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Menezes A, Julião G, Mariath F, Ferreira AL, Oliveira-Nunes MC, Gallucci L, Evaristo JAM, Nogueira FCS, Pereira DDA, Carneiro K. Epigenetic Mechanisms Histone Deacetylase-Dependent Regulate the Glioblastoma Angiogenic Matrisome and Disrupt Endothelial Cell Behavior In Vitro. Mol Cell Proteomics 2024; 23:100722. [PMID: 38272115 PMCID: PMC10883839 DOI: 10.1016/j.mcpro.2024.100722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/09/2023] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor and different efforts have been employed in the search for new drugs and therapeutic protocols for GBM. Epitranscriptomics has shed light on new druggable Epigenetic therapies specifically designed to modulate GBM biology and behavior such as Histone Deacetylase inhibitors (iHDAC). Although the effects of iHDAC on GBM have been largely explored, there is a lack of information on the underlaying mechanisms HDAC-dependent that modulate the repertoire of GBM secreted molecules focusing on the set of Extracellular Matrix (ECM) associated proteins, the Matrisome, that may impact the surrounding tumor microenvironment. To acquire a better comprehension of the impacts of HDAC activity on the GBM Matrisome, we studied the alterations on the Matrisome-associated ECM regulators, Core Matrisome ECM glycoproteins, ECM-affiliated proteins and Proteoglycans upon HDAC inhibition in vitro as well as their relationship with glioma pathophysiological/clinical features and angiogenesis. For this, U87MG GBM cells were treated for with iHDAC or vehicle (control) and the whole secretome was processed by Mass Spectrometry NANOLC-MS/MS. In silico analyses revealed that proteins associated to the Angiogenic Matrisome (AngioMatrix), including Decorin, ADAM10, ADAM12 and ADAM15 were differentially regulated in iHDAC versus control secretome. Interestingly, genes coding for the Matrisome proteins differentially regulated were found mutated in patients and were correlated to glioma pathophysiological/clinical features. In vitro functional assays, using HBMEC endothelial cells exposed to the secretome of control or iHDAC treated GBM cells, coupled to 2D and 3D GBM cell culture system, showed impaired migratory capacity of endothelial cells and disrupted tubulogenesis in a Fibronectin and VEGF independent fashion. Collectively, our study provides understanding of epigenetic mechanisms HDAC-dependent to key Matrisomal proteins that may contribute to identify new druggable Epigenetic therapies or gliomagenesis biomarkers with relevant implications to improve therapeutic protocols for this malignancy.
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Affiliation(s)
- Aline Menezes
- Instituto de Ciências Biomédicas e Programa de Pós-graduação em Medicina (Anatomia Patológica), UFRJ/RJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Glaucia Julião
- Instituto de Ciências Biomédicas e Programa de Pós-graduação em Medicina (Anatomia Patológica), UFRJ/RJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Mariath
- Laboratório de Estudos Avançados em Jornalismo, UNICAMP/SP, São Paulo, São Paulo, Brazil
| | - Ana Luiza Ferreira
- Instituto de Ciências Biomédicas e Programa de Pós-graduação em Medicina (Anatomia Patológica), UFRJ/RJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Lara Gallucci
- Instituto de Ciências Biomédicas e Programa de Pós-graduação em Medicina (Anatomia Patológica), UFRJ/RJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Fábio César Sousa Nogueira
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise de Abreu Pereira
- Programa de Oncobiologia Celular e Molecular, Coordenação de Pesquisa, Instituto Nacional do Câncer- INCA/RJ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Katia Carneiro
- Instituto de Ciências Biomédicas e Programa de Pós-graduação em Medicina (Anatomia Patológica), UFRJ/RJ, Rio de Janeiro, Rio de Janeiro, Brazil.
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Long S, Yan Y, Xu H, Wang L, Jiang J, Xu Z, Liu R, Zhou Q, Huang X, Chen J, Li Z, Wei W, Li X. Insights into the regulatory role of RNA methylation modifications in glioma. J Transl Med 2023; 21:810. [PMID: 37964279 PMCID: PMC10644640 DOI: 10.1186/s12967-023-04653-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023] Open
Abstract
Epitranscriptomic abnormalities, which are highly prevalent in primary central nervous system malignancies, have been identified as crucial contributors to the development and progression of gliomas. RNA epitranscriptomic modifications, particularly the reversible modification methylation, have been observed throughout the RNA cycle. Epitranscriptomic modifications, which regulate RNA transcription and translation, have profound biological implications. These modifications are associated with the development of several cancer types. Notably, three main protein types-writers, erasers, and readers, in conjunction with other related proteins, mediate these epitranscriptomic changes. This review primarily focuses on the role of recently identified RNA methylation modifications in gliomas, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), and N1-methyladenosine (m1A). We delved into their corresponding writers, erasers, readers, and related binding proteins to propose new approaches and prognostic indicators for patients with glioma.
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Affiliation(s)
- Shengrong Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yu Yan
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Hongyu Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Lesheng Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiazhi Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ziyue Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Runming Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Qiangqiang Zhou
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaopeng Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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Hastings JF, Latham SL, Kamili A, Wheatley MS, Han JZ, Wong-Erasmus M, Phimmachanh M, Nobis M, Pantarelli C, Cadell AL, O’Donnell YE, Leong KH, Lynn S, Geng FS, Cui L, Yan S, Achinger-Kawecka J, Stirzaker C, Norris MD, Haber M, Trahair TN, Speleman F, De Preter K, Cowley MJ, Bogdanovic O, Timpson P, Cox TR, Kolch W, Fletcher JI, Fey D, Croucher DR. Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma. SCIENCE ADVANCES 2023; 9:eabp8314. [PMID: 36867694 PMCID: PMC9984174 DOI: 10.1126/sciadv.abp8314] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Gene expression noise is known to promote stochastic drug resistance through the elevated expression of individual genes in rare cancer cells. However, we now demonstrate that chemoresistant neuroblastoma cells emerge at a much higher frequency when the influence of noise is integrated across multiple components of an apoptotic signaling network. Using a JNK activity biosensor with longitudinal high-content and in vivo intravital imaging, we identify a population of stochastic, JNK-impaired, chemoresistant cells that exist because of noise within this signaling network. Furthermore, we reveal that the memory of this initially random state is retained following chemotherapy treatment across a series of in vitro, in vivo, and patient models. Using matched PDX models established at diagnosis and relapse from individual patients, we show that HDAC inhibitor priming cannot erase the memory of this resistant state within relapsed neuroblastomas but improves response in the first-line setting by restoring drug-induced JNK activity within the chemoresistant population of treatment-naïve tumors.
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Affiliation(s)
- Jordan F. Hastings
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sharissa L. Latham
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Alvin Kamili
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Madeleine S. Wheatley
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jeremy Z. R. Han
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Marie Wong-Erasmus
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Monica Phimmachanh
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Max Nobis
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chiara Pantarelli
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Antonia L. Cadell
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Yolande E. I. O’Donnell
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - King Ho Leong
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sophie Lynn
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Fan-Suo Geng
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Lujing Cui
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Sabrina Yan
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Joanna Achinger-Kawecka
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Clare Stirzaker
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Murray D. Norris
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Michelle Haber
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Mark J. Cowley
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Ozren Bogdanovic
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Paul Timpson
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Thomas R. Cox
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jamie I. Fletcher
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
- Children’s Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - David R. Croucher
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
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Defining a Correlative Transcriptional Signature Associated with Bulk Histone H3 Acetylation Levels in Adult Glioblastomas. Cells 2023; 12:cells12030374. [PMID: 36766715 PMCID: PMC9913072 DOI: 10.3390/cells12030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Glioblastoma (GB) is the most prevalent primary brain cancer and the most aggressive form of glioma because of its poor prognosis and high recurrence. To confirm the importance of epigenetics in glioma, we explored The Cancer Gene Atlas (TCGA) database and we found that several histone/DNA modifications and chromatin remodeling factors were affected at transcriptional and genetic levels in GB compared to lower-grade gliomas. We associated these alterations in our own cohort of study with a significant reduction in the bulk levels of acetylated lysines 9 and 14 of histone H3 in high-grade compared to low-grade tumors. Within GB, we performed an RNA-seq analysis between samples exhibiting the lowest and highest levels of acetylated H3 in the cohort; these results are in general concordance with the transcriptional changes obtained after histone deacetylase (HDAC) inhibition of GB-derived cultures that affected relevant genes in glioma biology and treatment (e.g., A2ML1, CD83, SLC17A7, TNFSF18). Overall, we identified a transcriptional signature linked to histone acetylation that was potentially associated with good prognosis, i.e., high overall survival and low rate of somatic mutations in epigenetically related genes in GB. Our study identifies lysine acetylation as a key defective histone modification in adult high-grade glioma, and offers novel insights regarding the use of HDAC inhibitors in therapy.
