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Cortellino S, Longo VD. Metabolites and Immune Response in Tumor Microenvironments. Cancers (Basel) 2023; 15:3898. [PMID: 37568713 PMCID: PMC10417674 DOI: 10.3390/cancers15153898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The remodeled cancer cell metabolism affects the tumor microenvironment and promotes an immunosuppressive state by changing the levels of macro- and micronutrients and by releasing hormones and cytokines that recruit immunosuppressive immune cells. Novel dietary interventions such as amino acid restriction and periodic fasting mimicking diets can prevent or dampen the formation of an immunosuppressive microenvironment by acting systemically on the release of hormones and growth factors, inhibiting the release of proinflammatory cytokines, and remodeling the tumor vasculature and extracellular matrix. Here, we discuss the latest research on the effects of these therapeutic interventions on immunometabolism and tumor immune response and future scenarios pertaining to how dietary interventions could contribute to cancer therapy.
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Affiliation(s)
- Salvatore Cortellino
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, 85028 Rionero in Vulture, Italy;
| | - Valter D. Longo
- IFOM, The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
- Longevity Institute, Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
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2
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Gandhirajan A, Roychowdhury S, Vachharajani V. Sirtuins and Sepsis: Cross Talk between Redox and Epigenetic Pathways. Antioxidants (Basel) 2021; 11:antiox11010003. [PMID: 35052507 PMCID: PMC8772830 DOI: 10.3390/antiox11010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/19/2022] Open
Abstract
Sepsis and septic shock are the leading causes of death among hospitalized patients in the US. The immune response in sepsis transitions from a pro-inflammatory and pro-oxidant hyper-inflammation to an anti-inflammatory and cytoprotective hypo-inflammatory phase. While 1/3rd sepsis-related deaths occur during hyper-, a vast majority of sepsis-mortality occurs during the hypo-inflammation. Hyper-inflammation is cytotoxic for the immune cells and cannot be sustained. As a compensatory mechanism, the immune cells transition from cytotoxic hyper-inflammation to a cytoprotective hypo-inflammation with anti-inflammatory/immunosuppressive phase. However, the hypo-inflammation is associated with an inability to clear invading pathogens, leaving the host susceptible to secondary infections. Thus, the maladaptive immune response leads to a marked departure from homeostasis during sepsis-phases. The transition from hyper- to hypo-inflammation occurs via epigenetic programming. Sirtuins, a highly conserved family of histone deacetylators and guardians of homeostasis, are integral to the epigenetic programming in sepsis. Through their anti-inflammatory and anti-oxidant properties, the sirtuins modulate the immune response in sepsis. We review the role of sirtuins in orchestrating the interplay between the oxidative stress and epigenetic programming during sepsis.
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Affiliation(s)
- Anugraha Gandhirajan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
| | - Sanjoy Roychowdhury
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
| | - Vidula Vachharajani
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; (A.G.); (S.R.)
- Department of Critical Care Medicine, Respiratory Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence:
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3
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Jiang W, Xia T, Liu C, Li J, Zhang W, Sun C. Remodeling the Epigenetic Landscape of Cancer-Application Potential of Flavonoids in the Prevention and Treatment of Cancer. Front Oncol 2021; 11:705903. [PMID: 34235089 PMCID: PMC8255972 DOI: 10.3389/fonc.2021.705903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics, including DNA methylation, histone modification, and noncoding RNA regulation, are physiological regulatory changes that affect gene expression without modifying the DNA sequence. Although epigenetic disorders are considered a sign of cell carcinogenesis and malignant events that affect tumor progression and drug resistance, in view of the reversible nature of epigenetic modifications, clinicians believe that associated mechanisms can be a key target for cancer prevention and treatment. In contrast, epidemiological and preclinical studies indicated that the epigenome is constantly reprogrammed by intake of natural organic compounds and the environment, suggesting the possibility of utilizing natural compounds to influence epigenetics in cancer therapy. Flavonoids, although not synthesized in the human body, can be consumed daily and are common in medicinal plants, vegetables, fruits, and tea. Recently, numerous reports provided evidence for the regulation of cancer epigenetics by flavonoids. Considering their origin in natural and food sources, few side effects, and remarkable biological activity, the epigenetic antitumor effects of flavonoids warrant further investigation. In this article, we summarized and analyzed the multi-dimensional epigenetic effects of all 6 subtypes of flavonoids (including flavonols, flavones, isoflavones, flavanones, flavanols, and anthocyanidin) in different cancer types. Additionally, our report also provides new insights and a promising direction for future research and development of flavonoids in tumor prevention and treatment via epigenetic modification, in order to realize their potential as cancer therapeutic agents.
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Affiliation(s)
- Weiyi Jiang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tingting Xia
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenfeng Zhang
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China.,Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
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4
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Feng Y, Endo M, Sugiyama H. Nucleosomes and Epigenetics from a Chemical Perspective. Chembiochem 2020; 22:595-612. [PMID: 32864867 DOI: 10.1002/cbic.202000332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Nucleosomes, which are the fundamental building blocks of chromatin, are highly dynamic, they play vital roles in the formation of higher-order chromatin structures and orchestrate gene regulation. Nucleosome structures, histone modifications, nucleosome-binding proteins, and their functions are being gradually unravelled with the development of epigenetics. With the continuous development of research approaches such as cryo-EM, FRET and next-generation sequencing for genome-wide analysis of nucleosomes, the understanding of nucleosomes is getting wider and deeper. Herein, we review recent progress in research on nucleosomes and epigenetics, from nucleosome structure to chromatin formation, with a focus on chemical aspects. Basic knowledge of the nucleosome (nucleosome structure, nucleosome position sequence, nucleosome assembly and remodeling), epigenetic modifications, chromatin structure, chemical biology methods and nucleosome, observation nucleosome by AFM, phase separation and nucleosomes are described in this review.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University Yoshida-Ushinomiyacho, Kyoto, 606-8501, Japan
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5
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Management of epigenomic networks entailed in coronavirus infections and COVID-19. Clin Epigenetics 2020; 12:118. [PMID: 32758273 PMCID: PMC7404079 DOI: 10.1186/s13148-020-00912-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) are highly diverse single-stranded RNA viruses owing to their susceptibility to numerous genomic mutations and recombination. Such viruses involve human and animal pathogens including the etiologic agents of acute respiratory tract illnesses: severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the highly morbific SARS-CoV-2. Coronavirus disease 2019 (COVID-19), an emerging disease with a quick rise in infected cases and deaths, was recently identified causing a worldwide pandemic. COVID-19 disease outcomes were found to increase in elderly and patients with a compromised immune system. Evidences indicated that the main culprit behind COVID-19 deaths is the cytokine storm, which is illustrated by an uncontrolled over-production of soluble markers of inflammation. The regulation process of coronavirus pathogenesis through molecular mechanism comprise virus-host interactions linked to viral entry, replication and transcription, escape, and immune system control. Recognizing coronavirus infections and COVID-19 through epigenetics lens will lead to potential alteration in gene expression thus limiting coronavirus infections. Focusing on epigenetic therapies reaching clinical trials, clinically approved epigenetic-targeted agents, and combination therapy of antivirals and epigenetic drugs is currently considered an effective and valuable approach for viral replication and inflammatory overdrive control.
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Kumar A, Kumari N, Nallabelli N, Sharma U, Rai A, Singh SK, Kakkar N, Prasad R. Expression profile of H3K4 demethylases with their clinical and pathological correlation in patients with clear cell renal cell carcinoma. Gene 2020; 739:144498. [PMID: 32097694 DOI: 10.1016/j.gene.2020.144498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 01/18/2023]
Abstract
OBJECTIVE Clear cell renal cell carcinoma (ccRCC) is one of the deadly diseases with poor metastatic disease prognosis. There is an urgent need to explore the potential molecular markers which can improve the prognosis of the disease. Histone demethylases have emerged as a powerful tool for cancer prognosis and therapeutics during the last decade. The implications of demethylases of histone 3 lysine 4 (H3K4) in ccRCC are however unrevealed. We therefore evaluated the expression of H3K4 demethylases in ccRCC, with emphasis on their clinical significance as a prognostic marker. METHODS Total 50 histopathological confirmed cases of ccRCC were enrolled in the study. The expression of seven H3K4 demethylases was determined by Real-Time PCR using gene specific primers and correlated with tumor stage, grade and metastasis. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the prognostic significance of H3K4 demethylases. RESULTS The median age of the patients was 54 years with predominance of male patients by 2.6-fold. Among seven genes viz FBXL10, LSD1, LSD2, KDM5A, KDM5B, KDM5C and KDM5D analyzed, LSD2 was found to be significantly associated with tumor stage and metastasis. The optimal cut-off value for LSD2 was 3.2 as calculated from ROC curve analysis for metastasis as well as TNM stage with area under curve of 0.74 and 0.78 respectively. In addition, LSD2 expression showed significant positive correlation with LSD1 expression in tumor metastasis. CONCLUSION The expression of LSD2 was associated with higher TNM stage and metastasis of the tumor and thus, might serve as a useful marker for ccRCC progression.
