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Jia D, Li X, Bocci F, Tripathi S, Deng Y, Jolly MK, Onuchic JN, Levine H. Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response. J Clin Med 2019; 8:E725. [PMID: 31121840 PMCID: PMC6572429 DOI: 10.3390/jcm8050725] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
Cancer cells can acquire a spectrum of stable hybrid epithelial/mesenchymal (E/M) states during epithelial-mesenchymal transition (EMT). Cells in these hybrid E/M phenotypes often combine epithelial and mesenchymal features and tend to migrate collectively commonly as small clusters. Such collectively migrating cancer cells play a pivotal role in seeding metastases and their presence in cancer patients indicates an adverse prognostic factor. Moreover, cancer cells in hybrid E/M phenotypes tend to be more associated with stemness which endows them with tumor-initiation ability and therapy resistance. Most recently, cells undergoing EMT have been shown to promote immune suppression for better survival. A systematic understanding of the emergence of hybrid E/M phenotypes and the connection of EMT with stemness and immune suppression would contribute to more effective therapeutic strategies. In this review, we first discuss recent efforts combining theoretical and experimental approaches to elucidate mechanisms underlying EMT multi-stability (i.e., the existence of multiple stable phenotypes during EMT) and the properties of hybrid E/M phenotypes. Following we discuss non-cell-autonomous regulation of EMT by cell cooperation and extracellular matrix. Afterwards, we discuss various metrics that can be used to quantify EMT spectrum. We further describe possible mechanisms underlying the formation of clusters of circulating tumor cells. Last but not least, we summarize recent systems biology analysis of the role of EMT in the acquisition of stemness and immune suppression.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
| | - Xuefei Li
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
| | - Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Chemistry, Rice University, Houston, TX 77005, USA.
| | - Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX 77005, USA.
| | - Youyuan Deng
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Applied Physics Graduate Program, Rice University, Houston, TX 77005, USA.
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Chemistry, Rice University, Houston, TX 77005, USA.
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA.
- Department of Physics, Northeastern University, Boston, MA 02115, USA.
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52
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Zañudo JGT, Guinn MT, Farquhar K, Szenk M, Steinway SN, Balázsi G, Albert R. Towards control of cellular decision-making networks in the epithelial-to-mesenchymal transition. Phys Biol 2019; 16:031002. [PMID: 30654341 PMCID: PMC6405305 DOI: 10.1088/1478-3975/aaffa1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three physiological contexts: embryonic development, wound healing, and metastasis. We describe the existing experimental systems and manipulations used to better understand the molecular participants and factors that influence EMT and metastasis. We review the mathematical models of the regulatory networks involved in EMT, with a particular emphasis on the network motifs (such as coupled feedback loops) that can generate intermediate hybrid states between the epithelial and mesenchymal states. Ultimately, the understanding gained about these networks should be translated into methods to control phenotypic outcomes, especially in the context of cancer therapeutic strategies. We present emerging theories of how to drive the dynamics of a network toward a desired dynamical attractor (e.g. an epithelial cell state) and emerging synthetic biology technologies to monitor and control the state of cells.
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Affiliation(s)
- Jorge Gómez Tejeda Zañudo
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Medical Oncology, Dana-Farber Cancer Center, Boston, MA 02215, USA
- Cancer Program, Eli and Edythe L. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - M. Tyler Guinn
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Medical Scientist Training Program, 101 Nicolls Road, Stony Brook, NY 11794, USA
| | - Kevin Farquhar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariola Szenk
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Steven N. Steinway
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794 USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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53
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Xing J, Tian XJ. Investigating epithelial-to-mesenchymal transition with integrated computational and experimental approaches. Phys Biol 2019; 16:031001. [PMID: 30665206 PMCID: PMC6609444 DOI: 10.1088/1478-3975/ab0032] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The transition between epithelial and mesenchymal (EMT) is a fundamental cellular process that plays critical roles in development, cancer metastasis, and tissue wound healing. EMT is not a binary process but involves multiple partial EMT states that give rise to a high degree of cell state plasticity. Here, we first reviewed several studies on theoretical predictions and experimental verification of these intermediate states, the role of partial EMT on kidney fibrosis development, and how quantitative signaling information controls cell commitment to partial or full EMT upon transient signals. Next, we summarized existing knowledge and open questions on the coupling between EMT and other biological processes, such as the cell cycle, epigenetic regulation, stemness, and apoptosis. Taken together, EMT is a model system that has attracted increasing interests for quantitative experimental and theoretical studies.
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Affiliation(s)
- Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, United States of America. UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States of America. To whom correspondence should be addressed
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54
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Phillips RM, Lam C, Wang H, Tran PT. Bittersweet tumor development and progression: Emerging roles of epithelial plasticity glycosylations. Adv Cancer Res 2019; 142:23-62. [PMID: 30885363 DOI: 10.1016/bs.acr.2019.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Altered metabolism is one of the hallmarks of cancer. The best-known cancer metabolic anomaly is an increase in aerobic glycolysis, which generates ATP and other basic building blocks, such as nucleotides, lipids, and proteins to support tumor cell growth and survival. Epithelial plasticity (EP) programs such as the epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are evolutionarily conserved processes that are essential for embryonic development. EP also plays an important role during tumor progression toward metastasis and treatment resistance, and new roles in the acceleration of tumorigenesis have been found. Recent evidence has linked EMT-related transcriptomic alterations with metabolic reprogramming in cancer cells, which include increased aerobic glycolysis. More recent studies have revealed a novel connection between EMT and altered glycosylation in tumor cells, in which EMT drives an increase in glucose uptake and flux into the hexosamine biosynthetic pathway (HBP). The HBP is a side-branch pathway from glycolysis which generates the end product uridine-5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc). A key downstream utilization of UDP-GlcNAc is for the post-translational modification O-GlcNAcylation which involves the attachment of the GlcNAc moiety to Ser/Thr/Asn residues of proteins. Global changes in protein O-GlcNAcylation are emerging as a general characteristic of cancer cells. In our recent study, we demonstrated that the EMT-HBP-O-GlcNAcylation axis drives the O-GlcNAcylation of key proteins such as c-Myc, which previous studies have shown to suppress oncogene-induced senescence (OIS) and contribute to accelerated tumorigenesis. Here, we review the HBP and O-GlcNAcylation and their putative roles in driving EMT-related cancer processes with examples to illuminate potential new therapeutic targets for cancer.
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Affiliation(s)
- Ryan M Phillips
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christine Lam
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hailun Wang
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| | - Phuoc T Tran
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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55
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Biswas K, Jolly MK, Ghosh A. Stability and mean residence times for hybrid epithelial/mesenchymal phenotype. Phys Biol 2019; 16:025003. [PMID: 30537698 DOI: 10.1088/1478-3975/aaf7b7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cancer metastasis and drug resistance remain unsolved clinical challenges. A phenotypic transition that is often implicated in both these processes is epithelial-mesenchymal transition (EMT) during which epithelial cells weaken their cell-cell adhesion and gain traits of migration and invasion, typical of mesenchymal cells. However, recent studies indicate that apart from these two states, cells can also exist in one or more hybrid E/M state(s), which plays an aggressive role in progression of the disease. Furthermore, computational and experimental studies have identified a variety of phenotypic stability factors (PSFs) that stabilize the hybrid E/M state(s) and can increase disease aggressiveness. In this work, we study EMT regulatory networks, in the presence of different PSFs, as dynamical systems subjected to random fluctuations. The cells thus explore different stable E, M, E/M states in the potential landscape and our aim is to quantify the residence time in each of these states. Our stochastic simulations indicate an universal feature that the mean residence time (MRT) in the hybrid E/M state is enhanced in the presence of PSFs. We demonstrate that the feature is consistent for a variety of PSFs, namely, GRHL2, OVOL, ΔNp63α, miR-145/OCT4, participating in the core EMT regulatory network. Our results reveal potential targets for pushing cells out of a hybrid E/M state and thus halting metastatic progression.
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Affiliation(s)
- Kuheli Biswas
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, India
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56
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Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression. CURRENT STEM CELL REPORTS 2019. [DOI: 10.1007/s40778-019-0150-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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57
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Abstract
The transition of epithelial cells into a mesenchymal state (epithelial-to-mesenchymal transition or EMT) is a highly dynamic process implicated in various biological processes. During EMT, cells do not necessarily exist in 'pure' epithelial or mesenchymal states. There are cells with mixed (or hybrid) features of the two, which are termed as the intermediate cell states (ICSs). While the exact functions of ICS remain elusive, together with EMT it appears to play important roles in embryogenesis, tissue development, and pathological processes such as cancer metastasis. Recent single cell experiments and advanced mathematical modeling have improved our capability in identifying ICS and provided a better understanding of ICS in development and disease. Here, we review the recent findings related to the ICS in/or EMT and highlight the challenges in the identification and functional characterization of ICS.