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McCornack C, Woodiwiss T, Hardi A, Yano H, Kim AH. The function of histone methylation and acetylation regulators in GBM pathophysiology. Front Oncol 2023; 13:1144184. [PMID: 37205197 PMCID: PMC10185819 DOI: 10.3389/fonc.2023.1144184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023] Open
Abstract
Glioblastoma (GBM) is the most common and lethal primary brain malignancy and is characterized by a high degree of intra and intertumor cellular heterogeneity, a starkly immunosuppressive tumor microenvironment, and nearly universal recurrence. The application of various genomic approaches has allowed us to understand the core molecular signatures, transcriptional states, and DNA methylation patterns that define GBM. Histone posttranslational modifications (PTMs) have been shown to influence oncogenesis in a variety of malignancies, including other forms of glioma, yet comparatively less effort has been placed on understanding the transcriptional impact and regulation of histone PTMs in the context of GBM. In this review we discuss work that investigates the role of histone acetylating and methylating enzymes in GBM pathogenesis, as well as the effects of targeted inhibition of these enzymes. We then synthesize broader genomic and epigenomic approaches to understand the influence of histone PTMs on chromatin architecture and transcription within GBM and finally, explore the limitations of current research in this field before proposing future directions for this area of research.
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Affiliation(s)
- Colin McCornack
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, United States
| | - Timothy Woodiwiss
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa, IA, United States
| | - Angela Hardi
- Bernard Becker Medical Library, Washington University School of Medicine, St. Louis, MO, United States
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
- *Correspondence: Albert H. Kim,
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Liu H, Yan G, Li L, Wang D, Wang Y, Jin S, Jin Z, Li L, Zhu L. RUNX3 mediates keloid fibroblast proliferation through deacetylation of EZH2 by SIRT1. BMC Mol Cell Biol 2022; 23:52. [PMID: 36476345 PMCID: PMC9730640 DOI: 10.1186/s12860-022-00451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Keloid is a benign proliferative fibrous disease featured by excessive fibroblast proliferation after skin injury. However, the mechanism of abnormal cell proliferation is still unclear. Herein, we investigated the mechanism of abnormal proliferation in keloids involving Sirtuin 1(SIRT1)/ Zeste Homolog 2 (EZH2)/ Runt-related transcription factor 3 (RUNX3). METHODS: HE staining was used to observe the histopathological changes. Western blot was performed to detect SIRT1/EZH2/RUNX3 and cell cycle related proteins. RT-PCR detected EZH2 mRNA. After knockdown of EZH2 or overexpression of RUNX3, cell proliferation and cell cycle was analyzed. Immunoprecipitation was used to detect acetylated EZH2. RESULTS The results showed that overexpression of RUNX3 inhibited cell proliferation and arrested cell cycle at G1/S phase, whereas inhibition of SIRT1 promoted cell proliferation and G1/S phase of the cell cycle. Knockdown of EZH2 promoted the expression of RUNX3, inhibited cell proliferation and shortened the progression of G1 to S phase. Simultaneous knockdown of EZH2 and inhibition of SIRT1 reversed these effects. Inhibition of SIRT1 increased its protein stability by increasing EZH2 acetylation, thereby reducing the expression of RUNX3 and promoting cell proliferation. CONCLUSIONS Conclusively, the SIRT1/EZH2/RUNX3 axis may be an important pathway in the regulation of abnormal proliferation in keloids.
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Affiliation(s)
- Hanye Liu
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.440752.00000 0001 1581 2747Department of Anatomy, Histology and Embryology, Medical College, Yanbian University, No. 977 Gongyuan Road, Yanji, 133002 People’s Republic of China
| | - Guanghai Yan
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.440752.00000 0001 1581 2747Department of Anatomy, Histology and Embryology, Medical College, Yanbian University, No. 977 Gongyuan Road, Yanji, 133002 People’s Republic of China
| | - Li Li
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.440752.00000 0001 1581 2747Department of Anatomy, Histology and Embryology, Medical College, Yanbian University, No. 977 Gongyuan Road, Yanji, 133002 People’s Republic of China
| | - Dandan Wang
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.440752.00000 0001 1581 2747Department of Anatomy, Histology and Embryology, Medical College, Yanbian University, No. 977 Gongyuan Road, Yanji, 133002 People’s Republic of China
| | - Yu Wang
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.459480.40000 0004 1758 0638Department of Dermatology, Yanbian University Hospital, Yanji, 133002 People’s Republic of China
| | - Shan Jin
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.459480.40000 0004 1758 0638Department of Dermatology, Yanbian University Hospital, Yanji, 133002 People’s Republic of China
| | - Zhehu Jin
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.459480.40000 0004 1758 0638Department of Dermatology, Yanbian University Hospital, Yanji, 133002 People’s Republic of China
| | - Liangchang Li
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.440752.00000 0001 1581 2747Department of Anatomy, Histology and Embryology, Medical College, Yanbian University, No. 977 Gongyuan Road, Yanji, 133002 People’s Republic of China
| | - Lianhua Zhu
- grid.440752.00000 0001 1581 2747Jilin Key Laboratory for Immune and Targeting Research On Common Allergic Diseases, Yanbian University, Yanji, 133000 People’s Republic of China ,grid.459480.40000 0004 1758 0638Department of Dermatology, Yanbian University Hospital, Yanji, 133002 People’s Republic of China
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Yang S, Xie S, Shi X, Su D, He B, Xu Y, Liu Z. Characterizing HDAC Pathway Copy Number Variation in Pan-Cancer. Pathol Oncol Res 2022; 28:1610288. [PMID: 35769830 PMCID: PMC9235358 DOI: 10.3389/pore.2022.1610288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/17/2022] [Indexed: 11/13/2022]
Abstract
Background: Histone deacetylase (HDAC) plays a crucial role in regulating the expression and activity of a variety of genes associated with tumor progression and immunotherapeutic processes. The aim of this study was to characterize HDAC pathway copy number variation (CNV) in pan-cancer. Methods: A total of 10,678 tumor samples involving 33 types of tumors from The Cancer Genome Atlas (TCGA) were included in the study. Results: HDAC pathway CNV and CNV gain were identified as prognostic risk factors for pan-cancer species. The differences of tumor characteristics including tumor mutational burden, tumor neoantigen burden, high-microsatellite instability, and microsatellite stable between HDAC pathway CNV altered-type group and wild-type group varied among the various cancer species. In some cancer types, HDAC pathway CNV alteration was positively correlated with loss of heterozygosity, CNV burden, ploidy, and homologous recombination defect score markers, while it was significantly negatively correlated with immune score and stroma score. There were significant differences in immune characteristics such as major histocompatibility complex class I (MHC-I), MHC-II, chemokines, cytolytic-activity, and IFN-γ between the two groups. Immune cycle characteristics varied from one cancer type to another. Conclusion: This study reveals a tumor and immune profile of HDAC pathway CNV as well as its unlimited potential in immune prognosis.