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Affiliation(s)
- Aman Kumar
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India; Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Niti Kumari
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nayudu Nallabelli
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India; Department of Ophthalmology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ujjawal Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashutosh Rai
- Department of Translational and Regenerative Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shrawan Kumar Singh
- Department of Urology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Nandita Kakkar
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajendra Prasad
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, India; Department of Biochemistry, MM Institute of Medical Science and Research, MM (Deemed to be University), Mullana, Ambala, Haryana, India.
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Shen J, Chen M, Lee D, Law CT, Wei L, Tsang FHC, Chin DWC, Cheng CLH, Lee JMF, Ng IOL, Wong CCL, Wong CM. Histone chaperone FACT complex mediates oxidative stress response to promote liver cancer progression. Gut 2020; 69:329-342. [PMID: 31439637 DOI: 10.1136/gutjnl-2019-318668] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Facilitates Chromatin Transcription (FACT) complex is a histone chaperone participating in DNA repair-related and transcription-related chromatin dynamics. In this study, we investigated its oncogenic functions, underlying mechanisms and therapeutic implications in human hepatocellular carcinoma (HCC). DESIGN We obtained HCC and its corresponding non-tumorous liver samples from 16 patients and identified FACT complex as the most upregulated histone chaperone by RNA-Seq. We further used CRISPR-based gene activation and knockout systems to demonstrate the functions of FACT complex in HCC growth and metastasis. Functional roles and mechanistic insights of FACT complex in oxidative stress response were investigated by ChIP assay, flow cytometry, gene expression assays and 4sU-DRB transcription elongation assay. Therapeutic effect of FACT complex inhibitor, Curaxin, was tested in both in vitro and in vivo models. RESULTS We showed that FACT complex was remarkably upregulated in HCC and contributed to HCC progression. Importantly, we unprecedentedly revealed an indispensable role of FACT complex in NRF2-driven oxidative stress response. Oxidative stress prevented NRF2 and FACT complex from KEAP1-mediated protein ubiquitination and degradation. Stabilised NRF2 and FACT complex form a positive feedback loop; NRF2 transcriptionally activates the FACT complex, while FACT complex promotes the transcription elongation of NRF2 and its downstream antioxidant genes through facilitating rapid nucleosome disassembly for the passage of RNA polymerase. Therapeutically, Curaxin effectively suppressed HCC growth and sensitised HCC cell to sorafenib. CONCLUSION In conclusion, our findings demonstrated that FACT complex is essential for the expeditious HCC oxidative stress response and is a potential therapeutic target for HCC treatment.
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Affiliation(s)
- Jialing Shen
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Mengnuo Chen
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Derek Lee
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Cheuk-Ting Law
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Lai Wei
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Felice Ho-Ching Tsang
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Carol Lai-Hung Cheng
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Joyce Man-Fong Lee
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong .,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong, Hong Kong .,Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, Hong Kong
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8
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McDevitt PJ, Schneck JL, Diaz E, Hou W, Huddleston MJ, Matico RE, McCormick PM, Kirkpatrick RB. A Scalable Platform for Producing Recombinant Nucleosomes with Codified Histone Methyltransferase Substrate Preferences. Protein Expr Purif 2019; 164:105455. [PMID: 31306746 DOI: 10.1016/j.pep.2019.105455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022]
Abstract
Wolf-Hirschhorn Syndrome Candidate 1 (WHSC1; also known as NSD2) is a SET domain-containing histone lysine methyltransferase. A chromosomal translocation occurs in 15-20% of multiple myeloma patients and is associated with increased production of WHSC1 and poor clinical prognosis. To define the substrate requirements of NSD2, we established a platform for the large-scale production of recombinant polynucleosomes, based on authentic human histone proteins, expressed in E. coli, and complexed with linearized DNA. A brief survey of methyltransferases whose substrate requirements are recorded in the literature yielded expected results, lending credence to the fitness of our approach. This platform was readily 'codified' with respect to both position and extent of methylation at histone 3 lysines 18 and 36 and led to the conclusion that the most readily discernible activity of NSD2 in contact with a nucleosome substrate is dimethylation of histone 3 lysine 36. We further explored reaction mechanism, and conclude a processive, rather than distributive mechanism best describes the interaction of NSD2 with intact nucleosome substrates. The methods developed feature scale and flexibility and are suited to thorough pharmaceutical-scale drug discovery campaigns.
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Affiliation(s)
- Patrick J McDevitt
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA.
| | - Jessica L Schneck
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Elsie Diaz
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Wangfang Hou
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Michael J Huddleston
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Rosalie E Matico
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Patricia M McCormick
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
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SETD1A protects from senescence through regulation of the mitotic gene expression program. Nat Commun 2019; 10:2854. [PMID: 31253781 PMCID: PMC6599037 DOI: 10.1038/s41467-019-10786-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/20/2019] [Indexed: 01/13/2023] Open
Abstract
SETD1A, a Set1/COMPASS family member maintaining histone-H3-lysine-4 (H3K4) methylation on transcriptionally active promoters, is overexpressed in breast cancer. Here, we show that SETD1A supports mitotic processes and consequentially, its knockdown induces senescence. SETD1A, through promoter H3K4 methylation, regulates several genes orchestrating mitosis and DNA-damage responses, and its depletion causes chromosome misalignment and segregation defects. Cell cycle arrest in SETD1A knockdown senescent cells is independent of mutations in p53, RB and p16, known senescence mediators; instead, it is sustained through transcriptional suppression of SKP2, which degrades p27 and p21. Rare cells escaping senescence by restoring SKP2 expression display genomic instability. In > 200 cancer cell lines and in primary circulating tumor cells, SETD1A expression correlates with genes promoting mitosis and cell cycle suggesting a broad role in suppressing senescence induced by aberrant mitosis. Thus, SETD1A is essential to maintain mitosis and proliferation and its suppression unleashes the tumor suppressive effects of senescence. SETD1A, a histone H3K4 methyltransferase that promotes gene expression, is required for embryonic development. Here, the authors show that SETD1A regulates the expression of mitotic genes and that SETD1A suppression induces senescence.
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Humphries B, Wang Z, Yang C. MicroRNA Regulation of Epigenetic Modifiers in Breast Cancer. Cancers (Basel) 2019; 11:E897. [PMID: 31252590 PMCID: PMC6678197 DOI: 10.3390/cancers11070897] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/16/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022] Open
Abstract
Epigenetics refers to the heritable changes in gene expression without a change in the DNA sequence itself. Two of these major changes include aberrant DNA methylation as well as changes to histone modification patterns. Alterations to the epigenome can drive expression of oncogenes and suppression of tumor suppressors, resulting in tumorigenesis and cancer progression. In addition to modifications of the epigenome, microRNA (miRNA) dysregulation is also a hallmark for cancer initiation and metastasis. Advances in our understanding of cancer biology demonstrate that alterations in the epigenome are not only a major cause of miRNA dysregulation in cancer, but that miRNAs themselves also indirectly drive these DNA and histone modifications. More explicitly, recent work has shown that miRNAs can regulate chromatin structure and gene expression by directly targeting key enzymes involved in these processes. This review aims to summarize these research findings specifically in the context of breast cancer. This review also discusses miRNAs as epigenetic biomarkers and as therapeutics, and presents a comprehensive summary of currently validated epigenetic targets in breast cancer.
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Affiliation(s)
- Brock Humphries
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48109; USA.
| | - Zhishan Wang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.
- Center for Research on Environment Disease, College of Medicine, University of Kentucky, Lexington, KY 40536; USA.