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Affiliation(s)
- Yutong Sha
- Department of Mathematics, University of California, Irvine, CA 92697, United States of America
- Co-first authors
| | - Daniel Haensel
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, United States of America
- Co-first authors
| | - Guadalupe Gutierrez
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, United States of America
| | - Huijing Du
- Department of Mathematics, University of Nebraska-Lincoln, Lincoln, NE 68588, United States of America
| | - Xing Dai
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, United States of America
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697, United States of America
- Department of Development and Cell Biology, University of California, Irvine, CA 92697, United States of America
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58
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Jia D, George JT, Tripathi SC, Kundnani DL, Lu M, Hanash SM, Onuchic JN, Jolly MK, Levine H. Testing the gene expression classification of the EMT spectrum. Phys Biol 2019; 16:025002. [PMID: 30557866 PMCID: PMC7179477 DOI: 10.1088/1478-3975/aaf8d4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The epithelial-mesenchymal transition (EMT) plays a central role in cancer metastasis and drug resistance-two persistent clinical challenges. Epithelial cells can undergo a partial or full EMT, attaining either a hybrid epithelial/mesenchymal (E/M) or mesenchymal phenotype, respectively. Recent studies have emphasized that hybrid E/M cells may be more aggressive than their mesenchymal counterparts. However, mechanisms driving hybrid E/M phenotypes remain largely elusive. Here, to better characterize the hybrid E/M phenotype (s) and tumor aggressiveness, we integrate two computational methods-(a) RACIPE-to identify the robust gene expression patterns emerging from the dynamics of a given gene regulatory network, and (b) EMT scoring metric-to calculate the probability that a given gene expression profile displays a hybrid E/M phenotype. We apply the EMT scoring metric to RACIPE-generated gene expression data generated from a core EMT regulatory network and classify the gene expression profiles into relevant categories (epithelial, hybrid E/M, mesenchymal). This categorization is broadly consistent with hierarchical clustering readouts of RACIPE-generated gene expression data. We also show how the EMT scoring metric can be used to distinguish between samples composed of exclusively hybrid E/M cells and those containing mixtures of epithelial and mesenchymal subpopulations using the RACIPE-generated gene expression data.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
- Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005, United States of America
- These authors contributed equally
| | - Jason T George
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, United States of America
- These authors contributed equally
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Deepali L Kundnani
- Red and Charline McCombs Institute for the Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Mingyang Lu
- The Jackson Laboratory, Bar Harbor, ME, United States of America
- Current address: Department of Biochemistry, All India Institute of Medical Sciences, Nagpur 440003, India
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
- Red and Charline McCombs Institute for the Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
- Department of Chemistry, Rice University, Houston, TX 77005, United States of America
- Department of Biosciences, Rice University, Houston, TX 77005, United States of America
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States of America
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
- Current address: Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, United States of America
- Department of Bioengineering, Rice University, Houston, TX 77005, United States of America
- Department of Biosciences, Rice University, Houston, TX 77005, United States of America
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, United States of America
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59
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Pastushenko I, Blanpain C. EMT Transition States during Tumor Progression and Metastasis. Trends Cell Biol 2018; 29:212-226. [PMID: 30594349 DOI: 10.1016/j.tcb.2018.12.001] [Citation(s) in RCA: 1592] [Impact Index Per Article: 265.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is a process in which epithelial cells acquire mesenchymal features. In cancer, EMT is associated with tumor initiation, invasion, metastasis, and resistance to therapy. Recently, it has been demonstrated that EMT is not a binary process, but occurs through distinct cellular states. Here, we review the recent studies that demonstrate the existence of these different EMT states in cancer and the mechanisms regulating their functions. We discuss the different functional characteristics, such as proliferation, propagation, plasticity, invasion, and metastasis associated with the distinct EMT states. We summarize the role of the transcriptional and epigenetic landscapes, gene regulatory network and their surrounding niche in controlling the transition through the different EMT states.
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Affiliation(s)
- Ievgenia Pastushenko
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Bruxelles, Brussels, Belgium; WELBIO, Université Libre de Bruxelles, Brussels, Belgium.
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60
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Bohère J, Mancheno-Ferris A, Al Hayek S, Zanet J, Valenti P, Akino K, Yamabe Y, Inagaki S, Chanut-Delalande H, Plaza S, Kageyama Y, Osman D, Polesello C, Payre F. Shavenbaby and Yorkie mediate Hippo signaling to protect adult stem cells from apoptosis. Nat Commun 2018; 9:5123. [PMID: 30504772 PMCID: PMC6269459 DOI: 10.1038/s41467-018-07569-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/12/2018] [Indexed: 01/06/2023] Open
Abstract
To compensate for accumulating damages and cell death, adult homeostasis (e.g., body fluids and secretion) requires organ regeneration, operated by long-lived stem cells. How stem cells can survive throughout the animal life remains poorly understood. Here we show that the transcription factor Shavenbaby (Svb, OvoL in vertebrates) is expressed in renal/nephric stem cells (RNSCs) of Drosophila and required for their maintenance during adulthood. As recently shown in embryos, Svb function in adult RNSCs further needs a post-translational processing mediated by the Polished rice (Pri) smORF peptides and impairing Svb function leads to RNSC apoptosis. We show that Svb interacts both genetically and physically with Yorkie (YAP/TAZ in vertebrates), a nuclear effector of the Hippo pathway, to activate the expression of the inhibitor of apoptosis DIAP1. These data therefore identify Svb as a nuclear effector in the Hippo pathway, critical for the survival of adult somatic stem cells.
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Affiliation(s)
- Jérôme Bohère
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Alexandra Mancheno-Ferris
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Sandy Al Hayek
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Jennifer Zanet
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Philippe Valenti
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Kohsuke Akino
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Yuya Yamabe
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
| | - Sachi Inagaki
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Hélène Chanut-Delalande
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
| | - Serge Plaza
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France
- Laboratoire de Recherche en Sciences Végétales (LSRV), CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, 31326, Castanet-Tolosan, France
| | - Yuji Kageyama
- Department of Biology, Graduate School of Science, Kobe, 657-8501, Japan
- Biosignal Research Center, Kobe University, 1-1 Rokko-dai, Nada, Kobe, 657-8501, Japan
| | - Dani Osman
- Faculty of Sciences III, Lebanese University, Tripoli, 1300, Lebanon
- Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300, Lebanon
| | - Cédric Polesello
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
| | - François Payre
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Bat 4R3, 118 route de Narbonne, F-31062, Toulouse, France.