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Affiliation(s)
- Shuming Yang
- Department of Oncology, Senior Department of Oncology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Shengzhi Xie
- Department of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xinying Shi
- Genecast Biotechnology Co., Ltd., Wuxi, China
| | - Dan Su
- Department of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Bo He
- Department of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yang Xu
- Department of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Zhefeng Liu
- Department of Oncology, Senior Department of Oncology, The Fifth Medical Center of PLA General Hospital, Beijing, China
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8
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Fang K, Tang DS, Yan CS, Ma J, Cheng L, Li Y, Wang G. Comprehensive Analysis of Necroptosis in Pancreatic Cancer for Appealing its Implications in Prognosis, Immunotherapy, and Chemotherapy Responses. Front Pharmacol 2022; 13:862502. [PMID: 35662734 PMCID: PMC9157651 DOI: 10.3389/fphar.2022.862502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Necroptosis represents a new target for cancer immunotherapy and is considered a form of cell death that overcomes apoptosis resistance and enhances tumor immunogenicity. Herein, we aimed to determine necroptosis subtypes and investigate the roles of necroptosis in pancreatic cancer therapy. Methods: Based on the expression of prognostic necroptosis genes in pancreatic cancer samples from TCGA and ICGC cohorts, a consensus clustering approach was implemented for robustly identifying necroptosis subtypes. Immunogenic features were evaluated according to immune cell infiltrations, immune checkpoints, HLA molecules, and cancer-immunity cycle. The sensitivity to chemotherapy agents was estimated using the pRRophetic package. A necroptosis-relevant risk model was developed with a multivariate Cox regression analysis. Results: Five necroptosis subtypes were determined for pancreatic cancer (C1∼C5) with diverse prognosis, immunogenic features, and chemosensitivity. In particular, C4 and C5 presented favorable prognosis and weakened immunogenicity; C2 had high immunogenicity; C1 had undesirable prognosis and high genetic mutations. C5 was the most sensitive to known chemotherapy agents (cisplatin, gemcitabine, docetaxel, and paclitaxel), while C4 displayed resistance to aforementioned agents. The necroptosis-relevant risk model could accurately predict prognosis, immunogenicity, and chemosensitivity. Conclusion: Our findings provided a conceptual framework for comprehending necroptosis in pancreatic cancer biology. Future work is required for evaluating its relevance in the design of combined therapeutic regimens and guiding the best choice for immuno- and chemotherapy.
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Affiliation(s)
- Kun Fang
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - De-Sheng Tang
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chang-Sheng Yan
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiamin Ma
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Long Cheng
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yilong Li
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Gang Wang
- Department of Pancreatic and Biliary Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Laboratory of Hepatosplenic Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
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9
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Chen N, Peng C, Li D. Epigenetic Underpinnings of Inflammation: A Key to Unlock the Tumor Microenvironment in Glioblastoma. Front Immunol 2022; 13:869307. [PMID: 35572545 PMCID: PMC9100418 DOI: 10.3389/fimmu.2022.869307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults, and immunotherapies and genetic therapies for GBM have evolved dramatically over the past decade, but GBM therapy is still facing a dilemma due to the high recurrence rate. The inflammatory microenvironment is a general signature of tumors that accelerates epigenetic changes in GBM and helps tumors avoid immunological surveillance. GBM tumor cells and glioma-associated microglia/macrophages are the primary contributors to the inflammatory condition, meanwhile the modification of epigenetic events including DNA methylation, non-coding RNAs, and histone methylation and deacetylases involved in this pathological process of GBM, finally result in exacerbating the proliferation, invasion, and migration of GBM. On the other hand, histone deacetylase inhibitors, DNA methyltransferases inhibitors, and RNA interference could reverse the inflammatory landscapes and inhibit GBM growth and invasion. Here, we systematically review the inflammatory-associated epigenetic changes and regulations in the microenvironment of GBM, aiming to provide a comprehensive epigenetic profile underlying the recognition of inflammation in GBM.
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Affiliation(s)
- Nian Chen
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Li
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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10
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Hoang PH, Landi MT. DNA Methylation in Lung Cancer: Mechanisms and Associations with Histological Subtypes, Molecular Alterations, and Major Epidemiological Factors. Cancers (Basel) 2022; 14:cancers14040961. [PMID: 35205708 PMCID: PMC8870477 DOI: 10.3390/cancers14040961] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/14/2021] [Accepted: 02/11/2022] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the major leading cause of cancer-related mortality worldwide. Multiple epigenetic factors-in particular, DNA methylation-have been associated with the development of lung cancer. In this review, we summarize the current knowledge on DNA methylation alterations in lung tumorigenesis, as well as their associations with different histological subtypes, common cancer driver gene mutations (e.g., KRAS, EGFR, and TP53), and major epidemiological risk factors (e.g., sex, smoking status, race/ethnicity). Understanding the mechanisms of DNA methylation regulation and their associations with various risk factors can provide further insights into carcinogenesis, and create future avenues for prevention and personalized treatments. In addition, we also highlight outstanding questions regarding DNA methylation in lung cancer to be elucidated in future studies.
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11
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Ciaccio R, De Rosa P, Aloisi S, Viggiano M, Cimadom L, Zadran SK, Perini G, Milazzo G. Targeting Oncogenic Transcriptional Networks in Neuroblastoma: From N-Myc to Epigenetic Drugs. Int J Mol Sci 2021; 22:12883. [PMID: 34884690 PMCID: PMC8657550 DOI: 10.3390/ijms222312883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Neuroblastoma (NB) is one of the most frequently occurring neurogenic extracranial solid cancers in childhood and infancy. Over the years, many pieces of evidence suggested that NB development is controlled by gene expression dysregulation. These unleashed programs that outline NB cancer cells make them highly dependent on specific tuning of gene expression, which can act co-operatively to define the differentiation state, cell identity, and specialized functions. The peculiar regulation is mainly caused by genetic and epigenetic alterations, resulting in the dependency on a small set of key master transcriptional regulators as the convergence point of multiple signalling pathways. In this review, we provide a comprehensive blueprint of transcriptional regulation bearing NB initiation and progression, unveiling the complexity of novel oncogenic and tumour suppressive regulatory networks of this pathology. Furthermore, we underline the significance of multi-target therapies against these hallmarks, showing how novel approaches, together with chemotherapy, surgery, or radiotherapy, can have substantial antineoplastic effects, disrupting a wide variety of tumorigenic pathways through combinations of different treatments.
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12
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Lambrou GI, Poulou M, Giannikou K, Themistocleous M, Zaravinos A, Braoudaki M. Differential and Common Signatures of miRNA Expression and Methylation in Childhood Central Nervous System Malignancies: An Experimental and Computational Approach. Cancers (Basel) 2021; 13:cancers13215491. [PMID: 34771655 PMCID: PMC8583574 DOI: 10.3390/cancers13215491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Epigenetic modifications are considered of utmost significance for tumor ontogenesis and progression. Especially, it has been found that miRNA expression, as well as DNA methylation plays a significant role in central nervous system tumors during childhood. A total of 49 resected brain tumors from children were used for further analysis. DNA methylation was identified with methylation-specific MLPA and, in particular, for the tumor suppressor genes CASP8, RASSF1, MGMT, MSH6, GATA5, ATM1, TP53, and CADM1. miRNAs were identified with microarray screening, as well as selected samples, were tested for their mRNA expression levels. CASP8, RASSF1 were the most frequently methylated genes in all tumor samples. Simultaneous methylation of genes manifested significant results with respect to tumor staging, tumor type, and the differentiation of tumor and control samples. There was no significant dependence observed with the methylation of one gene promoter, rather with the simultaneous presence of all detected methylated genes' promoters. miRNA expression was found to be correlated to gene methylation. Epigenetic regulation appears to be of major importance in tumor progression and pathophysiology, making it an imperative field of study.
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Affiliation(s)
- George I. Lambrou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Myrto Poulou
- Department of Medical Genetics, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
| | - Marios Themistocleous
- Department of Neurosurgery, “Aghia Sofia” Children’s Hospital, 11527 Athens, Greece;
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 2404, Cyprus
- Basic and Translational Cancer Research Center (BTCRC), Cancer Genetics, Genomics and Systems Biology Group, European University Cyprus, Nicosia 1516, Cyprus
- Correspondence: (A.Z.); (M.B.)
| | - Maria Braoudaki
- Department of Life and Environmental Sciences, School of Life and Health Sciences, University of Hertfordshire, Hertfordshire AL10 9AB, UK
- Correspondence: (A.Z.); (M.B.)
