1
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Yu PC, Hou D, Chang B, Liu N, Xu CH, Chen X, Hu CL, Liu T, Wang X, Zhang Q, Liu P, Jiang Y, Fei MY, Zong LJ, Zhang JY, Liu H, Chen BY, Chen SB, Wang Y, Li ZJ, Li X, Deng CH, Ren YY, Zhao M, Jiang S, Wang R, Jin J, Yang S, Xue K, Shi J, Chang CK, Shen S, Wang Z, He PC, Chen Z, Chen SJ, Sun XJ, Wang L. SMARCA5 reprograms AKR1B1-mediated fructose metabolism to control leukemogenesis. Dev Cell 2024; 59:1954-1971.e7. [PMID: 38776924 DOI: 10.1016/j.devcel.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
A significant variation in chromatin accessibility is an epigenetic feature of leukemia. The cause of this variation in leukemia, however, remains elusive. Here, we identify SMARCA5, a core ATPase of the imitation switch (ISWI) chromatin remodeling complex, as being responsible for aberrant chromatin accessibility in leukemia cells. We find that SMARCA5 is required to maintain aberrant chromatin accessibility for leukemogenesis and then promotes transcriptional activation of AKR1B1, an aldo/keto reductase, by recruiting transcription co-activator DDX5 and transcription factor SP1. Higher levels of AKR1B1 are associated with a poor prognosis in leukemia patients and promote leukemogenesis by reprogramming fructose metabolism. Moreover, pharmacological inhibition of AKR1B1 has been shown to have significant therapeutic effects in leukemia mice and leukemia patient cells. Thus, our findings link the aberrant chromatin state mediated by SMARCA5 to AKR1B1-mediated endogenous fructose metabolism reprogramming and shed light on the essential role of AKR1B1 in leukemogenesis, which may provide therapeutic strategies for leukemia.
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Affiliation(s)
- Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dan Hou
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Binhe Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Na Liu
- Department of Hematology, Institute of Hematology, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinchi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ting Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Qunling Zhang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yilun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Liu
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shu-Bei Chen
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muying Zhao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Roujia Wang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jiacheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shaoxin Yang
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Kai Xue
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Shi
- Department of Hematology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Shuhong Shen
- Key Laboratory of Pediatric Hematology & Oncology of the Ministry of Health of China, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei 230027, China
| | - Peng-Cheng He
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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2
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Yang H, Lan L. Transcription-coupled DNA repair protects genome stability upon oxidative stress-derived DNA strand breaks. FEBS Lett 2024. [PMID: 38813713 DOI: 10.1002/1873-3468.14938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
Elevated oxidative stress, which threatens genome stability, has been detected in almost all types of cancers. Cells employ various DNA repair pathways to cope with DNA damage induced by oxidative stress. Recently, a lot of studies have provided insights into DNA damage response upon oxidative stress, specifically in the context of transcriptionally active genomes. Here, we summarize recent studies to help understand how the transcription is regulated upon DNA double strand breaks (DSB) and how DNA repair pathways are selectively activated at the damage sites coupling with transcription. The role of RNA molecules, especially R-loops and RNA modifications during the DNA repair process, is critical for protecting genome stability. This review provides an update on how cells protect transcribed genome loci via transcription-coupled repair pathways.
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Affiliation(s)
- Haibo Yang
- Department of Urology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Lan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
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3
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Brown LJ, Achinger-Kawecka J, Portman N, Clark S, Stirzaker C, Lim E. Epigenetic Therapies and Biomarkers in Breast Cancer. Cancers (Basel) 2022; 14:474. [PMID: 35158742 PMCID: PMC8833457 DOI: 10.3390/cancers14030474] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/07/2022] [Accepted: 01/14/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic therapies remain a promising, but still not widely used, approach in the management of patients with cancer. To date, the efficacy and use of epigenetic therapies has been demonstrated primarily in the management of haematological malignancies, with limited supportive data in solid malignancies. The most studied epigenetic therapies in breast cancer are those that target DNA methylation and histone modification; however, none have been approved for routine clinical use. The majority of pre-clinical and clinical studies have focused on triple negative breast cancer (TNBC) and hormone-receptor positive breast cancer. Even though the use of epigenetic therapies alone in the treatment of breast cancer has not shown significant clinical benefit, these therapies show most promise in use in combinations with other treatments. With improving technologies available to study the epigenetic landscape in cancer, novel epigenetic alterations are increasingly being identified as potential biomarkers of response to conventional and epigenetic therapies. In this review, we describe epigenetic targets and potential epigenetic biomarkers in breast cancer, with a focus on clinical trials of epigenetic therapies. We describe alterations to the epigenetic landscape in breast cancer and in treatment resistance, highlighting mechanisms and potential targets for epigenetic therapies. We provide an updated review on epigenetic therapies in the pre-clinical and clinical setting in breast cancer, with a focus on potential real-world applications. Finally, we report on the potential value of epigenetic biomarkers in diagnosis, prognosis and prediction of response to therapy, to guide and inform the clinical management of breast cancer patients.
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Affiliation(s)
- Lauren Julia Brown
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Joanna Achinger-Kawecka
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Neil Portman
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Susan Clark
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Elgene Lim
- School of Clinical Medicine, St. Vincent’s Campus, University of New South Wales (UNSW), Sydney, NSW 2010, Australia; (L.J.B.); (J.A.-K.); (N.P.); (S.C.); (C.S.)