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61
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Jolly MK, Somarelli JA, Sheth M, Biddle A, Tripathi SC, Armstrong AJ, Hanash SM, Bapat SA, Rangarajan A, Levine H. Hybrid epithelial/mesenchymal phenotypes promote metastasis and therapy resistance across carcinomas. Pharmacol Ther 2018; 194:161-184. [PMID: 30268772 DOI: 10.1016/j.pharmthera.2018.09.007] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer metastasis and therapy resistance are the major unsolved clinical challenges, and account for nearly all cancer-related deaths. Both metastasis and therapy resistance are fueled by epithelial plasticity, the reversible phenotypic transitions between epithelial and mesenchymal phenotypes, including epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET). EMT and MET have been largely considered as binary processes, where cells detach from the primary tumor as individual units with many, if not all, traits of a mesenchymal cell (EMT) and then convert back to being epithelial (MET). However, recent studies have demonstrated that cells can metastasize in ways alternative to traditional EMT paradigm; for example, they can detach as clusters, and/or occupy one or more stable hybrid epithelial/mesenchymal (E/M) phenotypes that can be the end point of a transition. Such hybrid E/M cells can integrate various epithelial and mesenchymal traits and markers, facilitating collective cell migration. Furthermore, these hybrid E/M cells may possess higher tumor-initiation and metastatic potential as compared to cells on either end of the EMT spectrum. Here, we review in silico, in vitro, in vivo and clinical evidence for the existence of one or more hybrid E/M phenotype(s) in multiple carcinomas, and discuss their implications in tumor-initiation, tumor relapse, therapy resistance, and metastasis. Together, these studies drive the emerging notion that cells in a hybrid E/M phenotype may occupy 'metastatic sweet spot' in multiple subtypes of carcinomas, and pathways linked to this (these) hybrid E/M state(s) may be relevant as prognostic biomarkers as well as a promising therapeutic targets.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
| | - Jason A Somarelli
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Maya Sheth
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Adrian Biddle
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, USA
| | - Andrew J Armstrong
- Duke Cancer Institute and Department of Medicine, Duke University Medical Center, Durham, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, USA
| | - Sharmila A Bapat
- National Center for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, India
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
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62
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Jolly MK, Preca BT, Tripathi SC, Jia D, George JT, Hanash SM, Brabletz T, Stemmler MP, Maurer J, Levine H. Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioeng 2018; 2:031908. [PMID: 31069317 PMCID: PMC6324214 DOI: 10.1063/1.5024874] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Aberrant activation of epithelial-mesenchymal transition (EMT) in carcinoma cells contributes to increased migration and invasion, metastasis, drug resistance, and tumor-initiating capacity. EMT is not always a binary process; rather, cells may exhibit a hybrid epithelial/mesenchymal (E/M) phenotype. ZEB1-a key transcription factor driving EMT-can both induce and maintain a mesenchymal phenotype. Recent studies have identified two novel autocrine feedback loops utilizing epithelial splicing regulatory protein 1 (ESRP1), hyaluronic acid synthase 2 (HAS2), and CD44 which maintain high levels of ZEB1. However, how the crosstalk between these feedback loops alters the dynamics of epithelial-hybrid-mesenchymal transition remains elusive. Here, using an integrated theoretical-experimental framework, we identify that these feedback loops can enable cells to stably maintain a hybrid E/M phenotype. Moreover, computational analysis identifies the regulation of ESRP1 as a crucial node, a prediction that is validated by experiments showing that knockdown of ESRP1 in stable hybrid E/M H1975 cells drives EMT. Finally, in multiple breast cancer datasets, high levels of ESRP1, ESRP1/HAS2, and ESRP1/ZEB1 correlate with poor prognosis, supporting the relevance of ZEB1/ESRP1 and ZEB1/HAS2 axes in tumor progression. Together, our results unravel how these interconnected feedback loops act in concert to regulate ZEB1 levels and to drive the dynamics of epithelial-hybrid-mesenchymal transition.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice
University, Houston, Texas 77030, USA
| | | | - Satyendra C. Tripathi
- Department of Clinical Cancer Prevention, UT MD
Anderson Cancer Center, Houston, Texas 77030,
USA
| | | | | | - Samir M. Hanash
- Department of Clinical Cancer Prevention, UT MD
Anderson Cancer Center, Houston, Texas 77030,
USA
| | - Thomas Brabletz
- Department of Experimental Medicine I,
Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander
University of Erlangen-Nürnberg, Erlangen 91054,
Germany
| | - Marc P. Stemmler
- Department of Experimental Medicine I,
Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander
University of Erlangen-Nürnberg, Erlangen 91054,
Germany
| | - Jochen Maurer
- Authors to whom correspondence should be addressed: and
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63
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van Staalduinen J, Baker D, Ten Dijke P, van Dam H. Epithelial-mesenchymal-transition-inducing transcription factors: new targets for tackling chemoresistance in cancer? Oncogene 2018; 37:6195-6211. [PMID: 30002444 DOI: 10.1038/s41388-018-0378-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 05/10/2018] [Accepted: 05/13/2018] [Indexed: 02/06/2023]
Abstract
Chemoresistance remains a major complication of cancer treatments. Recent data provide strong evidence that chemoresistance is linked to epithelial-mesenchymal transition (EMT), a latent developmental process, which is re-activated during cancer progression. EMT involves transcriptional reprogramming and is driven by specific EMT transcription factors (EMT-TFs). In this review, we provide support for the idea that EMT-TFs contribute to the development of resistance against cancer therapy and discuss how EMT-TFs might be targeted to advance novel therapeutic approaches to the treatment of cancer.
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Affiliation(s)
- Jente van Staalduinen
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - David Baker
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands.
| | - Hans van Dam
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
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64
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Bocci F, Jolly MK, George JT, Levine H, Onuchic JN. A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling. Oncotarget 2018; 9:29906-29920. [PMID: 30042822 PMCID: PMC6057462 DOI: 10.18632/oncotarget.25692] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and cancer stem cell (CSCs) formation are two fundamental and well-studied processes contributing to cancer metastasis and tumor relapse. Cells can undergo a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype or a complete EMT to attain a mesenchymal one. Similarly, cells can reversibly gain or lose 'stemness'. This plasticity in cell states is modulated by signaling pathways such as Notch. However, the interconnections among the cell states enabled by EMT, CSCs and Notch signaling remain elusive. Here, we devise a computational model to investigate the coupling among the core decision-making circuits for EMT, CSCs and Notch. Our model predicts that hybrid E/M cells are most likely to associate with stem-like traits and enhanced Notch-Jagged signaling – a pathway implicated in therapeutic resistance. Further, we show that the position of the 'stemness window' on the 'EMT axis' is varied by altering the coupling strength between EMT and CSC circuits, and/or modulating Notch signaling. Finally, we analyze the gene expression profile of CSCs from several cancer types and observe a heterogeneous distribution along the 'EMT axis', suggesting that different subsets of CSCs may exist with varying phenotypes along the epithelial-mesenchymal axis. We further investigate therapeutic perturbations such as treatment with metformin, a drug associated with decreased cancer incidence and increased lifespan of patients. Our mechanism-based model explains how metformin can both inhibit EMT and blunt the aggressive potential of CSCs simultaneously, by driving the cells out of a hybrid E/M stem-like state with enhanced Notch-Jagged signaling.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jason Thomas George
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA.,Department of Bioengineering, Rice University, Houston, TX 77005, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Department of Chemistry, Rice University, Houston, TX 77005, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.,Department of Biosciences, Rice University, Houston, TX 77005, USA
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65
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A hybrid computational model for collective cell durotaxis. Biomech Model Mechanobiol 2018; 17:1037-1052. [DOI: 10.1007/s10237-018-1010-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/17/2018] [Indexed: 12/17/2022]
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66
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Bozzi F, Brich S, Dagrada GP, Negri T, Conca E, Cortelazzi B, Belfiore A, Perrone F, Gualeni AV, Gloghini A, Cabras A, Brenca M, Maestro R, Zaffaroni N, Casali P, Bertulli R, Deraco M, Pilotti S. Epithelioid peritoneal mesothelioma: a hybrid phenotype within a mesenchymal-epithelial/epithelial-mesenchymal transition framework. Oncotarget 2018; 7:75503-75517. [PMID: 27705913 PMCID: PMC5342756 DOI: 10.18632/oncotarget.12262] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/13/2016] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to reconsider the biological characteristics of epithelioid malignant peritoneal mesothelioma (E-MpM) in the light of new concepts about epithelial mesenchymal transition and mesenchymal epithelial reverse transition (EMT/MErT) and the role of epigenetic reprogramming in this context. To this end we profiled surgical specimens and derived cells cultures by a number of complementary approaches i.e. immunohistochemistry, immunofluorescence, in situ hybridization, biochemistry, pluripotent stem cell arrays, treatments with cytokines, growth factors and specific inhibitors.The analyses of the surgical specimens showed that i) EZH2 is expressed throughout the spectrum of MpM, ii) that E-MpM (including the high-grade undifferentiated form) are characterised by c-MYC and miRNA 17-5p expression, and iii) that progression to sarcomatoid MpM is dictated by EMT regulators. They also showed that E-MpM expressed c-MET and are enriched in E- and P-cadherins- and VEGFR2-expressing CSCs, thus strongly supporting a role for MErT reprogramming in endowing E-MpM tumour cells with stemness and plasticity, and hence with a drug resistant phenotype. The cell culture-based experiments confirmed the stemness traits and plasticity of E-MpM, and support the view that EZH2 is a druggable target in this tumor.