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13
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Han JZR, Hastings JF, Phimmachanh M, Fey D, Kolch W, Croucher DR. Personalized Medicine for Neuroblastoma: Moving from Static Genotypes to Dynamic Simulations of Drug Response. J Pers Med 2021; 11:395. [PMID: 34064704 PMCID: PMC8151552 DOI: 10.3390/jpm11050395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
High-risk neuroblastoma is an aggressive childhood cancer that is characterized by high rates of chemoresistance and frequent metastatic relapse. A number of studies have characterized the genetic and epigenetic landscape of neuroblastoma, but due to a generally low mutational burden and paucity of actionable mutations, there are few options for applying a comprehensive personalized medicine approach through the use of targeted therapies. Therefore, the use of multi-agent chemotherapy remains the current standard of care for neuroblastoma, which also conceptually limits the opportunities for developing an effective and widely applicable personalized medicine approach for this disease. However, in this review we outline potential approaches for tailoring the use of chemotherapy agents to the specific molecular characteristics of individual tumours by performing patient-specific simulations of drug-induced apoptotic signalling. By incorporating multiple layers of information about tumour-specific aberrations, including expression as well as mutation data, these models have the potential to rationalize the selection of chemotherapeutics contained within multi-agent treatment regimens and ensure the optimum response is achieved for each individual patient.
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Affiliation(s)
- Jeremy Z. R. Han
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (J.Z.R.H.); (J.F.H.); (M.P.)
| | - Jordan F. Hastings
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (J.Z.R.H.); (J.F.H.); (M.P.)
| | - Monica Phimmachanh
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (J.Z.R.H.); (J.F.H.); (M.P.)
| | - Dirk Fey
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; (D.F.); (W.K.)
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; (D.F.); (W.K.)
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - David R. Croucher
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; (J.Z.R.H.); (J.F.H.); (M.P.)
- St Vincent’s Hospital Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
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14
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Abstract
Neuroblastoma (NB) is a pediatric cancer of the sympathetic nervous system and one of the most common solid tumors in infancy. Amplification of MYCN, copy number alterations, numerical and segmental chromosomal aberrations, mutations, and rearrangements on a handful of genes, such as ALK, ATRX, TP53, RAS/MAPK pathway genes, and TERT, are attributed as underlying causes that give rise to NB. However, the heterogeneous nature of the disease-along with the relative paucity of recurrent somatic mutations-reinforces the need to understand the interplay of genetic factors and epigenetic alterations in the context of NB. Epigenetic mechanisms tightly control gene expression, embryogenesis, imprinting, chromosomal stability, and tumorigenesis, thereby playing a pivotal role in physio- and pathological settings. The main epigenetic alterations include aberrant DNA methylation, disrupted patterns of posttranslational histone modifications, alterations in chromatin composition and/or architecture, and aberrant expression of non-coding RNAs. DNA methylation and demethylation are mediated by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) proteins, respectively, while histone modifications are coordinated by histone acetyltransferases and deacetylases (HATs, HDACs), and histone methyltransferases and demethylases (HMTs, HDMs). This article focuses predominately on the crosstalk between the epigenome and NB, and the implications it has on disease diagnosis and treatment.
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15
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Chellamuthu A, Gray SG. The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer. Cells 2020; 9:cells9081758. [PMID: 32708015 PMCID: PMC7463552 DOI: 10.3390/cells9081758] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine is often associated as an epigenetic modifier in DNA. However, it is also found increasingly in a plethora of RNA species, predominantly transfer RNAs, but increasingly found in cytoplasmic and mitochondrial ribosomal RNAs, enhancer RNAs, and a number of long noncoding RNAs. Moreover, this modification can also be found in messenger RNAs and has led to an increasing appreciation that RNA methylation can functionally regulate gene expression and cellular activities. In mammalian cells, the addition of m5C to RNA cytosines is carried out by enzymes of the NOL1/NOP2/SUN domain (NSUN) family as well as the DNA methyltransferase homologue DNMT2. In this regard, NSUN2 is a critical RNA methyltransferase for adding m5C to mRNA. In this review, using non-small cell lung cancer and other cancers as primary examples, we discuss the recent developments in the known functions of this RNA methyltransferase and its potential critical role in cancer.
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Affiliation(s)
- Anitha Chellamuthu
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
| | - Steven G. Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
- Thoracic Oncology Research Group, St. James’s Hospital, Dublin D08 RX0X, Ireland
- Correspondence:
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16
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Liu Y, Wang L, Zhu L, Ran B, Wang Z. Bisphenol A disturbs transcription of steroidogenic genes in ovary of rare minnow Gobiocypris rarus via the abnormal DNA and histone methylation. CHEMOSPHERE 2020; 240:124935. [PMID: 31563720 DOI: 10.1016/j.chemosphere.2019.124935] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
Increasing studies have established the toxic effects of BPA on development and reproduction in animals. In present study, we investigated epigenetic effects on the transcription of several ovarian steroidogenic genes in rare minnows Gobiocypris rarus after BPA exposure at 15 μgL-1 for 21, 42 and 63 d. Results showed that short term BPA exposure (21 d) caused significant increase of both estradiol and testerone levels whereas long term exposure (63 d) led to significant decrease of them. The oocytes development was hindered after BPA exposure. BPA treatments for 21 and 42 d resulted in significant increase of genome DNA methylation in ovary while 63-d exposure caused marked decrease. The histone trimethylation levels (H3K4me3, H3K9me3 and H3K27me3) in the ovary were also disturbed by BPA. H3K9me3 was significantly decreased after 21 d whereas it was markedly increased after 42 and 63 d. The 42-d exposure caused significant decrease for H3K4me3. Meanwhile, 42- and 63-d BPA exposure led to significant decrease of H3K27me3. DNA methylation could involve in gene expression regulation of cyp17a1 and cyp19a1a after BPA exposure. After short (21 d) and long term (63 d) BPA exposure, the respective mRNA expression down-regulation and up-regulation of star, cyp11a1, and cyp17a1 were mediated by H3K9me3. This study suggests that epigenetic modulation including DNA and histone methylation could be responsible for the detrimental effects on ovary development upon BPA exposure in G. rarus. It is speculated that BPA exposures for short or long term duration could disturb the steroidogenesis in entirely different mechanisms.
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Affiliation(s)
- Yan Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Long Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Benhui Ran
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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17
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García-Costela M, Escudero-Feliú J, Puentes-Pardo JD, San Juán SM, Morales-Santana S, Ríos-Arrabal S, Carazo Á, León J. Circadian Genes as Therapeutic Targets in Pancreatic Cancer. Front Endocrinol (Lausanne) 2020; 11:638. [PMID: 33042011 PMCID: PMC7516350 DOI: 10.3389/fendo.2020.00638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/06/2020] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer is one of the most lethal cancers worldwide due to its symptoms, early metastasis, and chemoresistance. Thus, the mechanisms contributing to pancreatic cancer progression require further exploration. Circadian rhythms are the daily oscillations of multiple biological processes regulated by an endogenous clock. Several evidences suggest that the circadian clock may play an important role in the cell cycle, cell proliferation and apoptosis. In addition, timing of chemotherapy or radiation treatment can influence the efficacy and toxicity treatment. Here, we revisit the studies on circadian clock as an emerging target for therapy in pancreatic cancer. We highlight those potential circadian genes regulators that are commonly affected in pancreatic cancer according to most recent reports.
