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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Dow LF, Case AM, Paustian MP, Pinkerton BR, Simeon P, Trippier PC. The evolution of small molecule enzyme activators. RSC Med Chem 2023; 14:2206-2230. [PMID: 37974956 PMCID: PMC10650962 DOI: 10.1039/d3md00399j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
There is a myriad of enzymes within the body responsible for maintaining homeostasis by providing the means to convert substrates to products as and when required. Physiological enzymes are tightly controlled by many signaling pathways and their products subsequently control other pathways. Traditionally, most drug discovery efforts focus on identifying enzyme inhibitors, due to upregulation being prevalent in many diseases and the existence of endogenous substrates that can be modified to afford inhibitor compounds. As enzyme downregulation and reduction of endogenous activators are observed in multiple diseases, the identification of small molecules with the ability to activate enzymes has recently entered the medicinal chemistry toolbox to afford chemical probes and potential therapeutics as an alternative means to intervene in diseases. In this review we highlight the progress made in the identification and advancement of non-kinase enzyme activators and their potential in treating various disease states.
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Affiliation(s)
- Louise F Dow
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Alfie M Case
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Megan P Paustian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Braeden R Pinkerton
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Princess Simeon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha NE 68106 USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center Omaha NE 68106 USA
- UNMC Center for Drug Discovery, University of Nebraska Medical Center Omaha NE 68106 USA
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3
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Xu L, Yan X, Wang J, Zhao Y, Liu Q, Fu J, Shi X, Su J. The Roles of Histone Deacetylases in the Regulation of Ovarian Cancer Metastasis. Int J Mol Sci 2023; 24:15066. [PMID: 37894746 PMCID: PMC10606123 DOI: 10.3390/ijms242015066] [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: 07/31/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Ovarian cancer is the most lethal gynecologic malignancy, and metastasis is the major cause of death in patients with ovarian cancer, which is regulated by the coordinated interplay of genetic and epigenetic mechanisms. Histone deacetylases (HDACs) are enzymes that can catalyze the deacetylation of histone and some non-histone proteins and that are involved in the regulation of a variety of biological processes via the regulation of gene transcription and the functions of non-histone proteins such as transcription factors and enzymes. Aberrant expressions of HDACs are common in ovarian cancer. Many studies have found that HDACs are involved in regulating a variety of events associated with ovarian cancer metastasis, including cell migration, invasion, and the epithelial-mesenchymal transformation. Herein, we provide a brief overview of ovarian cancer metastasis and the dysregulated expression of HDACs in ovarian cancer. In addition, we discuss the roles of HDACs in the regulation of ovarian cancer metastasis. Finally, we discuss the development of compounds that target HDACs and highlight their importance in the future of ovarian cancer therapy.
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Affiliation(s)
- Long Xu
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
- School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China
| | - Xiaoyu Yan
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Jian Wang
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Yuanxin Zhao
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Qingqing Liu
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Jiaying Fu
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Xinyi Shi
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
| | - Jing Su
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun 130021, China; (L.X.); (X.Y.); (J.W.); (Y.Z.); (Q.L.); (J.F.); (X.S.)
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4
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Pan Y, van der Watt PJ, Kay SA. E-box binding transcription factors in cancer. Front Oncol 2023; 13:1223208. [PMID: 37601651 PMCID: PMC10437117 DOI: 10.3389/fonc.2023.1223208] [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: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
E-boxes are important regulatory elements in the eukaryotic genome. Transcription factors can bind to E-boxes through their basic helix-loop-helix or zinc finger domain to regulate gene transcription. E-box-binding transcription factors (EBTFs) are important regulators of development and essential for physiological activities of the cell. The fundamental role of EBTFs in cancer has been highlighted by studies on the canonical oncogene MYC, yet many EBTFs exhibit common features, implying the existence of shared molecular principles of how they are involved in tumorigenesis. A comprehensive analysis of TFs that share the basic function of binding to E-boxes has been lacking. Here, we review the structure of EBTFs, their common features in regulating transcription, their physiological functions, and their mutual regulation. We also discuss their converging functions in cancer biology, their potential to be targeted as a regulatory network, and recent progress in drug development targeting these factors in cancer therapy.
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Affiliation(s)
- Yuanzhong Pan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pauline J. van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Steve A. Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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5
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Suzuki T, Conant A, Curow C, Alexander A, Ioffe Y, Unternaehrer JJ. Role of epithelial-mesenchymal transition factor SNAI1 and its targets in ovarian cancer aggressiveness. JOURNAL OF CANCER METASTASIS AND TREATMENT 2023; 9:25. [PMID: 38009093 PMCID: PMC10673625 DOI: 10.20517/2394-4722.2023.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy in the USA. For over twenty years, epithelial-mesenchymal transition (EMT) has been characterized extensively in development and disease. The dysregulation of this process in cancer has been identified as a mechanism by which epithelial tumors become more aggressive, allowing them to survive and invade distant tissues. This occurs in part due to the increased expression of the EMT transcription factor, SNAI1 (Snail). In the case of epithelial ovarian cancer, Snail has been shown to contribute to cancer invasion, stemness, chemoresistance, and metabolic changes. Thus, in this review, we focus on summarizing current findings on the role of EMT (specifically, factors downstream of Snail) in determining ovarian cancer aggressiveness.
