1
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Pang QY, Chiu YC, Huang RYJ. Regulating epithelial-mesenchymal plasticity from 3D genome organization. Commun Biol 2024; 7:750. [PMID: 38902393 PMCID: PMC11190238 DOI: 10.1038/s42003-024-06441-w] [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: 09/26/2022] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a dynamic process enabling polarized epithelial cells to acquire mesenchymal features implicated in development and carcinoma progression. As our understanding evolves, it is clear the reversible execution of EMT arises from complex epigenomic regulation involving histone modifications and 3-dimensional (3D) genome structural changes, leading to a cascade of transcriptional events. This review summarizes current knowledge on chromatin organization in EMT, with a focus on hierarchical structures of the 3D genome and chromatin accessibility changes.
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Affiliation(s)
- Qing You Pang
- Neuro-Oncology Research Laboratory, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ruby Yun-Ju Huang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
- Center for Advanced Computing and Imaging in Biomedicine, National Taiwan University, Taipei, 10051, Taiwan.
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore.
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2
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Wang D, Du G, Chen X, Wang J, Liu K, Zhao H, Cheng C, He Y, Jing N, Xu P, Bao W, Xi X, Zhang Y, Wang N, Liu Y, Sun Y, Zhang K, Zhang P, Gao WQ, Zhu HH. Zeb1-controlled metabolic plasticity enables remodeling of chromatin accessibility in the development of neuroendocrine prostate cancer. Cell Death Differ 2024; 31:779-791. [PMID: 38654072 PMCID: PMC11164927 DOI: 10.1038/s41418-024-01295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Cell plasticity has been found to play a critical role in tumor progression and therapy resistance. However, our understanding of the characteristics and markers of plastic cellular states during cancer cell lineage transition remains limited. In this study, multi-omics analyses show that prostate cancer cells undergo an intermediate state marked by Zeb1 expression with epithelial-mesenchymal transition (EMT), stemness, and neuroendocrine features during the development of neuroendocrine prostate cancer (NEPC). Organoid-formation assays and in vivo lineage tracing experiments demonstrate that Zeb1+ epithelioid cells are putative cells of origin for NEPC. Mechanistically, Zeb1 transcriptionally regulates the expression of several key glycolytic enzymes, thereby predisposing tumor cells to utilize glycolysis for energy metabolism. During this process, lactate accumulation-mediated histone lactylation enhances chromatin accessibility and cellular plasticity including induction of neuro-gene expression, which promotes NEPC development. Collectively, Zeb1-driven metabolic rewiring enables the epigenetic reprogramming of prostate cancer cells to license the adeno-to-neuroendocrine lineage transition.
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Affiliation(s)
- Deng Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Genyu Du
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Xinyu Chen
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Jinming Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Kaiyuan Liu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Huifang Zhao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Chaping Cheng
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Yuman He
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Na Jing
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Penghui Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wei Bao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Xialian Xi
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Yingchao Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Nan Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Yiyun Liu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Yujiao Sun
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Kai Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China
| | - Pengcheng Zhang
- School of Biomedical Engineering, Shanghai Tech University, Shanghai, 201210, China
| | - Wei-Qiang Gao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China.
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Helen He Zhu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center & Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine and School of Biomedical Engineering, Shanghai, 200127, China.
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3
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Acloque H, Yang J, Theveneau E. Epithelial-to-mesenchymal plasticity from development to disease: An introduction to the special issue. Genesis 2024; 62:e23581. [PMID: 38098257 PMCID: PMC11021161 DOI: 10.1002/dvg.23581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Epithelial-Mesenchymal Transition (EMT) refers to the ability of cells to switch between epithelial and mesenchymal states, playing critical roles in embryonic development, wound healing, fibrosis, and cancer metastasis. Here, we discuss some examples that challenge the use of specific markers to define EMT, noting that their expression may not always correspond to the expected epithelial or mesenchymal identity. In concordance with recent development in the field, we emphasize the importance of generalizing the use of the term Epithelial-Mesenchymal Plasticity (EMP), to better capture the diverse and context-dependent nature of the bidirectional journey that cells can undertake between the E and M phenotypes. We highlight the usefulness of studying a wide range of physiological EMT scenarios, stress the value of the dynamic of expression of EMP regulators and advocate, whenever possible, for more systematic functional assays to assess cellular states.
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Affiliation(s)
- Hervé Acloque
- INRAE, AgroParisTech, GABI, Université Paris Saclay, Jouy en Josas, France
| | - Jing Yang
- Department of Pharmacology and of Pediatrics, Moores Cancer Center, University of California San Diego, School of Medicine, La Jolla, California, USA
| | - Eric Theveneau
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
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4
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Advani R, Luzzi S, Scott E, Dalgliesh C, Weischenfeldt J, Munkley J, Elliott DJ. Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer. Oncogene 2023; 42:3161-3168. [PMID: 37752235 PMCID: PMC10589096 DOI: 10.1038/s41388-023-02838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Prostate cancer progression is connected to the activity of conventional oncogenes and tumour suppressors and driven by circulating steroid hormones. A key issue has been how to identify and care for aggressively developing prostate tumours. Here we discuss how expression of the splicing regulators ESRP1 and ESRP2, and how their role as "masterminds" of epithelial splicing patterns, have been identified as markers of aggressively proliferating prostate primary tumours. We suggest that the origin of prostate cancer within epithelial cells, and the subsequent association of ESRP1 and ESRP2 expression with more aggressive disease progression, identify ESRP1 and ESRP2 as lineage survival oncogenes. To move this field on in the future it will be important to identify the gene expression targets controlled by ESRP1/2 that regulate prostate cancer proliferation. Potential future therapies could be designed to target ESRP1 and ESRP2 protein activity or their regulated splice isoforms in aggressive prostate tumours. Design of these therapies is potentially complicated by the risk of producing a more mesenchymal splicing environment that might promote tumour metastasis.
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Affiliation(s)
- Rahul Advani
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Sara Luzzi
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Emma Scott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Caroline Dalgliesh
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jennifer Munkley
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - David J Elliott
- Newcastle University Biosciences Institute (NUBI) and Newcastle University Cancer Centre, Newcastle University, Newcastle Upon Tyne, NE1 3BZ, United Kingdom.
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5
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Toriumi K, Onodera Y, Takehara T, Mori T, Hasei J, Shigi K, Iwawaki N, Ozaki T, Akagi M, Nakanishi M, Teramura T. LRRC15 expression indicates high level of stemness regulated by TWIST1 in mesenchymal stem cells. iScience 2023; 26:106946. [PMID: 37534184 PMCID: PMC10391581 DOI: 10.1016/j.isci.2023.106946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 04/09/2023] [Accepted: 05/19/2023] [Indexed: 08/04/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are used as a major source for cell therapy, and its application is expanding in various diseases. On the other hand, reliable method to evaluate quality and therapeutic properties of MSC is limited. In this study, we focused on TWIST1 that is a transcription factor regulating stemness of MSCs and found that the transmembrane protein LRRC15 tightly correlated with the expression of TWIST1 and useful to expect TWIST1-regulated stemness of MSCs. The LRRC15-positive MSC populations in human and mouse bone marrow tissues highly expressed stemness-associated transcription factors and therapeutic cytokines, and showed better therapeutic effect in bleomycin-induced pulmonary fibrosis model mice. This study provides evidence for the important role of TWIST1 in the MSC stemness, and for the utility of the LRRC15 protein as a marker to estimate stem cell quality in MSCs before cell transplantation.
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Affiliation(s)
- Kensuke Toriumi
- Department of Orthopedic Surgery, Kindai University Faculty of Medicine, Osaka-sayama, Osaka, Japan
| | - Yuta Onodera
- Institute of Advanced Clinical Medicine, Kindai University Hospital, Osaka-sayama, Osaka, Japan
| | - Toshiyuki Takehara
- Institute of Advanced Clinical Medicine, Kindai University Hospital, Osaka-sayama, Osaka, Japan
| | - Tatsufumi Mori
- Life Science Institute, Kindai University, Osaka-sayama, Osaka, Japan
| | - Joe Hasei
- Department of Orthopedic Surgery, Okayama University Faculty of Medicine, Okayama, Okayama, Japan
| | - Kanae Shigi
- Institute of Advanced Clinical Medicine, Kindai University Hospital, Osaka-sayama, Osaka, Japan
| | - Natsumi Iwawaki
- Institute of Advanced Clinical Medicine, Kindai University Hospital, Osaka-sayama, Osaka, Japan
| | - Toshifumi Ozaki
- Department of Orthopedic Surgery, Okayama University Faculty of Medicine, Okayama, Okayama, Japan
| | - Masao Akagi
- Department of Orthopedic Surgery, Kindai University Faculty of Medicine, Osaka-sayama, Osaka, Japan
| | | | - Takeshi Teramura
- Institute of Advanced Clinical Medicine, Kindai University Hospital, Osaka-sayama, Osaka, Japan
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6
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Akhmetkaliyev A, Alibrahim N, Shafiee D, Tulchinsky E. EMT/MET plasticity in cancer and Go-or-Grow decisions in quiescence: the two sides of the same coin? Mol Cancer 2023; 22:90. [PMID: 37259089 DOI: 10.1186/s12943-023-01793-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/20/2023] [Indexed: 06/02/2023] Open
Abstract
Epithelial mesenchymal transition (EMT) and mesenchymal epithelial transition (MET) are genetic determinants of cellular plasticity. These programs operate in physiological (embryonic development, wound healing) and pathological (organ fibrosis, cancer) conditions. In cancer, EMT and MET interfere with various signalling pathways at different levels. This results in gross alterations in the gene expression programs, which affect most, if not all hallmarks of cancer, such as response to proliferative and death-inducing signals, tumorigenicity, and cell stemness. EMT in cancer cells involves large scale reorganisation of the cytoskeleton, loss of epithelial integrity, and gain of mesenchymal traits, such as mesenchymal type of cell migration. In this regard, EMT/MET plasticity is highly relevant to the Go-or-Grow concept, which postulates the dichotomous relationship between cell motility and proliferation. The Go-or-Grow decisions are critically important in the processes in which EMT/MET plasticity takes the central stage, mobilisation of stem cells during wound healing, cancer relapse, and metastasis. Here we outline the maintenance of quiescence in stem cell and metastatic niches, focusing on the implication of EMT/MET regulatory networks in Go-or-Grow switches. In particular, we discuss the analogy between cells residing in hybrid quasi-mesenchymal states and GAlert, an intermediate phase allowing quiescent stem cells to enter the cell cycle rapidly.
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Affiliation(s)
- Azamat Akhmetkaliyev
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan
| | | | - Darya Shafiee
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan
| | - Eugene Tulchinsky
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, 020000, Kazakhstan.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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7
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Castro-Muñoz LJ, Vázquez Ulloa E, Sahlgren C, Lizano M, De La Cruz-Hernández E, Contreras-Paredes A. Modulating epigenetic modifications for cancer therapy (Review). Oncol Rep 2023; 49:59. [PMID: 36799181 PMCID: PMC9942256 DOI: 10.3892/or.2023.8496] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/08/2022] [Indexed: 02/12/2023] Open
Abstract
Cancer is a global public health concern. Alterations in epigenetic processes are among the earliest genomic aberrations occurring during cancer development and are closely related to progression. Unlike genetic mutations, aberrations in epigenetic processes are reversible, which opens the possibility for novel pharmacological treatments. Non‑coding RNAs (ncRNAs) represent an essential epigenetic mechanism, and emerging evidence links ncRNAs to carcinogenesis. Epigenetic drugs (epidrugs) are a group of promising target therapies for cancer treatment acting as coadjuvants to reverse drug resistance in cancer. The present review describes central epigenetic aberrations during malignant transformation and explains how epidrugs target DNA methylation, histone modifications and ncRNAs. Furthermore, clinical trials focused on evaluating the effect of these epidrugs alone or in combination with other anticancer therapies and other ncRNA‑based therapies are discussed. The use of epidrugs promises to be an effective tool for reversing drug resistance in some patients with cancer.