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Affiliation(s)
- María García-Costela
- Research Unit, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
| | - Julia Escudero-Feliú
- Research Unit, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
| | - Jose D. Puentes-Pardo
- Research Unit, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
- Jose D. Puentes-Pardo
| | - Sara Moreno San Juán
- Cytometry and Michroscopy Research Service, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
| | - Sonia Morales-Santana
- Proteomic Research Service, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
- Endocrinology Unit, Endocrinology Division, CIBER of Fragility and Healthy Aging (CIBERFES), San Cecilio University Hospital, Granada, Spain
| | - Sandra Ríos-Arrabal
- Research Unit, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
- *Correspondence: Sandra Ríos-Arrabal
| | - Ángel Carazo
- Genomic Research Service, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
| | - Josefa León
- Research Unit, Biosanitary Research Institute of Granada, ibs.GRANADA, Granada, Spain
- Clinical Management Unit of Digestive Disease, San Cecilio University Hospital, Granada, Spain
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18
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Spaety ME, Gries A, Badie A, Venkatasamy A, Romain B, Orvain C, Yanagihara K, Okamoto K, Jung AC, Mellitzer G, Pfeffer S, Gaiddon C. HDAC4 Levels Control Sensibility toward Cisplatin in Gastric Cancer via the p53-p73/BIK Pathway. Cancers (Basel) 2019; 11:cancers11111747. [PMID: 31703394 PMCID: PMC6896094 DOI: 10.3390/cancers11111747] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/23/2019] [Accepted: 10/31/2019] [Indexed: 02/08/2023] Open
Abstract
Gastric cancer (GC) remains a health issue due to the low efficiency of therapies, such as cisplatin. This unsatisfactory situation highlights the necessity of finding factors impacting GC sensibility to therapies. We analyzed the cisplatin pangenomic response in cancer cells and found HDAC4 as a major epigenetic regulator being inhibited. HDAC4 mRNA repression was partly mediated by the cisplatin-induced expression of miR-140. At a functional level, HDAC4 inhibition favored cisplatin cytotoxicity and reduced tumor growth. Inversely, overexpression of HDAC4 inhibits cisplatin cytotoxicity. Importantly, HDAC4 expression was found to be elevated in gastric tumors compared to healthy tissues, and in particular in specific molecular subgroups. Furthermore, mutations in HDAC4 correlate with good prognosis. Pathway analysis of genes whose expression in patients correlated strongly with HDAC4 highlighted DNA damage, p53 stabilization, and apoptosis as processes downregulated by HDAC4. This was further confirmed by silencing of HDAC4, which favored cisplatin-induced apoptosis characterized by cleavage of caspase 3 and induction of proapoptotic genes, such as BIK, in part via a p53-dependent mechanism. Altogether, these results reveal HDAC4 as a resistance factor for cisplatin in GC cells that impacts on patients' survival.
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Affiliation(s)
- Marie-Elodie Spaety
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France;
| | - Alexandre Gries
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
| | - Amandine Badie
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
| | - Aina Venkatasamy
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Radiology Department, Centre Hospitalier Universitaire (CHU) Hautepierre, 67200 Strasbourg, France
| | - Benoit Romain
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Digestive Surgery department, CHU Hautepierre, 67200 Strasbourg, France
| | - Christophe Orvain
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
| | | | - Koji Okamoto
- National Cancer Research Center, Tokyo 104_0045, Japan; (K.Y.); (K.O.)
| | - Alain C. Jung
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Centre de Lutte contre le Cancer Paul Strauss (CLCC), 67065 Strasbourg, France
| | - Georg Mellitzer
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Centre de Lutte contre le Cancer Paul Strauss (CLCC), 67065 Strasbourg, France
| | - Sébastien Pfeffer
- Architecture and Reactivity of RNA, Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France;
| | - Christian Gaiddon
- Laboratory STREINTH (Stress Response and Innovative Therapies), Inserm IRFAC UMR_S1113, Université de Strasbourg, 3 av. Molière, 67200 Strasbourg, France; (M.-E.S.); (A.G.); (A.B.); (A.V.); (B.R.); (C.O.); (A.C.J.); (G.M.)
- Centre de Lutte contre le Cancer Paul Strauss (CLCC), 67065 Strasbourg, France
- Correspondence:
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19
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Orouji E, Utikal J. Tackling malignant melanoma epigenetically: histone lysine methylation. Clin Epigenetics 2018; 10:145. [PMID: 30466474 PMCID: PMC6249913 DOI: 10.1186/s13148-018-0583-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
Post-translational histone modifications such as acetylation and methylation can affect gene expression. Histone acetylation is commonly associated with activation of gene expression whereas histone methylation is linked to either activation or repression of gene expression. Depending on the site of histone modification, several histone marks can be present throughout the genome. A combination of these histone marks can shape global chromatin architecture, and changes in patterns of marks can affect the transcriptomic landscape. Alterations in several histone marks are associated with different types of cancers, and these alterations are distinct from marks found in original normal tissues. Therefore, it is hypothesized that patterns of histone marks can change during the process of tumorigenesis. This review focuses on histone methylation changes (both removal and addition of methyl groups) in malignant melanoma, a deadly skin cancer, and the implications of specific inhibitors of these modifications as a combinatorial therapeutic approach.
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Affiliation(s)
- Elias Orouji
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, 1901 East Rd. South Campus Research Building 4, Houston, TX, 77054, USA. .,Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany.
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
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20
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Levinzon L, Madigan M, Nguyen V, Hasic E, Conway M, Cherepanoff S. Tumour Expression of Histone Deacetylases in Uveal Melanoma. Ocul Oncol Pathol 2018; 5:153-161. [PMID: 31049320 DOI: 10.1159/000490038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Purpose To determine the expression of histone deacetylase enzymes in uveal melanoma tumour cells. Procedures This is an observational immunohistochemical study of 16 formalin-fixed, paraffin-embedded eyes enucleated for uveal melanoma between January 2001 and March 2002. Haematoxylin and eosin paraffin sections were reviewed for histopathological parameters according to the American Joint Committee on Cancer 7th edition. Sections were then immunohistochemically stained for histone deacetylases 1, 2, 3, 4 and 6 and sirtuin 2 using an automated Leica Bond II platform and Fast Red chromogen, then digitally scanned using Aperio software before assessment of staining. Results Nuclear expression of histone deacetylases 1, 2, 3, 4 and 6 and of sirtuin 2 was confirmed in uveal melanoma tumour cells. In addition, the tumour cells showed cytoplasmic expression of histone deacetylases 4 and 6 and sirtuin 2. Nuclear and cytoplasmic immunostaining was also seen in intraocular tissues uninvolved by the tumour. Conclusion Uveal melanoma tumour cells express histone deacetylases 1, 2, 3, 4 and 6 and sirtuin 2, confirming potential tissue targets for histone deacetylase inhibitors.
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Affiliation(s)
- Louis Levinzon
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Michele Madigan
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Vuong Nguyen
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Enisa Hasic
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Max Conway
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
| | - Svetlana Cherepanoff
- Save Site Institute, Sydney Medical School, The University of Sydney, Sydney Eye Hospital, Sydney, New South Wales, Australia
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21
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Polonis K, Blackburn PR, Urrutia RA, Lomberk GA, Kruisselbrink T, Cousin MA, Boczek NJ, Hoppman NL, Babovic-Vuksanovic D, Klee EW, Pichurin PN. Co-occurrence of a maternally inherited DNMT3A duplication and a paternally inherited pathogenic variant in EZH2 in a child with growth retardation and severe short stature: atypical Weaver syndrome or evidence of a DNMT3A dosage effect? Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002899. [PMID: 29802153 PMCID: PMC6071565 DOI: 10.1101/mcs.a002899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/18/2018] [Indexed: 11/24/2022] Open
Abstract
Overgrowth syndromes are a clinically heterogeneous group of disorders characterized by localized or generalized tissue overgrowth and varying degrees of developmental and intellectual disability. An expanding list of genes associated with overgrowth syndromes include the histone methyltransferase genes EZH2 and NSD1, which cause Weaver and Sotos syndrome, respectively, and the DNA methyltransferase (DNMT3A) gene that results in Tatton-Brown–Rahman syndrome (TBRS). Here, we describe a 5-year-old female with a paternally inherited pathogenic mutation in EZH2 (c.2050C>T, p.Arg684Cys) and a maternally inherited 505-kb duplication of uncertain significance at 2p23.3 (encompassing five genes, including DNMT3A) who presented with intrauterine growth restriction, slow postnatal growth, short stature, hypotonia, developmental delay, and neuroblastoma diagnosed at the age of 8 mo. Her father had tall stature, dysmorphic facial features, and intellectual disability consistent with Weaver syndrome, whereas her mother had short stature, cognitive delays, and chronic nonprogressive leukocytosis. It has been previously shown that EZH2 directly controls DNA methylation through physical association with DNMTs, including DNMT3A, with concomitant H3K27 methylation and CpG promoter methylation leading to repression of EZH2 target genes. Interestingly, NSD1 is involved in H3K36 methylation, a mark associated with transcriptional activation, and exhibits exquisite dosage sensitivity leading to overgrowth when deleted and severe undergrowth when duplicated in vivo. Although there is currently no evidence of dosage effects for DNMT3A, the co-occurrence of a duplication involving this gene and a pathogenic alteration in EZH2 in a patient with severe undergrowth is suggestive of a similar paradigm and further study is warranted.