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Affiliation(s)
- Tise Suzuki
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Ashlyn Conant
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
| | - Casey Curow
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- University of Redlands, Department of Biology, Redlands, CA 92373, USA
| | - Audrey Alexander
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Division of Natural and Mathematical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA
| | - Yevgeniya Ioffe
- Department of Gynecology and Obstetrics, Division of Gynecologic Oncology, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Juli J Unternaehrer
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92354, USA
- Department of Gynecology and Obstetrics, Loma Linda University, Loma Linda, CA 92354, USA
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6
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Yoodee S, Thongboonkerd V. Epigenetic regulation of epithelial-mesenchymal transition during cancer development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 380:1-61. [PMID: 37657856 DOI: 10.1016/bs.ircmb.2023.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
Epithelial-mesenchymal transition (EMT) plays essential roles in promoting malignant transformation of epithelial cells, leading to cancer progression and metastasis. During EMT-induced cancer development, a wide variety of genes are dramatically modified, especially down-regulation of epithelial-related genes and up-regulation of mesenchymal-related genes. Expression of other EMT-related genes is also modified during the carcinogenic process. Especially, epigenetic modifications are observed in the EMT-related genes, indicating their involvement in cancer development. Mechanically, epigenetic modifications of histone, DNA, mRNA and non-coding RNA stably change the EMT-related gene expression at transcription and translation levels. Herein, we summarize current knowledge on epigenetic regulatory mechanisms observed in EMT process relate to cancer development in humans. The better understanding of epigenetic regulation of EMT during cancer development may lead to improvement of drug design and preventive strategies in cancer therapy.
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Affiliation(s)
- Sunisa Yoodee
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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7
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Anerillas C, Altés G, Gorospe M. MAPKs in the early steps of senescence implemEMTation. Front Cell Dev Biol 2023; 11:1083401. [PMID: 37009481 PMCID: PMC10060890 DOI: 10.3389/fcell.2023.1083401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Evidence is accumulating that the earliest stages of the DNA damage response can direct cells toward senescence instead of other cell fates. In particular, tightly regulated signaling through Mitogen-Activated Protein Kinases (MAPKs) in early senescence can lead to a sustained pro-survival program and suppress a pro-apoptotic program. Importantly, an epithelial-to-mesenchymal Transition (EMT)-like program appears essential for preventing apoptosis and favoring senescence following DNA damage. In this review, we discuss how MAPKs might influence EMT features to promote a senescent phenotype that increases cell survival at the detriment of tissue function.
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8
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Casey MJ, Call AM, Thorpe AV, Jette CA, Engel ME, Stewart RA. The scaffolding function of LSD1/KDM1A reinforces a negative feedback loop to repress stem cell gene expression during primitive hematopoiesis. iScience 2022; 26:105737. [PMID: 36594016 PMCID: PMC9803847 DOI: 10.1016/j.isci.2022.105737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/15/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Lsd1/Kdm1a functions both as a histone demethylase enzyme and as a scaffold for assembling chromatin modifier and transcription factor complexes to regulate gene expression. The relative contributions of Lsd1's demethylase and scaffolding functions during embryogenesis are not known. Here, we analyze two independent zebrafish lsd1/kdm1a mutant lines and show Lsd1 is required to repress primitive hematopoietic stem cell gene expression. Lsd1 rescue constructs containing point mutations that selectively abrogate its demethylase or scaffolding capacity demonstrate the scaffolding function of Lsd1, not its demethylase activity, is required for repression of gene expression in vivo. Lsd1's SNAG-binding domain mediates its scaffolding function and reinforces a negative feedback loop to repress the expression of SNAG-domain-containing genes during embryogenesis, including gfi1 and snai1/2. Our findings reveal a model in which the SNAG-binding and scaffolding function of Lsd1, and its associated negative feedback loop, provide transient and reversible regulation of gene expression during hematopoietic development.
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Affiliation(s)
- Mattie J. Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Alexandra M. Call
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Annika V. Thorpe
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Cicely A. Jette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA
| | - Michael E. Engel
- Department of Pediatric Hematology/Oncology, Emily Couric Cancer Center, University of Virginia, Charlottesville, VA 22903, USA,Corresponding author
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT 84112, USA,Corresponding author
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9
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Engineered nanoparticles as emerging gene/drug delivery systems targeting the nuclear factor-κB protein and related signaling pathways in cancer. Biomed Pharmacother 2022; 156:113932. [DOI: 10.1016/j.biopha.2022.113932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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10
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Human Cytomegalovirus Induces Vitamin-D Resistance In Vitro by Dysregulating the Transcriptional Repressor Snail. Viruses 2022; 14:v14092004. [PMID: 36146811 PMCID: PMC9505537 DOI: 10.3390/v14092004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
Vitamin-D supplementation is considered to play a beneficial role against multiple viruses due to its immune-regulating and direct antimicrobial effects. In contrast, the human cytomegalovirus (HCMV) has shown to be resistant to treatment with vitamin D in vitro by downregulation of the vitamin-D receptor. In this study, we aimed to elucidate the mechanism and possible biological consequences of vitamin-D resistance during HCMV infection. Mechanistically, HCMV induced vitamin-D resistance by downregulating the vitamin-D receptor (VDR) within hours of lytic infection. We found that the VDR was inhibited at the promoter level, and treatment with histone deacetylase inhibitors could restore VDR expression. VDR downregulation highly correlated with the upregulation of the transcriptional repressor Snail1, a mechanism likely contributing to the epigenetic inactivation of the VDR promoter, since siRNA-mediated knockdown of Snail partly restored levels of VDR expression. Finally, we found that direct addition of the vitamin-D-inducible antimicrobial peptide LL-37 strongly and significantly reduced viral titers in infected fibroblasts, highlighting VDR biological relevance and the potential of vitamin-D-inducible peptides for the antiviral treatment of vitamin-D deficient patients.