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Affiliation(s)
| | - Elenaé Vázquez Ulloa
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Marcela Lizano
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico 04510, Mexico
| | - Erick De La Cruz-Hernández
- Laboratory of Research in Metabolic and Infectious Diseases, Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Tabasco 86650, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Correspondence to: Professor Adriana Contreras-Paredes, Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Avenue San Fernando, Col. Sección XVI, Tlalpan, Ciudad de Mexico 14080, Mexico, E-mail:
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8
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Saha S, Pradhan N, B N, Mahadevappa R, Minocha S, Kumar S. Cancer plasticity: Investigating the causes for this agility. Semin Cancer Biol 2023; 88:138-156. [PMID: 36584960 DOI: 10.1016/j.semcancer.2022.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Cancer is not a hard-wired phenomenon but an evolutionary disease. From the onset of carcinogenesis, cancer cells continuously adapt and evolve to satiate their ever-growing proliferation demands. This results in the formation of multiple subtypes of cancer cells with different phenotypes, cellular compositions, and consequently displaying varying degrees of tumorigenic identity and function. This phenomenon is referred to as cancer plasticity, during which the cancer cells exist in a plethora of cellular states having distinct phenotypes. With the advent of modern technologies equipped with enhanced resolution and depth, for example, single-cell RNA-sequencing and advanced computational tools, unbiased cancer profiling at a single-cell resolution are leading the way in understanding cancer cell rewiring both spatially and temporally. In this review, the processes and mechanisms that give rise to cancer plasticity include both intrinsic genetic factors such as epigenetic changes, differential expression due to changes in DNA, RNA, or protein content within the cancer cell, as well as extrinsic environmental factors such as tissue perfusion, extracellular milieu are detailed and their influence on key cancer plasticity hallmarks such as epithelial-mesenchymal transition (EMT) and cancer cell stemness (CSCs) are discussed. Due to therapy evasion and drug resistance, tumor heterogeneity caused by cancer plasticity has major therapeutic ramifications. Hence, it is crucial to comprehend all the cellular and molecular mechanisms that control cellular plasticity. How this process evades therapy, and the therapeutic avenue of targeting cancer plasticity must be diligently investigated.
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Affiliation(s)
- Shubhraneel Saha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Nikita Pradhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Neha B
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ravikiran Mahadevappa
- Department of Biotechnology, School of Science, Gandhi Institute of Technology and Management, Deemed to be University, Bengaluru, Karnataka 562163, India
| | - Shilpi Minocha
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Saran Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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9
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Sukocheva OA, Lukina E, Friedemann M, Menschikowski M, Hagelgans A, Aliev G. The crucial role of epigenetic regulation in breast cancer anti-estrogen resistance: Current findings and future perspectives. Semin Cancer Biol 2022; 82:35-59. [PMID: 33301860 DOI: 10.1016/j.semcancer.2020.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/22/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) cell de-sensitization to Tamoxifen (TAM) or other selective estrogen receptor (ER) modulators (SERM) is a complex process associated with BC heterogeneity and the transformation of ER signalling. The most influential resistance-related mechanisms include modifications in ER expression and gene regulation patterns. During TAM/SERM treatment, epigenetic mechanisms can effectively silence ER expression and facilitate the development of endocrine resistance. ER status is efficiently regulated by specific epigenetic tools including hypermethylation of CpG islands within ER promoters, increased histone deacetylase activity in the ER promoter, and/or translational repression by miRNAs. Over-methylation of the ER α gene (ESR1) promoter by DNA methyltransferases was associated with poor prognosis and indicated the development of resistance. Moreover, BC progression and spreading were marked by transformed chromatin remodelling, post-translational histone modifications, and expression of specific miRNAs and/or long non-coding RNAs. Therefore, targeted inhibition of histone acetyltransferases (e.g. MYST3), deacetylases (e.g. HDAC1), and/or demethylases (e.g. lysine-specific demethylase LSD1) was shown to recover and increase BC sensitivity to anti-estrogens. Indicated as a powerful molecular instrument, the administration of epigenetic drugs can regain ER expression along with the activation of tumour suppressor genes, which can in turn prevent selection of resistant cells and cancer stem cell survival. This review examines recent advances in the epigenetic regulation of endocrine drug resistance and evaluates novel anti-resistance strategies. Underlying molecular mechanisms of epigenetic regulation will be discussed, emphasising the utilization of epigenetic enzymes and their inhibitors to re-program irresponsive BCs.
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Affiliation(s)
- Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia.
| | - Elena Lukina
- Discipline of Biology, College of Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Albert Hagelgans
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital `Carl Gustav Carus`, Technical University of Dresden, Dresden 01307, Germany
| | - Gjumrakch Aliev
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119991, Russia; Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, 142432, Russia; Federal State Budgetary Institution «Research Institute of Human Morphology», 3, Tsyurupy Str., Moscow, 117418, Russian Federation; GALLY International Research Institute, San Antonio, TX, 78229, USA.
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10
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Cook DP, Wrana JL. A specialist-generalist framework for epithelial-mesenchymal plasticity in cancer. Trends Cancer 2022; 8:358-368. [DOI: 10.1016/j.trecan.2022.01.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
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11
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Milton AV, Konrad DB. Epithelial-mesenchymal transition and H 2O 2 signaling - a driver of disease progression and a vulnerability in cancers. Biol Chem 2022; 403:377-390. [PMID: 35032422 DOI: 10.1515/hsz-2021-0341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/18/2021] [Indexed: 12/20/2022]
Abstract
Mutation-selective drugs constitute a great advancement in personalized anticancer treatment with increased quality of life and overall survival in cancers. However, the high adaptability and evasiveness of cancers can lead to disease progression and the development of drug resistance, which cause recurrence and metastasis. A common characteristic in advanced neoplastic cancers is the epithelial-mesenchymal transition (EMT) which is strongly interconnected with H2O2 signaling, increased motility and invasiveness. H2O2 relays its signal through the installation of oxidative posttranslational modifications on cysteines. The increased H2O2 levels that are associated with an EMT confer a heightened sensitivity towards the induction of ferroptosis as a recently discovered vulnerability.
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Affiliation(s)
- Anna V Milton
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstr. 5-13, Haus C, D-81377 Munich, Germany
| | - David B Konrad
- Department of Pharmacy, Ludwig Maximilian University of Munich, Butenandtstr. 5-13, Haus C, D-81377 Munich, Germany
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12
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Johnson KS, Hussein S, Chakraborty P, Muruganantham A, Mikhail S, Gonzalez G, Song S, Jolly MK, Toneff MJ, Benton ML, Lin YC, Taube JH. CTCF Expression and Dynamic Motif Accessibility Modulates Epithelial-Mesenchymal Gene Expression. Cancers (Basel) 2022; 14:cancers14010209. [PMID: 35008373 PMCID: PMC8750563 DOI: 10.3390/cancers14010209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/14/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reversal, mesenchymal-epithelial transition (MET) drive tissue reorganization critical for early development. In carcinomas, processing through EMT, MET, or partial states promotes migration, invasion, dormancy, and metastatic colonization. As a reversible process, EMT is inherently regulated at epigenetic and epigenomic levels. To understand the epigenomic nature of reversible EMT and its partial states, we characterized chromatin accessibility dynamics, transcriptomic output, protein expression, and cellular phenotypes during stepwise reversible EMT. We find that the chromatin insulating protein machinery, including CTCF, is suppressed and re-expressed, coincident with broad alterations in chromatin accessibility, during EMT/MET, and is lower in triple-negative breast cancer cell lines with EMT features. Through an analysis of chromatin accessibility using ATAC-seq, we identify that early phases of EMT are characterized by enrichment for AP-1 family member binding motifs, but also by a diminished enrichment for CTCF binding motifs. Through a loss-of-function analysis, we demonstrate that the suppression of CTCF alters cellular plasticity, strengthening the epithelial phenotype via the upregulation of epithelial markers E-cadherin/CDH1 and downregulation of N-cadherin/CDH2. Conversely, the upregulation of CTCF leads to the upregulation of EMT gene expression and an increase in mesenchymal traits. These findings are indicative of a role of CTCF in regulating epithelial-mesenchymal plasticity and gene expression.
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Affiliation(s)
- Kelsey S. Johnson
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shaimaa Hussein
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | - Arvind Muruganantham
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Sheridan Mikhail
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Giovanny Gonzalez
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Shuxuan Song
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (P.C.); (M.K.J.)
| | | | | | - Yin C. Lin
- Baylor Institute for Immunology Research, Baylor Scott & White, Dallas, TX 75246, USA; (S.H.); (Y.C.L.)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA; (K.S.J.); (A.M.); (S.M.); (G.G.); (S.S.)
- Dan L. Duncan Cancer Center, Houston, TX 76706, USA
- Correspondence:
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13
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Wang G, Han JJ. Connections between metabolism and epigenetic modifications in cancer. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:199-221. [PMID: 37724300 PMCID: PMC10388788 DOI: 10.1515/mr-2021-0015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/19/2021] [Indexed: 09/20/2023]
Abstract
How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
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Affiliation(s)
- Guangchao Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jingdong J. Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
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14
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Ramirez Moreno M, Stempor PA, Bulgakova NA. Interactions and Feedbacks in E-Cadherin Transcriptional Regulation. Front Cell Dev Biol 2021; 9:701175. [PMID: 34262912 PMCID: PMC8273600 DOI: 10.3389/fcell.2021.701175] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/04/2021] [Indexed: 01/07/2023] Open
Abstract
Epithelial tissues rely on the adhesion between participating cells to retain their integrity. The transmembrane protein E-cadherin is the major protein that mediates homophilic adhesion between neighbouring cells and is, therefore, one of the critical components for epithelial integrity. E-cadherin downregulation has been described extensively as a prerequisite for epithelial-to-mesenchymal transition and is a hallmark in many types of cancer. Due to this clinical importance, research has been mostly focused on understanding the mechanisms leading to transcriptional repression of this adhesion molecule. However, in recent years it has become apparent that re-expression of E-cadherin is a major step in the progression of many cancers during metastasis. Here, we review the currently known molecular mechanisms of E-cadherin transcriptional activation and inhibition and highlight complex interactions between individual mechanisms. We then propose an additional mechanism, whereby the competition between adhesion complexes and heterochromatin protein-1 for binding to STAT92E fine-tunes the levels of E-cadherin expression in Drosophila but also regulates other genes promoting epithelial robustness. We base our hypothesis on both existing literature and our experimental evidence and suggest that such feedback between the cell surface and the nucleus presents a powerful paradigm for epithelial resilience.
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Affiliation(s)
- Miguel Ramirez Moreno
- Department of Biomedical Science and Bateson Centre, The University of Sheffield, Sheffield, England
| | | | - Natalia A Bulgakova
- Department of Biomedical Science and Bateson Centre, The University of Sheffield, Sheffield, England
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15
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Endothelin-1 enhances the regenerative capability of human bone marrow-derived mesenchymal stem cells in a sciatic nerve injury mouse model. Biomaterials 2021; 275:120980. [PMID: 34198163 DOI: 10.1016/j.biomaterials.2021.120980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/31/2021] [Accepted: 06/17/2021] [Indexed: 12/22/2022]
Abstract
We expanded the application of endothelin-1 (EDN1) by treating human mesenchymal stem cell (hMSC) organotypic spinal cord slice cultures with EDN1. EDN1-treated hMSCs significantly enhanced neuronal outgrowth. The underlying mechanism of this effect was evaluated via whole-genome methylation. EDN1 increased whole-genome demethylation and euchromatin. To observe demethylation downstream of EDN1, deaminases and glycosylases were screened, and APOBEC1 was found to cause global demethylation and OCT4 gene activation. The sequence of methyl-CpG-binding domain showed similar patterns between EDN1- and APOBEC1-induced demethylation. SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily A member 4 (SMARC A4) and SMARC subfamily D, member 2 (SMARC D2) were screened via methyl-CpG-binding domain sequencing as a modulator in response to EDN1. Chromatin immunoprecipitation of the H3K9me3, H3K27me3, and H3K4me4 binding sequences on the APOBEC1 promoter was analyzed following treatment with or without siSMARC A4 or siSMARC D2. The results suggested that SMARC A4 and SMARC D2 induced a transition from H3K9me3 to H3K4me3 in the APOBEC1 promoter region following EDN1 treatment. Correlations between EDN1 pathways and therapeutic efficacy in hBM-MSCs were determined in a sciatic nerve injury mouse model. Thus, EDN1 may be a useful novel-concept bioactive peptide and biomaterial component for improving hMSC regenerative capability.