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
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4
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Alterations of Chromatin Regulators in the Pathogenesis of Urinary Bladder Urothelial Carcinoma. Cancers (Basel) 2021; 13:cancers13236040. [PMID: 34885146 PMCID: PMC8656749 DOI: 10.3390/cancers13236040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Urinary bladder cancer is one of the ten major cancers worldwide, with higher incidences in males, in smokers, and in highly industrialized countries. New therapies beyond cytotoxic chemotherapy are urgently needed to improve treatment of these tumors. A better understanding of the mechanisms underlying their development may help in this regard. Recently, it was discovered that a group of proteins regulating the state of chromatin and thus gene expression is exceptionally and frequently affected by gene mutations in bladder cancers. Altered function of these mutated chromatin regulators must therefore be fundamental in their development, but how and why is poorly understood. Here we review the current knowledge on changes in chromatin regulators and discuss their possible consequences for bladder cancer development and options for new therapies. Abstract Urothelial carcinoma (UC) is the most frequent histological type of cancer in the urinary bladder. Genomic changes in UC activate MAPK and PI3K/AKT signal transduction pathways, which increase cell proliferation and survival, interfere with cell cycle and checkpoint control, and prevent senescence. A more recently discovered additional category of genetic changes in UC affects chromatin regulators, including histone-modifying enzymes (KMT2C, KMT2D, KDM6A, EZH2), transcription cofactors (CREBBP, EP300), and components of the chromatin remodeling complex SWI/SNF (ARID1A, SMARCA4). It is not yet well understood how these changes contribute to the development and progression of UC. Therefore, we review here the emerging knowledge on genomic and gene expression alterations of chromatin regulators and their consequences for cell differentiation, cellular plasticity, and clonal expansion during UC pathogenesis. Our analysis identifies additional relevant chromatin regulators and suggests a model for urothelial carcinogenesis as a basis for further mechanistic studies and targeted therapy development.
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Kim HI, Kim TH, Yoo JY, Young SL, Lessey BA, Ku BJ, Jeong JW. ARID1A and PGR proteins interact in the endometrium and reveal a positive correlation in endometriosis. Biochem Biophys Res Commun 2021; 550:151-157. [PMID: 33706098 DOI: 10.1016/j.bbrc.2021.02.144] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/28/2021] [Indexed: 11/16/2022]
Abstract
Endometriosis is a disorder in which endometrial cells normally limited to the lining of the uterus proliferate outside the uterine cavity and can cause pelvic pain and infertility. ARID1A levels are significantly reduced in the eutopic endometrium from women with endometriosis. Uterine specific Arid1a knock-out mice were infertile due to loss of epithelial progesterone receptor (PGR) signaling. However, the functional association of ARID1A and PGR in endometriosis has not been studied. We examined the expression patterns and co-localization of ARID1A and PGR in eutopic endometrium from women with and without endometriosis using immunostaining and Western blot analysis. ARID1A and PGR proteins co-localized in the epithelium during the proliferative and the early secretory phases. Our immunoprecipitation analysis and proximity ligation assay (PLA) revealed physical interaction between ARID1A and PGR-A but not PGR-B in the mouse and human endometrium. ARID1A levels positively correlated with PGR levels in the eutopic endometrium of women with endometriosis. Our results bring new perspectives on the molecular mechanisms involved in endometrial receptivity and progesterone resistance in endometriosis. The interrelationship between ARID1A and PGR may contribute to explaining the non-receptive endometrium in endometriosis-related infertility.
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Affiliation(s)
- Hong Im Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Tae Hoon Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Jung-Yoon Yoo
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA; Life Science Institute, Repure Life Science, Seoul, 03722, Republic of Korea
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Bruce A Lessey
- Department of Obstetrics and Gynecology, Wake Forest Baptist Health, Winston-Salem, NC, 27157, USA
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon, 35015, Republic of Korea.
| | - Jae-Wook Jeong
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA.
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6
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Giles KA, Gould CM, Achinger-Kawecka J, Page SG, Kafer GR, Rogers S, Luu PL, Cesare AJ, Clark SJ, Taberlay PC. BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer. Clin Epigenetics 2021; 13:37. [PMID: 33596994 PMCID: PMC7888175 DOI: 10.1186/s13148-021-01023-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour. Results Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest. Conclusions Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01023-7.
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Affiliation(s)
- Katherine A Giles
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia.,Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia
| | - Cathryn M Gould
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Scott G Page
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Phuc-Loi Luu
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Susan J Clark
- Epigenetics Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, 2000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, TAS, Hobart, 7000, Australia.
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7
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Contessoto VG, Cheng RR, Hajitaheri A, Dodero-Rojas E, Mello MF, Lieberman-Aiden E, Wolynes P, Di Pierro M, Onuchic JN. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Res 2021; 49:D172-D182. [PMID: 33021634 PMCID: PMC7778995 DOI: 10.1093/nar/gkaa818] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/05/2020] [Accepted: 10/02/2020] [Indexed: 11/30/2022] Open
Abstract
We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.
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Affiliation(s)
- Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Brazilian Biorenewables National Laboratory-LNBR, Brazilian Center for Research in Energy and Materials-CNPEM, Campinas, SP 13083-100, Brazil
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil
| | - Ryan R Cheng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arya Hajitaheri
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Computer Science, University of Houston, Houston, TX 77204, USA
| | - Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Theoretical and Computational Physics Laboratory, University of Costa Rica, San José 5 11501, Costa Rica
| | - Matheus F Mello
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Erez Lieberman-Aiden
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
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8
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Shi Y, Qi W, Xu Q, Wang Z, Cao X, Zhou L, Ye L. The role of epigenetics in the reproductive toxicity of environmental endocrine disruptors. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:78-88. [PMID: 33217042 DOI: 10.1002/em.22414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Environmental endocrine disruptors (EEDs) seriously endanger human health by interfering with the normal function of reproductive systems. In males, EEDs can affect sperm formation and semen quality as well spermatogenesis, ultimately reducing fertility. In females, EEDs can affect uterine development and the expression levels of reproduction-related genes, ultimately reducing female fertility and the normal development of the fetus. There are a large number of putative mechanisms by which EEDs can induce reproductive toxicity, and many studies have shown the involvement of epigenetics. In this review, we summarize the role of DNA methylation, noncoding RNAs, genomic imprinting, chromatin remodeling and histone modification in the reproductive toxicity of EEDs.