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11
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Singh T, Kaur P, Singh P, Singh S, Munshi A. Differential molecular mechanistic behavior of HDACs in cancer progression. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:171. [PMID: 35972597 DOI: 10.1007/s12032-022-01770-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022]
Abstract
Genetic aberration including mutation in oncogenes and tumor suppressor genes transforms normal cells into tumor cells. Epigenetic modifications work concertedly with genetic factors in controlling cancer development. Histone acetyltransferases (HATs), histone deacetylases (HDACs), DNA methyltransferases (DNMTs) and chromatin structure modifier are prospective epigenetic regulators. Specifically, HDACs are histone modifiers regulating the expression of genes implicated in cell survival, growth, apoptosis, and metabolism. The majority of HDACs are highly upregulated in cancer, whereas some have a varied function and expression in cancer progression. Distinct HDACs have a positive and negative role in controlling cancer progression. HDACs are also significantly involved in tumor cells acquiring metastatic and angiogenic potential in order to withstand the anti-tumor microenvironment. HDACs' role in modulating metabolic genes has also been associated with tumor development and survival. This review highlights and discusses the molecular mechanisms of HDACs by which they regulate cell survival, apoptosis, metastasis, invasion, stemness potential, angiogenesis, and epithelial to mesenchymal transitions (EMT) in tumor cells. HDACs are the potential target for anti-cancer drug development and various inhibitors have been developed and FDA approved for a variety of cancers. The primary HDAC inhibitors with proven anti-cancer efficacy have also been highlighted in this review.
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Affiliation(s)
- Tashvinder Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India
| | - Prabhsimran Kaur
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India
| | | | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India.
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, 151401, India.
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12
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Ding X, Zhu Z, Lapek J, McMillan EA, Zhang A, Chung CY, Dubbury S, Lapira J, Firdaus S, Kang X, Gao J, Oyer J, Chionis J, Rollins RA, Li L, Niessen S, Bagrodia S, Zhang L, VanArsdale T. PARP1-SNAI2 transcription axis drives resistance to PARP inhibitor, Talazoparib. Sci Rep 2022; 12:12501. [PMID: 35864202 PMCID: PMC9304387 DOI: 10.1038/s41598-022-16623-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
The synthetic lethal association between BRCA deficiency and poly (ADP-ribose) polymerase (PARP) inhibition supports PARP inhibitor (PARPi) clinical efficacy in BRCA-mutated tumors. PARPis also demonstrate activity in non-BRCA mutated tumors presumably through induction of PARP1-DNA trapping. Despite pronounced clinical response, therapeutic resistance to PARPis inevitably develops. An abundance of knowledge has been built around resistance mechanisms in BRCA-mutated tumors, however, parallel understanding in non-BRCA mutated settings remains insufficient. In this study, we find a strong correlation between the epithelial-mesenchymal transition (EMT) signature and resistance to a clinical PARPi, Talazoparib, in non-BRCA mutated tumor cells. Genetic profiling demonstrates that SNAI2, a master EMT transcription factor, is transcriptionally induced by Talazoparib treatment or PARP1 depletion and this induction is partially responsible for the emerging resistance. Mechanistically, we find that the PARP1 protein directly binds to SNAI2 gene promoter and suppresses its transcription. Talazoparib treatment or PARP1 depletion lifts PARP1-mediated suppression and increases chromatin accessibility around SNAI2 promoters, thus driving SNAI2 transcription and drug resistance. We also find that depletion of the chromatin remodeler CHD1L suppresses SNAI2 expression and reverts acquired resistance to Talazoparib. The PARP1/CHD1L/SNAI2 transcription axis might be therapeutically targeted to re-sensitize Talazoparib in non-BRCA mutated tumors.
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Affiliation(s)
- Xia Ding
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
| | - Zhou Zhu
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,AstraZeneca, Inc., Gaithersburg, MD, 20878, USA
| | - John Lapek
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Belharra Therapeutics, Inc., San Diego, CA, 92121, USA
| | - Elizabeth A McMillan
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Odyssey Therapeutics., San Diego, CA, 92121, USA
| | - Alexander Zhang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Chi-Yeh Chung
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Sara Dubbury
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Bristol Myers Squibb., San Diego, CA, 92121, USA
| | - Jennifer Lapira
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Sarah Firdaus
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Xiaolin Kang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Jingjin Gao
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Turning Point Therapeutics., San Diego, CA, 92121, USA
| | - Jon Oyer
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - John Chionis
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Genesis Therapeutics., San Diego, CA, 92121, USA
| | | | - Lianjie Li
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Sherry Niessen
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.,Belharra Therapeutics, Inc., San Diego, CA, 92121, USA
| | - Shubha Bagrodia
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA
| | - Lianglin Zhang
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
| | - Todd VanArsdale
- Oncology Research Unit, Pfizer, Inc., San Diego, CA, 92121, USA.
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13
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Pang QY, Tan TZ, Sundararajan V, Chiu YC, Chee EYW, Chung VY, Choolani MA, Huang RYJ. 3D genome organization in the epithelial-mesenchymal transition spectrum. Genome Biol 2022; 23:121. [PMID: 35637517 PMCID: PMC9150291 DOI: 10.1186/s13059-022-02687-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
Background The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests that regulation of EMT may occur at a higher order of three-dimensional genome level. Results We perform Hi-C analysis and combine ChIP-seq data across cancer cell lines representing different EMT states. We demonstrate that the epithelial and mesenchymal genes are regulated distinctively. We find that EMT genes are regulated within their topologically associated domains (TADs), with only a subset of mesenchymal genes being influenced by A/B compartment switches, indicating topological remodeling is required in the transcriptional regulation of these genes. At the TAD level, epithelial and mesenchymal genes are associated with different regulatory trajectories. The epithelial gene-residing TADs are enriched with H3K27me3 marks in the mesenchymal-like states. The mesenchymal gene-residing TADs, which do not show enrichment of H3K27me3 in epithelial-like states, exhibit increased interaction frequencies with regulatory elements in the mesenchymal-like states. Conclusions We propose a novel workflow coupling immunofluorescence and dielectrophoresis to unravel EMT heterogeneity at single-cell resolution. The predicted three-dimensional structures of chromosome 10, harboring Vimentin, identify cell clusters of different states. Our results pioneer a novel avenue to decipher the complexities underlying the regulation of EMT and may infer the barriers of plasticity in the 3D genome context. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02687-x.