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Li D, Zhang L, Zhang Y, Guan S, Gong X, Wang X. Maternal exposure to perfluorooctanoic acid (PFOA) causes liver toxicity through PPAR-α pathway and lowered histone acetylation in female offspring mice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:18866-18875. [PMID: 31062244 DOI: 10.1007/s11356-019-05258-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/22/2019] [Indexed: 05/27/2023]
Abstract
The study was conducted to investigate the liver toxicity in female offspring mice induced by maternal exposure to perfluorooctanoic acid (PFOA). Fifty pregnant Kunming mice were randomly divided into 5 groups with 10 of each, which were treated with 0.2 mL PFOA solution dissolved with deionized water at 0, 1, 2.5, 5, and 10 mg/kg BW, respectively, from the pregnancy day (PND) 0 to day 17. Female offspring mice were sacrificed to collect serum and liver at postpartum day 21. The results showed that PFOA significantly reduced the body weight at weaning and the survival rate of the female offspring mice (P < 0.01) increased the liver index of the pups (P < 0.01). Meanwhile, PFOA also caused hepatic bleeding, local necrosis, and enlargement of hepatocytes and vacuolization. The levels of serum AST, ALT, SOD, and CAT in PFOA treatment group were upregulated significantly (P < 0.01). The expressions of Acot1, Acox1, and Acsl1 genes were increased significantly (P < 0.01). The expression of PPAR-α gene was decreased significantly (P < 0.01). There was no significant difference in the expression of Cpt1a gene among the 5 groups. HAT activity was reduced significantly and HDAC activity was increased significantly. The expression of anti-acetyl-histone H3 and acetyl-histone H4 was reduced significantly. Thus, our findings indicate that exposure to PFOA during pregnancy affects the growth and development of the pups and causes liver damage, disrupting the secretion of enzymes involved in fatty acid oxidation induced by PPAR-α, leading to liver oxidative stress and a decrease in the degree of histone acetylation. Elevated HDAC may aggravate downstream fatty acid metabolism disorders through PPAR-α.
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Affiliation(s)
- Danyang Li
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Linchao Zhang
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Yan Zhang
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Shuo Guan
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Xincheng Gong
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China
| | - Xiaodan Wang
- College of Traditional Chinese Veterinary Medicine, Agricultural University of Hebei, Baoding, 071001, China.
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Kumar A, Kumari N, Nallabelli N, Prasad R. Pathogenic and Therapeutic Role of H3K4 Family of Methylases and Demethylases in Cancers. Indian J Clin Biochem 2019; 34:123-132. [PMID: 31092985 DOI: 10.1007/s12291-019-00828-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Histone modifications occupy an essential position in the epigenetic landscape of the cell, and their alterations have been linked to cancers. Histone 3 lysine 4 (H3K4) methylation has emerged as a critical epigenetic cue for the regulation of gene transcription through dynamic modulation by several H3K4 methyltransferases (writers) and demethylases (erasers). Any disturbance in the delicate balance of writers and erasers can result in the mis-regulation of H3K4 methylation, which has been demonstrated in several human cancers. Therefore, H3K4 methylation has been recognized as a putative therapeutic or prognostic tool and drug trials of different inhibitors of this process have demonstrated promising results. Henceforth, more detailed knowledge of H3K4 methylation is utmost important for elucidating the complex cellular processes, which might help in improving the disease outcome. The primary focus of this review will be directed on deciphering the role of H3K4 methylation along with its writers/erasers in different cancers.
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Affiliation(s)
- Aman Kumar
- 1Department of Biochemistry, Postgraduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, India
| | - Niti Kumari
- 1Department of Biochemistry, Postgraduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, India
| | - Nayudu Nallabelli
- 2Department of Endocrinology, Postgraduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, India
| | - Rajendra Prasad
- 1Department of Biochemistry, Postgraduate Institute of Medical Education and Research (PGIMER), Sector 12, Chandigarh, India
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13
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Liu Z, Gao Y, Li X. Cancer epigenetics and the potential of epigenetic drugs for treating solid tumors. Expert Rev Anticancer Ther 2018; 19:139-149. [PMID: 30470148 DOI: 10.1080/14737140.2019.1552139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Epigenetic modification without DNA sequence mutation plays an important role in cancer development. Some small molecular inhibitors targeting key epigenetic molecules have been approved by the Food and Drug Administration to treat hematological malignancies. However, the anticancer effects of these drugs on solid tumors are not satisfactory, and the mechanisms of action remain largely unknown. Areas covered: The review summarizes the latest research on cancer epigenetics and discusses the potentials and limitations of using epigenetic drugs to treat solid tumors. An analysis of possible reasons for epigenetic drug treatment failure in solid tumors in some clinical trials is discussed along with prospects for future development. Expert commentary: Next-generation small molecule inhibitors will target novel epigenetic regulators with high cancer specificity. Combined modalities exploiting epigenetic drugs with chemo-/radiotherapy, molecular-targeting drugs, and immunotherapy will be able to effectively treat solid tumors in the near future.
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Affiliation(s)
- Zhenghui Liu
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Yingxue Gao
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Xiong Li
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
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14
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Smith E, Zhou W, Shindiapina P, Sif S, Li C, Baiocchi RA. Recent advances in targeting protein arginine methyltransferase enzymes in cancer therapy. Expert Opin Ther Targets 2018; 22:527-545. [PMID: 29781349 PMCID: PMC6311705 DOI: 10.1080/14728222.2018.1474203] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Exploration in the field of epigenetics has revealed the diverse roles of the protein arginine methyltransferase (PRMT) family of proteins in multiple disease states. These findings have led to the development of specific inhibitors and discovery of several new classes of drugs with potential to treat both benign and malignant conditions. Areas covered: We provide an overview on the role of PRMT enzymes in healthy and malignant cells, highlighting the role of arginine methylation in specific pathways relevant to cancer pathogenesis. Additionally, we describe structure and catalytic activity of PRMT and discuss the mechanisms of action of novel small molecule inhibitors of specific members of the arginine methyltransferase family. Expert opinion: As the field of PRMT biology advances, it's becoming clear that this class of enzymes is highly relevant to maintaining normal physiologic processes as well and disease pathogenesis. We discuss the potential impact of PRMT inhibitors as a broad class of drugs, including the pleiotropic effects, off target effects the need for more detailed PRMT-centric interactomes, and finally, the potential for targeting this class of enzymes in clinical development of experimental therapeutics for cancer.
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Affiliation(s)
- Emily Smith
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Wei Zhou
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Polina Shindiapina
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Said Sif
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Chenglong Li
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Robert A. Baiocchi
- The Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
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15
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Liu Q, Cai X, Yang D, Chen Y, Wang Y, Shao L, Wang MW. Cycloalkane analogues of sinefungin as EHMT1/2 inhibitors. Bioorg Med Chem 2017; 25:4579-4594. [DOI: 10.1016/j.bmc.2017.06.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 01/26/2023]
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16
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Morel D, Almouzni G, Soria JC, Postel-Vinay S. Targeting chromatin defects in selected solid tumors based on oncogene addiction, synthetic lethality and epigenetic antagonism. Ann Oncol 2017; 28:254-269. [DOI: 10.1093/annonc/mdw552] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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17
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Abstract
Insulin resistance is one of the defining features of type 2 diabetes and the metabolic syndrome and accompanies many other clinical conditions, ranging from obesity to lipodystrophy to glucocorticoid excess. Extraordinary efforts have gone into defining the mechanisms that underlie insulin resistance, with most attention focused on altered signalling as well as mitochondrial and endoplasmic reticulum stress. Here, nuclear mechanisms of insulin resistance, including transcriptional and epigenomic effects, will be discussed. Three levels of control involving transcription factors, transcriptional cofactors, and chromatin-modifying enzymes will be considered. Well-studied examples of the first include PPAR-γ in adipose tissue and the glucocorticoid receptor and FoxO1 in a variety of insulin-sensitive tissues. These proteins work in concert with cofactors such as PGC-1α and CRTC2, and chromatin-modifying enzymes including DNA methyltransferases and histone acetyltransferases, to regulate key genes that promote insulin-stimulated glucose uptake, gluconeogenesis or other pathways that affect systemic insulin action. Furthermore, genetic variation associated with increased risk of type 2 diabetes is often related to altered transcription factor binding, either by affecting the transcription factor itself, or more commonly by changing the binding affinity of a noncoding regulatory region. Finally, several avenues for therapeutic exploitation in the battle against metabolic disease will be discussed, including small-molecule inhibitors and activators of these factors and their related pathways.
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Affiliation(s)
- E D Rosen
- Division of Endocrinology and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
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18
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Liu Q, Wang MW. Histone lysine methyltransferases as anti-cancer targets for drug discovery. Acta Pharmacol Sin 2016; 37:1273-1280. [PMID: 27397541 DOI: 10.1038/aps.2016.64] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/03/2016] [Indexed: 12/22/2022] Open
Abstract
Post-translational epigenetic modification of histones is controlled by a number of histone-modifying enzymes. Such modification regulates the accessibility of DNA and the subsequent expression or silencing of a gene. Human histone methyltransferases (HMTs)constitute a large family that includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). There is increasing evidence showing a correlation between HKMTs and cancer pathogenesis. Here, we present an overview of representative HKMTs, including their biological and biochemical properties as well as the profiles of small molecule inhibitors for a comprehensive understanding of HKMTs in drug discovery.