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Affiliation(s)
- Yanbin Shi
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Wen Qi
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Qi Xu
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Zheng Wang
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Xiaolian Cao
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Liting Zhou
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
| | - Lin Ye
- Department of Occupational and Environmental Health, School of Public Health, Jilin University, Changchun, China
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9
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Leruste A, Chauvin C, Pouponnot C, Bourdeaut F, Waterfall JJ, Piaggio E. Immune responses in genomically simple SWI/SNF-deficient cancers. Cancer 2020; 127:172-180. [PMID: 33079397 DOI: 10.1002/cncr.33172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/27/2020] [Accepted: 07/23/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Amaury Leruste
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Céline Chauvin
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Celio Pouponnot
- CNRS UMR 3347, INSERM U1021, Curie Institute Research Center, PSL Research University, Orsay, France
| | - Franck Bourdeaut
- Translational Research in Pediatric Oncology (RTOP) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France.,SIREDO Pediatric Cancer Center, Curie Institute, Paris, France.,Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France
| | - Joshua J Waterfall
- Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France.,Integrative Functional Genomics of Cancer (IFGC) team, INSERM U830, Curie Institute Research Center, PSL Research University, Paris, France
| | - Eliane Piaggio
- Translational Research Department, Curie Institute Research Center, PSL Research University, Paris, France.,Translational Immunotherapy (TransImm) team, INSERM U932, Curie Institute Research Center, PSL Research University, Paris, France
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10
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Abstract
Cell-free DNA (cfDNA) has the potential to enable non-invasive detection of disease states and progression. Beyond its sequence, cfDNA also represents the nucleosomal landscape of cell(s)-of-origin and captures the dynamics of the epigenome. In this review, we highlight the emergence of cfDNA epigenomic methods that assess disease beyond the scope of mutant tumour genotyping. Detection of tumour mutations is the gold standard for sequencing methods in clinical oncology. However, limitations inherent to mutation targeting in cfDNA, and the possibilities of uncovering molecular mechanisms underlying disease, have made epigenomics of cfDNA an exciting alternative. We discuss the epigenomic information revealed by cfDNA, and how epigenomic methods exploit cfDNA to detect and characterize cancer. Future applications of cfDNA epigenomic methods to act complementarily and orthogonally to current clinical practices has the potential to transform cancer management and improve cancer patient outcomes.
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Affiliation(s)
| | | | - Srinivas Ramachandran
- RNA Bioscience Initiative, and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Mail Stop: 8101, 12801 East 17th Avenue L18–9102, Aurora, CO 80045, USA
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11
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Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep 2020; 27:1781-1793.e4. [PMID: 31067463 DOI: 10.1016/j.celrep.2019.04.048] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022] Open
Abstract
Sarcomatoid urothelial bladder cancer (SARC) displays a high propensity for distant metastasis and is associated with short survival. We report a comprehensive genomic analysis of 28 cases of SARC and 84 cases of conventional urothelial carcinoma (UC), with the TCGA cohort of 408 muscle-invasive bladder cancers serving as the reference. SARCs show a distinct mutational landscape, with enrichment of TP53, RB1, and PIK3CA mutations. They are related to the basal molecular subtype of conventional UCs and could be divided into epithelial-basal and more clinically aggressive mesenchymal subsets on the basis of TP63 and its target gene expression levels. Other analyses reveal that SARCs are driven by downregulation of homotypic adherence genes and dysregulation of the EMT network, and nearly half exhibit a heavily infiltrated immune phenotype. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer.
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Affiliation(s)
- Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Hui Yao
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yan Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shizhen Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Miao Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Barton Grossman
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - James Edward Ferguson
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - He Huang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vipulkumar Dadhania
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith Baggerly
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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12
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Inactivation of Arid1a in the endometrium is associated with endometrioid tumorigenesis through transcriptional reprogramming. Nat Commun 2020; 11:2717. [PMID: 32483112 PMCID: PMC7264300 DOI: 10.1038/s41467-020-16416-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
Somatic inactivating mutations of ARID1A, a SWI/SNF chromatin remodeling gene, are prevalent in human endometrium-related malignancies. To elucidate the mechanisms underlying how ARID1A deleterious mutation contributes to tumorigenesis, we establish genetically engineered murine models with Arid1a and/or Pten conditional deletion in the endometrium. Transcriptomic analyses on endometrial cancers and precursors derived from these mouse models show a close resemblance to human uterine endometrioid carcinomas. We identify transcriptional networks that are controlled by Arid1a and have an impact on endometrial tumor development. To verify findings from the murine models, we analyze ARID1AWT and ARID1AKO human endometrial epithelial cells. Using a system biology approach and functional studies, we demonstrate that ARID1A-deficiency lead to loss of TGF-β tumor suppressive function and that inactivation of ARID1A/TGF-β axis promotes migration and invasion of PTEN-deleted endometrial tumor cells. These findings provide molecular insights into how ARID1A inactivation accelerates endometrial tumor progression and dissemination, the major causes of cancer mortality. ARID1A, which is often mutated in human endometrial cancer, is a component of the SWI/SNF chromatin remodelling complex. Here, the authors show that Arid1a mutations in the mouse endometrium and primary human endometrial epithelial cells cause widespread reprogramming of gene transcription and result in a loss of response to TGFβ.
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13
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Wu Y, Zhao Y, Huan L, Zhao J, Zhou Y, Xu L, Hu Z, Liu Y, Chen Z, Wang L, Huang S, He X, Liang L. An LTR Retrotransposon-Derived Long Noncoding RNA lncMER52A Promotes Hepatocellular Carcinoma Progression by Binding p120-Catenin. Cancer Res 2019; 80:976-987. [PMID: 31874857 DOI: 10.1158/0008-5472.can-19-2115] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/13/2019] [Accepted: 12/19/2019] [Indexed: 12/24/2022]
Abstract
Long terminal repeat (LTR) retrotransposons are a major class of transposable elements, accounting for 8.67% of the human genome. LTRs can serve as regulatory sequences and drive transcription of tissue or cancer-specific transcripts. However, the role of these LTR-activated transcripts, especially long non-coding RNAs (lncRNA), in cancer development remains largely unexplored. Here, we identified a novel lncRNA derived from MER52A retrotransposons (lncMER52A) that was exclusively expressed in hepatocellular carcinoma (HCC). HCC patients with higher lncMER52A had advanced TNM stage, less differentiated tumors, and shorter overall survival. LncMER52A promoted invasion and metastasis of HCC cells in vitro and in vivo. Mechanistically, lncMER52A stabilized p120-catenin and triggered the activation of Rho GTPase downstream of p120-catenin. Furthermore, we found that chromatin accessibility was crucial for the expression of lncMER52A. In addition, YY1 transcription factor bound to the cryptic MER52A LTR promoter and drove lncMER52A transcription in HCC. In conclusion, we identified an LTR-activated lncMER52A, which promoted the progression of HCC cells via stabilizing p120-catenin and activating p120-ctn/Rac1/Cdc42 axis. LncMER52A could serve as biomarker and therapeutic target for patients with HCC. SIGNIFICANCE: A novel long noncoding RNA lncMER52 modulates cell migration and invasion via posttranslational control of p120-catenin protein stability. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/5/976/F1.large.jpg.