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Affiliation(s)
- Qing You Pang
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University Health System, Singapore, 119077, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, 117599, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, 117599, Singapore.,Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore, 117599, Singapore
| | - Vignesh Sundararajan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, 117599, Singapore
| | - Yi-Chia Chiu
- School of Medicine, College of Medicine, National Taiwan University, No. 1, Ren-Ai Road Section I, Taipei, 10051, Taiwan
| | - Edward Yu Wing Chee
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, 117599, Singapore
| | - Vin Yee Chung
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, 117599, Singapore
| | - Mahesh A Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University Health System, Singapore, 119077, Singapore
| | - Ruby Yun-Ju Huang
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University Health System, Singapore, 119077, Singapore. .,School of Medicine, College of Medicine, National Taiwan University, No. 1, Ren-Ai Road Section I, Taipei, 10051, Taiwan. .,Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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14
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Chen M, Li S, Srinivasasainagendra V, Sharma M, Li Z, Tiwari H, Tollefsbol TO, Li Y. Maternal soybean genistein on prevention of later-life breast cancer through inherited epigenetic regulations. Carcinogenesis 2022; 43:190-202. [PMID: 35084457 PMCID: PMC9036993 DOI: 10.1093/carcin/bgac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer has strong developmental origins and maternal nutrition composition may influence later-life breast cancer risk in the offspring. Our study focused on a bioactive dietary component, genistein (GE) enriched in soybean products, to investigate specific timing of maternal GE exposure that may influence preventive efficacy of GE on offspring breast cancer later in life, and to explore the potential epigenetic mechanisms. Our results indicate a time-dependent effect of maternal GE exposure on early-life breast cancer development in offspring mice. Through integrated transcriptome and methylome analyses, we identified several candidate genes showing significantly differential gene expression and DNA methylation changes. We further found maternal long-term GE treatment can induce inherited epigenetic landmark changes in a candidate tumor suppressor gene, Trp63, resulting in transcriptional activation of Trp63 and induction of the downstream target genes. Our results suggest that maternal long-term exposure to soybean GE may influence early-life epigenetic reprogramming processes, which may contribute to its temporal preventive effects on breast cancer in the offspring. This study provides important mechanistic insights into an appropriate maternal administration of soybean products on prevention of breast cancer later in offspring life.
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Affiliation(s)
- Min Chen
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Manvi Sharma
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zhenhai Li
- Department of Obstetrics, Gynecology & Women’s Heath, University of Missouri, Columbia, Missouri, USA
| | - Hemant Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yuanyuan Li
- Department of Obstetrics, Gynecology & Women’s Heath, University of Missouri, Columbia, Missouri, USA
- Department of Surgery, University of Missouri, Columbia, Missouri, USA
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15
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Clugston A, Bodnar A, Cerqueira DM, Phua YL, Lawler A, Boggs K, Pfenning A, Ho J, Kostka D. Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. Genomics 2022; 114:278-291. [PMID: 34942352 PMCID: PMC8792369 DOI: 10.1016/j.ygeno.2021.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 01/03/2023]
Abstract
Mammalian nephrons originate from a population of nephron progenitor cells, and changes in these cells' transcriptomes contribute to the cessation of nephrogenesis, an important determinant of nephron number. To characterize microRNA (miRNA) expression and identify putative cis-regulatory regions, we collected nephron progenitor cells from mouse kidneys at embryonic day 14.5 and postnatal day zero and assayed small RNA expression and transposase-accessible chromatin. We detect expression of 1104 miRNA (114 with expression changes), and 46,374 chromatin accessible regions (2103 with changes in accessibility). Genome-wide, our data highlight processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways. Furthermore, they identify new candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in nephron progenitor cell differentiation. Finally, we associate expression-changing miRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements and target genes. These analyses highlight new putative cis-regulatory loci for miRNA in nephron progenitors.
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Affiliation(s)
- Andrew Clugston
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Andrew Bodnar
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Débora Malta Cerqueira
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Yu Leng Phua
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Alyssa Lawler
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kristy Boggs
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andreas Pfenning
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
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16
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Nowak E, Bednarek I. Aspects of the Epigenetic Regulation of EMT Related to Cancer Metastasis. Cells 2021; 10:3435. [PMID: 34943943 PMCID: PMC8700111 DOI: 10.3390/cells10123435] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/28/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Epithelial to mesenchymal transition (EMT) occurs during the pathological process associated with tumor progression and is considered to influence and promote the metastatic cascade. Characterized by loss of cell adhesion and apex base polarity, EMT enhances cell motility and metastasis. The key markers of the epithelial to mesenchymal transition are proteins characteristic of the epithelial phenotype, e.g., E-cadherin, cytokeratins, occludin, or desmoplakin, the concentration and activity of which are reduced during this process. On the other hand, as a result of acquiring the characteristics of mesenchymal cells, an increased amount of N-cadherin, vimentin, fibronectin, or vitronectin is observed. Importantly, epithelial cells undergo partial EMT where some of the cells show both epithelial and mesenchymal characteristics. The significant influence of epigenetic regulatory mechanisms is observed in the gene expression involved in EMT. Among the epigenetic modifications accompanying incorrect genetic reprogramming in cancer are changes in the level of DNA methylation within the CpG islands and posttranslational covalent changes of histone proteins. All observed modifications, which are stable but reversible changes, affect the level of gene expression leading to the development and progression of the disease, and consequently affect the uncontrolled growth of the population of cancer cells.