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16
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Reisenauer KN, Tao Y, Das P, Song S, Svatek H, Patel SD, Mikhail S, Ingros A, Sheesley P, Masi M, Boari A, Evidente A, Kornienko A, Romo D, Taube J. Epithelial-mesenchymal transition sensitizes breast cancer cells to cell death via the fungus-derived sesterterpenoid ophiobolin A. Sci Rep 2021; 11:10652. [PMID: 34017048 PMCID: PMC8137940 DOI: 10.1038/s41598-021-89923-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/21/2021] [Indexed: 12/30/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) imparts properties of cancer stem-like cells, including resistance to frequently used chemotherapies, necessitating the identification of molecules that induce cell death specifically in stem-like cells with EMT properties. Herein, we demonstrate that breast cancer cells enriched for EMT features are more sensitive to cytotoxicity induced by ophiobolin A (OpA), a sesterterpenoid natural product. Using a model of experimentally induced EMT in human mammary epithelial (HMLE) cells, we show that EMT is both necessary and sufficient for OpA sensitivity. Moreover prolonged, sub-cytotoxic exposure to OpA is sufficient to suppress EMT-imparted CSC features including sphere formation and resistance to doxorubicin. In vivo growth of CSC-rich mammary cell tumors, is suppressed by OpA treatment. These data identify a driver of EMT-driven cytotoxicity with significant potential for use either in combination with standard chemotherapy or for tumors enriched for EMT features.
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Affiliation(s)
| | - Yongfeng Tao
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Provas Das
- Department of Biology, Baylor University, Waco, TX, USA
| | - Shuxuan Song
- Department of Biology, Baylor University, Waco, TX, USA
| | | | | | | | - Alec Ingros
- Department of Biology, Baylor University, Waco, TX, USA
| | | | - Marco Masi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Naples, Italy
| | - Angela Boari
- Institute of Sciences and Food Production, CNR, Bari, Italy
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte Sant'Angelo, Naples, Italy
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Daniel Romo
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Joseph Taube
- Department of Biology, Baylor University, Waco, TX, USA.
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17
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Harn HIC, Wang SP, Lai YC, Van Handel B, Liang YC, Tsai S, Schiessl IM, Sarkar A, Xi H, Hughes M, Kaemmer S, Tang MJ, Peti-Peterdi J, Pyle AD, Woolley TE, Evseenko D, Jiang TX, Chuong CM. Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration of laboratory and spiny mice. Nat Commun 2021; 12:2595. [PMID: 33972536 PMCID: PMC8110808 DOI: 10.1038/s41467-021-22822-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
Tissue regeneration is a process that recapitulates and restores organ structure and function. Although previous studies have demonstrated wound-induced hair neogenesis (WIHN) in laboratory mice (Mus), the regeneration is limited to the center of the wound unlike those observed in African spiny (Acomys) mice. Tissue mechanics have been implicated as an integral part of tissue morphogenesis. Here, we use the WIHN model to investigate the mechanical and molecular responses of laboratory and African spiny mice, and report these models demonstrate opposing trends in spatiotemporal morphogenetic field formation with association to wound stiffness landscapes. Transcriptome analysis and K14-Cre-Twist1 transgenic mice show the Twist1 pathway acts as a mediator for both epidermal-dermal interactions and a competence factor for periodic patterning, differing from those used in development. We propose a Turing model based on tissue stiffness that supports a two-scale tissue mechanics process: (1) establishing a morphogenetic field within the wound bed (mm scale) and (2) symmetry breaking of the epidermis and forming periodically arranged hair primordia within the morphogenetic field (μm scale). Thus, we delineate distinct chemo-mechanical events in building a Turing morphogenesis-competent field during WIHN of laboratory and African spiny mice and identify its evo-devo advantages with perspectives for regenerative medicine.
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Affiliation(s)
- Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- International Research Center of Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Pei Wang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- International Research Center of Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
| | - Yung-Chih Lai
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Ben Van Handel
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Stephanie Tsai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
- School of Dentistry, National Taiwan University, Taipei, Taiwan
| | - Ina Maria Schiessl
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Arijita Sarkar
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Haibin Xi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Hughes
- International Research Center of Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
| | - Stefan Kaemmer
- Park Systems Inc., 3040 Olcott Street, Santa Clara, CA, 95054, USA
| | - Ming-Jer Tang
- International Research Center of Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan, Taiwan
- Department of Physiology, Medical College, National Cheng Kung University, Tainan, Taiwan
| | - Janos Peti-Peterdi
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - April D Pyle
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Thomas E Woolley
- Cardiff School of Mathematics, Cardiff University, Senghennydd Road, Cardiff, UK
| | - Denis Evseenko
- Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Research and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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18
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Polycomb-group proteins in the initiation and progression of cancer. J Genet Genomics 2021; 48:433-443. [PMID: 34266781 DOI: 10.1016/j.jgg.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/23/2021] [Accepted: 03/28/2021] [Indexed: 12/13/2022]
Abstract
The Polycomb group (PcG) proteins are a family of chromatin regulators and critical for the maintenance of cellular identity. The PcG machinery can be categorized into at least three multi-protein complexes, namely Polycomb Repressive Complex 1 (PRC1), PRC2, and Polycomb Repressive DeUBiquitinase (PR-DUB). Their deregulation has been associated with human cancer initiation and progression. Here we review the updated understanding for PcG proteins in transcription regulation and DNA damage repair and highlight increasing links to the hallmarks in cancer. Accordingly, we discuss some of the recent advances in drug development or strategies against cancers caused by the gain or loss of PcG functions.
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19
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A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2. Cancers (Basel) 2021; 13:cancers13071609. [PMID: 33807227 PMCID: PMC8037024 DOI: 10.3390/cancers13071609] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Epithelial-mesenchymal transition (EMT) is a key process in cancer progression through which cells weaken their cell-cell adhesion and gain mobility and invasive traits. Besides chemical signaling, recent studies have established the connection of EMT to mechanical microenvironment, such as the stiffness of extracellular matrix (ECM). LOXL2 is representative of a family of enzymes that promotes fiber cross-linking in ECM. With increased cross-linking comes increased stiffness, which induces EMT that can, in turn, elevate LOXL2 levels. As such, a positive feedback loop among EMT, LOXL2, and ECM stiffness can be formed. We built a mathematical model on a core biochemical reaction network featuring this feedback loop, and showed how strongly it drives EMT. We also illustrated mechanistically how cross-linking connects with stiffness, using a mechanical model of collagen (a major component of ECM). Using this theoretical framework, we demonstrated the heterogeneity of LOXL2/stiffness and its implications on migrating cancer cells that could seed metastasis, the growth of secondary malignant tumors. This framework can inspire experimental studies of more fine-grained mechanotransduction and biomechanical heterogeneity in cancers. Abstract The epithelial-mesenchymal transition (EMT) plays a critical role in cancer progression, being responsible in many cases for the onset of the metastatic cascade and being integral in the ability of cells to resist drug treatment. Most studies of EMT focus on its induction via chemical signals such as TGF-β or Notch ligands, but it has become increasingly clear that biomechanical features of the microenvironment such as extracellular matrix (ECM) stiffness can be equally important. Here, we introduce a coupled feedback loop connecting stiffness to the EMT transcription factor ZEB1, which acts via increasing the secretion of LOXL2 that leads to increased cross-linking of collagen fibers in the ECM. This increased cross-linking can effectively increase ECM stiffness and increase ZEB1 levels, thus setting a positive feedback loop between ZEB1 and ECM stiffness. To investigate the impact of this non-cell-autonomous effect, we introduce a computational approach capable of connecting LOXL2 concentration to increased stiffness and thereby to higher ZEB1 levels. Our results indicate that this positive feedback loop, once activated, can effectively lock the cells in a mesenchymal state. The spatial-temporal heterogeneity of the LOXL2 concentration and thus the mechanical stiffness also has direct implications for migrating cells that attempt to escape the primary tumor.
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20
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Prominent Role of Histone Modifications in the Regulation of Tumor Metastasis. Int J Mol Sci 2021; 22:ijms22052778. [PMID: 33803458 PMCID: PMC7967218 DOI: 10.3390/ijms22052778] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor aggressiveness and progression is highly dependent on the process of metastasis, regulated by the coordinated interplay of genetic and epigenetic mechanisms. Metastasis involves several steps of epithelial to mesenchymal transition (EMT), anoikis resistance, intra- and extravasation, and new tissue colonization. EMT is considered as the most critical process allowing cancer cells to switch their epithelial characteristics and acquire mesenchymal properties. Emerging evidence demonstrates that epigenetics mechanisms, DNA methylation, histone modifications, and non-coding RNAs participate in the widespread changes of gene expression that characterize the metastatic phenotype. At the chromatin level, active and repressive histone post-translational modifications (PTM) in association with pleiotropic transcription factors regulate pivotal genes involved in the initiation of the EMT process as well as in intravasation and anoikis resistance, playing a central role in the progression of tumors. Herein, we discuss the main epigenetic mechanisms associated with the different steps of metastatic process, focusing in particular on the prominent role of histone modifications and the modifying enzymes that mediate transcriptional regulation of genes associated with tumor progression. We further discuss the development of novel treatment strategies targeting the reversibility of histone modifications and highlight their importance in the future of cancer therapy.
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21
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Das P, Taube JH. Regulating Methylation at H3K27: A Trick or Treat for Cancer Cell Plasticity. Cancers (Basel) 2020; 12:E2792. [PMID: 33003334 PMCID: PMC7600873 DOI: 10.3390/cancers12102792] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Properly timed addition and removal of histone 3 lysine 27 tri-methylation (H3K27me3) is critical for enabling proper differentiation throughout all stages of development and, likewise, can guide carcinoma cells into altered differentiation states which correspond to poor prognoses and treatment evasion. In early embryonic stages, H3K27me3 is invoked to silence genes and restrict cell fate. Not surprisingly, mutation or altered functionality in the enzymes that regulate this pathway results in aberrant methylation or demethylation that can lead to malignancy. Likewise, changes in expression or activity of these enzymes impact cellular plasticity, metastasis, and treatment evasion. This review focuses on current knowledge regarding methylation and de-methylation of H3K27 in cancer initiation and cancer cell plasticity.
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Affiliation(s)
| | - Joseph H. Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA;
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22
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Khot M, Sreekumar D, Jahagirdar S, Kulkarni A, Hari K, Faseela EE, Sabarinathan R, Jolly MK, Sengupta K. Twist1 induces chromosomal instability (CIN) in colorectal cancer cells. Hum Mol Genet 2020; 29:1673-1688. [PMID: 32337580 PMCID: PMC7322571 DOI: 10.1093/hmg/ddaa076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Twist1 is a basic helix-loop-helix transcription factor, essential during early development in mammals. While Twist1 induces epithelial-to-mesenchymal transition (EMT), here we show that Twist1 overexpression enhances nuclear and mitotic aberrations. This is accompanied by an increase in whole chromosomal copy number gains and losses, underscoring the role of Twist1 in inducing chromosomal instability (CIN) in colorectal cancer cells. Array comparative genomic hybridization (array CGH) analysis further shows sub-chromosomal deletions, consistent with an increased frequency of DNA double strand breaks (DSBs). Remarkably, Twist1 overexpression downmodulates key cell cycle checkpoint factors-Bub1, BubR1, Mad1 and Mad2-that regulate CIN. Mathematical simulations using the RACIPE tool show a negative correlation of Twist1 with E-cadherin and BubR1. Data analyses of gene expression profiles of patient samples from The Cancer Genome Atlas (TCGA) reveal a positive correlation between Twist1 and mesenchymal genes across cancers, whereas the correlation of TWIST1 with CIN and DSB genes is cancer subtype-specific. Taken together, these studies highlight the mechanistic involvement of Twist1 in the deregulation of factors that maintain genome stability during EMT in colorectal cancer cells. Twist1 overexpression enhances genome instability in the context of EMT that further contributes to cellular heterogeneity. In addition, these studies imply that Twist1 downmodulates nuclear lamins that further alter spatiotemporal organization of the cancer genome and epigenome. Notwithstanding their genetic background, colorectal cancer cells nevertheless maintain their overall ploidy, while the downstream effects of Twist1 enhance CIN and DNA damage enriching for sub-populations of aggressive cancer cells.
