a novel therapeutic target. But more details of interaction between FoxM1 and other signaling pathways need to be clarified in the future.
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98
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D'Afonseca V, Gónzalez G, Salazar M, Arencibia AD. Computational analyses on genetic alterations in the NSD genes family and the implications for colorectal cancer development. Ecancermedicalscience 2020; 14:1001. [PMID: 32153656 PMCID: PMC7032942 DOI: 10.3332/ecancer.2020.1001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Indexed: 12/21/2022] Open
Abstract
Colorectal cancer (CRC) is a prevalent tumour throughout the world. CRC symptoms appear only in advanced stages causing decrease in survival of patients. Therefore, it is necessary to establish new strategies to detect CRC through subclinical screening. Genetic alterations and differential expression of genes that codify histone methyltransferases (HMTs) are linked to tumourigenesis of CRC. One important group of genes that codify HMTs are the NSD family composed of NSD1, NSD2 and NSD3 genes. This family participates in several cancer processes as oncogenes, harbouring several genetic alterations and presenting differential expression in tumour cells. To investigate the implications of NSD genes in CRC cancer, we described the genomic landscape of all NSD family members in a cohort of CRC patients from publicly available cancer datasets. We identified associations among recurrent copy number alterations (CNAs), mutations and differential gene expression concerning clinical outcome. We found in CRC repositories that NSD1 harbours a missense mutation in SET domain—the catalytic region—that probably could decrease its activity. In addition, we found an association between the low expressions of NSD1 and NSD2 and decrease of survival probability in CRC patients. Finally, we reported that NSD3 showed the highest rate of gene amplification, which was highly correlated to its mRNA expression, a common feature of many cancer drivers. Our results highlight the potential use of the NSD1 and NSD2 gene as prognostic markers of poor prognosis in CRC patients. Additionally, we appointed the use of the NSD3 gene as a putative cancer driver gene in CRC given that this gene harbours the highest rate of genetic amplification. All our findings are leading to novel strategies to predict and control CRC, however, some studies need to be conducted to validate these findings.
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Affiliation(s)
- Vívian D'Afonseca
- Vicerectory in Research and Postgraduation, University Catholic of Maule, Talca 3605, Chile.,Center of Biotechnology in Naturals Research, University Catholic of Maule, Talca 3605, Chile
| | - Glória Gónzalez
- Center of Biotechnology in Naturals Research, University Catholic of Maule, Talca 3605, Chile
| | - Marcela Salazar
- Vicerectory in Research and Postgraduation, University Catholic of Maule, Talca 3605, Chile.,Center of Biotechnology in Naturals Research, University Catholic of Maule, Talca 3605, Chile
| | - Ariel D Arencibia
- Center of Biotechnology in Naturals Research, University Catholic of Maule, Talca 3605, Chile
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99
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Yamazaki S, Gukasyan HJ, Wang H, Uryu S, Sharma S. Translational Pharmacokinetic-Pharmacodynamic Modeling for an Orally Available Novel Inhibitor of Epigenetic Regulator Enhancer of Zeste Homolog 2. J Pharmacol Exp Ther 2020; 373:220-229. [PMID: 32094296 DOI: 10.1124/jpet.119.263491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/12/2020] [Indexed: 11/22/2022] Open
Abstract
PF06821497 has been identified as an orally available small-molecule enhancer of zeste homolog 2 inhibitor. The objectives of the present study were to characterize pharmacokinetic-pharmacodynamic-disease relationships of PF06821497 in xenograft mouse models with diffuse large B-cell lymphoma (Karpas422). An indirect-response model reasonably fit dose-dependent pharmacodynamic responses [histone H3 on lysine 27 (H3K27) me3 inhibition] with an unbound EC 50 of 76 nM, whereas a signal-transduction model sufficiently fit dose-dependent disease responses (tumor growth inhibition) with an unbound tumor stasis concentration (T sc ) of 168 nM. Thus, effective concentration for 70% of maximal effect (EC70) for H3K27me3 inhibition was roughly comparable to T sc , suggesting that 70% H3K27me3 inhibition could be required for tumor stasis. Consistently, an integrated pharmacokinetic-pharmacodynamic-disease model adequately describing tumor growth inhibition also suggested that ∼70% H3K27me3 inhibition was associated with tumor stasis. Based on these results, we would propose that an EC70 estimate for H3K27me3 inhibition corresponding to tumor stasis could be considered a minimum target efficacious concentration of PF06821497 in cancer patients. SIGNIFICANCE STATEMENT: Using a mathematical modeling approach, the quantitative relationships of an orally available anticancer small-molecule enhancer of zeste homolog 2 inhibitor, PF06821497, were characterized among pharmacokinetics, pharmacodynamic biomarker inhibition, and disease responses in nonclinical xenograft models with diffuse large B-cell lymphoma. The modeling results suggest that >70% histone H3 on lysine 27 (H3K27) me3 inhibition would be required for tumor stasis (i.e., 100% tumor growth inhibition). Accordingly, we would propose that an effective concentration for 70% of maximal effect estimate for H3K27me3 inhibition could be considered a minimum target efficacious concentration of PF06821497 in cancer patients.
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Affiliation(s)
- Shinji Yamazaki
- Pharmacokinetics, Dynamics and Metabolism (S.Y.), Pharmaceutical Science (H.J.G.), and Oncology Research Unit (H.W., S.U., S.S.), Pfizer Worldwide Research & Development, San Diego, California
| | - Hovhannes J Gukasyan
- Pharmacokinetics, Dynamics and Metabolism (S.Y.), Pharmaceutical Science (H.J.G.), and Oncology Research Unit (H.W., S.U., S.S.), Pfizer Worldwide Research & Development, San Diego, California
| | - Hui Wang
- Pharmacokinetics, Dynamics and Metabolism (S.Y.), Pharmaceutical Science (H.J.G.), and Oncology Research Unit (H.W., S.U., S.S.), Pfizer Worldwide Research & Development, San Diego, California
| | - Sean Uryu
- Pharmacokinetics, Dynamics and Metabolism (S.Y.), Pharmaceutical Science (H.J.G.), and Oncology Research Unit (H.W., S.U., S.S.), Pfizer Worldwide Research & Development, San Diego, California
| | - Shikhar Sharma
- Pharmacokinetics, Dynamics and Metabolism (S.Y.), Pharmaceutical Science (H.J.G.), and Oncology Research Unit (H.W., S.U., S.S.), Pfizer Worldwide Research & Development, San Diego, California
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100
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Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
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Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
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