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Affiliation(s)
- Yangjun Wu
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yiming Zhao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Huan
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yuqiang Zhou
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Linguo Xu
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yizhe Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Linhui Liang
- Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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14
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The emerging role of epigenetic therapeutics in immuno-oncology. Nat Rev Clin Oncol 2019; 17:75-90. [PMID: 31548600 DOI: 10.1038/s41571-019-0266-5] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
Abstract
The past decade has seen the emergence of immunotherapy as a prime approach to cancer treatment, revolutionizing the management of many types of cancer. Despite the promise of immunotherapy, most patients do not have a response or become resistant to treatment. Thus, identifying combinations that potentiate current immunotherapeutic approaches will be crucial. The combination of immune-checkpoint inhibition with epigenetic therapy is one such strategy that is being tested in clinical trials, encompassing a variety of cancer types. Studies have revealed key roles of epigenetic processes in regulating immune cell function and mediating antitumour immunity. These interactions make combined epigenetic therapy and immunotherapy an attractive approach to circumvent the limitations of immunotherapy alone. In this Review, we highlight the basic dynamic mechanisms underlying the synergy between immunotherapy and epigenetic therapies and detail current efforts to translate this knowledge into clinical benefit for patients.
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15
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Mota STS, Vecchi L, Zóia MAP, Oliveira FM, Alves DA, Dornelas BC, Bezerra SM, Andrade VP, Maia YCP, Neves AF, Goulart LR, Araújo TG. New Insights into the Role of Polybromo-1 in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20122852. [PMID: 31212728 PMCID: PMC6627401 DOI: 10.3390/ijms20122852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 01/22/2023] Open
Abstract
The human protein Polybromo-1 (PBMR1/BAF180) is a component of the SWI/SNF chromatin-remodeling complex that has been reported to be deregulated in tumors. However, its role in prostate cancer (PCa) is largely unknown. In this study, we described the PBRM1 transcriptional levels and the protein expression/localization in tissues of PCa patients and in prostatic cell lines. Increased PBRM1 mRNA levels were found in PCa samples, when compared to benign disease, and were correlated with higher Gleason score. We also verified that only the nuclear localization of PBRM1 protein is correlated with a more aggressive disease and high Prostate-Specific Antigen (PSA) levels in tissue microarrays. Intriguing expression patterns of mRNA and protein were identified in the cell lines. Although PBRM1 protein was restricted to the nuclei, in tumor cell lines in non-neoplastic cells, it was also present in vesicular-like structures that were dispersed within the cytoplasm. We knocked-down PBRM1 in the castration-resistant PCa (CRPC) cell line PC-3 and we verified that PBRM1 promotes the expression of several markers of aggressiveness, including EpCAM, TGF-β, and N-Cadherin. Therefore, our data supported the hypothesis that PBRM1 displays a pivotal role in the promotion and maintenance of the malignant behavior of PCa, especially in CRPC.
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Affiliation(s)
- Sara T S Mota
- Laboratory of Genetics and Biotechnology, Institute of Biotechnology, Federal University of Uberlandia, Patos de Minas-MG 387400-128, Brazil.
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | - Lara Vecchi
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | - Mariana A P Zóia
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | - Fabrícia M Oliveira
- Faculty of Mathematics, Federal University of Uberlandia, Patos de Minas-MG 387400-128, Brazil.
| | - Douglas A Alves
- Laboratory of Genetics and Biotechnology, Institute of Biotechnology, Federal University of Uberlandia, Patos de Minas-MG 387400-128, Brazil.
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | - Bruno C Dornelas
- Pathology Division, Internal Medicine, University Hospital, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | | | | | - Yara C P Maia
- Medical Faculty, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
| | - Adriana F Neves
- Laboratory of Molecular Biology, Federal University of Goias-GO, Goiânia-GO 75704-020, Brazil.
| | - Luiz Ricardo Goulart
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
- University of California Davis, Department of Medical Microbiology and Immunology, Davis, CA 95616, USA.
| | - Thaise G Araújo
- Laboratory of Genetics and Biotechnology, Institute of Biotechnology, Federal University of Uberlandia, Patos de Minas-MG 387400-128, Brazil.
- Laboratory of Nanobiotechnology, Institute of Biotechnology, Federal University of Uberlandia, Uberlandia-MG 38400-902, Brazil.