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Affiliation(s)
- Maithilee Khot
- B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Dyuthi Sreekumar
- B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanika Jahagirdar
- B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Apoorva Kulkarni
- B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Kishore Hari
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | | | - Radhakrishnan Sabarinathan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Kundan Sengupta
- B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India
- To whom correspondence should be addressed at: B-216, Chromosome Biology Lab (CBL), Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pashan, Pune 411008, India. Tel: +91 20 25908071; Fax: +91-20-20251566;
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23
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Nguyen TM, Alchalabi S, Oluwatoyosi A, Ropri AS, Herschkowitz JI, Rosen JM. New twists on long noncoding RNAs: from mobile elements to motile cancer cells. RNA Biol 2020; 17:1535-1549. [PMID: 32522127 DOI: 10.1080/15476286.2020.1760535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The purpose of this review is to highlight several areas of lncRNA biology and cancer that we hope will provide some new insights for future research. These include the relationship of lncRNAs and the epithelial to mesenchymal transition (EMT) with a focus on transcriptional and alternative splicing mechanisms and mRNA stability through miRNAs. In addition, we highlight the potential role of enhancer e-lncRNAs, the importance of transposable elements in lncRNA biology, and finally the emerging area of using antisense oligonucleotides (ASOs) and small molecules to target lncRNAs and their therapeutic implications.
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Affiliation(s)
- Tuan M Nguyen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School , Boston, MA, USA.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School , Boston, MA, USA
| | - Sumayya Alchalabi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Adewunmi Oluwatoyosi
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
| | - Ali S Ropri
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jason I Herschkowitz
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, SUNY , Rensselaer, NY, USA
| | - Jeffrey M Rosen
- Department of Molecular & Cellular Biology, Baylor College of Medicine , Houston, TX, USA
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24
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Lu Y, Chan YT, Tan HY, Li S, Wang N, Feng Y. Epigenetic regulation in human cancer: the potential role of epi-drug in cancer therapy. Mol Cancer 2020; 19:79. [PMID: 32340605 PMCID: PMC7184703 DOI: 10.1186/s12943-020-01197-3] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is dynamic and heritable modifications to the genome that occur independently of DNA sequence. It requires interactions cohesively with various enzymes and other molecular components. Aberrant epigenetic alterations can lead to inappropriate onset of genetic expressions and promote tumorigenesis. As the epigenetic modifiers are susceptible to extrinsic factors and reversible, they are becoming promising targets in multiple cancer therapies. Recently, various epi-drugs have been developed and implicated in clinical use. The use of epi-drugs alone, or in combination with chemotherapy or immunotherapy, has shown compelling outcomes, including augmentation of anti-tumoral effects, overcoming drug resistance, and activation of host immune response.
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Affiliation(s)
- Yuanjun Lu
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Hor-Yue Tan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Sha Li
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
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25
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Wang Q, Jiang S, Liu J, Ma G, Zheng J, Zhang Y. DEP Domain Containing 1 Promotes Proliferation, Invasion, and Epithelial-Mesenchymal Transition in Colorectal Cancer by Enhancing Expression of Suppressor of Zest 12. Cancer Biother Radiopharm 2020; 36:36-44. [PMID: 32343606 DOI: 10.1089/cbr.2019.3460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Objective: DEP domain containing 1 (DEPDC1), aberrantly upregulated in various tumors, has been shown to be involved in the occurrence and development of tumors. This study aims to investigate pathophysiological roles of DEPDC1 in colorectal cancer (CRC). Materials and Methods: Expression level of DEPDC1 and suppressor of zest 12 (SUZ12) in CRC tissues and cell lines were analyzed by quantitative real-time polymerase chain reaction and immunohistochemistry. Staining with 5-bromo-2-deoxyuridine staining and colony formation assays were conducted to evaluate cell proliferation. Transwell or wound healing assay to evaluate invasion or migration, respectively. The effect on epithelial-mesenchymal transition (EMT) of CRC was determined by Western blot. Results: DEPDC1 and SUZ12 were increased in CRC tissues and cell lines. Silence of DEPDC1 suppressed cell proliferation, migration, and invasion of CRC. Moreover, DEPDC1 knockdown suppressed EMT of CRC. Mechanistically, the authors demonstrated silencing DEPDC1 decreased protein expression of SUZ12 and led to a remarkable reduction of trimethylation on the lysine 27 residue of histone H3 (H3K27Me3). Inhibitory ability of DEPDC1 knockdown on CRC progression was reversed by overexpression of SUZ12. Conclusions: DEPDC1 promoted CRC progression through regulation of SUZ12-mediated H3K27Me3, illuminating a novel DEPDC1-SUZ12 molecular axis as regulator in CRC progression and suggesting potential implications in treatment of CRC.
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Affiliation(s)
- Qiang Wang
- Department of Surgical Oncology, Mindong Hospital Affiliated to Fujian Medical University, Ningde, China
| | - Shijian Jiang
- Department of Surgical Oncology, Mindong Hospital Affiliated to Fujian Medical University, Ningde, China
| | - Jianchao Liu
- Department of General Surgery, Liaocheng People's Hospital, Liaocheng, China
| | - Genshun Ma
- Department of General Surgery, Liaocheng People's Hospital, Liaocheng, China
| | - Jianrui Zheng
- Department of Pathology, Mindong Hospital Affiliated to Fujian Medical University, Ningde, China
| | - Yajun Zhang
- Department of General Surgery, Liaocheng People's Hospital, Liaocheng, China
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26
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Boles NC, Fernandes M, Swigut T, Srinivasan R, Schiff L, Rada-Iglesias A, Wang Q, Saini JS, Kiehl T, Stern JH, Wysocka J, Blenkinsop TA, Temple S. Epigenomic and Transcriptomic Changes During Human RPE EMT in a Stem Cell Model of Epiretinal Membrane Pathogenesis and Prevention by Nicotinamide. Stem Cell Reports 2020; 14:631-647. [PMID: 32243845 PMCID: PMC7160390 DOI: 10.1016/j.stemcr.2020.03.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 12/21/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) is a biological process involved in tissue morphogenesis and disease that causes dramatic changes in cell morphology, migration, proliferation, and gene expression. The retinal pigment epithelium (RPE), which supports the neural retina, can undergo EMT, producing fibrous epiretinal membranes (ERMs) associated with vision-impairing clinical conditions, such as macular pucker and proliferative vitreoretinopathy (PVR). We found that co-treatment with TGF-β and TNF-α (TNT) accelerates EMT in adult human RPE stem cell-derived RPE cell cultures. We captured the global epigenomic and transcriptional changes elicited by TNT treatment of RPE and identified putative active enhancers associated with actively transcribed genes, including a set of upregulated transcription factors that are candidate regulators. We found that the vitamin B derivative nicotinamide downregulates these key transcriptional changes, and inhibits and partially reverses RPE EMT, revealing potential therapeutic routes to benefit patients with ERM, macular pucker and PVR.
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Affiliation(s)
| | - Marie Fernandes
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomasz Swigut
- Department of Chemical and Systems Biology, Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rajini Srinivasan
- Department of Chemical and Systems Biology, Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Lauren Schiff
- Neural Stem Cell Institute, Rensselaer NY 12144, USA
| | | | - Qingjie Wang
- Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | | | - Thomas Kiehl
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey H Stern
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | | | - Sally Temple
- Neural Stem Cell Institute, Rensselaer NY 12144, USA.
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27
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Xu Y, Ouyang C, Lyu D, Lin Z, Zheng W, Xiao F, Xu Z, Ding L. Diabetic nephropathy execrates epithelial-to-mesenchymal transition (EMT) via miR-2467-3p/Twist1 pathway. Biomed Pharmacother 2020; 125:109920. [PMID: 32050151 DOI: 10.1016/j.biopha.2020.109920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/12/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
Although diabetic nephropathy (DN) is induced by a complicate interplay of multiple factors, the underlying mechanisms remain poorly characterized, even the treatment. Herein, we show that both of DN patients and STZ-induced type 1 diabetic rat exhibit the reduction both of urinary and circulating miR-2467-3p. We identify a negative correlation between miR-2467-3p levels and renal dysfunction. Administration of miR-2467-3p prevents diabetes-induced renal dysfunction and represses renal fibrosis in STZ-induced type 1 diabetic rats. Conversely, anti-miR-2467 overexpression exacerbates renal dysfunction and fibrosis in STZ-induced rats. In diabetic condition, the reduction of miR-2467-3p promotes expression of Twist1, inducing epithelial-to-mesenchymal transition (EMT), resulting in renal fibrosis and kidney dysfunction. Together, our study presents miR-2467/Twist1/EMT as a regulatory axis of renal dysfunction in DN.
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Affiliation(s)
- Yan Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350004, China
| | - Changhan Ouyang
- Hubei Key Laboratory of Cardiovascular, Cerebrovascular and Metabolic Disorders, Hubei University of Science and Technology, Xianning, 437100, China
| | - Dayin Lyu
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Zhangmei Lin
- School of Clinical Medicine, Fujian Medical University, Fuzhou, 350004, China
| | - Wencai Zheng
- School of Clinical Medicine, Fujian Medical University, Fuzhou, 350004, China
| | - Fan Xiao
- School of Clinical Medicine, Fujian Medical University, Fuzhou, 350004, China
| | - Zhimin Xu
- School of Clinical Medicine, Fujian Medical University, Fuzhou, 350004, China
| | - Lexi Ding
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, 410008, China.
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28
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Chung VY, Tan TZ, Ye J, Huang RL, Lai HC, Kappei D, Wollmann H, Guccione E, Huang RYJ. The role of GRHL2 and epigenetic remodeling in epithelial-mesenchymal plasticity in ovarian cancer cells. Commun Biol 2019; 2:272. [PMID: 31372511 PMCID: PMC6656769 DOI: 10.1038/s42003-019-0506-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Cancer cells exhibit phenotypic plasticity during epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) involving intermediate states. To study genome-wide epigenetic remodeling associated with EMT plasticity, we integrate the analyses of DNA methylation, ChIP-sequencing of five histone marks (H3K4me1, H3K4me3, H3K27Ac, H3K27me3 and H3K9me3) and transcriptome profiling performed on ovarian cancer cells with different epithelial/mesenchymal states and on a knockdown model of EMT suppressor Grainyhead-like 2 (GRHL2). We have identified differentially methylated CpG sites associated with EMT, found at promoters of epithelial genes and GRHL2 binding sites. GRHL2 knockdown results in CpG methylation gain and nucleosomal remodeling (reduction in permissive marks H3K4me3 and H3K27ac; elevated repressive mark H3K27me3), resembling the changes observed across progressive EMT states. Epigenetic-modifying agents such as 5-azacitidine, GSK126 and mocetinostat further reveal cell state-dependent plasticity upon GRHL2 overexpression. Overall, we demonstrate that epithelial genes are subject to epigenetic control during intermediate phases of EMT/MET involving GRHL2.