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Affiliation(s)
- Fabio Bozzi
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Brich
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,MOSE-DEA University of Trieste, Trieste, Italy
| | - Gian Paolo Dagrada
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tiziana Negri
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Barbara Cortelazzi
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonino Belfiore
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ambra Vittoria Gualeni
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Annunziata Gloghini
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Antonello Cabras
- Department of Diagnostic Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Brenca
- Experimental Oncology 1, Centro di Riferimento Oncologico, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Roberta Maestro
- Experimental Oncology 1, Centro di Riferimento Oncologico, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Casali
- Adult Mesenchymal Tumor Medical Oncology Unit, Department of Cancer Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rossella Bertulli
- Adult Mesenchymal Tumor Medical Oncology Unit, Department of Cancer Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marcello Deraco
- Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvana Pilotti
- Laboratory of Experimental Molecular Pathology, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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67
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Sekhon K, Bucay N, Majid S, Dahiya R, Saini S. MicroRNAs and epithelial-mesenchymal transition in prostate cancer. Oncotarget 2018; 7:67597-67611. [PMID: 27588490 PMCID: PMC5341899 DOI: 10.18632/oncotarget.11708] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/25/2016] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) is a leading cause of male cancer-related deaths. A significant fraction of prostate tumors are very aggressive, often metastasizing to bone, causing significant morbidity and mortality. Also, PCa is associated with high rates of recurrence, often attributed to the existence of cancer stem cells. Epithelial-mesenchymal transition (EMT), a process characterized by decreased expression of epithelial genes and increased expression of mesenchymal genes, plays a critical role in tumor invasion, metastasis and recurrence. In PCa, EMT has been implicated particularly in the context of metastatic disease and microRNAs have emerged as critical post-transcriptional regulators of PCa EMT. In this review, we summarize the role of miRNAs in PCa EMT that play a role in progression, metastasis and recurrence. Studies till date suggest that microRNAs mediate efficient and reversible control of PCa EMT via multiple mechanisms including either by (i) directly repressing single or multiple EMT-TFs or regulating cytoskeletal components (epithelial/mesenchymal genes) or (ii) regulating key signaling pathways involved in EMT. Oncogenic microRNAs often act as EMT promoters by repressing epithelial characteristics and tumor suppressive miRNAs act by inhibiting mesenchymal progression. Further, EMT is mechanistically linked to stem cell signatures in PCa and several miRNAs implicated in EMT have been reported to influence PCa stem cells. Loss of EMT-inhibiting miRNAs and/or gain of EMT promoting miRNAs lead to induction of PCa EMT, leading to tumor progression, metastasis and recurrence. Restoring expression of tumor suppressive miRNAs and inhibiting oncogenic miRNAs represent potential therapeutic opportunities to prevent disease metastasis and recurrence.
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Affiliation(s)
- Kirandeep Sekhon
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA, USA
| | - Nathan Bucay
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA, USA
| | - Shahana Majid
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA, USA
| | - Sharanjot Saini
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, CA, USA
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68
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Jolly MK, Tripathi SC, Jia D, Mooney SM, Celiktas M, Hanash SM, Mani SA, Pienta KJ, Ben-Jacob E, Levine H. Stability of the hybrid epithelial/mesenchymal phenotype. Oncotarget 2017; 7:27067-84. [PMID: 27008704 PMCID: PMC5053633 DOI: 10.18632/oncotarget.8166] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/07/2016] [Indexed: 12/16/2022] Open
Abstract
Epithelial-to-Mesenchymal Transition (EMT) and its reverse – Mesenchymal to Epithelial Transition (MET) – are hallmarks of cellular plasticity during embryonic development and cancer metastasis. During EMT, epithelial cells lose cell-cell adhesion and gain migratory and invasive traits either partially or completely, leading to a hybrid epithelial/mesenchymal (hybrid E/M) or a mesenchymal phenotype respectively. Mesenchymal cells move individually, but hybrid E/M cells migrate collectively as observed during gastrulation, wound healing, and the formation of tumor clusters detected as Circulating Tumor Cells (CTCs). Typically, the hybrid E/M phenotype has largely been tacitly assumed to be transient and ‘metastable’. Here, we identify certain ‘phenotypic stability factors’ (PSFs) such as GRHL2 that couple to the core EMT decision-making circuit (miR-200/ZEB) and stabilize hybrid E/M phenotype. Further, we show that H1975 lung cancer cells can display a stable hybrid E/M phenotype and migrate collectively, a behavior that is impaired by knockdown of GRHL2 and another previously identified PSF - OVOL. In addition, our computational model predicts that GRHL2 can also associate hybrid E/M phenotype with high tumor-initiating potential, a prediction strengthened by the observation that the higher levels of these PSFs may be predictive of poor patient outcome. Finally, based on these specific examples, we deduce certain network motifs that can stabilize the hybrid E/M phenotype. Our results suggest that partial EMT, i.e. a hybrid E/M phenotype, need not be ‘metastable’, and strengthen the emerging notion that partial EMT, but not necessarily a complete EMT, is associated with aggressive tumor progression.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX, USA
| | - Steven M Mooney
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Muge Celiktas
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Red and Charline McCombs Institute for The Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth J Pienta
- The James Brady Urological Institute, and Departments of Urology, Oncology, Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX, USA.,School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Physics and Astronomy, Rice University, Houston, TX, USA.,Department of Biosciences, Rice University, Houston, TX, USA
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69
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George JT, Jolly MK, Xu S, Somarelli JA, Levine H. Survival Outcomes in Cancer Patients Predicted by a Partial EMT Gene Expression Scoring Metric. Cancer Res 2017; 77:6415-6428. [PMID: 28947416 PMCID: PMC5690883 DOI: 10.1158/0008-5472.can-16-3521] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 06/12/2017] [Accepted: 09/19/2017] [Indexed: 12/19/2022]
Abstract
Metastasis is a significant contributor to morbidity and mortality for many cancer patients and remains a major obstacle for effective treatment. In many tissue types, metastasis is fueled by the epithelial-to-mesenchymal transition (EMT)-a dynamic process characterized by phenotypic and morphologic changes concomitant with increased migratory and invasive potential. Recent experimental and theoretical evidence suggests that cells can be stably halted en route to EMT in a hybrid E/M phenotype. Cells in this phenotype tend to move collectively, forming clusters of circulating tumor cells that are key tumor-initiating agents. Here, we developed an inferential model built on the gene expression of multiple cancer subtypes to devise an EMT metric that characterizes the degree to which a given cell line exhibits hybrid E/M features. Our model identified drivers and fine-tuners of epithelial-mesenchymal plasticity and recapitulated the behavior observed in multiple in vitro experiments across cancer types. We also predicted and experimentally validated the hybrid E/M status of certain cancer cell lines, including DU145 and A549. Finally, we demonstrated the relevance of predicted EMT scores to patient survival and observed that the role of the hybrid E/M phenotype in characterizing tumor aggressiveness is tissue and subtype specific. Our algorithm is a promising tool to quantify the EMT spectrum, to investigate the correlation of EMT score with cancer treatment response and survival, and to provide an important metric for systematic clinical risk stratification and treatment. Cancer Res; 77(22); 6415-28. ©2017 AACR.
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Affiliation(s)
- Jason T George
- Center for Theoretical Biological Physics, Rice University, Houston, Texas
- Department of Bioengineering, Rice University, Houston, Texas
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Shengnan Xu
- Duke Cancer Institute & Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jason A Somarelli
- Duke Cancer Institute & Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, Texas.
- Department of Bioengineering, Rice University, Houston, Texas
- Department of Physics and Astronomy, Rice University, Houston, Texas
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70
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Abstract
Background The Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential and drug-resistance. Recent research has argued that epithelial (E) cells can undergo either a partial EMT to attain a hybrid epithelial/mesenchymal (E/M) phenotype that typically displays collective migration, or a complete EMT to adopt a mesenchymal (M) phenotype that shows individual migration. The core EMT regulatory network - miR-34/SNAIL/miR-200/ZEB1 - has been identified by various studies, but how this network regulates the transitions among the E, E/M, and M phenotypes remains controversial. Two major mathematical models - ternary chimera switch (TCS) and cascading bistable switches (CBS) - that both focus on the miR-34/SNAIL/miR-200/ZEB1 network, have been proposed to elucidate the EMT dynamics, but a detailed analysis of how well either or both of these two models can capture recent experimental observations about EMT dynamics remains to be done. Results Here, via an integrated experimental and theoretical approach, we first show that both these two models can be used to understand the two-step transition of EMT - E→E/M→M, the different responses of SNAIL and ZEB1 to exogenous TGF-β and the irreversibility of complete EMT. Next, we present new experimental results that tend to discriminate between these two models. We show that ZEB1 is present at intermediate levels in the hybrid E/M H1975 cells, and that in HMLE cells, overexpression of SNAIL is not sufficient to initiate EMT in the absence of ZEB1 and FOXC2. Conclusions These experimental results argue in favor of the TCS model proposing that miR-200/ZEB1 behaves as a three-way decision-making switch enabling transitions among the E, hybrid E/M and M phenotypes.