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16
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Giles KA, Gould CM, Du Q, Skvortsova K, Song JZ, Maddugoda MP, Achinger-Kawecka J, Stirzaker C, Clark SJ, Taberlay PC. Integrated epigenomic analysis stratifies chromatin remodellers into distinct functional groups. Epigenetics Chromatin 2019; 12:12. [PMID: 30755246 PMCID: PMC6371444 DOI: 10.1186/s13072-019-0258-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/05/2019] [Indexed: 12/19/2022] Open
Abstract
Background ATP-dependent chromatin remodelling complexes are responsible for establishing and maintaining the positions of nucleosomes. Chromatin remodellers are targeted to chromatin by transcription factors and non-coding RNA to remodel the chromatin into functional states. However, the influence of chromatin remodelling on shaping the functional epigenome is not well understood. Moreover, chromatin remodellers have not been extensively explored as a collective group across two-dimensional and three-dimensional epigenomic layers. Results Here, we have integrated the genome-wide binding profiles of eight chromatin remodellers together with DNA methylation, nucleosome positioning, histone modification and Hi-C chromosomal contacts to reveal that chromatin remodellers can be stratified into two functional groups. Group 1 (BRG1, SNF2H, CHD3 and CHD4) has a clear preference for binding at ‘actively marked’ chromatin and Group 2 (BRM, INO80, SNF2L and CHD1) for ‘repressively marked’ chromatin. We find that histone modifications and chromatin architectural features, but not DNA methylation, stratify the remodellers into these functional groups. Conclusions Our findings suggest that chromatin remodelling events are synchronous and that chromatin remodellers themselves should be considered simultaneously and not as individual entities in isolation or necessarily by structural similarity, as they are traditionally classified. Their coordinated function should be considered by preference for chromatin features in order to gain a more accurate and comprehensive picture of chromatin regulation. Electronic supplementary material The online version of this article (10.1186/s13072-019-0258-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine A Giles
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Cathryn M Gould
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Qian Du
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Ksenia Skvortsova
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Jenny Z Song
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Madhavi P Maddugoda
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Joanna Achinger-Kawecka
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Sydney, NSW, 2000, Australia
| | - Clare Stirzaker
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Sydney, NSW, 2000, Australia
| | - Susan J Clark
- Epigenetics Research, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Sydney, NSW, 2000, Australia
| | - Phillippa C Taberlay
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, 2000, Australia. .,School of Medicine, Collage of Health and Medicine, University of Tasmania, Hobart, TAS, 7000, Australia.
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17
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The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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18
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The Role of DNA/Histone Modifying Enzymes and Chromatin Remodeling Complexes in Testicular Germ Cell Tumors. Cancers (Basel) 2018; 11:cancers11010006. [PMID: 30577487 PMCID: PMC6357018 DOI: 10.3390/cancers11010006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
It is well established that cancer cells exhibit alterations in chromatin structure and accessibility. Indeed, the dysregulation of many protein-coding players with enzymatic activity (DNA and histone-modifying enzymes) and chromatin remodelers have been depicted in various tumor models in recent years. Still, little attention has been directed towards testicular germ cell tumors (TGCTs)-representing the most common neoplasm among young adult Caucasian men-with most studies focusing on exploring the role of DNA methyltransferases (DNMTs) and DNA demethylases (TETs). TGCTs represent a complex tumor model, associated with developmental and embryogenesis-related phenomena, and display seldom (cyto)genetic aberrations, leaving room for Epigenetics to explain such morphological and clinical diversity. Herein, we have summarized the major findings that were reported in literature regarding the dysregulation of DNA/histone-modifying enzymes and chromatin remodelers in TGCTs. Additionally, we performed in silico analysis of The Cancer Genome Atlas database to find the most relevant of those players in TGCTs. We concluded that several DNA/histone-modifying enzymes and chromatin remodelers may serve as biomarkers for subtyping, dictating prognosis and survival, and, possibly, for serving as targets of directed, less toxic therapies.
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19
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Abstract
Differentiation of stem cells into highly specialised cells requires gene expression changes brought about by remodelling of the chromatin architecture. During this lineage-commitment process, the majority of DNA needs to be packaged into inactive heterochromatin, allowing only a subset of regulatory elements to remain open and functionally required genes to be expressed. Epigenetic mechanisms such as DNA methylation, post-translational modifications to histone tails, and nucleosome positioning all potentially contribute to the changes in higher order chromatin structure during differentiation. The mammary gland is a particularly useful model to study these complex epigenetic processes since the majority of its development is postnatal, the gland is easily accessible, and development occurs in a highly reproducible manner. Inappropriate epigenetic remodelling can also drive tumourigenesis; thus, insights into epigenetic remodelling during mammary gland development advance our understanding of breast cancer aetiology. We review the current literature surrounding DNA methylation and histone modifications in the developing mammary gland and its implications for breast cancer.
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Affiliation(s)
- Holly Holliday
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Laura A Baker
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Simon R Junankar
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia
| | - Susan J Clark
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.,Epigenetics Research Program, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre, Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, NSW, 2010, Australia.
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20
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Comprehensive assessment of the expression of the SWI/SNF complex defines two distinct prognostic subtypes of ovarian clear cell carcinoma. Oncotarget 2018; 7:54758-54770. [PMID: 27340867 PMCID: PMC5342379 DOI: 10.18632/oncotarget.10181] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/01/2016] [Indexed: 12/18/2022] Open
Abstract
Somatic mutations in the ARID1A tumor-suppressor gene have been frequently identified in ovarian clear cell carcinoma (CCC) cases. BAF250a encoded by ARID1A is a member of the SWI/SNF complex, but the expression and mutation status of other SWI/SNF subunits have not been explored. The current study aimed to elucidate the biological and clinical significance of the SWI/SNF complex subunits, by assessing the expression and mutation status of SWI/SNF subunits, and distinct genomic aberrations associated with their expression. Of 82 CCC specimens, 38 samples presented no BAF250a expression, and 50 samples exhibited the loss of at least one subunit of the SWI/SNF complex. Cases which lack at least one SWI/SNF complex component exhibited significantly more advanced stages, faster growth and stronger nuclear atypia compared with SWI/SNF-positive samples (p<0.05). Although BAF250a expression is not related to poor prognosis, the group presenting the loss of at least one SWI/SNF complex subunit exhibited significantly shorter overall and progression-free survivals (p<0.05). A multivariate analysis suggested that the expression status of the SWI/SNF complex serves as an independent prognostic factor (p<0.005). The cases positive for all SWI/SNF subunits demonstrated significantly greater DNA copy number alterations, such as amplification at chromosomes 8q.24.3 and 20q.13.2-20q.13.33 (including ZNF217) and deletion at chromosomes 13q12.11-13q14.3 (including RB1), 17p13.2-17p13.1 (including TP53) and 19p13.2-19p13.12. In conclusion, the CCCs exhibiting the loss of one or multiple SWI/SNF complex subunits demonstrated aggressive behaviors and poor prognosis, whereas the CCCs with positive expression for all SWI/SNF components presented more copy number alterations and a favorable prognosis.