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Affiliation(s)
- Vin Yee Chung
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Jieru Ye
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
| | - Rui-Lan Huang
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, 11031 Taipei, Taiwan
| | - Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, 11031 Taipei, Taiwan
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596 Singapore
| | - Heike Wollmann
- Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673 Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673 Singapore
| | - Ruby Yun-Ju Huang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore
- School of Medicine, College of Medicine, National Taiwan University, 10051 Taipei, Taiwan
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29
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Adhikary S, Chakravarti D, Terranova C, Sengupta I, Maitituoheti M, Dasgupta A, Srivastava DK, Ma J, Raman AT, Tarco E, Sahin AA, Bassett R, Yang F, Tapia C, Roy S, Rai K, Das C. Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor. Nat Commun 2019; 10:1398. [PMID: 30923315 PMCID: PMC6438984 DOI: 10.1038/s41467-019-08986-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/09/2019] [Indexed: 12/17/2022] Open
Abstract
The roles of Plant Homeodomain (PHD) fingers in catalysis of histone modifications are unknown. We demonstrated that the PHD finger of Ubiquitin Protein Ligase E3 Component N-Recognin7 (UBR7) harbors E3 ubiquitin ligase activity toward monoubiquitination of histone H2B at lysine120 (H2BK120Ub). Purified PHD finger or full-length UBR7 monoubiquitinated H2BK120 in vitro, and loss of UBR7 drastically reduced H2BK120Ub genome-wide binding sites in MCF10A cells. Low UBR7 expression was correlated with occurrence of triple-negative breast cancer and metastatic tumors. Consistently, UBR7 knockdown enhanced the invasiveness, induced epithelial-to-mesenchymal transition and promoted metastasis. Conversely, ectopic expression of UBR7 restored these cellular phenotypes and reduced tumor growth. Mechanistically, UBR7 loss reduced H2BK120Ub levels on cell adhesion genes, including CDH4, and upregulated the Wnt/β-Catenin signaling pathway. CDH4 overexpression could partially revert UBR7-dependent cellular phenotypes. Collectively, our results established UBR7 as a histone H2B monoubiquitin ligase that suppresses tumorigenesis and metastasis of triple-negative breast cancer.
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Affiliation(s)
- Santanu Adhikary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Deepavali Chakravarti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Isha Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India
| | - Mayinuer Maitituoheti
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anirban Dasgupta
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Dushyant Kumar Srivastava
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India
| | - Junsheng Ma
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ayush T Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Emily Tarco
- Department of Translational Molecular Pathology and Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fei Yang
- Department of Translational Molecular Pathology and Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Coya Tapia
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Siddhartha Roy
- Structural Biology and Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, 700032, India.
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata, 700064, India.
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30
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Zhou C, Wang Y, Zhang J, Su J, An Q, Liu X, Zhang M, Wang Y, Liu J, Zhang Y. H3K27me3 is an epigenetic barrier while KDM6A overexpression improves nuclear reprogramming efficiency. FASEB J 2019; 33:4638-4652. [PMID: 30673507 DOI: 10.1096/fj.201801887r] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aberrant epigenetic reprogramming is a major factor of developmental failure of cloned embryos. Histone H3 lysine 27 trimethylation (H3K27me3), a histone mark for transcriptional repression, plays important roles in mammalian embryonic development and induced pluripotent stem cell (iPSC) generation. The global loss of H3K27me3 marks may facilitate iPSC generation in mice and humans. However, the H3K27me3 level and its role in bovine somatic cell nuclear transfer (SCNT) reprogramming remain poorly understood. Here, we show that SCNT embryos exhibit global H3K27me3 hypermethylation from the 2- to 8-cell stage and that its removal by ectopically expressed H3K27me3 lysine demethylase (KDM)6A greatly improves nuclear reprogramming efficiency. In contrast, H3K27me3 reduction by H3K27me3 methylase enhancer of zeste 2 polycomb repressive complex knockdown or donor cell treatment with the enhancer of zeste 2 polycomb repressive complex-selective inhibitor GSK343 suppressed blastocyst formation by SCNT embryos. KDM6A overexpression enhanced the transcription of genes involved in cell adhesion and cellular metabolism and X-linked genes. Furthermore, we identified methyl-CpG-binding domain protein 3-like 2, which was reactivated by KDM6A, as a factor that is required for effective reprogramming in bovines. These results show that H3K27me3 functions as an epigenetic barrier and that KDM6A overexpression improves SCNT efficiency by facilitating transcriptional reprogramming.-Zhou, C., Wang, Y., Zhang, J., Su, J., An, Q., Liu, X., Zhang, M., Wang, Y., Liu, J., Zhang, Y. H3K27me3 is an epigenetic barrier while KDM6A overexpression improves nuclear reprogramming efficiency.
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Affiliation(s)
- Chuan Zhou
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yizhi Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Quanli An
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xin Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Min Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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31
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Skrypek N, Bruneel K, Vandewalle C, De Smedt E, Soen B, Loret N, Taminau J, Goossens S, Vandamme N, Berx G. ZEB2 stably represses RAB25 expression through epigenetic regulation by SIRT1 and DNMTs during epithelial-to-mesenchymal transition. Epigenetics Chromatin 2018; 11:70. [PMID: 30445998 PMCID: PMC6240308 DOI: 10.1186/s13072-018-0239-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/09/2018] [Indexed: 12/29/2022] Open
Abstract
Background Epithelial mesenchymal transition (EMT) is tightly regulated by a network of transcription factors (EMT-TFs). Among them is the nuclear factor ZEB2, a member of the zinc-finger E-box binding homeobox family. ZEB2 nuclear localization has been identified in several cancer types, and its overexpression is correlated with the malignant progression. ZEB2 transcriptionally represses epithelial genes, such as E-cadherin (CDH1), by directly binding to the promoter of the genes it regulates and activating mesenchymal genes by a mechanism in which there is no full agreement. Recent studies showed that EMT-TFs interact with epigenetic regulatory enzymes that alter the epigenome, thereby providing another level of control. The role of epigenetic regulation on ZEB2 function is not well understood. In this study, we aimed to characterize the epigenetic effect of ZEB2 repressive function on the regulation of a small Rab GTPase RAB25. Results Using cellular models with conditional ZEB2 expression, we show a clear transcriptional repression of RAB25 and CDH1. RAB25 contributes to the partial suppression of ZEB2-mediated cell migration. Furthermore, a highly significant reverse correlation between RAB25 and ZEB2 expression in several human cancer types could be identified. Mechanistically, ZEB2 binds specifically to E-box sequences on the RAB25 promoter. ZEB2 binding is associated with the local increase in DNA methylation requiring DNA methyltransferases as well as histone deacetylation (H3K9Ac) depending on the activity of SIRT1. Surprisingly, SIRT1 and DNMTs did not interact directly with ZEB2, and while SIRT1 inhibition decreased the stability of long-term repression, it did not prevent down-regulation of RAB25 and CDH1 by ZEB2. Conclusions ZEB2 expression is resulting in drastic changes at the chromatin level with both clear DNA hypermethylation and histone modifications. Here, we revealed that SIRT1-mediated H3K9 deacetylation helps to maintain gene repression but is not required for the direct ZEB2 repressive function. Targeting epigenetic enzymes to prevent EMT is an appealing approach to limit cancer dissemination, but inhibiting SIRT1 activity alone might have limited effect and will require drug combination to efficiently prevent EMT. Electronic supplementary material The online version of this article (10.1186/s13072-018-0239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Skrypek
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kenneth Bruneel
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Cindy Vandewalle
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva De Smedt
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bieke Soen
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Nele Loret
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Joachim Taminau
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Centre for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Inflammation Research Center, Ghent, Belgium.,VIB-UGent Center for Inflammation Research, Technologiepark 927, 9052, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, 9052, Zwijnaarde, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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32
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Le AVP, Szaumkessel M, Tan TZ, Thiery JP, Thompson EW, Dobrovic A. DNA Methylation Profiling of Breast Cancer Cell Lines along the Epithelial Mesenchymal Spectrum-Implications for the Choice of Circulating Tumour DNA Methylation Markers. Int J Mol Sci 2018; 19:ijms19092553. [PMID: 30154364 PMCID: PMC6164039 DOI: 10.3390/ijms19092553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/29/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
(1) Background: Epithelial–mesenchymal plasticity (EMP) is a dynamic process whereby epithelial carcinoma cells reversibly acquire morphological and invasive characteristics typical of mesenchymal cells. Identifying the methylation differences between epithelial and mesenchymal states may assist in the identification of optimal DNA methylation biomarkers for the blood-based monitoring of cancer. (2) Methods: Methylation-sensitive high-resolution melting (MS-HRM) was used to examine the promoter methylation status of a panel of established and novel markers in a range of breast cancer cell lines spanning the epithelial–mesenchymal spectrum. Pyrosequencing was used to validate the MS-HRM results. (3) Results: VIM, DKK3, and CRABP1 were methylated in the majority of epithelial breast cancer cell lines, while methylation of GRHL2, MIR200C, and CDH1 was restricted to mesenchymal cell lines. Some markers that have been used to assess minimal residual disease such as AKR1B1 and APC methylation proved to be specific for epithelial breast cell lines. However, RASSF1A, RARβ, TWIST1, and SFRP2 methylation was seen in both epithelial and mesenchymal cell lines, supporting their suitability for a multimarker panel. (4) Conclusions: Profiling DNA methylation shows a distinction between epithelial and mesenchymal phenotypes. Understanding how DNA methylation varies between epithelial and mesenchymal phenotypes may lead to more rational selection of methylation-based biomarkers for circulating tumour DNA analysis.
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Affiliation(s)
- Anh Viet-Phuong Le
- Olivia Newton John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
- Department of Surgery, St. Vincent's Hospital, University of Melbourne, Melbourne, VIC 3065, Australia.
| | - Marcin Szaumkessel
- Olivia Newton John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, 14 Medical Drive, National University of Singapore, Singapore 117599, Singapore.
| | - Jean-Paul Thiery
- Cancer Science Institute of Singapore, 14 Medical Drive, National University of Singapore, Singapore 117599, Singapore.
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology, Gustave Roussy, Université Paris-Sud, 94805 Villejuif, France.
| | - Erik W Thompson
- Department of Surgery, St. Vincent's Hospital, University of Melbourne, Melbourne, VIC 3065, Australia.
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Alexander Dobrovic
- Olivia Newton John Cancer Research Institute, Heidelberg, VIC 3084, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC 3010, Australia.
- School of Cancer Medicine, La Trobe University Bundoora, Bundoora, VIC 3086, Australia.
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33
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Jelinek J, Madzo J. DREAM: A Simple Method for DNA Methylation Profiling by High-throughput Sequencing. Methods Mol Biol 2018; 1465:111-27. [PMID: 27581143 DOI: 10.1007/978-1-4939-4011-0_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The digital restriction enzyme analysis of methylation (DREAM) is a simple method for DNA methylation analysis at tens of thousands of CpG sites across the genome. The method creates specific signatures at unmethylated and methylated CpG sites by sequential digests of genomic DNA with restriction endonucleases SmaI and XmaI, respectively. Both enzymes have the same CCCGGG recognition site; however, they differ in their sensitivity to CpG methylation and their cutting pattern. SmaI cuts only unmethylated sites leaving blunt 5'-GGG ends. XmaI cuts remaining methylated CC(me)CGG sites leaving 5'-CCGGG ends. Restriction fragments with distinct signatures at their ends are ligated to Illumina sequencing adaptors with sample-specific barcodes. High-throughput sequencing of pooled libraries follows. Sequencing reads are mapped to the restriction sites in the reference genome, and signatures corresponding to methylation status of individual DNA molecules are resolved. Methylation levels at target CpG sites are calculated as the proportion of sequencing reads with the methylated signature to the total number of reads mapping to the particular restriction site. Aligning the reads to the reference genome of any species is straightforward, since the method does not rely on bisulfite conversion of DNA. Sequencing of 25 million reads per human DNA library yields over 50,000 unique CpG sites with high coverage enabling accurate determination of DNA methylation levels. DREAM has a background less than 1 % making it suitable for accurate detection of low methylation levels. In summary, the method is simple, robust, highly reproducible, and cost-effective.