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19
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Matboli M, El-Nakeep S, Hossam N, Habieb A, Azazy AEM, Ebrahim AE, Nagy Z, Abdel-Rahman O. Exploring the role of molecular biomarkers as a potential weapon against gastric cancer: A review of the literature. World J Gastroenterol 2016; 22:5896-5908. [PMID: 27468184 PMCID: PMC4948264 DOI: 10.3748/wjg.v22.i26.5896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is a global health problem and a major cause of cancer-related death with high recurrence rates ranging from 25% to 40% for GC patients staging II-IV. Unfortunately, while the majority of GC patients usually present with advanced tumor stage; there is still limited evidence-based therapeutic options. Current approach to GC management consists mainly of; endoscopy followed by, gastrectomy and chemotherapy or chemo-radiotherapy. Recent studies in GC have confirmed that it is a heterogeneous disease. Many molecular characterization studies have been performed in GC. Recent discoveries of the molecular pathways underlying the disease have opened the door to more personalized treatment and better predictable outcome. The identification of molecular markers is a useful tool for clinical managementin GC patients, assisting in diagnosis, evaluation of response to treatment and development of novel therapeutic modalities. While chemotherapeutic agents have certain physiological effects on the tumor cells, the prediction of the response is different from one type of tumor to the other. The specificity of molecular biomarkers is a principal feature driving their application in anticancer therapies. Here we are trying to focus on the role of molecular pathways of GC and well-established molecular markers that can guide the therapeutic management.
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20
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Kaminska B, Mota M, Pizzi M. Signal transduction and epigenetic mechanisms in the control of microglia activation during neuroinflammation. Biochim Biophys Acta Mol Basis Dis 2016; 1862:339-51. [DOI: 10.1016/j.bbadis.2015.10.026] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/12/2015] [Accepted: 10/28/2015] [Indexed: 12/21/2022]
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Abstract
Epigenetics is currently one of the most promising areas of study in the field of biomedical research. Scientists have dedicated their efforts to studying epigenetic mechanisms in cancer for centuries. Additionally, the field has expanded from simply studying DNA methylation to other areas, such as histone modification, non-coding RNA, histone variation, nucleosome location, and chromosome remodeling. In ocular tumors, a large amount of epigenetic exploration has expanded from single genes to the genome-wide level. Most importantly, because epigenetic changes are reversible, several epigenetic drugs have been developed for the treatment of cancer. Herein, we review the current understanding of epigenetic mechanisms in ocular tumors, including but not limited to retinoblastoma and uveal melanoma. Furthermore, the development of new pharmacological strategies is summarized.
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Affiliation(s)
- Xuyang Wen
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Linna Lu
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Zhang He
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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22
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Li X, Li C, Sun G. Histone Acetylation and Its Modifiers in the Pathogenesis of Diabetic Nephropathy. J Diabetes Res 2016; 2016:4065382. [PMID: 27379253 PMCID: PMC4917685 DOI: 10.1155/2016/4065382] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/17/2016] [Indexed: 12/19/2022] Open
Abstract
Diabetic nephropathy (DN) remains a leading cause of mortality worldwide despite advances in its prevention and management. A comprehensive understanding of factors contributing to DN is required to develop more effective therapeutic options. It is becoming more evident that histone acetylation (HAc), as one of the epigenetic mechanisms, is thought to be associated with the etiology of diabetic vascular complications such as diabetic retinopathy (DR), diabetic cardiomyopathy (DCM), and DN. Histone acetylases (HATs) and histone deacetylases (HDACs) are the well-known regulators of reversible acetylation in the amino-terminal domains of histone and nonhistone proteins. In DN, however, the roles of histone acetylation (HAc) and these enzymes are still controversial. Some new evidence has revealed that HATs and HDACs inhibitors are renoprotective in cellular and animal models of DN, while, on the other hand, upregulation of HAc has been implicated in the pathogenesis of DN. In this review, we focus on the recent advances on the roles of HAc and their covalent enzymes in the development and progression of DN in certain cellular processes including fibrosis, inflammation, hypertrophy, and oxidative stress and discuss how targeting these enzymes and their inhibitors can ultimately lead to the therapeutic approaches for treating DN.
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Affiliation(s)
- Xiaoxia Li
- Department of Nephrology, The Second Hospital of Jilin University, Changchun 130041, China
| | - Chaoyuan Li
- Department of Nephrology, The Second Hospital of Jilin University, Changchun 130041, China
| | - Guangdong Sun
- Department of Nephrology, The Second Hospital of Jilin University, Changchun 130041, China
- *Guangdong Sun:
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23
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Busch C, Burkard M, Leischner C, Lauer UM, Frank J, Venturelli S. Epigenetic activities of flavonoids in the prevention and treatment of cancer. Clin Epigenetics 2015; 7:64. [PMID: 26161152 PMCID: PMC4497414 DOI: 10.1186/s13148-015-0095-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/17/2015] [Indexed: 02/07/2023] Open
Abstract
Aberrant epigenetic modifications are described in an increasing number of pathological conditions, including neurodegenerative diseases, cardiovascular diseases, diabetes mellitus type 2, obesity and cancer. The general reversibility of epigenetic changes makes them an attractive and promising target e.g. in the treatment of cancer. Thus, a growing number of epigenetically active compounds are currently tested in clinical trials for their therapeutic potential. Interestingly, many phytochemicals present in plant foods, particularly flavonoids, are suggested to be able to alter epigenetic cellular mechanisms. Flavonoids are natural phenol compounds that form a large group of secondary plant metabolites with interesting biological activities. They can be categorized into six major subclasses, which display diverse properties affecting the two best characterized epigenetic mechanisms: modulation of the DNA methylation status and histone acetylation. High dietary flavonoid intake has strongly been suggested to reduce the risk of numerous cancer entities in a large body of epidemiological studies. Established health-promoting effects of diets rich in fruit and vegetables are faced by efforts to use purified flavonoids as supplements or pharmaceuticals, whereupon data on the latter applications remain controversial. The purpose of this review is to give an overview of current research on flavonoids to further elucidate their potential in cancer prevention and therapy, thereby focusing on their distinct epigenetic activities.
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Affiliation(s)
- Christian Busch
- Division of Dermatologic Oncology, Department of Dermatology and Allergology, Medical University Hospital, Tuebingen, Germany
| | - Markus Burkard
- Division of Dermatologic Oncology, Department of Dermatology and Allergology, Medical University Hospital, Tuebingen, Germany ; Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Christian Leischner
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Jan Frank
- Institute of Biological Chemistry and Nutrition, University of Hohenheim, Stuttgart, Germany
| | - Sascha Venturelli
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
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24
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Ospelt C, Gay S. Epigenetics in rheumatology. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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25
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Marmorstein R, Zhou MM. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol 2014; 6:a018762. [PMID: 24984779 DOI: 10.1101/cshperspect.a018762] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone acetylation marks are written by histone acetyltransferases (HATs) and read by bromodomains (BrDs), and less commonly by other protein modules. These proteins regulate many transcription-mediated biological processes, and their aberrant activities are correlated with several human diseases. Consequently, small molecule HAT and BrD inhibitors with therapeutic potential have been developed. Structural and biochemical studies of HATs and BrDs have revealed that HATs fall into distinct subfamilies containing a structurally related core for cofactor binding, but divergent flanking regions for substrate-specific binding, catalysis, and autoregulation. BrDs adopt a conserved left-handed four-helix bundle to recognize acetyllysine; divergent loop residues contribute to substrate-specific acetyllysine recognition.
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Affiliation(s)
- Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10065
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26
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Leveridge M, Buxton R, Argyrou A, Francis P, Leavens B, West A, Rees M, Hardwicke P, Bridges A, Ratcliffe S, Chung CW. Demonstrating Enhanced Throughput of RapidFire Mass Spectrometry through Multiplexing Using the JmjD2d Demethylase as a Model System. ACTA ACUST UNITED AC 2013; 19:278-86. [DOI: 10.1177/1087057113496276] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Using mass spectrometry to detect enzymatic activity offers several advantages over fluorescence-based methods. Automation of sample handling and analysis using platforms such as the RapidFire (Agilent Technologies, Lexington, MA) has made these assays amenable to medium-throughput screening (of the order of 100,000 wells). However, true high-throughput screens (HTS) of large compound collections (>1 million) are still considered too time-consuming to be feasible. Here we propose a simple multiplexing strategy that can be used to increase the throughput of RapidFire, making it viable for HTS. The method relies on the ability to analyze pooled samples from several reactions simultaneously and to deconvolute their origin using “mass-tagged” substrates. Using the JmjD2d H3K9me3 demethylase as a model system, we demonstrate the practicality of this method to achieve a 4-fold increase in throughput. This was achieved without any loss of assay quality. This multiplex strategy could easily be scaled to give even greater reductions in analysis time.