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Affiliation(s)
- Katarzyna Polonis
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick R Blackburn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Epigenomics Translational Program, Mayo Clinic, Rochester, Minnesota 55905, USA.,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Teresa Kruisselbrink
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Nicole L Hoppman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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22
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Paradise BD, Barham W, Fernandez-Zapico ME. Targeting Epigenetic Aberrations in Pancreatic Cancer, a New Path to Improve Patient Outcomes? Cancers (Basel) 2018; 10:cancers10050128. [PMID: 29710783 PMCID: PMC5977101 DOI: 10.3390/cancers10050128] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer has one of the highest mortality rates among all types of cancers. The disease is highly aggressive and typically diagnosed in late stage making it difficult to treat. Currently, the vast majority of therapeutic regimens have only modest curative effects, and most of them are in the surgical/neo-adjuvant setting. There is a great need for new and more effective treatment strategies in common clinical practice. Previously, pathogenesis of pancreatic cancer was attributed solely to genetic mutations; however, recent advancements in the field have demonstrated that aberrant activation of epigenetic pathways contributes significantly to the pathogenesis of the disease. The identification of these aberrant activated epigenetic pathways has revealed enticing targets for the use of epigenetic inhibitors to mitigate the phenotypic changes driven by these cascades. These pathways have been found to be responsible for overactivation of growth signaling pathways and silencing of tumor suppressors and other cell cycle checkpoints. Furthermore, new miRNA signatures have been uncovered in pancreatic ductal adenocarcinoma (PDAC) patients, further widening the window for therapeutic opportunity. There has been success in preclinical settings using both epigenetic inhibitors as well as miRNAs to slow disease progression and eliminate diseased tissues. In addition to their utility as anti-proliferative agents, the pharmacological inhibitors that target epigenetic regulators (referred to here as readers, writers, and erasers for their ability to recognize, deposit, and remove post-translational modifications) have the potential to reconfigure the epigenetic landscape of diseased cells and disrupt the cancerous phenotype. The potential to “reprogram” cancer cells to revert them to a healthy state presents great promise and merits further investigation.
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Affiliation(s)
- Brooke D Paradise
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA.
| | - Whitney Barham
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
- Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA.
| | - Martín E Fernandez-Zapico
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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23
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Archer TC, Mahoney EL, Pomeroy SL. Medulloblastoma: Molecular Classification-Based Personal Therapeutics. Neurotherapeutics 2017; 14:265-273. [PMID: 28386677 PMCID: PMC5398996 DOI: 10.1007/s13311-017-0526-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent advances in cancer genomics have revealed 4 distinct subgroups of medulloblastomas, each with unique transcription profiles, DNA alterations and clinical outcome. Molecular classification of medulloblastomas improves predictions of clinical outcome, allowing more accurate matching of intensity of conventional treatments with chemotherapy and radiation to overall prognosis and setting the stage for the introduction of targeted therapies.
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Affiliation(s)
- Tenley C Archer
- Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | | | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
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24
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Song B, Cui H, Li Y, Cheng C, Yang B, Wang F, Kong P, Li H, Zhang L, Jia Z, Bi Y, Wang J, Zhou Y, Liu J, Wang J, Zhao Z, Zhang Y, Hu X, Shi R, Yang J, Liu H, Yan T, Li Y, Xu E, Qian Y, Xi Y, Guo S, Chen Y, Wang J, Li G, Liang J, Jia J, Chen X, Guo J, Wang T, Zhang Y, Li Q, Wang C, Cheng X, Zhan Q, Cui Y. Mutually exclusive mutations in NOTCH1 and PIK3CA associated with clinical prognosis and chemotherapy responses of esophageal squamous cell carcinoma in China. Oncotarget 2016; 7:3599-613. [PMID: 26528858 PMCID: PMC4823130 DOI: 10.18632/oncotarget.6120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/24/2015] [Indexed: 12/23/2022] Open
Abstract
Background Recurrent genetic abnormalities that correlate with clinical features could be used to determine patients' prognosis, select treatments and predict responses to therapy. Esophageal squamous cell carcinoma (ESCC) contains genomic alterations of undefined clinical significance. We aimed to identify mutually exclusive mutations that are frequently detected in ESCCs and characterized their associations with clinical variables. Methods We analyzed next-generation-sequencing data from 104 ESCCs from Taihang Mountain region of China; 96 pairs were selected for deep target-capture-based validation and analysis of clinical and pathology data. We used model proposed by Szczurek to identify exclusive mutations and to associate these with pathology findings. Univariate and multivariate analyses with Cox proportional hazards model were used to examine the association between mutations and overall survival and response to chemotherapy. Findings were validated in an analysis of samples from 89 patients with ESCC from Taihang Mountain. Results We identified statistically significant mutual exclusivity between mutations in NOTCH1 and PIK3CA in ESCC samples. Mutations in NOTCH1 were associated with well-differentiated, early-stage malignancy and less metastasis to regional lymph nodes. Nonetheless, patients with NOTCH1 mutations had shorter survival times than patients without NOTCH1 mutations, and failed to respond to chemotherapy. In contrast, patients with mutations in PIK3CA had better responses to chemotherapy and longer survival times than patients without PIK3CA mutations. Conclusions In a genetic analysis of ESCCs from patients in China, we identified mutually exclusive mutations in NOTCH1 and PIK3CA. These findings might increase our understanding of ESCC development and be used as prognostic factors.
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Affiliation(s)
- Bin Song
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Oncology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Heyang Cui
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yaoping Li
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Caixia Cheng
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Pathology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Bin Yang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Fang Wang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Pengzhou Kong
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hongyi Li
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ling Zhang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhiwu Jia
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanghui Bi
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | | | - Yong Zhou
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Jing Liu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Juan Wang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhenxiang Zhao
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanyan Zhang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaoling Hu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruyi Shi
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jie Yang
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Haiyan Liu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Nuclear medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ting Yan
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yike Li
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Enwei Xu
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Yu Qian
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanfeng Xi
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Shiping Guo
- Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Yunqing Chen
- Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Jinfen Wang
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Guodong Li
- Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi, China
| | - Jianfang Liang
- Department of Pathology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Junmei Jia
- Department of Oncology, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xing Chen
- Department of Endoscopy, Shanxi Provincial People's Hospital, Taiyuan, Shanxi, China
| | - Jiansheng Guo
- Department of General Surgery, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Tong Wang
- Department of Statistics, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yanbo Zhang
- Department of Statistics, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Qingshan Li
- School of Pharmaceutical Sciences, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Chuangui Wang
- Key Laboratory of Medical Cell Biology, College of Translational Medicine, China Medical University, Shenyang, China
| | - Xiaolong Cheng
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongping Cui
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
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25
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Luo H, Jiang Y, Ma S, Chang H, Yi C, Cao H, Gao Y, Guo H, Hou J, Yan J, Sheng Y, Ren X. EZH2 promotes invasion and metastasis of laryngeal squamous cells carcinoma via epithelial-mesenchymal transition through H3K27me3. Biochem Biophys Res Commun 2016; 479:253-259. [DOI: 10.1016/j.bbrc.2016.09.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
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26
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Wu X, Cao N, Fenech M, Wang X. Role of Sirtuins in Maintenance of Genomic Stability: Relevance to Cancer and Healthy Aging. DNA Cell Biol 2016; 35:542-575. [DOI: 10.1089/dna.2016.3280] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Xiayu Wu
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Neng Cao
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
| | - Michael Fenech
- Genome Health and Personalized Nutrition, Commonwealth Scientific and Industrial Research Organization Food and Nutrition, Adelaide, South Australia, Australia
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, Yunnan, China
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27
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Shen YF, Wei AM, Kou Q, Zhu QY, Zhang L. Histone deacetylase 4 increases progressive epithelial ovarian cancer cells via repression of p21 on fibrillar collagen matrices. Oncol Rep 2015; 35:948-54. [PMID: 26572940 DOI: 10.3892/or.2015.4423] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 11/05/2022] Open
Abstract
Histone deacetylase (HDAC) 4 is an emerging target in cancer therapeutics, but little is known about the function of HDAC4 in gynecologic malignancies. Therefore we investigated the mechanism of HDAC4 promoting the proliferation of epithelial ovarian cancer cells (OV). In this study, we observed that the proliferation of cells with HDAC4 inhibitor Trichostatin A (TSA) treatment was markedly decreased, Further, we showed that epithelial ovarian cancer tissues with stage III/IV had higher HDAC4 expression, compared to that with stage I/II. We examined first that the HDAC4 expression was increased in response to fibrillar collagen matrices. In addition, we found that HDAC4 was retained in the nucleus by regulation of PP1α, which regulated HDAC4 cellular fraction via phosphorylation of HDAC4. In addition, we found that HDAC4 bound to Sp1 in epithelial ovarian cancer cells. Finally, ovarian cancer cell line OVCAR3 was evaluated via gain/loss-of-function of HDAC4 by either overexpression of HDCA4 or knock-down of HDAC4 with shRNA. We examined both protein and mRNA of p21 by western blotting and qPCR. We performed analysis of colony formation in matrigel and migration by ECIS. Our results suggest that the accumulation of HDAC4 induced by fibrillar collagen matrices in the nucleus via co-localization of PP1α, leads to repression of the mRNA/protein of p21 and in turn promotes the proliferation and migration of epithelial ovarian cancer cells.