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Affiliation(s)
- Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 North Broad Street, Rm 339 F, PAHB, Philadelphia, PA, 19140, USA.
| | - Jozef Madzo
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
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Lu MY, Liao YW, Chen PY, Hsieh PL, Fang CY, Wu CY, Yen ML, Peng BY, Wang DP, Cheng HC, Wu CZ, Shih YH, Wang DJ, Yu CC, Tsai LL. Targeting LncRNA HOTAIR suppresses cancer stemness and metastasis in oral carcinomas stem cells through modulation of EMT. Oncotarget 2017; 8:98542-98552. [PMID: 29228709 PMCID: PMC5716749 DOI: 10.18632/oncotarget.21614] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/26/2017] [Indexed: 12/25/2022] Open
Abstract
Increasing evidence indicates that long non-coding RNAs (lncRNAs) regulate diverse cellular processes, such as cell growth, apoptosis and tumorigenesis. However, the functional roles of lncRNAs and mechanistic analysis of their interplays with oncogenic pathways in oral cancer remain largely unknown. In the current study, we examined the significance of lncRNA HOTAIR (HOX transcript antisense RNA) in tumor progression of oral squamous cell carcinomas (OSCC). We found the expression of HOTAIR was upregulated in tumor tissues, especially in the metastatic samples. And it was also observed in metastatic OSCC cell lines. Silence of HOTAIR in oral carcinomas stem cells (OCSC) significantly inhibited their cancer stemness, invasiveness and tumourigenicity in xenotransplantation models. By contrast, overexpression of HOTAIR in OSCC enhanced their metastatic potential and epithelial-mesenchymal transition (EMT) characteristics. And we showed that the expression of HOTAIR was positively related to mesenchymal markers and inversely correlated with epithelial marker in clinical samples. Moreover, Kaplan-Meier survival analysis suggested that high level of HOTAIR was a strong predictor of poor survival in OSCC patients. Collectively, our data demonstrated that HOTAIR-mediated cancer stemness and metastasis are associated with the regulation of EMT and HOTAIR may serve as a therapeutic target in OSCC.
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Affiliation(s)
- Ming-Yi Lu
- School of Dentistry, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Wen Liao
- School of Dentistry, Chung Shan Medical University, Taichung, Taiwan
| | - Pei-Yin Chen
- School of Dentistry, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Pei-Ling Hsieh
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Yuan Fang
- Department of Dentistry, Taipei Municipal Wanfang Hospital, Taipei, Taiwan.,School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chia-Yu Wu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ming-Liang Yen
- Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Bou-Yue Peng
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Dayen Peter Wang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Hsin-Chung Cheng
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Ching-Zong Wu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yung-Hsun Shih
- Department of Dentistry, Taipei Municipal Wanfang Hospital, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Duen-Jeng Wang
- Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
| | - Cheng-Chia Yu
- School of Dentistry, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan.,Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Lo-Lin Tsai
- Department of Dentistry, Taipei Municipal Wanfang Hospital, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan
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35
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The Histone Variant H2A.Z Is a Master Regulator of the Epithelial-Mesenchymal Transition. Cell Rep 2017; 21:943-952. [DOI: 10.1016/j.celrep.2017.09.086] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/17/2017] [Accepted: 09/25/2017] [Indexed: 11/20/2022] Open
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36
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Fujita Y, Masuda K, Hamada J, Shoda K, Naruto T, Hamada S, Miyakami Y, Kohmoto T, Watanabe M, Takahashi R, Tange S, Saito M, Kudo Y, Fujiwara H, Ichikawa D, Tangoku A, Otsuji E, Imoto I. KH-type splicing regulatory protein is involved in esophageal squamous cell carcinoma progression. Oncotarget 2017; 8:101130-101145. [PMID: 29254151 PMCID: PMC5731861 DOI: 10.18632/oncotarget.20926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/25/2017] [Indexed: 11/25/2022] Open
Abstract
KH-type splicing regulatory protein (KHSRP) is a multifunctional RNA-binding protein, which is involved in several post-transcriptional aspects of RNA metabolism, including microRNA (miRNA) biogenesis. It affects distinct cell functions in different tissues and can have an impact on various pathological conditions. In the present study, we investigated the oncogenic functions of KHSRP and their underlying mechanisms in the pathogenesis of esophageal squamous cell carcinoma (ESCC). KHSRP expression levels were elevated in ESCC tumors when compared with those in non-tumorous tissues by immunohistochemistry, and cytoplasmic KHSRP overexpression was found to be an independent prognosticator for worse overall survival in a cohort of 104 patients with ESCC. KHSRP knockdown inhibited growth, migration, and invasion of ESCC cells. KHSRP knockdown also inhibited the maturation of cancer-associated miRNAs, such as miR-21, miR-130b, and miR-301, and induced the expression of their target mRNAs, such as BMP6, PDCD4, and TIMP3, resulting in the inhibition of epithelial-to-mesenchymal transition. Our findings uncover a novel oncogenic function of KHSRP in esophageal tumorigenesis and implicate its use as a marker for prognostic evaluation and as a putative therapeutic target in ESCC.
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Affiliation(s)
- Yuji Fujita
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kiyoshi Masuda
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Junichi Hamada
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsutoshi Shoda
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan.,Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takuya Naruto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Satoshi Hamada
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yuko Miyakami
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Tomohiro Kohmoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Miki Watanabe
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Rizu Takahashi
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Shoichiro Tange
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Masako Saito
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yasusei Kudo
- Department of Oral Molecular Pathology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Hitoshi Fujiwara
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Ichikawa
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan.,First Department of Surgery, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Akira Tangoku
- Department of Thoracic, Endocrine Surgery and Oncology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Eigo Otsuji
- Division of Digestive Surgery, Department of Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Issei Imoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
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37
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Skrypek N, Goossens S, De Smedt E, Vandamme N, Berx G. Epithelial-to-Mesenchymal Transition: Epigenetic Reprogramming Driving Cellular Plasticity. Trends Genet 2017; 33:943-959. [PMID: 28919019 DOI: 10.1016/j.tig.2017.08.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/20/2017] [Accepted: 08/10/2017] [Indexed: 12/11/2022]
Abstract
Epithelial-to-mesenchymal transition (EMT) is a process in which epithelial cells lose their junctions and polarity to gain a motile mesenchymal phenotype. EMT is essential during embryogenesis and adult physiological processes like wound healing, but is aberrantly activated in pathological conditions like fibrosis and cancer. A series of transcription factors (EMT-inducing transcription factor; EMT-TF) regulate the induction of EMT by repressing the transcription of epithelial genes while activating mesenchymal genes through mechanisms still debated. The nuclear interaction of EMT-TFs with larger protein complexes involved in epigenetic genome modulation has attracted recent attention to explain functions of EMT-TFs during reprogramming and cellular differentiation. In this review, we discuss recent advances in understanding the interplay between epigenetic regulators and EMT transcription factors and how these findings could be used to establish new therapeutic approaches to tackle EMT-related diseases.
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Affiliation(s)
- Nicolas Skrypek
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; These authors contributed equally
| | - Steven Goossens
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Centre for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium; These authors contributed equally
| | - Eva De Smedt
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Niels Vandamme
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Inflammation Research Center (IRC), VIB, Ghent, Belgium
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department for Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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38
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Taube JH, Sphyris N, Johnson KS, Reisenauer KN, Nesbit TA, Joseph R, Vijay GV, Sarkar TR, Bhangre NA, Song JJ, Chang JT, Lee MG, Soundararajan R, Mani SA. The H3K27me3-demethylase KDM6A is suppressed in breast cancer stem-like cells, and enables the resolution of bivalency during the mesenchymal-epithelial transition. Oncotarget 2017; 8:65548-65565. [PMID: 29029452 PMCID: PMC5630352 DOI: 10.18632/oncotarget.19214] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
The deposition of the activating H3K4me3 and repressive H3K27me3 histone modifications within the same promoter, forming a so-called bivalent domain, maintains gene expression in a repressed but transcription-ready state. We recently reported a significantly increased incidence of bivalency following an epithelial-mesenchymal transition (EMT), a process associated with the initiation of the metastatic cascade. The reverse process, known as the mesenchymal-epithelial transition (MET), is necessary for efficient colonization. Here, we identify numerous genes associated with differentiation, proliferation and intercellular adhesion that are repressed through the acquisition of bivalency during EMT, and re-expressed following MET. The majority of EMT-associated bivalent domains arise through H3K27me3 deposition at H3K4me3-marked promoters. Accordingly, we show that the expression of the H3K27me3-demethylase KDM6A is reduced in cells that have undergone EMT, stem-like subpopulations of mammary cell lines and stem cell-enriched triple-negative breast cancers. Importantly, KDM6A levels are restored following MET, concomitant with CDH1/E-cadherin reactivation through H3K27me3 removal. Moreover, inhibition of KDM6A, using the H3K27me3-demethylase inhibitor GSK-J4, prevents the re-expression of bivalent genes during MET. Our findings implicate KDM6A in the resolution of bivalency accompanying MET, and suggest KDM6A inhibition as a viable strategy to suppress metastasis formation in breast cancer.
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Affiliation(s)
- Joseph H. Taube
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Biology, Baylor University, Waco, Texas, USA
- Institute of Biomedical Sciences, Baylor University, Waco, Texas, USA
| | - Nathalie Sphyris
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | - Robiya Joseph
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Geraldine V. Vijay
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tapasree R. Sarkar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Integrative Bioscience, Texas A & M University, College Station, Texas, USA
| | - Neeraja A. Bhangre
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joon Jin Song
- Depatment of Statistical Science, Baylor University, Waco, Texas, USA
| | - Jeffrey T. Chang
- Center for Clinical and Translational Sciences, The University of Texas Health Science Center at Houston, Texas, USA
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Texas, USA
| | - Min Gyu Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sendurai A. Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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39
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DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. Oncogene 2017; 36:5551-5566. [PMID: 28581528 DOI: 10.1038/onc.2017.159] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/08/2017] [Accepted: 04/14/2017] [Indexed: 12/26/2022]
Abstract
Widespread genome hypo-methylation and promoter hyper-methylation of epithelium-specific genes are hallmarks of stable epithelial-to-mesenchymal transition (EMT), which in prostate cancer (PCa) correlates with castration resistance, cancer stem cells generation, chemoresistance and worst prognosis. Exploiting our consolidated 'ex-vivo' system, we show that cancer-associated fibroblasts (CAFs) released factors have pivotal roles in inducing genome methylation changes required for EMT and stemness in EMT-prone PCa cells. By global DNA methylation analysis and RNA-Seq, we provide compelling evidence that conditioned media from CAFs explanted from two unrelated patients with advanced PCa, stimulates concurrent DNA hypo- and hyper-methylation required for EMT and stemness in PC3 and DU145, but not in LN-CaP and its derivative C4-2B, PCa cells. CpG island (CGI) hyper-methylation associates with repression of genes required for epithelial maintenance and invasion antagonism, whereas activation of EMT markers and stemness genes correlate with CGI hypo-methylation. Remarkably, methylation variations and EMT-regulated transcripts almost completely reverse qualitatively and quantitatively during MET. Unsupervised clustering analysis of the PRAD TCGA data set with the differentially expressed (DE) and methylated EMT signature, identified a gene cluster of DE genes defined by a CAF+ and AR- phenotype and worst diagnosis. This gene cluster includes the relevant factors for EMT and stemness, which display DNA methylation variations in regulatory regions inversely correlated to their expression changes, thus strongly sustaining the ex-vivo data. DNMT3A-dependent methylation is essential for silencing epithelial maintenance and EMT counteracting genes, such as CDH1 and GRHL2, that is, the direct repressor of ZEB1, the key transcriptional factor for EMT and stemness. Accordingly, DNMT3A knock-down prevents EMT entry. These results shed light on the mechanisms of establishment and maintenance of coexisting DNA hypo- and hyper-methylation patterns during cancer progression, the generation of EMT and cell stemness in advanced PCa, and may pave the way to new therapeutic implications.