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71
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Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. J R Soc Interface 2017; 13:rsif.2015.1106. [PMID: 27170649 PMCID: PMC4892257 DOI: 10.1098/rsif.2015.1106] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/15/2016] [Indexed: 01/14/2023] Open
Abstract
Metastasis can involve repeated cycles of epithelial-to-mesenchymal transition (EMT) and its reverse mesenchymal-to-epithelial transition. Cells can also undergo partial transitions to attain a hybrid epithelial/mesenchymal (E/M) phenotype that allows the migration of adhering cells to form a cluster of circulating tumour cells. These clusters can be apoptosis-resistant and possess an increased metastatic propensity as compared to the cells that undergo a complete EMT (mesenchymal cells). Hence, identifying the key players that can regulate the formation and maintenance of such clusters may inform anti-metastasis strategies. Here, we devise a mechanism-based theoretical model that links cell–cell communication via Notch-Delta-Jagged signalling with the regulation of EMT. We demonstrate that while both Notch-Delta and Notch-Jagged signalling can induce EMT in a population of cells, only Jagged-dominated Notch signalling, but not Delta-dominated signalling, can lead to the formation of clusters containing hybrid E/M cells. Our results offer possible mechanistic insights into the role of Jagged in tumour progression, and offer a framework to investigate the effects of other microenvironmental signals during metastasis.
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Affiliation(s)
- Marcelo Boareto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA Institute of Physics, University of Sao Paulo, Sao Paulo 05508, Brazil
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA Department of Bioengineering, Rice University, Houston, TX 77005-1827, USA
| | - Aaron Goldman
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Mika Pietilä
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX 77030, USA Metastasis Research Center, MD Anderson Cancer Center, Houston, TX 77025, USA
| | - Shiladitya Sengupta
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA Department of Bioengineering, Rice University, Houston, TX 77005-1827, USA Department of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA Department of Biosciences, Rice University, Houston, TX 77005-1827, USA
| | - Jose' N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA Department of Chemistry, Rice University, Houston, TX 77005-1827, USA Department of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA Department of Biosciences, Rice University, Houston, TX 77005-1827, USA
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72
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Characterization of epithelial-mesenchymal transition intermediate/hybrid phenotypes associated to resistance to EGFR inhibitors in non-small cell lung cancer cell lines. Oncotarget 2017; 8:103340-103363. [PMID: 29262566 PMCID: PMC5732732 DOI: 10.18632/oncotarget.21132] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 08/23/2017] [Indexed: 01/06/2023] Open
Abstract
Increasing evidence points to a key role played by epithelial-mesenchymal transition (EMT) in cancer progression and drug resistance. In this study, we used wet and in silico approaches to investigate whether EMT phenotypes are associated to resistance to target therapy in a non-small cell lung cancer model system harboring activating mutations of the epidermal growth factor receptor. The combination of different analysis techniques allowed us to describe intermediate/hybrid and complete EMT phenotypes respectively in HCC827- and HCC4006-derived drug-resistant human cancer cell lines. Interestingly, intermediate/hybrid EMT phenotypes, a collective cell migration and increased stem-like ability associate to resistance to the epidermal growth factor receptor inhibitor, erlotinib, in HCC827 derived cell lines. Moreover, the use of three complementary approaches for gene expression analysis supported the identification of a small EMT-related gene list, which may have otherwise been overlooked by standard stand-alone methods for gene expression analysis.
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73
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Klymenko Y, Kim O, Stack MS. Complex Determinants of Epithelial: Mesenchymal Phenotypic Plasticity in Ovarian Cancer. Cancers (Basel) 2017; 9:cancers9080104. [PMID: 28792442 PMCID: PMC5575607 DOI: 10.3390/cancers9080104] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/02/2017] [Accepted: 08/06/2017] [Indexed: 02/07/2023] Open
Abstract
Unlike most epithelial malignancies which metastasize hematogenously, metastasis of epithelial ovarian cancer (EOC) occurs primarily via transcoelomic dissemination, characterized by exfoliation of cells from the primary tumor, avoidance of detachment-induced cell death (anoikis), movement throughout the peritoneal cavity as individual cells and multi-cellular aggregates (MCAs), adhesion to and disruption of the mesothelial lining of the peritoneum, and submesothelial matrix anchoring and proliferation to generate widely disseminated metastases. This exceptional microenvironment is highly permissive for phenotypic plasticity, enabling mesenchymal-to-epithelial (MET) and epithelial-to-mesenchymal (EMT) transitions. In this review, we summarize current knowledge on EOC heterogeneity in an EMT context, outline major regulators of EMT in ovarian cancer, address controversies in EMT and EOC chemoresistance, and highlight computational modeling approaches toward understanding EMT/MET in EOC.
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Affiliation(s)
- Yuliya Klymenko
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46617, USA.
- Medical Sciences Program, Indiana University School of Medicine, Bloomington, IN 47405, USA.
| | - Oleg Kim
- Department of Applied and Computational Mathematics and Statistics, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46617, USA.
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA.
| | - M Sharon Stack
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46617, USA.
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74
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Burger GA, Danen EHJ, Beltman JB. Deciphering Epithelial-Mesenchymal Transition Regulatory Networks in Cancer through Computational Approaches. Front Oncol 2017; 7:162. [PMID: 28824874 PMCID: PMC5540937 DOI: 10.3389/fonc.2017.00162] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/18/2017] [Indexed: 12/14/2022] Open
Abstract
Epithelial–mesenchymal transition (EMT), the process by which epithelial cells can convert into motile mesenchymal cells, plays an important role in development and wound healing but is also involved in cancer progression. It is increasingly recognized that EMT is a dynamic process involving multiple intermediate or “hybrid” phenotypes rather than an “all-or-none” process. However, the role of EMT in various cancer hallmarks, including metastasis, is debated. Given the complexity of EMT regulation, computational modeling has proven to be an invaluable tool for cancer research, i.e., to resolve apparent conflicts in experimental data and to guide experiments by generating testable hypotheses. In this review, we provide an overview of computational modeling efforts that have been applied to regulation of EMT in the context of cancer progression and its associated tumor characteristics. Moreover, we identify possibilities to bridge different modeling approaches and point out outstanding questions in which computational modeling can contribute to advance our understanding of pathological EMT.
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Affiliation(s)
- Gerhard A Burger
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Erik H J Danen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Joost B Beltman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
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75
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Jolly MK, Ward C, Eapen MS, Myers S, Hallgren O, Levine H, Sohal SS. Epithelial-mesenchymal transition, a spectrum of states: Role in lung development, homeostasis, and disease. Dev Dyn 2017. [DOI: 10.1002/dvdy.24541] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics; Rice University; Houston Texas
| | - Chris Ward
- Institute of Cellular Medicine; Newcastle University; Newcastle upon Tyne United Kingdom
| | - Mathew Suji Eapen
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
- NHMRC Centre of Research Excellence for Chronic Respiratory Disease; University of Tasmania; Hobart Tasmania Australia
| | - Stephen Myers
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
| | - Oskar Hallgren
- Department of Experimental Medical Sciences; Department of Respiratory Medicine and Allergology, Lund University; Sweden
| | - Herbert Levine
- Center for Theoretical Biological Physics; Rice University; Houston Texas
| | - Sukhwinder Singh Sohal
- School of Health Sciences; Faculty of Health, University of Tasmania, Launceston, University of Tasmania; Hobart Tasmania Australia
- NHMRC Centre of Research Excellence for Chronic Respiratory Disease; University of Tasmania; Hobart Tasmania Australia
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76
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Santamaria PG, Moreno‐Bueno G, Portillo F, Cano A. EMT: Present and future in clinical oncology. Mol Oncol 2017; 11:718-738. [PMID: 28590039 PMCID: PMC5496494 DOI: 10.1002/1878-0261.12091] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022] Open
Abstract
Epithelial/mesenchymal transition (EMT) has emerged as a key regulator of metastasis by facilitating tumor cell invasion and dissemination to distant organs. Recent evidences support that the reverse mesenchymal/epithelial transition (MET) is required for metastatic outgrowth; moreover, the existence of hybrid epithelial/mesenchymal (E/M) phenotypes is increasingly being reported in different tumor contexts. The accumulated data strongly support that plasticity between epithelial and mesenchymal states underlies the dissemination and metastatic potential of carcinoma cells. However, the translation into the clinics of EMT and epithelial plasticity processes presents enormous challenges and still remains a controversial issue. In this review, we will evaluate current evidences for translational applicability of EMT and depict an overview of the most recent EMT in vivo models, EMT marker analyses in human samples as well as potential EMT therapeutic approaches and ongoing clinical trials. We foresee that standardized analyses of EMT markers in solid and liquid tumor biopsies in addition to innovative tools targeting the E/M states will become promising strategies for future translation to the clinical setting.