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Affiliation(s)
- Yu-Fei Shen
- State Key Laboratory of Reproductive Medicine, Department of Gynecology and Obstetrics, Nanjing Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 210029, P.R. China
| | - Ai-Min Wei
- State Key Laboratory of Reproductive Medicine, Department of Gynecology and Obstetrics, Nanjing Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 210029, P.R. China
| | - Qing Kou
- State Key Laboratory of Reproductive Medicine, Department of Gynecology and Obstetrics, Nanjing Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 210029, P.R. China
| | - Qiao-Ying Zhu
- State Key Laboratory of Reproductive Medicine, Department of Gynecology and Obstetrics, Nanjing Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 210029, P.R. China
| | - Lei Zhang
- State Key Laboratory of Reproductive Medicine, Department of Gynecology and Obstetrics, Nanjing Maternal and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 210029, P.R. China
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28
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Barbier-Torres L, Beraza N, Fernández-Tussy P, Lopitz-Otsoa F, Fernández-Ramos D, Zubiete-Franco I, Varela-Rey M, Delgado TC, Gutiérrez V, Anguita J, Pares A, Banales JM, Villa E, Caballería J, Alvarez L, Lu SC, Mato JM, Martínez-Chantar ML. Histone deacetylase 4 promotes cholestatic liver injury in the absence of prohibitin-1. Hepatology 2015; 62:1237-48. [PMID: 26109312 PMCID: PMC4589448 DOI: 10.1002/hep.27959] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/21/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Prohibitin-1 (PHB1) is an evolutionarily conserved pleiotropic protein that participates in diverse processes depending on its subcellular localization and interactome. Recent data have indicated a diverse role for PHB1 in the pathogenesis of obesity, cancer, and inflammatory bowel disease, among others. Data presented here suggest that PHB1 is also linked to cholestatic liver disease. Expression of PHB1 is markedly reduced in patients with primary biliary cirrhosis and biliary atresia or with Alagille syndrome, two major pediatric cholestatic conditions. In the experimental model of bile duct ligation, silencing of PHB1 induced liver fibrosis, reduced animal survival, and induced bile duct proliferation. Importantly, the modulatory effect of PHB1 is not dependent on its known mitochondrial function. Also, PHB1 interacts with histone deacetylase 4 (HDAC4) in the presence of bile acids. Hence, PHB1 depletion leads to increased nuclear HDAC4 content and its associated epigenetic changes. Remarkably, HDAC4 silencing and the administration of the HDAC inhibitor parthenolide during obstructive cholestasis in vivo promote genomic reprogramming, leading to regression of the fibrotic phenotype in liver-specific Phb1 knockout mice. CONCLUSION PHB1 is an important mediator of cholestatic liver injury that regulates the activity of HDAC4, which controls specific epigenetic markers; these results identify potential novel strategies to treat liver injury and fibrosis, particularly as a consequence of chronic cholestasis.
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Affiliation(s)
- Lucía Barbier-Torres
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Naiara Beraza
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Pablo Fernández-Tussy
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Fernando Lopitz-Otsoa
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - David Fernández-Ramos
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Imanol Zubiete-Franco
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Marta Varela-Rey
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Teresa C Delgado
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Virginia Gutiérrez
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Juan Anguita
- CIC bioGUNE, Proteomics Unit, Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - Albert Pares
- Liver Unit. Hospital Clínic. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd). IDIBAPS. Barcelona, Spain
| | - Jesús M Banales
- Biodonostia Research Health Institute, Donostia University Hospital (HUD), University of the Basque Country (UPV/EHU), Ikerbasque, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), San Sebastian, Spain
| | - Erica Villa
- Department of Gastroenterology, Azienda Ospedaliero-Universitaria & University of Modena and Reggio Emilia, Modena, Italy
| | - Juan Caballería
- Liver Unit. Hospital Clínic. Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd). IDIBAPS. Barcelona, Spain
| | - Luis Alvarez
- La Paz University Hospital Health Research Institute-IdiPAZ, Madrid, Spain
| | - Shelly C Lu
- Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, California 90048; USC Research Center for Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033
| | - Jose M Mato
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
| | - María Luz Martínez-Chantar
- CIC bioGUNE, Metabolomics Unit, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
- Corresponding Author: Martinez-Chantar ML, CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain. Tel: +34-944-061318; Fax: +34-944-061301
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Murata H, Yoshimoto K, Hatae R, Akagi Y, Mizoguchi M, Hata N, Kuga D, Nakamizo A, Amano T, Sayama T, Iihara K. Detection of proneural/mesenchymal marker expression in glioblastoma: temporospatial dynamics and association with chromatin-modifying gene expression. J Neurooncol 2015; 125:33-41. [PMID: 26272600 DOI: 10.1007/s11060-015-1886-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 08/08/2015] [Indexed: 12/30/2022]
Abstract
Proneural and mesenchymal are two subtypes of glioblastoma identified by gene expression profiling. In this study, the primary aim was to detect markers to develop a clinically applicable method for distinguishing proneural and mesenchymal glioblastoma. The secondary aims were to investigate the temporospatial dynamics of these markers and to explore the association between these markers and the expression of chromatin-modifying genes. One hundred thirty-three glioma samples (grade II: 14 samples, grade III: 18, grade IV: 101) were analyzed. We quantified the expression of 6 signature genes associated with proneural and mesenchymal glioblastoma by quantitative reverse transcription-polymerase chain reaction. We assigned proneural (PN) and mesenchymal (MES) scores based on the average of the 6 markers and calculated a predominant metagene (P-M) score by subtracting the MES from the PN score. We used these scores to analyze correlations with malignant transformation, tumor recurrence, tumor heterogeneity, chromatin-modifying gene expression, and HDAC7 expression. The MES score positively correlated with tumor grade, whereas the PN score did not. The P-M score was able to distinguish the proneural and mesenchymal subtypes. It was decreased in cases of tumor recurrence and malignant transformation and showed variability within a tumor, suggesting intratumoral heterogeneity. The PN score correlated with the expression of multiple histone-modifying genes, whereas the MES score was associated only with HDAC7 expression. Thus, we demonstrated a simple and straightforward method of quantifying proneural/mesenchymal markers in glioblastoma. Of note, HDAC7 expression might be a novel therapeutic target in glioblastoma treatment.