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40
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Oliveira-Barros EG, Nicolau-Neto P, Da Costa NM, Pinto LFR, Palumbo A, Nasciutti LE. Prostate cancer molecular profiling: the Achilles heel for the implementation of precision medicine. Cell Biol Int 2017; 41:1239-1245. [DOI: 10.1002/cbin.10785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 05/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Eliane Gouvêa Oliveira-Barros
- Programa de Pesquisa em Biologia Celular e do Desenvolvimento; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; CEP: 21941-902 Rio de Janeiro Brazil
| | - Pedro Nicolau-Neto
- Programa de Carcinogênese Molecular; Centro de Pesquisas (CPQ); Instituto Nacional de Câncer (INCA); Rua André Cavalcanti, 37-Centro CEP: 20231-050 Rio de Janeiro Brazil
| | - Nathalia Meireles Da Costa
- Programa de Carcinogênese Molecular; Centro de Pesquisas (CPQ); Instituto Nacional de Câncer (INCA); Rua André Cavalcanti, 37-Centro CEP: 20231-050 Rio de Janeiro Brazil
| | - Luís Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular; Centro de Pesquisas (CPQ); Instituto Nacional de Câncer (INCA); Rua André Cavalcanti, 37-Centro CEP: 20231-050 Rio de Janeiro Brazil
| | - Antonio Palumbo
- Programa de Pesquisa em Biologia Celular e do Desenvolvimento; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; CEP: 21941-902 Rio de Janeiro Brazil
- Programa de Carcinogênese Molecular; Centro de Pesquisas (CPQ); Instituto Nacional de Câncer (INCA); Rua André Cavalcanti, 37-Centro CEP: 20231-050 Rio de Janeiro Brazil
| | - Luiz Eurico Nasciutti
- Programa de Pesquisa em Biologia Celular e do Desenvolvimento; Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; CEP: 21941-902 Rio de Janeiro Brazil
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41
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Malek R, Gajula RP, Williams RD, Nghiem B, Simons BW, Nugent K, Wang H, Taparra K, Lemtiri-Chlieh G, Yoon AR, True L, An SS, DeWeese TL, Ross AE, Schaeffer EM, Pienta KJ, Hurley PJ, Morrissey C, Tran PT. TWIST1-WDR5- Hottip Regulates Hoxa9 Chromatin to Facilitate Prostate Cancer Metastasis. Cancer Res 2017; 77:3181-3193. [PMID: 28484075 DOI: 10.1158/0008-5472.can-16-2797] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/03/2017] [Accepted: 04/19/2017] [Indexed: 12/22/2022]
Abstract
TWIST1 is a transcription factor critical for development that can promote prostate cancer metastasis. During embryonic development, TWIST1 and HOXA9 are coexpressed in mouse prostate and then silenced postnatally. Here we report that TWIST1 and HOXA9 coexpression are reactivated in mouse and human primary prostate tumors and are further enriched in human metastases, correlating with survival. TWIST1 formed a complex with WDR5 and the lncRNA Hottip/HOTTIP, members of the MLL/COMPASS-like H3K4 methylases, which regulate chromatin in the Hox/HOX cluster during development. TWIST1 overexpression led to coenrichment of TWIST1 and WDR5 as well as increased H3K4me3 chromatin at the Hoxa9/HOXA9 promoter, which was dependent on WDR5. Expression of WDR5 and Hottip/HOTTIP was also required for TWIST1-induced upregulation of HOXA9 and aggressive cellular phenotypes such as invasion and migration. Pharmacologic inhibition of HOXA9 prevented TWIST1-induced aggressive prostate cancer cellular phenotypes in vitro and metastasis in vivo This study demonstrates a novel mechanism by which TWIST1 regulates chromatin and gene expression by cooperating with the COMPASS-like complex to increase H3K4 trimethylation at target gene promoters. Our findings highlight a TWIST1-HOXA9 embryonic prostate developmental program that is reactivated during prostate cancer metastasis and is therapeutically targetable. Cancer Res; 77(12); 3181-93. ©2017 AACR.
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Affiliation(s)
- Reem Malek
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rajendra P Gajula
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Russell D Williams
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Belinda Nghiem
- Department of Urology, University of Washington, Seattle, Washington
| | - Brian W Simons
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Katriana Nugent
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hailun Wang
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kekoa Taparra
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ghali Lemtiri-Chlieh
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arum R Yoon
- Department of Environmental Health Sciences, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Lawrence True
- Department of Pathology, University of Washington, Seattle, Washington
| | - Steven S An
- Department of Environmental Health Sciences, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley E Ross
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward M Schaeffer
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kenneth J Pienta
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paula J Hurley
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Phuoc T Tran
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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42
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Patel SA, Vanharanta S. Epigenetic determinants of metastasis. Mol Oncol 2017; 11:79-96. [PMID: 27756687 PMCID: PMC5423227 DOI: 10.1016/j.molonc.2016.09.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/12/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic analyses of cancer progression in patient samples and model systems have thus far failed to identify specific mutational drivers of metastasis. Yet, at least in experimental systems, metastatic cancer clones display stable traits that can facilitate progression through the many steps of metastasis. How cancer cells establish and maintain the transcriptional programmes required for metastasis remains mostly unknown. Emerging evidence suggests that metastatic traits may arise from epigenetically altered transcriptional output of the oncogenic signals that drive tumour initiation and early progression. Molecular dissection of such mechanisms remains a central challenge for a comprehensive understanding of the origins of metastasis.
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Affiliation(s)
- Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, CB2 0XZ, United Kingdom
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, CB2 0XZ, United Kingdom.
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43
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Lee JY, Kong G. Roles and epigenetic regulation of epithelial-mesenchymal transition and its transcription factors in cancer initiation and progression. Cell Mol Life Sci 2016; 73:4643-4660. [PMID: 27460000 PMCID: PMC11108467 DOI: 10.1007/s00018-016-2313-z] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 02/07/2023]
Abstract
The epithelial-mesenchymal transition (EMT) is a crucial developmental process by which epithelial cells undergo a mesenchymal phenotypic change. During EMT, epigenetic mechanisms including DNA methylation and histone modifications are involved in the regulation of EMT-related genes. The epigenetic gene silencing of the epithelial marker E-cadherin has been well characterized. In particular, three major transcriptional repressors of E-cadherin, Snail, ZEB, and Twist families, also known as EMT-inducing transcription factors (EMT-TFs), play a crucial role in this process by cooperating with multiple epigenetic modifiers. Furthermore, recent studies have identified the novel epigenetic modifiers that control the expression of EMT-TFs, and these modifiers have emerged as critical regulators of cancer development and as novel therapeutic targets for human cancer. In this review, the diverse functions of EMT-TFs in cancer progression, the cooperative mechanisms of EMT-TFs with epigenetic modifiers, and epigenetic regulatory roles for the expression of EMT-TFs will be discussed.
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Affiliation(s)
- Jeong-Yeon Lee
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul, Republic of Korea
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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44
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Sun L, Fang J. Epigenetic regulation of epithelial-mesenchymal transition. Cell Mol Life Sci 2016; 73:4493-4515. [PMID: 27392607 PMCID: PMC5459373 DOI: 10.1007/s00018-016-2303-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/10/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is an essential process for morphogenesis and organ development which reversibly enables polarized epithelial cells to lose their epithelial characteristics and to acquire mesenchymal properties. It is now evident that the aberrant activation of EMT is also a critical mechanism to endow epithelial cancer cells with migratory and invasive capabilities associated with metastatic competence. This dedifferentiation program is mediated by a small cohort of pleiotropic transcription factors which orchestrate a complex array of epigenetic mechanisms for the wide-spread changes in gene expression. Here, we review major epigenetic mechanisms with an emphasis on histone modifications and discuss their implications in EMT and tumor progression. We also highlight mechanisms underlying transcription regulation concerted by various chromatin-modifying proteins and EMT-inducing transcription factors at different molecular layers. Owing to the reversible nature of epigenetic modifications, a thorough understanding of their functions in EMT will not only provide new insights into our knowledge of cancer progression and metastasis, but also facilitate the development of diagnostic and therapeutic strategies for human malignancy.
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Affiliation(s)
- Lidong Sun
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jia Fang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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45
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Yun J, Song SH, Kim HP, Han SW, Yi EC, Kim TY. Dynamic cohesin-mediated chromatin architecture controls epithelial-mesenchymal plasticity in cancer. EMBO Rep 2016; 17:1343-59. [PMID: 27466323 PMCID: PMC5007572 DOI: 10.15252/embr.201541852] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 06/03/2016] [Accepted: 06/22/2016] [Indexed: 01/26/2023] Open
Abstract
Epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) are important interconnected events in tumorigenesis controlled by complex genetic networks. However, the cues that activate EMT-initiating factors and the mechanisms that reversibly connect EMT/MET are not well understood. Here, we show that cohesin-mediated chromatin organization coordinates EMT/MET by regulating mesenchymal genes. We report that RAD21, a subunit of the cohesin complex, is expressed in epithelial breast cancer cells, whereas its expression is decreased in mesenchymal cancer. Depletion of RAD21 in epithelial cancer cells causes transcriptional activation of TGFB1 and ITGA5, inducing EMT. Reduced binding of RAD21 changes intrachromosomal chromatin interactions within the TGFB1 and ITGA5 loci, creating an active transcriptional environment. Similarly, stem cell-like cancer cells also show an open chromatin structure at both genes, which correlates with high expression levels and mesenchymal fate characteristics. Conversely, overexpression of RAD21 in mesenchymal cancer cells induces MET-specific expression patterns. These findings indicate that dynamic cohesin-mediated chromatin structures are responsible for the initiation and regulation of essential EMT-related cell fate changes in cancer.
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Affiliation(s)
- Jiyeon Yun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology Seoul National University College of Medicine, Seoul, Korea Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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46
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Zhao Q, Gui T, Qian Q, Li L, Shen K. B-cell-specific Moloney murine leukemia virus integration site 1: potential stratification factor and therapeutic target for epithelial ovarian cancer. Onco Targets Ther 2016; 9:5203-8. [PMID: 27578986 PMCID: PMC5001671 DOI: 10.2147/ott.s109443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Epithelial ovarian cancer, a vexing challenge for clinical management, still lacks biomarkers for early diagnosis, precise stratification, and prognostic evaluation of patients. B-cell-specific Moloney murine leukemia virus integration site 1 (BMI1), a member of the polycomb group of proteins, engages in diverse cellular processes, including proliferation, differentiation, senescence, and stem cell renewal. In addition, BMI1, as a cancer stem-cell marker, participates in tumorigenesis through various pathways. Rewardingly, recent studies have also revealed a relationship between BMI1 expression and the clinical grade/stage, therapy response, and survival outcome in a majority of human malignancies, including epithelial ovarian cancer. Therefore, BMI1 might serve as a potential stratification factor and treatment target for epithelial ovarian cancer, pending evidence from further investigations.
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Affiliation(s)
- Qianying Zhao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing
| | - Ting Gui
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing
| | - Qiuhong Qian
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing; Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Shandong, People's Republic of China
| | - Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing
| | - Keng Shen
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing
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47
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Ho SM, Cheong A, Adgent MA, Veevers J, Suen AA, Tam NNC, Leung YK, Jefferson WN, Williams CJ. Environmental factors, epigenetics, and developmental origin of reproductive disorders. Reprod Toxicol 2016; 68:85-104. [PMID: 27421580 DOI: 10.1016/j.reprotox.2016.07.011] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/21/2016] [Accepted: 07/09/2016] [Indexed: 12/31/2022]
Abstract
Sex-specific differentiation, development, and function of the reproductive system are largely dependent on steroid hormones. For this reason, developmental exposure to estrogenic and anti-androgenic endocrine disrupting chemicals (EDCs) is associated with reproductive dysfunction in adulthood. Human data in support of "Developmental Origins of Health and Disease" (DOHaD) comes from multigenerational studies on offspring of diethylstilbestrol-exposed mothers/grandmothers. Animal data indicate that ovarian reserve, female cycling, adult uterine abnormalities, sperm quality, prostate disease, and mating behavior are susceptible to DOHaD effects induced by EDCs such as bisphenol A, genistein, diethylstilbestrol, p,p'-dichlorodiphenyl-dichloroethylene, phthalates, and polyaromatic hydrocarbons. Mechanisms underlying these EDC effects include direct mimicry of sex steroids or morphogens and interference with epigenomic sculpting during cell and tissue differentiation. Exposure to EDCs is associated with abnormal DNA methylation and other epigenetic modifications, as well as altered expression of genes important for development and function of reproductive tissues. Here we review the literature exploring the connections between developmental exposure to EDCs and adult reproductive dysfunction, and the mechanisms underlying these effects.