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Affiliation(s)
- Melanie Leveridge
- Department of Screening and Compound Profiling, GlaxoSmithKline, Stevenage, UK
| | - Rachel Buxton
- Biological Reagents and Assay Development, GlaxoSmithKline, Stevenage, UK
| | - Argyrides Argyrou
- Biological Reagents and Assay Development, GlaxoSmithKline, Stevenage, UK
| | - Peter Francis
- Computational and Structural Chemistry, GlaxoSmithKline, Stevenage, UK
| | - Bill Leavens
- Computational and Structural Chemistry, GlaxoSmithKline, Stevenage, UK
| | - Andy West
- Computational and Structural Chemistry, GlaxoSmithKline, Stevenage, UK
| | - Mike Rees
- Biological Reagents and Assay Development, GlaxoSmithKline, Stevenage, UK
| | - Philip Hardwicke
- Biological Reagents and Assay Development, GlaxoSmithKline, Stevenage, UK
| | - Angela Bridges
- Biological Reagents and Assay Development, GlaxoSmithKline, Stevenage, UK
| | - Steven Ratcliffe
- Computational and Structural Chemistry, GlaxoSmithKline, Stevenage, UK
| | - Chun-wa Chung
- Computational and Structural Chemistry, GlaxoSmithKline, Stevenage, UK
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27
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Knackstedt RW, Moseley VR, Wargovich MJ. Epigenetic mechanisms underlying diet-sourced compounds in the prevention and treatment of gastrointestinal cancer. Anticancer Agents Med Chem 2013; 12:1203-10. [PMID: 22931412 DOI: 10.2174/187152012803833053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 06/06/2012] [Accepted: 06/07/2012] [Indexed: 12/31/2022]
Abstract
The development of colon cancer, the third most diagnosed cancer and third leading cause of cancer deaths in the United States, can be influenced by genetic predispositions and environmental exposures. As 80% of colon cancer cases are sporadic in nature, much interest lies in determining risk factors that may foster its development, as well as identifying compounds that could inhibit colon cancer development or halt progression. A major risk factor for sporadic colon cancer is a high fat, Western diet which has been linked to a cancer-prone, pro-inflammatory state. Cultures which place an emphasis on fresh fruits and vegetables demonstrate lower colon cancer incidences. Diet not only has the potential to encourage colon cancer development, but recent evidence demonstrates that certain dietary natural products can halt colon cancer development and progression via epigenetic regulation. Epigenetic dysregulation may contribute to inflammation-driven diseases, such as cancer, and can lead to the inappropriate silencing of genes necessary to inhibit cancer development. Natural compounds have shown the ability to reverse epigenetic dysregulation in in vitro and in vivo models. As current allopathic medicines aimed at reversing epigenetic silencing are accompanied with the risk of toxicity and side effects, much interest lies in being able to harness the disease preventing properties in natural products. Here, we discuss the epidemiology of colon cancer, describe the need for natural approaches to inhibit disease development and highlight natural products which have been shown to inhibit gastrointestinal cancer initiation and progression in vitro or in vivo through epigenetic modulation.
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Affiliation(s)
- Rebecca W Knackstedt
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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28
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Dangi-Garimella S, Sahai V, Ebine K, Kumar K, Munshi HG. Three-dimensional collagen I promotes gemcitabine resistance in vitro in pancreatic cancer cells through HMGA2-dependent histone acetyltransferase expression. PLoS One 2013; 8:e64566. [PMID: 23696899 PMCID: PMC3655998 DOI: 10.1371/journal.pone.0064566] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 04/16/2013] [Indexed: 12/29/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is associated with a pronounced collagen-rich stromal reaction that has been shown to contribute to chemo-resistance. We have previously shown that PDAC cells are resistant to gemcitabine chemotherapy in the collagen microenvironment because of increased expression of the chromatin remodeling protein high mobility group A2 (HMGA2). We have now found that human PDAC tumors display higher levels of histone H3K9 and H3K27 acetylation in fibrotic regions. We show that relative to cells grown on tissue culture plastic, PDAC cells grown in three-dimensional collagen gels demonstrate increased histone H3K9 and H3K27 acetylation, along with increased expression of p300, PCAF and GCN5 histone acetyltransferases (HATs). Knocking down HMGA2 attenuates the effect of collagen on histone H3K9 and H3K27 acetylation and on collagen-induced p300, PCAF and GCN5 expression. We also show that human PDAC tumors with HMGA2 demonstrate increased histone H3K9 and H3K27 acetylation. Additionally, we show that cells in three-dimensional collagen gels demonstrate increased protection against gemcitabine. Significantly, down-regulation of HMGA2 or p300, PCAF and GCN5 HATs sensitizes the cells to gemcitabine in three-dimensional collagen. Overall, our results increase our understanding of how the collagen microenvironment contributes to chemo-resistance in vitro and identify HATs as potential therapeutic targets against this deadly cancer.
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Affiliation(s)
- Surabhi Dangi-Garimella
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (SD); (HGM)
| | - Vaibhav Sahai
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Kazumi Ebine
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Krishan Kumar
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Hidayatullah G. Munshi
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Northwestern University, Chicago, Illinois, United States of America
- The Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (SD); (HGM)
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29
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Serravallo M, Jagdeo J, Glick SA, Siegel DM, Brody NI. Sirtuins in dermatology: applications for future research and therapeutics. Arch Dermatol Res 2013; 305:269-82. [PMID: 23377138 DOI: 10.1007/s00403-013-1320-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 01/13/2013] [Accepted: 01/21/2013] [Indexed: 12/31/2022]
Abstract
Sirtuins are a family of seven proteins in humans (SIRT1-SIRT7) that are involved in multiple cellular processes relevant to dermatology. The role of sirtuins in other organ systems is established. However, the importance of these proteins in dermatology is less defined. Recently, sirtuins gained international attention because of their role as "longevity proteins" that may extend and enhance human life. Sirtuins function in the cell via histone deacetylase and/or adenosine diphosphate ribosyltransferase enzymatic activity that target histone and non-histone substrates, including transcription regulators, tumor suppressors, structural proteins, DNA repair proteins, cell signaling proteins, transport proteins, and enzymes. Sirtuins are involved in cellular pathways related to skin structure and function, including aging, ultraviolet-induced photoaging, inflammation, epigenetics, cancer, and a variety of cellular functions including cell cycle, DNA repair and proliferation. This review highlights sirtuin-related cellular pathways, therapeutics and pharmacological targets in atopic dermatitis, bullous dermatoses, collagen vascular disorders, psoriasis, systemic lupus erythematosus, hypertrophic and keloid scars, cutaneous infections, and non-melanoma and melanoma skin cancer. Also discussed is the role of sirtuins in the following genodermatoses: ataxia telangiectasia, Cowden's syndrome, dyskeratosis congenita, Rubenstein-Taybi, Werner syndrome, and xeroderma pigmentosum. The pathophysiology of these inherited diseases is not well understood, and sirtuin-related processes represent potential therapeutic targets for diseases lacking suitable alternative treatments. The goal of this review is to bring attention to the dermatology community, physicians, and scientists, the importance of sirtuins in dermatology and provide a foundation and impetus for future discussion, research and pharmacologic discovery.
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Affiliation(s)
- Melissa Serravallo
- Department of Dermatology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
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30
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Nair SS, Kumar R. Chromatin remodeling in cancer: a gateway to regulate gene transcription. Mol Oncol 2012; 6:611-9. [PMID: 23127546 PMCID: PMC3538127 DOI: 10.1016/j.molonc.2012.09.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/30/2012] [Indexed: 01/01/2023] Open
Abstract
Cancer cells are remarkably adaptive to diverse survival strategies, probably due to its ability to interpret signaling cues differently than the normal cells. It appears as if cancer cells are constantly sampling, selecting and adapting signaling pathways to favor its proliferation. This process of successful adaptive evolution eventually renders a retractile nature to therapeutic regimens, fueling to the process of cancer progression. Based on plethora of available information, it is now evident that multiple signaling pathways eventually converge, perhaps, in a tempo-spatial manner, onto DNA template-dependent dynamic processes. Considering the complexity and packaging of eukaryotic genome, this process involves energy-dependent sub-events mediated by chromatin remodelers. Chromatin remodeler proteins function as gatekeepers and constitute a major determinant of accessibility of accessory factors to nucleosome DNA, allowing a wide repertoire of biological functions. And thus, aberrant expression or epigenetic modulation of remodeler proteins confers a unique ability to cancer cells to reprogram its genome for the maintenance of oncogenic phenotypes. Cancer cells can uniquely select a multi-subunit remodeler proteome for oncogenic advantage. This review summarizes our current understanding and importance of remodeler and chromatin proteins in cancer biology and also highlights the paradoxical role of proteins with or without dual-regulator functions. It is our hope that an in-depth understanding of these events is likely to provide a next set of opportunities for novel strategies for targeted cancer therapeutics.