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Affiliation(s)
- Patricia G. Santamaria
- Departamento de BioquímicaInstituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC‐UAM)Universidad Autónoma de Madrid (UAM)IdiPAZCIBERONCMadridSpain
| | - Gema Moreno‐Bueno
- Departamento de BioquímicaInstituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC‐UAM)Universidad Autónoma de Madrid (UAM)IdiPAZCIBERONCMadridSpain
- Fundación MD Anderson InternationalMadridSpain
| | - Francisco Portillo
- Departamento de BioquímicaInstituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC‐UAM)Universidad Autónoma de Madrid (UAM)IdiPAZCIBERONCMadridSpain
| | - Amparo Cano
- Departamento de BioquímicaInstituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC‐UAM)Universidad Autónoma de Madrid (UAM)IdiPAZCIBERONCMadridSpain
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77
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Ito T, Tsuji G, Ohno F, Nakahara T, Uchi H, Furue M. Potential role of the OVOL1-OVOL2 axis and c-Myc in the progression of cutaneous squamous cell carcinoma. Mod Pathol 2017; 30:919-927. [PMID: 28339425 DOI: 10.1038/modpathol.2016.169] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 11/09/2022]
Abstract
OVOL1 and OVOL2 are ubiquitously conserved genes encoding C2H2 zinc-finger transcription factors in mammals. They promote epithelial cell proliferation, differentiation, and mesenchymal-to-epithelial transition, coordinately mediated via the Wnt signaling pathway. We previously reported that human OVOL1 and OVOL2 were preferentially expressed in the normal epidermis and hair follicles as well as their tumors, and found that OVOL1 is upregulated in Bowen's disease and downregulated in cutaneous squamous cell carcinoma. The aims of this study were to elucidate the potential role of the OVOL1-OVOL2 axis in Bowen's disease and squamous cell carcinoma, and to reveal the relationship between OVOL and c-Myc, a proto-oncogene that plays a pivotal role in the malignancy of epithelial tumors. We investigated 20 Bowen's disease and 20 squamous cell carcinoma clinical samples and a human squamous cell carcinoma cell line (A431) using immunohistochemical staining and molecular biological approaches. Immunohistochemical analysis revealed that OVOL1 was upregulated in Bowen's disease and markedly downregulated in squamous cell carcinoma; conversely, c-Myc was downregulated in Bowen's disease and upregulated in squamous cell carcinoma. OVOL2 was markedly upregulated in the nucleus of Bowen's disease cells, but the distribution of OVOL2 expression in squamous cell carcinoma varied widely; OVOL2 was typically expressed in the cytoplasm, but only sporadically in the nucleus. Furthermore, knockdown of OVOL1 using a specific small interfering RNA increased the mRNA and protein levels of c-Myc and OVOL2. Knockdown of OVOL2 did not significantly affect the mRNA and protein levels of either c-Myc or OVOL1. These results suggest that OVOL1 is an upstream suppressor of c-Myc and OVOL2, and the OVOL1-OVOL2 axis is a modulator of c-Myc, coordinately regulating the invasiveness of cutaneous squamous cell carcinoma. Taken together, this study suggests that the OVOL1-OVOL2 axis is a key modulator of c-Myc expression in the shift from in situ epidermal malignancy (Bowen's disease) to invasive squamous cell carcinoma.
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Affiliation(s)
- Takamichi Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Gaku Tsuji
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Research and Clinical Center for Yusho and Dioxin, Kyushu University, Fukuoka, Japan
| | - Fumitaka Ohno
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Nakahara
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Division of Skin Surface Sensing, Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroshi Uchi
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masutaka Furue
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Research and Clinical Center for Yusho and Dioxin, Kyushu University, Fukuoka, Japan.,Division of Skin Surface Sensing, Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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78
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Jia D, Jolly MK, Kulkarni P, Levine H. Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory. Cancers (Basel) 2017; 9:E70. [PMID: 28640191 PMCID: PMC5532606 DOI: 10.3390/cancers9070070] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 01/11/2023] Open
Abstract
Waddington's epigenetic landscape, a famous metaphor in developmental biology, depicts how a stem cell progresses from an undifferentiated phenotype to a differentiated one. The concept of "landscape" in the context of dynamical systems theory represents a high-dimensional space, in which each cell phenotype is considered as an "attractor" that is determined by interactions between multiple molecular players, and is buffered against environmental fluctuations. In addition, biological noise is thought to play an important role during these cell-fate decisions and in fact controls transitions between different phenotypes. Here, we discuss the phenotypic transitions in cancer from a dynamical systems perspective and invoke the concept of "cancer attractors"-hidden stable states of the underlying regulatory network that are not occupied by normal cells. Phenotypic transitions in cancer occur at varying levels depending on the context. Using epithelial-to-mesenchymal transition (EMT), cancer stem-like properties, metabolic reprogramming and the emergence of therapy resistance as examples, we illustrate how phenotypic plasticity in cancer cells enables them to acquire hybrid phenotypes (such as hybrid epithelial/mesenchymal and hybrid metabolic phenotypes) that tend to be more aggressive and notoriously resilient to therapies such as chemotherapy and androgen-deprivation therapy. Furthermore, we highlight multiple factors that may give rise to phenotypic plasticity in cancer cells, such as (a) multi-stability or oscillatory behaviors governed by underlying regulatory networks involved in cell-fate decisions in cancer cells, and (b) network rewiring due to conformational dynamics of intrinsically disordered proteins (IDPs) that are highly enriched in cancer cells. We conclude by discussing why a therapeutic approach that promotes "recanalization", i.e., the exit from "cancer attractors" and re-entry into "normal attractors", is more likely to succeed rather than a conventional approach that targets individual molecules/pathways.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005, USA.
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
| | - Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
- Department of Biosciences, Rice University, Houston, TX 77005, USA.