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Affiliation(s)
- Ewa Nowak
- Department of Biotechnology and Genetic Engineering, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland;
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17
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Ray SK, Mukherjee S. Epigenetic Reprogramming and Landscape of Transcriptomic Interactions: Impending Therapeutic Interference of Triple-Negative Breast Cancer in Molecular Medicine. Curr Mol Med 2021; 22:835-850. [PMID: 34872474 DOI: 10.2174/1566524021666211206092437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
The mechanisms governing the development and progression of cancers are believed to be the consequence of hereditary deformities and epigenetic modifications. Accordingly, epigenetics has become an incredible and progressively explored field of research to discover better prevention and therapy for neoplasia, especially triple-negative breast cancer (TNBC). It represents 15-20% of all invasive breast cancers and will, in general, have bellicose histological highlights and poor clinical outcomes. In the early phases of triple-negative breast carcinogenesis, epigenetic deregulation modifies chromatin structure and influences the plasticity of cells. It up-keeps the oncogenic reprogramming of malignant progenitor cells with the acquisition of unrestrained selfrenewal capacities. Genomic impulsiveness in TNBC prompts mutations, copy number variations, as well as genetic rearrangements, while epigenetic remodeling includes an amendment by DNA methylation, histone modification, and noncoding RNAs of gene expression profiles. It is currently evident that epigenetic mechanisms assume a significant part in the pathogenesis, maintenance, and therapeutic resistance of TNBC. Although TNBC is a heterogeneous malaise that is perplexing to describe and treat, the ongoing explosion of genetic and epigenetic research will help to expand these endeavors. Latest developments in transcriptome analysis have reformed our understanding of human diseases, including TNBC at the molecular medicine level. It is appealing to envision transcriptomic biomarkers to comprehend tumor behavior more readily regarding its cellular microenvironment. Understanding these essential biomarkers and molecular changes will propel our capability to treat TNBC adequately. This review will depict the different aspects of epigenetics and the landscape of transcriptomics in triple-negative breast carcinogenesis and their impending application for diagnosis, prognosis, and treatment decision with the view of molecular medicine.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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18
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Epithelial Mesenchymal Transition and its transcription factors. Biosci Rep 2021; 42:230017. [PMID: 34708244 PMCID: PMC8703024 DOI: 10.1042/bsr20211754] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Epithelial–mesenchymal transition or EMT is an extremely dynamic process involved in conversion of epithelial cells into mesenchymal cells, stimulated by an ensemble of signaling pathways, leading to change in cellular morphology, suppression of epithelial characters and acquisition of properties such as enhanced cell motility and invasiveness, reduced cell death by apoptosis, resistance to chemotherapeutic drugs etc. Significantly, EMT has been found to play a crucial role during embryonic development, tissue fibrosis and would healing, as well as during cancer metastasis. Over the years, work from various laboratories have identified a rather large number of transcription factors (TFs) including the master regulators of EMT, with the ability to regulate the EMT process directly. In this review, we put together these EMT TFs and discussed their role in the process. We have also tried to focus on their mechanism of action, their interdependency, and the large regulatory network they form. Subsequently, it has become clear that the composition and structure of the transcriptional regulatory network behind EMT probably varies based upon various physiological and pathological contexts, or even in a cell/tissue type-dependent manner.
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19
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Noguchi S, Hirano K, Tanimoto N, Shimada T, Akiyoshi H. SLUG is upregulated and induces epithelial mesenchymal transition in canine oral squamous cell carcinoma. Vet Comp Oncol 2021; 20:134-141. [PMID: 34310030 DOI: 10.1111/vco.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/11/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022]
Abstract
SLUG, encoded by the Snai2 gene, is known to play a role in epithelial-mesenchymal transition (EMT), which contributes to cell invasion and metastasis in some types of human carcinomas. However, the mechanisms and roles of EMT in canine squamous cell carcinoma (SCC) have not yet been elucidated. We have previously established canine oral SCC cell lines, including tonsillar SCC, and in this study, we evaluated the effects of SLUG on the phenotypes regarding EMT of canine SCC cells. First, immunohistochemical analysis revealed that SLUG is upregulated in canine oral SCC tissues compared to that in non-tumoural oral mucosa. Furthermore, gain-of-function and loss-of-function of SLUG revealed that SLUG partly contributed to migration and invasion of cells, as well as the upregulation of EMT markers such as vimentin and SNAIL. Thus, the current study suggests that SLUG promotes cell migration and invasion through EMT induction in canine oral SCC, as well as human cancers.
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Affiliation(s)
- Shunsuke Noguchi
- Laboratory of Veterinary Radiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Kazuya Hirano
- Laboratory of Veterinary Radiology, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Osaka, Japan
| | - Nanami Tanimoto
- Laboratory of Veterinary Radiology, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Osaka, Japan
| | - Terumasa Shimada
- Veterinary Medical Center, Osaka Prefecture University, Osaka, Japan
| | - Hideo Akiyoshi
- Laboratory of Veterinary Surgery, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
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20
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Subbalakshmi AR, Sahoo S, Biswas K, Jolly MK. A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT). Cells Tissues Organs 2021; 211:689-702. [PMID: 33567424 DOI: 10.1159/000512520] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity comprises reversible transitions among epithelial, hybrid epithelial/mesenchymal (E/M) and mesenchymal phenotypes, and underlies various aspects of aggressive tumor progression such as metastasis, therapy resistance, and immune evasion. The process of cells attaining one or more hybrid E/M phenotypes is termed as partial epithelial mesenchymal transition (EMT). Cells in hybrid E/M phenotype(s) can be more aggressive than those in either fully epithelial or mesenchymal state. Thus, identifying regulators of hybrid E/M phenotypes is essential to decipher the rheostats of phenotypic plasticity and consequent accelerators of metastasis. Here, using a computational systems biology approach, we demonstrate that SLUG (SNAIL2) - an EMT-inducing transcription factor - can inhibit cells from undergoing a complete EMT and thus stabilize them in hybrid E/M phenotype(s). It expands the parametric range enabling the existence of a hybrid E/M phenotype, thereby behaving as a phenotypic stability factor. Our simulations suggest that this specific property of SLUG emerges from the topology of the regulatory network it forms with other key regulators of epithelial-mesenchymal plasticity. Clinical data suggest that SLUG associates with worse patient prognosis across multiple carcinomas. Together, our results indicate that SLUG can stabilize hybrid E/M phenotype(s).