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Affiliation(s)
- Sujit S Nair
- Department of Biochemistry and Molecular Biology, The McCormick Genomic and Proteomic Center, The School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
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Castellano S, Spannhoff A, Milite C, Dal Piaz F, Cheng D, Tosco A, Viviano M, Yamani A, Cianciulli A, Sala M, Cura V, Cavarelli J, Novellino E, Mai A, Bedford MT, Sbardella G. Identification of small-molecule enhancers of arginine methylation catalyzed by coactivator-associated arginine methyltransferase 1. J Med Chem 2012; 55:9875-90. [PMID: 23095008 PMCID: PMC3508294 DOI: 10.1021/jm301097p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Arginine methylation is a common post-translational modification that is crucial in modulating gene expression at multiple critical levels. The arginine methyltransferases (PRMTs) are envisaged as promising druggable targets, but their role in physiological and pathological pathways is far from being clear due to the limited number of modulators reported to date. In this effort, enzyme activators can be invaluable tools useful as gain-of-function reagents to interrogate the biological roles in cells and in vivo of PRMTs. Yet the identification of such molecules is rarely pursued. Herein we describe a series of aryl ureido acetamido indole carboxylates (dubbed "uracandolates"), able to increase the methylation of histone (H3) or nonhistone (polyadenylate-binding protein 1, PABP1) substrates induced by coactivator-associated arginine methyltransferase 1 (CARM1), both in in vitro and cellular settings. To the best of our knowledge, this is the first report of compounds acting as CARM1 activators.
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Affiliation(s)
- Sabrina Castellano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Astrid Spannhoff
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Ciro Milite
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Fabrizio Dal Piaz
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Donghang Cheng
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Alessandra Tosco
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Monica Viviano
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Abdellah Yamani
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Agostino Cianciulli
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Marina Sala
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), UDS, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, IGBMC (Institut de Génétique et Biologie Moléculaire et Cellulaire), UDS, CNRS, INSERM, 67404 Illkirch Cedex, France
| | - Ettore Novellino
- Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonello Mai
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P.le A. Moro 5, I-00185 Roma, Italy
| | - Mark T. Bedford
- University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957, USA
| | - Gianluca Sbardella
- Dipartimento di Scienze Farmaceutiche e Biomediche, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Ponte Don Melillo, I-84084 Fisciano (SA), Italy
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Gilbert ER, Liu D. Epigenetics: the missing link to understanding β-cell dysfunction in the pathogenesis of type 2 diabetes. Epigenetics 2012; 7:841-52. [PMID: 22810088 PMCID: PMC3427279 DOI: 10.4161/epi.21238] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Type 2 diabetes (T2D) is a growing health problem worldwide. While peripheral insulin resistance is common during obesity and aging in both animals and people, progression to T2D is largely due to insulin secretory dysfunction and significant apoptosis of functional β-cells, leading to an inability to compensate for insulin resistance. It is recognized that environmental factors and nutrition play an important role in the pathogenesis of diabetes. However, our knowledge surrounding molecular mechanisms by which these factors trigger β-cell dysfunction and diabetes is still limited. Recent discoveries raise the possibility that epigenetic changes in response to environmental stimuli may play an important role in the development of diabetes. In this paper, we review emerging knowledge regarding epigenetic mechanisms that may be involved in β-cell dysfunction and pathogenesis of diabetes, including the role of nutrition, oxidative stress and inflammation. We will mainly focus on the role of DNA methylation and histone modifications but will also briefly review data on miRNA effects on the pancreatic islets. Further studies aimed at better understanding how epigenetic regulation of gene expression controls β-cell function may reveal potential therapeutic targets for prevention and treatment of diabetes.
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Affiliation(s)
- Elizabeth R. Gilbert
- Department of Animal and Poultry Sciences; College of Agriculture and Life Sciences; Virginia Tech; Blacksburg, VA USA
| | - Dongmin Liu
- Department of Human Nutrition, Foods and Exercise; College of Agriculture and Life Sciences; Virginia Tech; Blacksburg, VA USA
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Guo SW. The endometrial epigenome and its response to steroid hormones. Mol Cell Endocrinol 2012; 358:185-96. [PMID: 22067514 DOI: 10.1016/j.mce.2011.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 10/21/2011] [Accepted: 10/21/2011] [Indexed: 01/21/2023]
Abstract
The human endometrium undergoes cyclic morphological and functional changes during the menstrual cycle. These changes are driven mainly by steroid hormones and orchestrated by a myriad of genes - many of which have been identified recently as being epigenetically regulated. Epigenetic modifications, including DNA methylation and histone acetylations, are shown recently to be involved in functional changes in endometrium and endometrial diseases. Since epigenetics itself is a rapidly evolving field, this review starts with an overview of epigenetics and its intrinsic connections with endometrial response to steroid hormones, highlighting its various levels of complexities. This is followed by a review of published and unpublished work on "writers", "erasers", and other players of endometrial epigenome. In the end, areas in need for future research in this area will be exposed.
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Affiliation(s)
- Sun-Wei Guo
- Shanghai Obstetric and Gynecologic Hospital, and Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University Shanghai College of Medicine, 419 Fangxie Road, Shanghai 200011, China.
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34
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Verbrugge I, Johnstone RW, Bots M. Promises and challenges of anticancer drugs that target the epigenome. Epigenomics 2012; 3:547-65. [PMID: 22126246 DOI: 10.2217/epi.11.82] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The occurrence of epigenetic aberrations in cancer and their role in promoting tumorigenesis has led to the development of various small molecule inhibitors that target epigenetic enzymes. In preclinical settings, many epigenetic inhibitors demonstrate promising activity against a variety of both hematological and solid tumors. The therapeutic efficacy of those inhibitors that have entered the clinic however, is restricted predominantly to hematological malignancies. Here we outline the observed epigenetic aberrations in various types of cancer and the clinical responses to epigenetic drugs. We furthermore discuss strategies to improve the responsiveness of both hematological and solid malignancies to epigenetic drugs.
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Affiliation(s)
- Inge Verbrugge
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne 3002, Victoria, Australia
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35
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Franci G, Miceli M, Altucci L. Targeting epigenetic networks with polypharmacology: a new avenue to tackle cancer. Epigenomics 2012; 2:731-42. [PMID: 22122079 DOI: 10.2217/epi.10.62] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The term 'epigenetic' fuses old and new concepts that refer to the modulation of gene expression in cellular heritability, fate, development and programming-reprogramming other than the DNA sequence itself. Epigenetic control of transcription is regulated by enzymes that mediate covalent modifications at gene-regulatory regions and histone proteins around which chromosomal DNA is wound. Many of the enzymes that mediate chromatin epigenetic reactions are deregulated in diseases such as cancer. Thus, small-molecule inhibitors that target chromatin-modifying enzymes represent a novel option for treatment, and DNA methyltransferase and histone deacetylase inhibitors have been approved for cancer treatment. Moreover, other classes of epi-enzymes (MS-275, SAHA) have been demonstrated to have strong disease association, and are currently being targeted for modulation. An epigenetic poly-pharmacological approach targeting multiple chromatin-modifying enzymes may represent a 'smart' option to treat cancer versus the current view on the selective and single pharmacological targeting of epigenetic enzymes.
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Schmidt HD, Sangrey GR, Darnell SB, Schassburger RL, Cha JHJ, Pierce RC, Sadri-Vakili G. Increased brain-derived neurotrophic factor (BDNF) expression in the ventral tegmental area during cocaine abstinence is associated with increased histone acetylation at BDNF exon I-containing promoters. J Neurochem 2012; 120:202-9. [PMID: 22043863 PMCID: PMC3243782 DOI: 10.1111/j.1471-4159.2011.07571.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent evidence suggests that the persistence of cocaine seeking during periods of protracted drug abstinence following chronic cocaine exposure is mediated, in part, by neuroadaptations in the mesolimbic dopamine system. Specifically, incubation of cocaine-seeking behavior coincides with increased brain-derived neurotrophic factor (BDNF) protein expression in the ventral tegmental area (VTA). However, the molecular mechanisms that regulate time-dependent changes in VTA BDNF protein expression during cocaine abstinence are unclear. The goal of these experiments was to determine whether VTA BDNF transcript levels are altered following cocaine abstinence and identify the molecular mechanisms regulating cocaine-induced changes in VTA BDNF transcription. Rats were allowed to self-administer cocaine (0.25 mg/infusion, i.v.) for 14 days on a fixed-ratio schedule of reinforcement followed by 7 days of forced drug abstinence. BDNF protein and exon I-containing transcripts were significantly increased in the VTA of cocaine-experienced rats following 7 days of forced drug abstinence compared to yoked saline controls. Cocaine-induced changes in BDNF mRNA were associated with increased acetylation of histone 3 and binding of CREB-binding protein to exon I-containing promoters in the VTA. Taken together, these results suggest that drug abstinence following cocaine self-administration remodels chromatin in the VTA resulting in increased expression of BDNF, which may contribute to neuroadaptations underlying cocaine craving and relapse.