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79
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Jolly MK, Tripathi SC, Somarelli JA, Hanash SM, Levine H. Epithelial/mesenchymal plasticity: how have quantitative mathematical models helped improve our understanding? Mol Oncol 2017; 11:739-754. [PMID: 28548388 PMCID: PMC5496493 DOI: 10.1002/1878-0261.12084] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/11/2017] [Accepted: 05/18/2017] [Indexed: 12/17/2022] Open
Abstract
Phenotypic plasticity, the ability of cells to reversibly alter their phenotypes in response to signals, presents a significant clinical challenge to treating solid tumors. Tumor cells utilize phenotypic plasticity to evade therapies, metastasize, and colonize distant organs. As a result, phenotypic plasticity can accelerate tumor progression. A well‐studied example of phenotypic plasticity is the bidirectional conversions among epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M) phenotype(s). These conversions can alter a repertoire of cellular traits associated with multiple hallmarks of cancer, such as metabolism, immune evasion, invasion, and metastasis. To tackle the complexity and heterogeneity of these transitions, mathematical models have been developed that seek to capture the experimentally verified molecular mechanisms and act as ‘hypothesis‐generating machines’. Here, we discuss how these quantitative mathematical models have helped us explain existing experimental data, guided further experiments, and provided an improved conceptual framework for understanding how multiple intracellular and extracellular signals can drive E/M plasticity at both the single‐cell and population levels. We also discuss the implications of this plasticity in driving multiple aggressive facets of tumor progression.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
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80
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Jolly MK, Ware KE, Gilja S, Somarelli JA, Levine H. EMT and MET: necessary or permissive for metastasis? Mol Oncol 2017; 11:755-769. [PMID: 28548345 PMCID: PMC5496498 DOI: 10.1002/1878-0261.12083] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/11/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
Epithelial‐to‐mesenchymal transition (EMT) and its reverse mesenchymal‐to‐epithelial transition (MET) have been suggested to play crucial roles in metastatic dissemination of carcinomas. These phenotypic transitions between states are not binary. Instead, carcinoma cells often exhibit a spectrum of epithelial/mesenchymal phenotype(s). While epithelial/mesenchymal plasticity has been observed preclinically and clinically, whether any of these phenotypic transitions are indispensable for metastatic outgrowth remains an unanswered question. Here, we focus on epithelial/mesenchymal plasticity in metastatic dissemination and propose alternative mechanisms for successful dissemination and metastases beyond the traditional EMT/MET view. We highlight multiple hypotheses that can help reconcile conflicting observations, and outline the next set of key questions that can offer valuable insights into mechanisms of metastasis in multiple tumor models.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Kathryn E Ware
- Duke Cancer Institute & Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Shivee Gilja
- Duke Cancer Institute & Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Jason A Somarelli
- Duke Cancer Institute & Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
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81
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Jolly MK, Levine H. Computational systems biology of epithelial-hybrid-mesenchymal transitions. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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82
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Jia D, Jolly MK, Harrison W, Boareto M, Ben-Jacob E, Levine H. Operating principles of tristable circuits regulating cellular differentiation. Phys Biol 2017; 14:035007. [PMID: 28443829 DOI: 10.1088/1478-3975/aa6f90] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Many cell-fate decisions during embryonic development are governed by a motif comprised of two transcription factors (TFs) A and B that mutually inhibit each other and may self-activate. This motif, called as a self-activating toggle switch (SATS), can typically have three stable states (phenotypes)-two corresponding to differentiated cell fates, each of which has a much higher level of one TF than the other-[Formula: see text] or [Formula: see text]-and the third state corresponding to an 'undecided' stem-like state with similar levels of both A and B-[Formula: see text]. Furthermore, two or more SATSes can be coupled together in various topologies in different contexts, thereby affecting the coordination between multiple cellular decisions. However, two questions remain largely unanswered: (a) what governs the co-existence and relative stability of these three stable states? (b) What orchestrates the decision-making of coupled SATSes? Here, we first demonstrate that the co-existence and relative stability of the three stable states in an individual SATS can be governed by the relative strength of self-activation, external signals activating and/or inhibiting A and B, and mutual degradation between A and B. Simultaneously, we investigate the effects of these factors on the decision-making of two coupled SATSes. Our results offer novel understanding into the operating principles of individual and coupled tristable self-activating toggle switches (SATSes) regulating cellular differentiation and can yield insights into synthesizing three-way genetic circuits and understanding of cellular reprogramming.
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Affiliation(s)
- Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, United States of America. Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005-1827, United States of America
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83
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Mooney SM, Talebian V, Jolly MK, Jia D, Gromala M, Levine H, McConkey BJ. The GRHL2/ZEB Feedback Loop-A Key Axis in the Regulation of EMT in Breast Cancer. J Cell Biochem 2017; 118:2559-2570. [PMID: 28266048 DOI: 10.1002/jcb.25974] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 12/17/2022]
Abstract
More than 90% of cancer-related deaths are caused by metastasis. Epithelial-to-Mesenchymal Transition (EMT) causes tumor cell dissemination while the reverse process, Mesenchymal-to-Epithelial Transition (MET) allows cancer cells to grow and establish a potentially deadly metastatic lesion. Recent evidence indicates that in addition to E and M, cells can adopt a stable hybrid Epithelial/Mesenchymal (E/M) state where they can move collectively leading to clusters of Circulating Tumor Cells-the "bad actors" of metastasis. EMT is postulated to occur in all four major histological breast cancer subtypes. Here, we identify a set of genes strongly correlated with CDH1 in 877 cancer cell lines, and differentially expressed genes in cell lines overexpressing ZEB1, SNAIL, and TWIST. GRHL2 and ESRP1 appear in both these sets and also correlate with CDH1 at the protein level in 40 breast cancer specimens. Next, we find that GRHL2 and CD24 expression coincide with an epithelial character in human mammary epithelial cells. Further, we show that high GRHL2 expression is highly correlated with worse relapse-free survival in all four subtypes of breast cancer. Finally, we integrate CD24, GRHL2, and ESRP1 into a mathematical model of EMT regulation to validate the role of these players in EMT. Our data analysis and modeling results highlight the relationships among multiple crucial EMT/MET drivers including ZEB1, GRHL2, CD24, and ESRP1, particularly in basal-like breast cancers, which are most similar to triple-negative breast cancer (TNBC) and are considered the most dangerous subtype. J. Cell. Biochem. 118: 2559-2570, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Steven M Mooney
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Vida Talebian
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Department of Bioengineering, Rice University, Houston 77005, Texas
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Program in Systems/Synthetic/Physical Biology, Rice University, Houston 77005, Texas
| | - Monica Gromala
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston 77005, Texas.,Program in Systems/Synthetic/Physical Biology, Rice University, Houston 77005, Texas.,Department of Physics and Astronomy, Rice University, Houston 77005, Texas
| | - Brendan J McConkey
- Department of Biology, University of Waterloo, Waterloo N2L3G1, ON, Canada
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84
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Mooney SM, Jolly MK, Levine H, Kulkarni P. Phenotypic plasticity in prostate cancer: role of intrinsically disordered proteins. Asian J Androl 2017; 18:704-10. [PMID: 27427552 PMCID: PMC5000791 DOI: 10.4103/1008-682x.183570] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A striking characteristic of cancer cells is their remarkable phenotypic plasticity, which is the ability to switch states or phenotypes in response to environmental fluctuations. Phenotypic changes such as a partial or complete epithelial to mesenchymal transition (EMT) that play important roles in their survival and proliferation, and development of resistance to therapeutic treatments, are widely believed to arise due to somatic mutations in the genome. However, there is a growing concern that such a deterministic view is not entirely consistent with multiple lines of evidence, which indicate that stochasticity may also play an important role in driving phenotypic plasticity. Here, we discuss how stochasticity in protein interaction networks (PINs) may play a key role in determining phenotypic plasticity in prostate cancer (PCa). Specifically, we point out that the key players driving transitions among different phenotypes (epithelial, mesenchymal, and hybrid epithelial/mesenchymal), including ZEB1, SNAI1, OVOL1, and OVOL2, are intrinsically disordered proteins (IDPs) and discuss how plasticity at the molecular level may contribute to stochasticity in phenotypic switching by rewiring PINs. We conclude by suggesting that targeting IDPs implicated in EMT in PCa may be a new strategy to gain additional insights and develop novel treatments for this disease, which is the most common form of cancer in adult men.
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Affiliation(s)
- Steven M Mooney
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005; Department of Bioengineering, Rice University, Houston, TX 77005; Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA
| | - Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
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85
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Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity. Proc Natl Acad Sci U S A 2017; 114:E2644-E2653. [PMID: 28289210 DOI: 10.1073/pnas.1700082114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack a unique 3D structure and comprise a large fraction of the human proteome play important roles in numerous cellular functions. Prostate-Associated Gene 4 (PAGE4) is an IDP that acts as a potentiator of the Activator Protein-1 (AP-1) transcription factor. Homeodomain-Interacting Protein Kinase 1 (HIPK1) phosphorylates PAGE4 at S9 and T51, but only T51 is critical for its activity. Here, we identify a second kinase, CDC-Like Kinase 2 (CLK2), which acts on PAGE4 and hyperphosphorylates it at multiple S/T residues, including S9 and T51. We demonstrate that HIPK1 is expressed in both androgen-dependent and androgen-independent prostate cancer (PCa) cells, whereas CLK2 and PAGE4 are expressed only in androgen-dependent cells. Cell-based studies indicate that PAGE4 interaction with the two kinases leads to opposing functions. HIPK1-phosphorylated PAGE4 (HIPK1-PAGE4) potentiates c-Jun, whereas CLK2-phosphorylated PAGE4 (CLK2-PAGE4) attenuates c-Jun activity. Consistent with the cellular data, biophysical measurements (small-angle X-ray scattering, single-molecule fluorescence resonance energy transfer, and NMR) indicate that HIPK1-PAGE4 exhibits a relatively compact conformational ensemble that binds AP-1, whereas CLK2-PAGE4 is more expanded and resembles a random coil with diminished affinity for AP-1. Taken together, the results suggest that the phosphorylation-induced conformational dynamics of PAGE4 may play a role in modulating changes between PCa cell phenotypes. A mathematical model based on our experimental data demonstrates how differential phosphorylation of PAGE4 can lead to transitions between androgen-dependent and androgen-independent phenotypes by altering the AP-1/androgen receptor regulatory circuit in PCa cells.