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Affiliation(s)
- Ayalur R Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Kuheli Biswas
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India,
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21
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Tripathi SC, Jolly MK, Mani SA, Levine H. Editorial: Characterizing the Multi-Faceted Dynamics of Tumor Cell Plasticity. Front Mol Biosci 2021; 7:630276. [PMID: 33553244 PMCID: PMC7855584 DOI: 10.3389/fmolb.2020.630276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston MA, United States
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22
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Cheng F, Dou J, Zhang Y, Wang X, Wei H, Zhang Z, Cao Y, Wu Z. Urolithin A Inhibits Epithelial-Mesenchymal Transition in Lung Cancer Cells via P53-Mdm2-Snail Pathway. Onco Targets Ther 2021; 14:3199-3208. [PMID: 34040386 PMCID: PMC8139733 DOI: 10.2147/ott.s305595] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The epithelial-to-mesenchymal transition (EMT) is a fundamental process in tumor progression that endows cancer cells with migratory and invasive potential. Snail, a zinc finger transcriptional repressor, plays an important role in the induction of EMT by directly repressing the key epithelial marker E-cadherin. Here, we assessed the effect of urolithin A, a major metabolite from pomegranate ellagitannins, on Snail expression and EMT process. METHODS The role of Snail in urolithin A-induced EMT inhibition in lung cancer cells was explored by wound healing assay and cell invasion assay. The qRT-PCR and CHX assay were performed to investigate how urolithin A regulates Snail expression. Immunoprecipitation assays were established to determine the effects of urolithin A in mdm2-Snail interaction. In addition, the expression of p53 was manipulated to explore its effect on the expression of mdm2 and Snail. RESULTS The urolithin A dose-dependently upregulated epithelial marker and decreased mesenchymal markers in lung cancer cells. In addition, exposure to urolithin A decreased cell migratory and invasive capacity. We have further demonstrated that urolithin A inhibits lung cancer cell EMT by decreasing Snail protein expression and activity. Mechanistically, urolithin A disrupts the interaction of p53 and mdm2 which leads Snail ubiquitination and degradation. CONCLUSION We conclude that urolithin A could inhibit EMT process by controlling mainly Snail expression. These results highlighted the role of pomegranate in regulation of EMT program in lung cancer.
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Affiliation(s)
- Feng Cheng
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Jintao Dou
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- School of Anesthesiology, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Yong Zhang
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- School of Clinical Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Xiang Wang
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Huijun Wei
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Zhijian Zhang
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Yuxiang Cao
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- Provincial Engineering Laboratory for Screening and Re-Evaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wannan Medical College, Wuhu, 241001, People’s Republic of China
| | - Zhihao Wu
- Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- Anhui Province Key Laboratory of Active Biological Macro-Molecules Research, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001, People’s Republic of China
- Correspondence: Zhihao Wu Research Laboratory of Tumor Microenvironment, Wannan Medical College, Wuhu, 241001, People’s Republic of China Email
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23
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Sunnaghatta Nagaraja S, Raviraj R, Selvakumar I, Dharmalingam D, Ramadas N, Chellappan DR, Ponnachipudhur Chinnaswamy P, Nagarajan D. Radiation-induced H3K9 tri-methylation in E-cadherin promoter during lung EMT: in vitro and in vivo approaches using vanillin. Free Radic Res 2020; 54:540-555. [PMID: 32842802 DOI: 10.1080/10715762.2020.1814274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radiotherapy is an important treatment regime for lung cancer, worldwide. However, radiation-induced pneumonitis and fibrosis are the treatment-limiting toxicities among patients who have undergone radiotherapy. The epithelial cells via epithelial to mesenchymal transition [EMT] acquires mesenchymal phenotype, which ultimately leads to fibrosis. Many investigations are focussed on understanding the signalling pathways mediating in EMT, however, the role of histone methylation is less understood in radiation-induced lung EMT. In the present study, we analysed the effect of vanillin, an antioxidant, on histone methylation during radiation-induced EMT. The thoracic region of Wistar rats was irradiated with a fractionated dose of X-ray (3 Gy/day) for two weeks (total of 30 Gy). The irradiated animals were sacrificed at the 8th and 16th weeks and tissues were used for analyses. Our data showed that radiation decreased the level of antioxidant enzymes such as SOD, catalase and reduced glutathione that would ultimately enhance oxidative stress in the tissues. Histopathological analysis revealed that radiation increased the infiltration of inflammatory cells to the tissue injury site. Total global histone methylation was increased upon irradiation, which was effectively prevented by vanillin administration. Vanillin enhanced E-cadherin expression and decreased the mesenchymal markers N-cadherin and vimentin in the irradiated lung tissue. The ChIP-qPCR analysis suggested that snail expression in the nucleus might involve in the enrichment of suppressive marker H3K9me3 on the E-cadherin promoter. Finally, we suggested that vanillin administration decreased radiation-induced oxidative stress and EMT expression. Additionally, irradiation increased the H3K9 methylation status with nuclear translocation of snail during lung EMT.