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21
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Porkka N, Valo S, Nieminen TT, Olkinuora A, Mäki-Nevala S, Eldfors S, Peltomäki P. Sequencing of Lynch syndrome tumors reveals the importance of epigenetic alterations. Oncotarget 2017; 8:108020-108030. [PMID: 29296220 PMCID: PMC5746122 DOI: 10.18632/oncotarget.22445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
Genomic instability and epigenetic aberrations are important classifiers of human tumors, yet, their interrelations are poorly understood. We used Lynch syndrome (LS) to address such relationships. Forty-five tumors (11 colorectal adenomas, 18 colorectal carcinomas, and 16 ovarian carcinomas) were profiled for CpG Island Methylator Phenotype (CIMP) and somatic mutations. All tumors showed high-degree microsatellite instability. Panel sequencing of 578 cancer-relevant genes revealed the average number of 1433, 1124, and 657 non-synonymous somatic mutations per colorectal adenoma, colorectal carcinoma, and ovarian carcinoma, respectively. Genes harboring mutations with allele frequency 25 % or higher in at least 31 % of tumors were regarded to be possible drivers. Among 72 and 10 such genes identified in colorectal and ovarian tumors, respectively, the most frequently mutated genes BRD4 and MLL2 (62 % of colorectal tumors) and ARID1A (50 % of ovarian carcinomas) are involved in epigenetic regulation. The total number of somatic mutations or mutant genes per tumor were significantly associated with CIMP. Our results suggest that even in an inherited disease, tumor type-specific epigenetic changes are significant and may result from regulatory changes (CIMP) or structural events (mutations of epigenetic regulatory genes). The findings are clinically relevant since many of the affected pathways can be therapeutically targeted.
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Affiliation(s)
- Noora Porkka
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Satu Valo
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Satu Mäki-Nevala
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Samuli Eldfors
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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22
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Varghese VK, Shukla V, Kabekkodu SP, Pandey D, Satyamoorthy K. DNA methylation regulated microRNAs in human cervical cancer. Mol Carcinog 2017; 57:370-382. [PMID: 29077234 DOI: 10.1002/mc.22761] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023]
Abstract
Regulation of miRNA gene expression by DNA promoter methylation may represent a key mechanism to drive cervical cancer progression. In order to understand the impact of DNA promoter methylation on miRNAs at various stages of cervical carcinogenesis, we performed DNA methylation microarray on Normal Cervical Epithelium (NCE), Cervical Intraepithelial Neoplasia (CIN I-III) and Squamous Cell Carcinoma (SCC) tissues to identify differentially methylated miRNAs followed by validation by bisulfite sequencing. Further, expression of miRNAs was analyzed by qRT-PCR in clinical tissues and cervical cancer cell lines. Transcriptional activity was determined by luciferase assay. We identified a total of 69 hypermethylated and hypomethylated miRNA promoters encompassing 78 CpG islands in all except Y chromosome, among the three groups. The candidate DNA promoters of miR-424 were significantly hypermethylated and miR-200b and miR-34c were significantly hypomethylated in SCC compared to NCE (P < 0.05). Expression of miR-424, miR-200b, and miR-34c were inversely correlated with promoter DNA methylation in tissue samples. Treatment of cell lines with 5-aza-2'-deoxycytidine showed differential expression in all three miRNAs. We observed a decrease in miRNA promoter activity following in vitro SssI methylase treatment of miR-424, miR-200b, and miR-34c. Luciferase assay demonstrated that miR-200b and miR-424 functionally interacts with 3'-UTR of HIPK3 and RBBP6 respectively and decreased their activity in presence of miR-200b and miR-424 mimics transfected in SiHa cells. Taken together, we have identified deregulation of miRNAs by aberrant DNA promoter methylation, leading to its transcriptional silencing during cervical carcinogenesis, which can be potential targets for diagnosis and therapy.
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Affiliation(s)
- Vinay K Varghese
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Shama P Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Deeksha Pandey
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
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23
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Pawlyn C, Kaiser MF, Heuck C, Melchor L, Wardell CP, Murison A, Chavan SS, Johnson DC, Begum DB, Dahir NM, Proszek PZ, Cairns DA, Boyle EM, Jones JR, Cook G, Drayson MT, Owen RG, Gregory WM, Jackson GH, Barlogie B, Davies FE, Walker BA, Morgan GJ. The Spectrum and Clinical Impact of Epigenetic Modifier Mutations in Myeloma. Clin Cancer Res 2016; 22:5783-5794. [PMID: 27235425 PMCID: PMC5124543 DOI: 10.1158/1078-0432.ccr-15-1790] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 03/24/2016] [Accepted: 04/27/2016] [Indexed: 12/14/2022]
Abstract
PURPOSE Epigenetic dysregulation is known to be an important contributor to myeloma pathogenesis but, unlike other B-cell malignancies, the full spectrum of somatic mutations in epigenetic modifiers has not been reported previously. We sought to address this using the results from whole-exome sequencing in the context of a large prospective clinical trial of newly diagnosed patients and targeted sequencing in a cohort of previously treated patients for comparison. EXPERIMENTAL DESIGN Whole-exome sequencing analysis of 463 presenting myeloma cases entered in the UK NCRI Myeloma XI study and targeted sequencing analysis of 156 previously treated cases from the University of Arkansas for Medical Sciences (Little Rock, AR). We correlated the presence of mutations with clinical outcome from diagnosis and compared the mutations found at diagnosis with later stages of disease. RESULTS In diagnostic myeloma patient samples, we identify significant mutations in genes encoding the histone 1 linker protein, previously identified in other B-cell malignancies. Our data suggest an adverse prognostic impact from the presence of lesions in genes encoding DNA methylation modifiers and the histone demethylase KDM6A/UTX The frequency of mutations in epigenetic modifiers appears to increase following treatment most notably in genes encoding histone methyltransferases and DNA methylation modifiers. CONCLUSIONS Numerous mutations identified raise the possibility of targeted treatment strategies for patients either at diagnosis or relapse supporting the use of sequencing-based diagnostics in myeloma to help guide therapy as more epigenetic targeted agents become available. Clin Cancer Res; 22(23); 5783-94. ©2016 AACR.