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Affiliation(s)
- Heath D Schmidt
- Center for Neurobiology and Behavior, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania School, Philadelphia, Pennsylvania, USA
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Abstract
There have been great advances in the neurological sciences in recent years including some in the higher functions of the brain such as memory but one of the more critical of these with close ties to memory is consciousness which remains an enigma. Revolutionary developments in genetics during the last two decades, referred to as epigenetics, have provided opportunity for discovery. The chromatin in the cell nucleus consists mainly of DNA nucleotides and histone proteins and the DNA is dynamically and epigenetically altered by the local actions of enzymes and trans-acting factors on the adjacent histone amino acids. DNA is also directly activated or inhibited by methyl groups and by non-coding RNAs. Epigenetics is a determinant in long-term cell memory consolidation and, as recently demonstrated in animal and human studies and described here, these effects enable a rapid and extraordinarily complex cognitive matching of cell memory to experience during consciousness.
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Thalhammer A, Mecinović J, Loenarz C, Tumber A, Rose NR, Heightman TD, Schofield CJ. Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates. Org Biomol Chem 2011; 9:127-35. [PMID: 21076780 PMCID: PMC4733660 DOI: 10.1039/c0ob00592d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Based on structural analysis of the human 2-oxoglutarate (2OG) dependent JMJD2 histone N(ε)-methyl lysyl demethylase family, 3-substituted pyridine 2,4-dicarboxylic acids were identified as potential inhibitors with possible selectivity over other human 2OG oxygenases. Microwave-assisted palladium-catalysed cross coupling methodology was developed to install a diverse set of substituents on the sterically demanding C-3 position of a pyridine 2,4-dicarboxylate scaffold. The subsequently prepared di-acids were tested for in vitro inhibition of the histone demethylase JMJD2E and another human 2OG oxygenase, prolyl-hydroxylase domain isoform 2 (PHD2, EGLN1). A subset of substitution patterns yielded inhibitors with selectivity for JMJD2E over PHD2, demonstrating that structure-based inhibitor design can enable selective inhibition of histone demethylases over related human 2OG oxygenases.
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Affiliation(s)
- Armin Thalhammer
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors. PLoS One 2010; 5:e15535. [PMID: 21124847 PMCID: PMC2990756 DOI: 10.1371/journal.pone.0015535] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 10/08/2010] [Indexed: 12/13/2022] Open
Abstract
Background Small molecule modulators of epigenetic processes are currently sought as basic probes for biochemical mechanisms, and as starting points for development of therapeutic agents. Nε-Methylation of lysine residues on histone tails is one of a number of post-translational modifications that together enable transcriptional regulation. Histone lysine demethylases antagonize the action of histone methyltransferases in a site- and methylation state-specific manner. Nε-Methyllysine demethylases that use 2-oxoglutarate as co-factor are associated with diverse human diseases, including cancer, inflammation and X-linked mental retardation; they are proposed as targets for the therapeutic modulation of transcription. There are few reports on the identification of templates that are amenable to development as potent inhibitors in vivo and large diverse collections have yet to be exploited for the discovery of demethylase inhibitors. Principal Findings High-throughput screening of a ∼236,000-member collection of diverse molecules arrayed as dilution series was used to identify inhibitors of the JMJD2 (KDM4) family of 2-oxoglutarate-dependent histone demethylases. Initial screening hits were prioritized by a combination of cheminformatics, counterscreening using a coupled assay enzyme, and orthogonal confirmatory detection of inhibition by mass spectrometric assays. Follow-up studies were carried out on one of the series identified, 8-hydroxyquinolines, which were shown by crystallographic analyses to inhibit by binding to the active site Fe(II) and to modulate demethylation at the H3K9 locus in a cell-based assay. Conclusions These studies demonstrate that diverse compound screening can yield novel inhibitors of 2OG dependent histone demethylases and provide starting points for the development of potent and selective agents to interrogate epigenetic regulation.
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Gräff J, Franklin TB, Mansuy IM. [Epigenetics and memory]. Biol Aujourdhui 2010; 204:131-7. [PMID: 20950557 DOI: 10.1051/jbio/2010007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Indexed: 11/15/2022]
Abstract
The epigenetic marking of chromatin in the brain has recently been recognized as an essential mechanism for brain functions such as learning and memory formation. It allows nerve cells not only to respond to environmental stimuli and modulate their profile of gene expression, but also to establish and maintain their own identity. The epigenetic code is conferred by a set of covalent modifications on the basic elements of chromatin, DNA and histone proteins. These changes are catalyzed by specific enzymes and mechanisms, which include DNA methylation, and post-translational modifications of histone proteins such as acetylation, phosphorylation, methylation and ubiquitination. They are both stable and highly dynamic, and are triggered during stimulation of neuronal circuits but can also persist thereafter. Their study in animal models has demonstrated their importance, and revealed some of their modes of function.
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Affiliation(s)
- Johannes Gräff
- Brain Research Institute, University of Zurich, Zurich, Switzerland
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42
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Wigle TJ, Provencher LM, Norris JL, Jin J, Brown PJ, Frye SV, Janzen WP. Accessing protein methyltransferase and demethylase enzymology using microfluidic capillary electrophoresis. CHEMISTRY & BIOLOGY 2010; 17:695-704. [PMID: 20659682 PMCID: PMC2914686 DOI: 10.1016/j.chembiol.2010.04.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 04/08/2010] [Accepted: 04/16/2010] [Indexed: 12/11/2022]
Abstract
The discovery of small molecules targeting the >80 enzymes that add (methyltransferases) or remove (demethylases) methyl marks from lysine and arginine residues, most notably present in histone tails, may yield unprecedented chemotherapeutic agents and facilitate regenerative medicine. To better enable chemical exploration of these proteins, we have developed a highly quantitative microfluidic capillary electrophoresis assay to enable full mechanistic studies of these enzymes and the kinetics of their inhibition. This technology separates small biomolecules, i.e., peptides, based on their charge-to-mass ratio. Methylation, however, does not alter the charge of peptide substrates. To overcome this limitation, we have employed a methylation-sensitive endoproteinase strategy to separate methylated from unmethylated peptides. The assay was validated on a lysine methyltransferase (G9a) and a lysine demethylase (LSD1) and was employed to investigate the inhibition of G9a by small molecules.
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Affiliation(s)
- Tim J. Wigle
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina, 2092 Genetic Medicine Building CB #7363, 120 Mason Farm Rd, Chapel, Hill, North Carolina, 27599-7363
| | | | - Jacqueline L. Norris
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina, 2092 Genetic Medicine Building CB #7363, 120 Mason Farm Rd, Chapel, Hill, North Carolina, 27599-7363
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina, 2092 Genetic Medicine Building CB #7363, 120 Mason Farm Rd, Chapel, Hill, North Carolina, 27599-7363
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, MaRS Centre South Tower, 101 College St., Suite 700, Toronto, Ontario, M5G 1L7
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina, 2092 Genetic Medicine Building CB #7363, 120 Mason Farm Rd, Chapel, Hill, North Carolina, 27599-7363
| | - William P. Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina, 2092 Genetic Medicine Building CB #7363, 120 Mason Farm Rd, Chapel, Hill, North Carolina, 27599-7363
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43
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Goody MF, Kelly MW, Lessard KN, Khalil A, Henry CA. Nrk2b-mediated NAD+ production regulates cell adhesion and is required for muscle morphogenesis in vivo: Nrk2b and NAD+ in muscle morphogenesis. Dev Biol 2010; 344:809-26. [PMID: 20566368 DOI: 10.1016/j.ydbio.2010.05.513] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/22/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
Abstract
Cell-matrix adhesion complexes (CMACs) play fundamental roles during morphogenesis. Given the ubiquitous nature of CMACs and their roles in many cellular processes, one question is how specificity of CMAC function is modulated. The clearly defined cell behaviors that generate segmentally reiterated axial skeletal muscle during zebrafish development comprise an ideal system with which to investigate CMAC function during morphogenesis. We found that Nicotinamide riboside kinase 2b (Nrk2b) cell autonomously modulates the molecular composition of CMACs in vivo. Nrk2b is required for normal Laminin polymerization at the myotendinous junction (MTJ). In Nrk2b-deficient embryos, at MTJ loci where Laminin is not properly polymerized, muscle fibers elongate into adjacent myotomes and are abnormally long. In yeast and human cells, Nrk2 phosphorylates Nicotinamide Riboside and generates NAD+ through an alternative salvage pathway. Exogenous NAD+ treatment rescues MTJ development in Nrk2b-deficient embryos, but not in laminin mutant embryos. Both Nrk2b and Laminin are required for localization of Paxillin, but not beta-Dystroglycan, to CMACs at the MTJ. Overexpression of Paxillin in Nrk2b-deficient embryos is sufficient to rescue MTJ integrity. Taken together, these data show that Nrk2b plays a specific role in modulating subcellular localization of discrete CMAC components that in turn plays roles in musculoskeletal development. Furthermore, these data suggest that Nrk2b-mediated synthesis of NAD+ is functionally upstream of Laminin adhesion and Paxillin subcellular localization during MTJ development. These results indicate a previously unrecognized complexity to CMAC assembly in vivo and also elucidate a novel role for NAD+ during morphogenesis.