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Affiliation(s)
| | - Raghavi Raviraj
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Ilakya Selvakumar
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | | | - Nirupama Ramadas
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | | | | | - Devipriya Nagarajan
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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24
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Sterneck E, Poria DK, Balamurugan K. Slug and E-Cadherin: Stealth Accomplices? Front Mol Biosci 2020; 7:138. [PMID: 32760736 PMCID: PMC7371942 DOI: 10.3389/fmolb.2020.00138] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
During physiological epithelial-mesenchymal transition (EMT), which is important for embryogenesis and wound healing, epithelial cells activate a program to remodel their structure and achieve a mesenchymal fate. In cancer cells, EMT confers increased invasiveness and tumor-initiating capacity, which contribute to metastasis and resistance to therapeutics. However, cellular plasticity that navigates between epithelial and mesenchymal states and maintenance of a hybrid or partial E/M phenotype appears to be even more important for cancer progression. Besides other core EMT transcription factors, the well-characterized Snail-family proteins Snail (SNAI1) and Slug (SNAI2) play important roles in both physiological and pathological EMT. Often mentioned in unison, they do, however, differ in their functions in many scenarios. Indeed, Slug expression does not always correlate with complete EMT or loss of E-cadherin (CDH1). For example, Slug plays important roles in mammary epithelial cell progenitor cell lineage commitment and differentiation, DNA damage responses, hematopoietic stem cell self-renewal, and in pathologies such as pulmonary fibrosis and atherosclerosis. In this Perspective, we highlight Slug functions in mammary epithelial cells and breast cancer as a “non-EMT factor” in basal epithelial cells and stem cells with focus reports that demonstrate co-expression of Slug and E-cadherin. We speculate that Slug and E-cadherin may cooperate in normal mammary gland and breast cancer/stem cells and advocate for functional assessment of such Slug+/E-cadherinlow/+ (SNAI2+/CDH1low/+) “basal-like epithelial” cells. Thus, Slug may be regarded as less of an EMT factor than driver of the basal epithelial cell phenotype.
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Affiliation(s)
- Esta Sterneck
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Dipak K Poria
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Kuppusamy Balamurugan
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
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25
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Wang Y, Shi Y, Tao M, Zhuang S, Liu N. Peritoneal fibrosis and epigenetic modulation. Perit Dial Int 2020; 41:168-178. [PMID: 32662737 DOI: 10.1177/0896860820938239] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Peritoneal dialysis (PD) is an effective treatment for patients with end-stage renal disease. However, peritoneal fibrosis (PF) is a common complication that ultimately leads to ultrafiltration failure and discontinuation of PD after long-term PD therapy. There is currently no effective therapy to prevent or delay this pathologic process. Recent studies have reported epigenetic modifications involved in PF, and accumulating evidence suggests that epigenetic therapies may have the potential to prevent and treat PF clinically. The major epigenetic modifications in PF include DNA methylation, histone modification, and noncoding RNAs. The mechanisms of epigenetic regulation in PF are complex, predominantly involving modification of signaling molecules, transcriptional factors, and genes. This review will describe the mechanisms of epigenetic modulation in PF and discuss the possibility of targeting them to prevent and treat this complication.
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Affiliation(s)
- Yi Wang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, China
| | - Yingfeng Shi
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, China
| | - Min Tao
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, China.,Department of Medicine, Rhode Island Hospital and Alpert Medical School, Brown University, Providence, RI, USA
| | - Na Liu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, China
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SNAI1-Driven Sequential EMT Changes Attributed by Selective Chromatin Enrichment of RAD21 and GRHL2. Cancers (Basel) 2020; 12:cancers12051140. [PMID: 32370157 PMCID: PMC7281482 DOI: 10.3390/cancers12051140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/06/2023] Open
Abstract
Over two decades of research on cancer-associated epithelial-mesenchymal transition (EMT) led us to ascertain the occurrence of transitional intermediate states (collectively referred to as the EMT spectrum). Among the molecular factors that drive EMT, SNAI1 plays an indispensable role in regulating other core transcription factors, and this regulation is highly context-dependent. However, molecular investigation on this context-dependent regulation is still lacking. Using two ovarian cancer cell lines, we show that SNAI1 regulation on other core EMT-TFs switches from a repressive control in highly epithelial cells to an activation signaling in intermediate epithelial cells. Upon further scrutiny, we identify that the expression of early epithelial genes PERP and ERBB3 are differentially regulated in SNAI1-induced sequential EMT changes. Mechanistically, we show that changes in PERP and ERBB3 transcript levels could be correlated to the selective enrichment loss of RAD21, a cohesin component, at the distal enhancer sites of PERP and ERBB3, which precedes that of the proximal promoter-associated sites. Furthermore, the RAD21 enrichment at the distal enhancer sites is dependent on GRHL2 expression. In a nutshell, the alteration of GRHL2-associated RAD21 enrichment in epithelial genes is crucial to redefine the transition of cellular states along the EMT spectrum.
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Guo Q, Cheng K, Wang X, Li X, Yu Y, Hua Y, Yang Z. Expression of HDAC1 and RBBP4 correlate with clinicopathologic characteristics and prognosis in breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:563-572. [PMID: 32269697 PMCID: PMC7137008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/07/2020] [Indexed: 06/11/2023]
Abstract
Retinoblastoma binding protein 4 (RBBP4) plays an important role in transcription, cell cycle, and proliferation. Immunohistochemistry was performed to assess HDAC1 and RBBP4 expression in 240 BC patients. The expression of HDAC1 and RBBP4 in 12 pairs of BC tissues and their normal tissues was determined by western blotting. Kaplan-Meier analysis and Cox's proportional hazards regression were applied to evaluate the prognostic significance of HDAC1 and RBBP4. HDAC1 and RBBP4 expression in BC was significantly higher than that in normal tissues. HDAC1 was positively correlated with RBBP4 in breast cancer. HDAC1 and RBBP4 were negatively correlated with ER and PR in BC, respectively. The patients with high expression of RBBP4 had a worse overall survival time. The expression of RBBP4 was found to be significantly correlated with lymph node metastasis. RBBP4 may play a major role though HDAC1 in the development, metastasis, and prognosis of BC.