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Affiliation(s)
| | | | - Christoph Heuck
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | | | - Alex Murison
- The Institute of Cancer Research, London, United Kingdom
| | - Shweta S Chavan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Dil B Begum
- The Institute of Cancer Research, London, United Kingdom
| | - Nasrin M Dahir
- The Institute of Cancer Research, London, United Kingdom
| | | | - David A Cairns
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Eileen M Boyle
- The Institute of Cancer Research, London, United Kingdom
| | - John R Jones
- The Institute of Cancer Research, London, United Kingdom
| | | | - Mark T Drayson
- Clinical Immunology, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Roger G Owen
- St James's University Hospital, Leeds, United Kingdom
| | - Walter M Gregory
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Graham H Jackson
- Department of Haematology, Newcastle University, Newcastle, United Kingdom
| | - Bart Barlogie
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Faith E Davies
- The Institute of Cancer Research, London, United Kingdom
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Brian A Walker
- The Institute of Cancer Research, London, United Kingdom
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Gareth J Morgan
- The Institute of Cancer Research, London, United Kingdom.
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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24
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Babaian A, Mager DL. Endogenous retroviral promoter exaptation in human cancer. Mob DNA 2016; 7:24. [PMID: 27980689 PMCID: PMC5134097 DOI: 10.1186/s13100-016-0080-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/11/2016] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.
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Affiliation(s)
- Artem Babaian
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z1L3 Canada ; Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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25
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Niu ZS, Niu XJ, Wang WH. Genetic alterations in hepatocellular carcinoma: An update. World J Gastroenterol 2016; 22:9069-9095. [PMID: 27895396 PMCID: PMC5107590 DOI: 10.3748/wjg.v22.i41.9069] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/20/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Although recent advances in therapeutic approaches for treating HCC have improved the prognoses of patients with HCC, this cancer is still associated with a poor survival rate mainly due to late diagnosis. Therefore, a diagnosis must be made sufficiently early to perform curative and effective treatments. There is a need for a deeper understanding of the molecular mechanisms underlying the initiation and progression of HCC because these mechanisms are critical for making early diagnoses and developing novel therapeutic strategies. Over the past decade, much progress has been made in elucidating the molecular mechanisms underlying hepatocarcinogenesis. In particular, recent advances in next-generation sequencing technologies have revealed numerous genetic alterations, including recurrently mutated genes and dysregulated signaling pathways in HCC. A better understanding of the genetic alterations in HCC could contribute to identifying potential driver mutations and discovering novel therapeutic targets in the future. In this article, we summarize the current advances in research on the genetic alterations, including genomic instability, single-nucleotide polymorphisms, somatic mutations and deregulated signaling pathways, implicated in the initiation and progression of HCC. We also attempt to elucidate some of the genetic mechanisms that contribute to making early diagnoses of and developing molecularly targeted therapies for HCC.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Molecular Diagnostic Techniques
- Molecular Targeted Therapy
- Mutation
- Patient Selection
- Phenotype
- Polymorphism, Single Nucleotide
- Precision Medicine
- Predictive Value of Tests
- Signal Transduction
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26
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Segedi M, Anderson LN, Espin-Garcia O, Borgida A, Bianco T, Cheng D, Chen Z, Patel D, Brown MC, Xu W, Reisman D, Gallinger S, Cotterchio M, Hung R, Liu G, Cleary SP. BRM polymorphisms, pancreatic cancer risk and survival. Int J Cancer 2016; 139:2474-81. [PMID: 27487558 DOI: 10.1002/ijc.30369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/31/2016] [Accepted: 06/20/2016] [Indexed: 12/30/2022]
Abstract
Variant alleles of two promoter polymorphisms in the BRM gene (BRM-741, BRM-1321), create MEF2D transcription binding sites that lead to epigenetic silencing of BRM, the key catalytic component of the SWI/SNF chromatin remodeling complex. BRM suppression can be reversed pharmacologically.(1) Our group and others have reported associations with lung, head and neck, hepatocellular cancer risk,(1-3) and with lung and esophageal cancer prognosis (ASCO 2013; abstract 11057 & 4077). Herein, we assessed risk and survival associations with pancreatic cancer. A provincial population-based case-control study was conducted with 623 histologically confirmed pancreatic adenocarcinoma cases and 1,192 age/gender distribution-matched controls.(4) Survival of cases was obtained through the Ontario Cancer Registry. Logistic and Cox proportional hazard regression models were fitted, adjusting for relevant covariates. Median age was 65 y; 52% were male; Stage I (8%), II (55%), III (14%), IV (23%); 53% after curative resection, 79% after chemotherapy; and 83% had died. In the risk analysis, adjusted odds ratios (aOR) were 1.01 (95% CI: 0.1-2.0) and 0.96 (95% CI: 0.7-1.3) for the homozygotes of BRM-741 and BRM-1321, respectively; aOR of double-homozygotes was 1.11 (95% CI: 0.80-1.53), compared to the double-wildtype. For the survival analysis, adjusted hazard ratios (aHR) were 2.19 (95% CI: 1.9-2.5) for BRM-741 and 1.94 (95% CI: 1.7-2.2) for BRM-1321, per unit increase in variant alleles. Compared with the double-wildtype, aHR for carrying no, one, and two double-homozygotes were 2.14 (95% CI: 1.6-2.8), 4.17 (95% CI: 3.0-5.7), 8.03 (95% CI: 5.7-11.4), respectively. In conclusion, two functional promoter BRM polymorphisms were not associated with pancreatic adenocarcinoma risk, but are strongly associated with survival.