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Affiliation(s)
- Hideki Murata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Yojiro Akagi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Akira Nakamizo
- Stroke Center, Steel Memorial Yawata Hospital, Fukuoka, Japan
| | - Toshiyuki Amano
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Tetsuro Sayama
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Koji Iihara
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
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30
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Yang Z, Jones A, Widschwendter M, Teschendorff AE. An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer. Genome Biol 2015; 16:140. [PMID: 26169266 PMCID: PMC4501092 DOI: 10.1186/s13059-015-0699-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/19/2015] [Indexed: 12/20/2022] Open
Abstract
Background One of the most important recent findings in cancer genomics is the identification of novel driver mutations which often target genes that regulate genome-wide chromatin and DNA methylation marks. Little is known, however, as to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types. Results Here we conduct an integrative pan-cancer-wide analysis of matched RNA-Seq and DNA methylation data across ten different cancer types. We identify seven tumor suppressor and eleven oncogenic epigenetic enzymes which display patterns of deregulation and association with genome-wide cancer DNA methylation patterns, which are largely independent of cancer type. In doing so, we provide evidence that genome-wide cancer hyper- and hypo- DNA methylation patterns are independent processes, controlled by distinct sets of epigenetic enzyme genes. Using causal network modeling, we predict a number of candidate drivers of cancer DNA hypermethylation and hypomethylation. Finally, we show that the genomic loci whose DNA methylation levels associate most strongly with expression of these putative drivers are highly consistent across cancer types. Conclusions This study demonstrates that there exist universal patterns of epigenomic deregulation that transcend cancer types, and that intra-tumor levels of genome-wide DNA hypomethylation and hypermethylation are controlled by distinct processes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0699-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhen Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Allison Jones
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andrew E Teschendorff
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
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31
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Lee P, Murphy B, Miller R, Menon V, Banik NL, Giglio P, Lindhorst SM, Varma AK, Vandergrift WA, Patel SJ, Das A. Mechanisms and clinical significance of histone deacetylase inhibitors: epigenetic glioblastoma therapy. Anticancer Res 2015; 35:615-625. [PMID: 25667438 PMCID: PMC6052863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glioblastoma is the most common and deadliest of malignant primary brain tumors (Grade IV astrocytoma) in adults. Current standard treatments have been improving but patient prognosis still remains unacceptably devastating. Glioblastoma recurrence is linked to epigenetic mechanisms and cellular pathways. Thus, greater knowledge of the cellular, genetic and epigenetic origin of glioblastoma is the key for advancing glioblastoma treatment. One rapidly growing field of treatment, epigenetic modifiers; histone deacetylase inhibitors (HDACis), has now shown much promise for improving patient outcomes through regulation of the acetylation states of histone proteins (a form of epigenetic modulation) and other non-histone protein targets. HDAC inhibitors have been shown, in a pre-clinical setting, to be effective anticancer agents via multiple mechanisms, by up-regulating expression of tumor suppressor genes, inhibiting oncogenes, inhibiting tumor angiogenesis and up-regulating the immune system. There are many HDAC inhibitors that are currently in pre-clinical and clinical stages of investigation for various types of cancers. This review will explain the theory of epigenetic cancer therapy, identify HDAC inhibitors that are being investigated for glioblastoma therapy, explain the mechanisms of therapeutic effects as demonstrated by pre-clinical and clinical studies and describe the current status of development of these drugs as they pertain to glioblastoma therapy.
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Affiliation(s)
- Philip Lee
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Ben Murphy
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Rickey Miller
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Vivek Menon
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Naren L Banik
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A. Ralph H. Johnson VA Medical Center, Charleston, SC, U.S.A
| | - Pierre Giglio
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A. Department of Neurological Surgery Ohio State University Wexner Medical College, Columbus, OH, U.S.A
| | - Scott M Lindhorst
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Abhay K Varma
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - William A Vandergrift
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Sunil J Patel
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A
| | - Arabinda Das
- Department of Neurology and Neurosurgery & MUSC Brain & Spine Tumor Program Medical University of South Carolina, Charleston, SC, U.S.A.
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Conway K, Edmiston SN, May R, Kuan PF, Chu H, Bryant C, Tse CK, Swift-Scanlan T, Geradts J, Troester MA, Millikan RC. DNA methylation profiling in the Carolina Breast Cancer Study defines cancer subclasses differing in clinicopathologic characteristics and survival. Breast Cancer Res 2014; 16:450. [PMID: 25287138 PMCID: PMC4303129 DOI: 10.1186/s13058-014-0450-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 09/24/2014] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Breast cancer is a heterogeneous disease, with several intrinsic subtypes differing by hormone receptor (HR) status, molecular profiles, and prognosis. However, the role of DNA methylation in breast cancer development and progression and its relationship with the intrinsic tumor subtypes are not fully understood. METHODS A microarray targeting promoters of cancer-related genes was used to evaluate DNA methylation at 935 CpG sites in 517 breast tumors from the Carolina Breast Cancer Study, a population-based study of invasive breast cancer. RESULTS Consensus clustering using methylation (β) values for the 167 most variant CpG loci defined four clusters differing most distinctly in HR status, intrinsic subtype (luminal versus basal-like), and p53 mutation status. Supervised analyses for HR status, subtype, and p53 status identified 266 differentially methylated CpG loci with considerable overlap. Genes relatively hypermethylated in HR+, luminal A, or p53 wild-type breast cancers included FABP3, FGF2, FZD9, GAS7, HDAC9, HOXA11, MME, PAX6, POMC, PTGS2, RASSF1, RBP1, and SCGB3A1, whereas those more highly methylated in HR-, basal-like, or p53 mutant tumors included BCR, C4B, DAB2IP, MEST, RARA, SEPT5, TFF1, THY1, and SERPINA5. Clustering also defined a hypermethylated luminal-enriched tumor cluster 3 that gene ontology analysis revealed to be enriched for homeobox and other developmental genes (ASCL2, DLK1, EYA4, GAS7, HOXA5, HOXA9, HOXB13, IHH, IPF1, ISL1, PAX6, TBX1, SOX1, and SOX17). Although basal-enriched cluster 2 showed worse short-term survival, the luminal-enriched cluster 3 showed worse long-term survival but was not independently prognostic in multivariate Cox proportional hazard analysis, likely due to the mostly early stage cases in this dataset. CONCLUSIONS This study demonstrates that epigenetic patterns are strongly associated with HR status, subtype, and p53 mutation status and may show heterogeneity within tumor subclass. Among HR+ breast tumors, a subset exhibiting a gene signature characterized by hypermethylation of developmental genes and poorer clinicopathologic features may have prognostic value and requires further study. Genes differentially methylated between clinically important tumor subsets have roles in differentiation, development, and tumor growth and may be critical to establishing and maintaining tumor phenotypes and clinical outcomes.
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Norum JH, Andersen K, Sørlie T. Lessons learned from the intrinsic subtypes of breast cancer in the quest for precision therapy. Br J Surg 2014; 101:925-38. [PMID: 24849143 DOI: 10.1002/bjs.9562] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 01/06/2023]
Abstract
BACKGROUND Wide variability in breast cancer, between patients and within each individual neoplasm, adds confounding complexity to the treatment of the disease. In clinical practice, hormone receptor status has been used to classify breast tumours and to guide treatment. Modern classification systems should take the wide tumour heterogeneity into account to improve patient outcome. METHODS This article reviews the identification of the intrinsic molecular subtypes of breast cancer, their prognostic and therapeutic implications, and the impact of tumour heterogeneity on cancer progression and treatment. The possibility of functionally addressing tumour-specific characteristics in in vivo models to inform decisions for precision therapies is also discussed. RESULTS Despite the robust breast tumour classification system provided by gene expression profiling, heterogeneity is also evident within these molecular portraits. A complicating factor in breast cancer classification is the process of selective clonality within developing neoplasms. Phenotypically and functionally distinct clones representing the intratumour heterogeneity might confuse molecular classification. Molecular portraits of the heterogeneous primary tumour might not necessarily reflect the subclone of cancer cells that causes the disease to relapse. Studies of reciprocal relationships between cancer cell subpopulations within developing tumours are therefore needed, and are possible only in genetically engineered mouse models or patient-derived xenograft models, in which the treatment-induced selection pressure on individual cell clones can be mimicked. CONCLUSION In the future, more refined classifications, based on integration of information at several molecular levels, are required to improve treatment guidelines. Large-scale translational research efforts paved the way for identification of the intrinsic subtypes, and are still fundamental for ensuring future progress in cancer care.
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Affiliation(s)
- J H Norum
- Department of Genetics, Institute of Cancer Research, Oslo, Norway; Cancer Stem Cell Innovation Centre, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
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