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Affiliation(s)
- Qingqun Guo
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Kai Cheng
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Xiaohong Wang
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Xiaoqiang Li
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Yue Yu
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Yitong Hua
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
| | - Zhenlin Yang
- Department of Thyroid and Breast Surgery, Binzhou Medical University Hospital Binzhou, Shandong, China
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Skrzypek K, Majka M. Interplay among SNAIL Transcription Factor, MicroRNAs, Long Non-Coding RNAs, and Circular RNAs in the Regulation of Tumor Growth and Metastasis. Cancers (Basel) 2020; 12:E209. [PMID: 31947678 PMCID: PMC7017348 DOI: 10.3390/cancers12010209] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
SNAIL (SNAI1) is a zinc finger transcription factor that binds to E-box sequences and regulates the expression of genes. It usually acts as a gene repressor, but it may also activate the expression of genes. SNAIL plays a key role in the regulation of epithelial to mesenchymal transition, which is the main mechanism responsible for the progression and metastasis of epithelial tumors. Nevertheless, it also regulates different processes that are responsible for tumor growth, such as the activity of cancer stem cells, the control of cell metabolism, and the regulation of differentiation. Different proteins and microRNAs may regulate the SNAIL level, and SNAIL may be an important regulator of microRNA expression as well. The interplay among SNAIL, microRNAs, long non-coding RNAs, and circular RNAs is a key event in the regulation of tumor growth and metastasis. This review for the first time discusses different types of regulation between SNAIL and non-coding RNAs with a focus on feedback loops and the role of competitive RNA. Understanding these mechanisms may help develop novel therapeutic strategies against cancer based on microRNAs.
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Affiliation(s)
- Klaudia Skrzypek
- Jagiellonian University Medical College, Faculty of Medicine, Institute of Pediatrics, Department of Transplantation, Wielicka 265, 30-663 Cracow, Poland
| | - Marcin Majka
- Jagiellonian University Medical College, Faculty of Medicine, Institute of Pediatrics, Department of Transplantation, Wielicka 265, 30-663 Cracow, Poland
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Huang C, Wu XF, Wang XL. Trichostatin a inhibits phenotypic transition and induces apoptosis of the TAF-treated normal colonic epithelial cells through regulation of TGF-β pathway. Int J Biochem Cell Biol 2019; 114:105565. [PMID: 31278993 DOI: 10.1016/j.biocel.2019.105565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 12/15/2022]
Abstract
Tumor-associated fibroblasts (TAFs) contribute to transdifferentiation of stromal cells in tumor microenvironment. Epithelial-mesenchymal transition (EMT) is a procedure of phenotypic remodeling of epithelial cells and extensively exists in local tumoral stroma. Histone deacetylase (HDAC) inhibitor Tricostatin A (TSA) and sodium butyrate (SB) are reported to play important roles in the regulation of biological behaviour of cancer cells. However, whether TSA or SB is involved in control of EMT in colon epithelial cells induced by TAFs remains unidentified. In present study, we used conditioned medium (CM) form TAF-like CCD-18Co cells to stimulate 2D- and 3D-cultured colon epithelial HCoEpiC cells for 24 h and 4 d. We found that the CCD-18Co CM triggered multiple morphological changes in HCoEpiCs including prolonged cell diameters, down-regulation of E-cadherin and up-regulation of vimentin and α-SMA. Besides, ZEB1 and Snail expression and migration were also promoted by the CM. These phenomena were abolised by 5 μg/ml LY364947, a TGF-β receptor inhibitor. CCD-18Co induced up-regulation of HDAC1 and HDAC2 in the 2D and 3D models, while no change of HDAC4 exprerssion was found. Treatment of 2 μg/ml TSA reversed the CCD-18Co-induced morphological changes and migration of the HCoEpiCs, and suppressed the downregulation of E-cadherin and upregulation of vimentin, α-SMA, ZEB1 and Snail. However, the suppressive effect of 4 mg/ml SB on the EMT was not observed. TSA down-regulated the expressions of Smad2/3, p-Smad2/3 amd HDAC4. Besides, TSA promoted the apoptosis rate (36.84 ± 6.52%) comparing with the CCD-18Co-treated HCoEpiCs (3.52 ± 0.85%, P < 0.05), with promotion of Bax (0.5893±0.0498 in 2D and 0.8867±0.0916 in 3D) and reduction of Bcl-2 (0.0476±0.0053 in 2D and 0.0294±0.0075 in 3D). TSA stimulated expression of phosphorylated-p38 MAPK in 2D (0.3472±0.0249) and 3D (0.3188±0.0248). After pre-treatment with p38 MAPK inhibitor VX-702 (0.5 mg/ml), the apoptosis rate of TSA was decreased in 2D (10.32%) and 3D (5.26%). Our observations demonstrate that epigenetic treatment with HDAC inhibitor TSA may be a useful therapeutic tool for the reversion of TAF-induced EMT in colon epithelium through mediating canonical Smads pathway and non-canonical p38 MAPK signalling.
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Affiliation(s)
- Chao Huang
- Department of Traditional Chinese Medicine, Affiliated Bao'an Hospital of Shenzhen, Southern Medical University, Shenzhen, 518100, China.
| | - Xiao-Fen Wu
- Department of Endocrinology, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, 730050, China
| | - Xiu-Lian Wang
- Health Management Centre, Affiliated Bao'an Hospital of Traditional Chinese Medicine of Shenzhen, Traditional Chinese Medicine University Of Guangzhou, Shenzhen, 518100, China
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