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Affiliation(s)
- Maja Segedi
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada.,Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Laura N Anderson
- Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Ayelet Borgida
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
| | - Teresa Bianco
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
| | - Dangxiao Cheng
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Zhuo Chen
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Devalben Patel
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - M Catherine Brown
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
| | - David Reisman
- Medical Oncology, University of Florida, Gainesville, FL
| | - Steven Gallinger
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
| | | | - Rayjean Hung
- Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada.
| | - Sean P Cleary
- Princess Margaret Cancer Centre-University Health Network-Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada.,Mount Sinai Hospital-Lunenfeld Research Institute, Toronto, ON, Canada
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27
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Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science 2016; 352:aad9780. [PMID: 27257261 DOI: 10.1126/science.aad9780] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression in metazoans is central for establishing cellular diversity, and its deregulation can result in pathological conditions. Although transcription factors are essential for implementing gene expression programs, they do not function in isolation and require the recruitment of various chromatin-modifying and -remodeling machineries. A classic example of developmental chromatin regulation is the balanced activities of the Polycomb group (PcG) proteins within the PRC1 and PRC2 complexes, and the Trithorax group (TrxG) proteins within the COMPASS family, which are highly mutated in a large number of human diseases. In this review, we will discuss the latest findings regarding the properties of the PcG and COMPASS families and the insight they provide into the epigenetic control of transcription under physiological and pathological settings.
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Affiliation(s)
- Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA.
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28
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Gurard-Levin ZA, Wilson LOW, Pancaldi V, Postel-Vinay S, Sousa FG, Reyes C, Marangoni E, Gentien D, Valencia A, Pommier Y, Cottu P, Almouzni G. Chromatin Regulators as a Guide for Cancer Treatment Choice. Mol Cancer Ther 2016; 15:1768-77. [PMID: 27196757 DOI: 10.1158/1535-7163.mct-15-1008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/26/2016] [Indexed: 12/22/2022]
Abstract
The limited capacity to predict a patient's response to distinct chemotherapeutic agents is a major hurdle in cancer management. The efficiency of a large fraction of current cancer therapeutics (radio- and chemotherapies) is influenced by chromatin structure. Reciprocally, alterations in chromatin organization may affect resistance mechanisms. Here, we explore how the misexpression of chromatin regulators-factors involved in the establishment and maintenance of functional chromatin domains-can inform about the extent of docetaxel response. We exploit Affymetrix and NanoString gene expression data for a set of chromatin regulators generated from breast cancer patient-derived xenograft models and patient samples treated with docetaxel. Random Forest classification reveals specific panels of chromatin regulators, including key components of the SWI/SNF chromatin remodeler, which readily distinguish docetaxel high-responders and poor-responders. Further exploration of SWI/SNF components in the comprehensive NCI-60 dataset reveals that the expression inversely correlates with docetaxel sensitivity. Finally, we show that loss of the SWI/SNF subunit BRG1 (SMARCA4) in a model cell line leads to enhanced docetaxel sensitivity. Altogether, our findings point toward chromatin regulators as biomarkers for drug response as well as therapeutic targets to sensitize patients toward docetaxel and combat drug resistance. Mol Cancer Ther; 15(7); 1768-77. ©2016 AACR.
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Affiliation(s)
- Zachary A Gurard-Levin
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France. Sorbonne Universités, UPMC Universite Paris 06, CNRS, UMR3664, Paris, France.
| | - Laurence O W Wilson
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France. Sorbonne Universités, UPMC Universite Paris 06, CNRS, UMR3664, Paris, France
| | - Vera Pancaldi
- Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez, Almagro, Madrid, Spain
| | - Sophie Postel-Vinay
- DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, France. Inserm Unit U981, Gustave Roussy, Villejuif, France. Université Paris Saclay, Université Paris-Sud, Faculté de Médicine, Le Kremlin Bicêtre, France
| | - Fabricio G Sousa
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Cecile Reyes
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Elisabetta Marangoni
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - David Gentien
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Alfonso Valencia
- Spanish National Cancer Research Centre (CNIO), c/Melchor Fernandez, Almagro, Madrid, Spain
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Paul Cottu
- Institut Curie, Medical Oncology, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France. Sorbonne Universités, UPMC Universite Paris 06, CNRS, UMR3664, Paris, France.
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29
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Anglesio MS, Bashashati A, Wang YK, Senz J, Ha G, Yang W, Aniba MR, Prentice LM, Farahani H, Li Chang H, Karnezis AN, Marra MA, Yong PJ, Hirst M, Gilks B, Shah SP, Huntsman DG. Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden. J Pathol 2015; 236:201-9. [PMID: 25692284 PMCID: PMC6680210 DOI: 10.1002/path.4516] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 12/21/2022]
Abstract
Endometriosis is a significant risk factor for clear cell and endometrioid ovarian cancers and is often found contiguous with these cancers. Using whole‐genome shotgun sequencing of seven clear cell ovarian carcinomas (CCC) and targeted sequencing in synchronous endometriosis, we have investigated how this carcinoma may evolve from endometriosis. In every case we observed multiple tumour‐associated somatic mutations in at least one concurrent endometriotic lesion. ARID1A and PIK3CA mutations appeared consistently in concurrent endometriosis when present in the primary CCC. In several cases, one or more endometriotic lesions carried the near‐complete complement of somatic mutations present in the index CCC tumour. Ancestral mutations were detected in both tumour‐adjacent and ‐distant endometriotic lesions, regardless of any cytological atypia. These findings provide objective evidence that multifocal benign endometriotic lesions are clonally related and that CCCs arising in these patients progress from endometriotic lesions that may already carry sufficient cancer‐associated mutations to be considered neoplasms themselves, albeit with low malignant potential. We speculate that genomically distinct classes of endometriosis exist and that ovarian endometriosis with high mutational burden represents one class at high risk for malignant transformation. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Michael S Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Yi Kan Wang
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Janine Senz
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Gavin Ha
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Winnie Yang
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Mohamed R Aniba
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Leah M Prentice
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Hossein Farahani
- Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Hector Li Chang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marco A Marra
- Michael Smith Genome Science Centre, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - Paul J Yong
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Martin Hirst
- Michael Smith Genome Science Centre, British Columbia Cancer Agency Research Center, Vancouver, Canada.,Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Anatomical Pathology, Vancouver General Hospital, Vancouver, Canada
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Molecular Oncology, British Columbia Cancer Agency Research Center, Vancouver, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
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