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Affiliation(s)
- Michelle F Goody
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
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44
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Campagna-Slater V, Schapira M. Finding Inspiration in the Protein Data Bank to Chemically Antagonize Readers of the Histone Code. Mol Inform 2010; 29:322-31. [PMID: 27463059 DOI: 10.1002/minf.201000018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2010] [Accepted: 03/02/2010] [Indexed: 12/12/2022]
Abstract
Members of the Royal family of proteins are readers of the histone code that contain aromatic cages capable of recognizing specific sequences and lysine methylation states on histone tails. These binding modules play a key role in epigenetic signalling, and are part of a larger group of epigenetic targets that are becoming increasingly attractive for drug discovery. In the current study, pharmacophore representations of the aromatic cages forming the methyl-lysine (Me-Lys) recognition site were used to search the Protein Data Bank (PDB) for ligand binding pockets possessing similar chemical and geometrical features in unrelated proteins. The small molecules bound to these sites were then extracted from the PDB, and clustered based on fragments binding to the aromatic cages. The compounds collected are numerous and structurally diverse, but point to a limited set of preferred chemotypes; these include quaternary ammonium, sulfonium, and primary, secondary and tertiary amine moieties, as well as aromatic, aliphatic or orthogonal rings, and bicyclic systems. The chemical tool-kit identified can be used to design antagonists of the Royal family and related proteins.
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Affiliation(s)
- Valérie Campagna-Slater
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 7thfloor, 101 College Street, Toronto, Ontario, Canada, M5G 1L7 fax: 416-946-0880
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 7thfloor, 101 College Street, Toronto, Ontario, Canada, M5G 1L7 fax: 416-946-0880. .,Department of Pharmacology and Toxicology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.
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Choudhuri S, Cui Y, Klaassen CD. Molecular targets of epigenetic regulation and effectors of environmental influences. Toxicol Appl Pharmacol 2010; 245:378-93. [PMID: 20381512 DOI: 10.1016/j.taap.2010.03.022] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 03/25/2010] [Accepted: 03/29/2010] [Indexed: 12/31/2022]
Abstract
The true understanding of what we currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DNA methylation, chromatin modification, as well as on the expression of small non-coding RNAs (ncRNAs) have expanded the scope of research on the etiology of various diseases including cancer. The current review briefly discusses the molecular mechanisms of epigenetic regulation and expands the discussion with examples on the role of environment, such as the immediate environment during development, in inducing epigenetic changes and modulating gene expression.
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Affiliation(s)
- Supratim Choudhuri
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Additive Safety, Division of Biotechnology and GRAS Notice Review, College Park, MD, USA.
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RCC1 uses a conformationally diverse loop region to interact with the nucleosome: a model for the RCC1-nucleosome complex. J Mol Biol 2010; 398:518-29. [PMID: 20347844 DOI: 10.1016/j.jmb.2010.03.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 02/24/2010] [Accepted: 03/19/2010] [Indexed: 01/15/2023]
Abstract
The binding of RCC1 (regulator of chromosome condensation 1) to chromatin is critical for cellular processes such as mitosis, nucleocytoplasmic transport, and nuclear envelope formation because RCC1 recruits the small GTPase Ran (Ras-related nuclear protein) to chromatin and sets up a Ran-GTP gradient around the chromosomes. However, the molecular mechanism by which RCC1 binds to nucleosomes, the repeating unit of chromatin, is not known. We have used biochemical approaches to test structural models for how the RCC1 beta-propeller protein could bind to the nucleosome. In contrast to the prevailing model, RCC1 does not appear to use the beta-propeller face opposite to its Ran-binding face to interact with nucleosomes. Instead, we find that RCC1 uses a conformationally flexible loop region we have termed the switchback loop in addition to its N-terminal tail to bind to the nucleosome. The juxtaposition of the RCC1 switchback loop to its Ran binding surface suggests a novel mechanism for how nucleosome-bound RCC1 recruits Ran to chromatin. Furthermore, this model accounts for previously unexplained observations for how Ran can interact with the nucleosome both dependent and independent of RCC1 and how binding of the nucleosome can enhance RCC1's Ran nucleotide exchange activity.
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47
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Abstract
Epigenetics is a rapidly growing field and holds great promise for a range of human diseases, including brain disorders such as Rett syndrome, anxiety and depressive disorders, schizophrenia, Alzheimer disease and Huntington disease. This review is concerned with the pharmacology of epigenetics to treat disorders of the epigenome whether induced developmentally or manifested/acquired later in life. In particular, we will focus on brain disorders and their treatment by drugs that modify the epigenome. While the use of DNA methyl transferase inhibitors and histone deacetylase inhibitors in in vitro and in vivo models have demonstrated improvements in disease-related deficits, clinical trials in humans have been less promising. We will address recent advances in our understanding of the complexity of the epigenome with its many molecular players, and discuss evidence for a compromised epigenome in the context of an ageing or diseased brain. We will also draw on examples of species differences that may exist between humans and model systems, emphasizing the need for more robust pre-clinical testing. Finally, we will discuss fundamental issues to be considered in study design when targeting the epigenome.
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Affiliation(s)
- Pritika Narayan
- Department of Pharmacology and the National Research Centre for Growth and Development, The University of Auckland, Auckland, New Zealand
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Weissman B, Knudsen KE. Hijacking the chromatin remodeling machinery: impact of SWI/SNF perturbations in cancer. Cancer Res 2009; 69:8223-30. [PMID: 19843852 DOI: 10.1158/0008-5472.can-09-2166] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is increasing evidence that alterations in chromatin remodeling play a significant role in human disease. The SWI/SNF chromatin remodeling complex family mobilizes nucleosomes and functions as a master regulator of gene expression and chromatin dynamics whose functional specificity is driven by combinatorial assembly of a central ATPase and association with 10 to 12 unique subunits. Although the biochemical consequence of SWI/SNF in model systems has been extensively reviewed, the present article focuses on the evidence linking SWI/SNF perturbations to cancer initiation and tumor progression in human disease.
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Affiliation(s)
- Bernard Weissman
- Department of Pathology and Laboratory and Lineberger Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
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Copeland RA, Solomon ME, Richon VM. Protein methyltransferases as a target class for drug discovery. Nat Rev Drug Discov 2009; 8:724-32. [PMID: 19721445 DOI: 10.1038/nrd2974] [Citation(s) in RCA: 371] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The protein methyltransferases (PMTs) - which methylate protein lysine and arginine residues and have crucial roles in gene transcription - are emerging as an important group of enzymes that play key parts in normal physiology and human diseases. The collection of human PMTs is a large and diverse group of enzymes that have a common mechanism of catalysis. Here, we review the biological, biochemical and structural data that together present PMTs as a novel, chemically tractable target class for drug discovery.
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Affiliation(s)
- Robert A Copeland
- Epizyme, Inc., 840 Memorial Drive, Cambridge, Massachussets 02139, USA.
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50
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Schrump DS. Cytotoxicity mediated by histone deacetylase inhibitors in cancer cells: mechanisms and potential clinical implications. Clin Cancer Res 2009; 15:3947-57. [PMID: 19509170 DOI: 10.1158/1078-0432.ccr-08-2787] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aberrant expression of epigenetic regulators of gene expression contributes to initiation and progression of cancer. During recent years, considerable research efforts have focused on the role of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in cancer cells, and the identification of pharmacologic agents that modulate gene expression via inhibition of HDACs. The following review highlights recent studies pertaining to HDAC expression in cancer cells, the plieotropic mechanisms by which HDAC inhibitors (HDACi) mediate antitumor activity, and the potential clinical implications of HDAC inhibition as a strategy for cancer therapy.
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Affiliation(s)
- David S Schrump
- Thoracic Oncology Section, Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-1201, USA.
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