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Affiliation(s)
- Shuk-Mei Ho
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Cincinnati Cancer Center, Cincinnati, OH, United States; Cincinnati Veteran Affairs Hospital Medical Center, Cincinnati, OH, United States.
| | - Ana Cheong
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Margaret A Adgent
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jennifer Veevers
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Cincinnati Cancer Center, Cincinnati, OH, United States
| | - Alisa A Suen
- Reproductive Medicine Group, Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States; Curriculum in Toxicology, UNC Chapel Hill, Chapel Hill, NC, United States
| | - Neville N C Tam
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Cincinnati Cancer Center, Cincinnati, OH, United States
| | - Yuet-Kin Leung
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Cincinnati Cancer Center, Cincinnati, OH, United States
| | - Wendy N Jefferson
- Reproductive Medicine Group, Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Carmen J Williams
- Reproductive Medicine Group, Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States.
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48
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Seisen T, Rouprêt M, Gomez F, Malouf GG, Shariat SF, Peyronnet B, Spano JP, Cancel-Tassin G, Cussenot O. A comprehensive review of genomic landscape, biomarkers and treatment sequencing in castration-resistant prostate cancer. Cancer Treat Rev 2016; 48:25-33. [PMID: 27327958 DOI: 10.1016/j.ctrv.2016.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 12/11/2022]
Abstract
Hormone-naïve prostate cancer and its castration-resistant state (CRPC) are clinically and genetically heterogeneous diseases. From initiation of prostate carcinogenesis to its evolution towards therapeutic resistance, various combinations of genetic and epigenetic events occur. Schematically, progression to CRPC could be divided in two distinct pathways, either dependent or independent of the androgen receptor activity. Nevertheless, because the better knowledge of the genetic landscape of CRPC is under way, limited clinical applications are available at the moment, underlying the usefulness of prognostic and predictive biomarkers in daily practice. Despite the promising prognostic value of circulating tumor cells, no biomarker has been currently validated as a surrogate for overall survival in CRPC patients. Inversely, considerable interest has been generated with the recent finding of the splice variant AR-V7 that allows to predict resistance to abiraterone acetate and enzalutamide. However, other predictive biomarkers would be necessary to accurately guide personalized sequencing of CRPC treatment, which now includes numerous possibilities based on the six validated drugs, without accounting for those currently under investigation in the ongoing randomized controlled trials. As a consequence, only rational sequencing, which consists in choosing an agent that is not expected to have cross-resistance with previous therapy, can be currently advised.
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Affiliation(s)
- Thomas Seisen
- Academic Department of Urology of La Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Faculté de Médecine Pierre et Marie Curie, University Paris 6, 75013 Paris, France; Institut Universitaire de Cancérologie, Pierre et Marie Curie, University Paris 6, GRC n° 5, CeRePP/ONCOTYPE-URO, 75013 Paris, France
| | - Morgan Rouprêt
- Academic Department of Urology of La Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Faculté de Médecine Pierre et Marie Curie, University Paris 6, 75013 Paris, France; Institut Universitaire de Cancérologie, Pierre et Marie Curie, University Paris 6, GRC n° 5, CeRePP/ONCOTYPE-URO, 75013 Paris, France.
| | - Florie Gomez
- Department of Urology, CHC Liege, Liège, Belgium
| | - Gabriel G Malouf
- Academic Department of Medical Oncology of La Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Faculté de Médecine Pierre et Marie Curie, University Paris 6, GRC n° 5, ONCOTYPE-URO, 75013 Paris, France
| | - Shahrokh F Shariat
- Academic Department of Urology and Comprehensive Cancer Center, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Benoit Peyronnet
- Academic Department of Urology, CHU Rennes and University of Rennes, France
| | - Jean-Philippe Spano
- Academic Department of Medical Oncology of La Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Faculté de Médecine Pierre et Marie Curie, University Paris 6, GRC n° 5, ONCOTYPE-URO, 75013 Paris, France
| | - Géraldine Cancel-Tassin
- Institut Universitaire de Cancérologie, Pierre et Marie Curie, University Paris 6, GRC n° 5, CeRePP/ONCOTYPE-URO, 75013 Paris, France
| | - Olivier Cussenot
- Institut Universitaire de Cancérologie, Pierre et Marie Curie, University Paris 6, GRC n° 5, CeRePP/ONCOTYPE-URO, 75013 Paris, France; Academic Department of Urology of Tenon, Assistance-Publique Hôpitaux de Paris, Faculté de Médecine Pierre et Marie Curie, University Paris 6, 75013 Paris, France
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49
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Malouf GG, Su X, Zhang J, Creighton CJ, Ho TH, Lu Y, Raynal NJM, Karam JA, Tamboli P, Allanick F, Mouawad R, Spano JP, Khayat D, Wood CG, Jelinek J, Tannir NM. DNA Methylation Signature Reveals Cell Ontogeny of Renal Cell Carcinomas. Clin Cancer Res 2016; 22:6236-6246. [PMID: 27256309 DOI: 10.1158/1078-0432.ccr-15-1217] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 04/28/2016] [Accepted: 05/12/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE DNA methylation is a heritable covalent modification that is developmentally regulated and is critical in tissue-type definition. Although genotype-phenotype correlations have been described for different subtypes of renal cell carcinoma (RCC), it is unknown if DNA methylation profiles correlate with morphological or ontology based phenotypes. Here, we test the hypothesis that DNA methylation signatures can discriminate between putative precursor cells in the nephron. EXPERIMENTAL DESIGNS We performed deep profiling of DNA methylation and transcriptome in diverse histopathological RCC subtypes and validated DNA methylation in an independent dataset as well as in The Cancer Genome Atlas Clear Cell and Chromophobe Renal Cell Carcinoma Datasets. RESULTS Our data provide the first mapping of methylome epi-signature and indicate that RCC subtypes can be grouped into two major epi-clusters: C1, which encompasses clear-cell RCC, papillary RCC, mucinous and spindle cell carcinomas and translocation RCC; C2, which comprises oncocytoma and chromophobe RCC. Interestingly, C1 epi-cluster displayed 3-fold more hypermethylation as compared with C2 epi-cluster. Of note, differentially methylated regions between C1 and C2 epi-clusters occur in gene bodies and intergenic regions, instead of gene promoters. Transcriptome analysis of C1 epi-cluster suggests a functional convergence on Polycomb targets, whereas C2 epi-cluster displays DNA methylation defects. Furthermore, we find that our epigenetic ontogeny signature is associated with worse outcomes of patients with clear-cell RCC. CONCLUSIONS Our data define the epi-clusters that can discriminate between distinct RCC subtypes and for the first time define the epigenetic basis for proximal versus distal tubule derived kidney tumors. Clin Cancer Res; 22(24); 6236-46. ©2016 AACR.
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Affiliation(s)
- Gabriel G Malouf
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France.
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianping Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, Arizona
- Center for Individualized Medicine, Epigenomics Group, Mayo Clinic, Rochester, Minnesota
| | - Yue Lu
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Noël J-M Raynal
- Fels Institute, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pheroze Tamboli
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frederick Allanick
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Roger Mouawad
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - David Khayat
- Department of Medical Oncology, Groupe Hospitalier Pitié-Salpêtrière, University Pierre and Marie Curie (Paris VI), Institut Universitaire de cancérologie, AP-HP, Paris, France
- AVEC Foundation Laboratory, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christopher G Wood
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jaroslav Jelinek
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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50
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Stacchiotti S, Astolfi A, Gronchi A, Fontana A, Pantaleo MA, Negri T, Brenca M, Tazzari M, Urbini M, Indio V, Colombo C, Radaelli S, Brich S, Dei Tos AP, Casali PG, Castelli C, Dagrada GP, Pilotti S, Maestro R. Evolution of Dermatofibrosarcoma Protuberans to DFSP-Derived Fibrosarcoma: An Event Marked by Epithelial-Mesenchymal Transition-like Process and 22q Loss. Mol Cancer Res 2016; 14:820-9. [PMID: 27256159 DOI: 10.1158/1541-7786.mcr-16-0068] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/16/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED Dermatofibrosarcoma protuberans (DFSP) is a rare and indolent cutaneous sarcoma. At times, a fibrosarcomatous transformation marked by a more aggressive clinical behavior may be present. We investigated the natural history and the molecular bases of progression from classic DFSP to the fibrosarcomatous form (FS-DFSP), looking, retrospectively, at the outcome of all patients affected by primary DFSP treated at our institution from 1993 to 2012 and analyzing the molecular profile of 5 DFSPs and 5 FS-DFSPs by an integrated genomics approach (whole transcriptome sequencing, copy number analysis, FISH, qRT-PCR, IHC). The presence of fibrosarcomatous features was identified in 20 (7.6%) patients out of 263 DFSP. All cases were treated with macroscopic complete surgery. A local relapse occurred in 4 of 23 patients who received a microscopic marginal surgery (2 classic DFSP, 2 FS-DFSP), while metastasis affected 2 patients, both FS-DFSP (10% of FS-DFSP), being the first event. DFSP evolution to FS-DFSP was paralleled by a transcriptional reprogramming. The recurrent loss of chromosome 22q appeared to contribute to this phenomenon by promoting the expression of epigenetic regulators, such as EZH2. Loss of the p16/CDKN2A/INK4A locus at 9p was also observed in two FS-DFSP metastatic cases. IMPLICATIONS FS-DFSP is a rare subgroup among DFSP, with a 10% metastatic risk, that was independent from local recurrence and that was not observed in DFSP, that were all cured by wide surgery. Chromosome 22q deletion might play a role in FS-DFSP, and p16 loss may convey a poor outcome. EZH2 dysregulation was also found and represents a druggable target. Mol Cancer Res; 14(9); 820-9. ©2016 AACR.
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Affiliation(s)
- Silvia Stacchiotti
- Adult Mesenchymal Tumour and Rare Cancer Medical Oncology Unit, Cancer Medicine Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Annalisa Astolfi
- Centro Interdipartimentale di Ricerche sul Cancro G. Prodi, Università di Bologna, Bologna, Italy
| | - Alessandro Gronchi
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Andrea Fontana
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Maria A Pantaleo
- Dipartimento di Medicina Sperimentale, Specialistica e Diagnostica, Università di Bologna, Bologna, Italy
| | - Tiziana Negri
- Department of Diagnostic Pathology and Laboratory, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Monica Brenca
- Unit of Experimental Oncology 1, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Marcella Tazzari
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Milena Urbini
- Centro Interdipartimentale di Ricerche sul Cancro G. Prodi, Università di Bologna, Bologna, Italy
| | - Valentina Indio
- Centro Interdipartimentale di Ricerche sul Cancro G. Prodi, Università di Bologna, Bologna, Italy
| | - Chiara Colombo
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Stefano Radaelli
- Melanoma and Sarcoma Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvia Brich
- Department of Diagnostic Pathology and Laboratory, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| | - Angelo P Dei Tos
- Department of Anatomic Pathology, General Hospital of Treviso, Treviso, Italy
| | - Paolo G Casali
- Adult Mesenchymal Tumour and Rare Cancer Medical Oncology Unit, Cancer Medicine Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Chiara Castelli
- Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Gian Paolo Dagrada
- Department of Diagnostic Pathology and Laboratory, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Silvana Pilotti
- Department of Diagnostic Pathology and Laboratory, Laboratory of Experimental Molecular Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Roberta Maestro
- Unit of Experimental Oncology 1, CRO Aviano National Cancer Institute, Aviano, Italy
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