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86
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Faddaoui A, Sheta R, Bachvarova M, Plante M, Gregoire J, Renaud MC, Sebastianelli A, Gobeil S, Morin C, Ghani K, Bachvarov D. Suppression of the grainyhead transcription factor 2 gene (GRHL2) inhibits the proliferation, migration, invasion and mediates cell cycle arrest of ovarian cancer cells. Cell Cycle 2017; 16:693-706. [PMID: 28278050 DOI: 10.1080/15384101.2017.1295181] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Previously, we have identified the Grainyhead transcription factor 2 gene (GRHL2) as notably hypomethylated in high-grade (HG) serous epithelial ovarian tumors, compared with normal ovarian tissues. GRHL2 is known for its functions in normal tissue development and wound healing. In the context of cancer, the role of GRHL2 is still ambiguous as both tumorigenic and tumor suppressive functions have been reported for this gene, although a role of GRHL2 in maintaining the epithelial status of cancer cells has been suggested. In this study, we report that GRHL2 is strongly overexpressed in both low malignant potential (LMP) and HG serous epithelial ovarian tumors, which probably correlates with its hypomethylated status. Suppression of the GRHL2 expression led to a sharp decrease in cell proliferation, migration and invasion and induced G1 cell cycle arrest in epithelial ovarian cancer (EOC) cells displaying either epithelial (A2780s) or mesenchymal (SKOV3) phenotypes. However, no phenotypic alterations were observed in these EOC cell lines following GRHL2 silencing. Gene expression profiling and consecutive canonical pathway and network analyses confirmed these data, as in both these EOC cell lines, GRHL2 ablation was associated with the downregulation of various genes and pathways implicated in cell growth and proliferation, cell cycle control and cellular metabolism. Taken together, our data are indicative for a strong oncogenic potential of the GRHL2 gene in EOC progression and support recent findings on the role of GRHL2 as one of the major phenotypic stability factors (PSFs) that stabilize the highly aggressive/metastatic hybrid epithelial/mesenchymal (E/M) phenotype of cancer cells.
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Affiliation(s)
- Adnen Faddaoui
- a Department of Molecular Medicine , Université Laval , Québec , Canada.,b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
| | - Razan Sheta
- a Department of Molecular Medicine , Université Laval , Québec , Canada.,b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
| | - Magdalena Bachvarova
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
| | - Marie Plante
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada.,c Department of Obstetrics and Gynecology , Université Laval , Québec , Canada
| | - Jean Gregoire
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada.,c Department of Obstetrics and Gynecology , Université Laval , Québec , Canada
| | - Marie-Claude Renaud
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada.,c Department of Obstetrics and Gynecology , Université Laval , Québec , Canada
| | - Alexandra Sebastianelli
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada.,c Department of Obstetrics and Gynecology , Université Laval , Québec , Canada
| | - Stephane Gobeil
- a Department of Molecular Medicine , Université Laval , Québec , Canada.,d Centre de Recherche du CHU de Québec , CHUL , Québec , Canada
| | - Chantale Morin
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
| | - Karim Ghani
- b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
| | - Dimcho Bachvarov
- a Department of Molecular Medicine , Université Laval , Québec , Canada.,b Centre de Recherche du CHU de Québec , L'Hôtel-Dieu de Québec , Québec , Canada
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87
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Sulaiman A, Yao ZM, Wang LS. Re-evaluating the role of epithelial-mesenchymal-transition in cancer progression. J Biomed Res 2016; 32:81-90. [PMID: 28546516 PMCID: PMC5895572 DOI: 10.7555/jbr.31.20160124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are essential for embryonic development and also important in cancer progression. In a conventional model, epithelial-like cancer cells transit to mesenchymal-like tumor cells with great motility via EMT transcription factors; these mesenchymal-like cells migrate through the circulation system, relocate to a suitable site and then convert back to an epithelial-like phenotype to regenerate the tumor. However, recent findings challenge this conventional model and support the existence of a stable hybrid epithelial/mesenchymal (E/M) tumor population. Hybrid E/M tumor cells exhibit both epithelial and mesenchymal properties, possess great metastatic and tumorigenic capacity and are associated with poorer patient prognosis. The hybrid E/M model and associated regulatory networks represent a conceptual change regarding tumor metastasis and organ colonization. It may lead to the development of novel treatment strategies to ultimately stop cancer progression and improve disease-free survival.
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Affiliation(s)
- Andrew Sulaiman
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada.,China-Canada Centre of Research for Digestive Diseases.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Ze-Min Yao
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada.,China-Canada Centre of Research for Digestive Diseases.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
| | - Li-Sheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Canada.,China-Canada Centre of Research for Digestive Diseases.,Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.,Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada
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88
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Fu H, Qi L, Chen L, He Y, Zhang N, Guo H. Expression of Ovol2 is related to epithelial characteristics and shows a favorable clinical outcome in hepatocellular carcinoma. Onco Targets Ther 2016; 9:5963-5973. [PMID: 27729805 PMCID: PMC5047729 DOI: 10.2147/ott.s110409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Metastasis involves epithelial–mesenchymal transition (EMT) and mesenchymal–epithelial transition. Ovol2 belongs to the Ovo-like family (Ovol) of evolutionarily conserved zinc-finger transcription factors that regulate gene expression in various differentiation processes. Recent studies have demonstrated that Ovols affect mesenchymal–epithelial transition by inducing the expression of miR-200 in a range of human cancers. Downregulated Ovol2 expression is involved in the invasion and metastasis of breast and prostate cancers, but little is known about its expression and prognostic value in other cancers, including hepatocellular carcinoma (HCC). This study was designed to explore the clinical and prognostic significance of Ovol2 in patients with HCC. The expression of Ovol2 in tumor samples from patients with HCC and HCC cell lines was examined using Western blotting, real-time polymerase chain reaction, and immunohistochemistry. The expression levels of EMT-related markers, including E-cadherin, N-cadherin, and vimentin, were detected in relation to Ovol2 expression. The prognostic significance of Ovol2 in patients with HCC was statistically analyzed by Kaplan–Meier and Cox regression analyses. Ovol2 expression was significantly lower in HCC tissues than in adjacent noncancerous tissues. Low expression of Ovol2 was detected in HCC tissues with poor histological differentiation, microvascular invasion, and cirrhosis. A significant relationship was observed between Ovol2 and EMT marker expression levels. Kaplan–Meier analysis showed that overall survival was significantly worse in patients with HCC with low Ovol2 expression, indicating that Ovol2 deletion was an independent predictor of unfavorable prognosis in patients with HCC. Elevated Ovol2 expression may suppress HCC cell invasion and metastasis via restricting EMT.
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Affiliation(s)
- Hui Fu
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital; The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer
| | - Lisha Qi
- The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer; Department of Pathology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Lu Chen
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital; The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer
| | - Yuchao He
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital; The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer
| | - Ning Zhang
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital; The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer
| | - Hua Guo
- Department of Tumor Cell Biology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital; The Key Laboratory of Tianjin Cancer Prevention and Treatment, National Clinical Research Center for Cancer
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89
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Jolly MK, Jia D, Boareto M, Mani SA, Pienta KJ, Ben-Jacob E, Levine H. Coupling the modules of EMT and stemness: A tunable 'stemness window' model. Oncotarget 2016; 6:25161-74. [PMID: 26317796 PMCID: PMC4694822 DOI: 10.18632/oncotarget.4629] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/10/2015] [Indexed: 12/19/2022] Open
Abstract
Metastasis of carcinoma involves migration of tumor cells to distant organs and initiate secondary tumors. Migration requires a complete or partial Epithelial-to-Mesenchymal Transition (EMT), and tumor-initiation requires cells possessing stemness. Epithelial cells (E) undergoing a complete EMT to become mesenchymal (M) have been suggested to be more likely to possess stemness. However, recent studies suggest that stemness can also be associated with cells undergoing a partial EMT (hybrid E/M phenotype). Therefore, the correlation between EMT and stemness remains elusive. Here, using a theoretical framework that couples the core EMT and stemness modules (miR-200/ZEB and LIN28/let-7), we demonstrate that the positioning of ‘stemness window’ on the ‘EMT axis’ need not be universal; rather it can be fine-tuned. Particularly, we present OVOL as an example of a modulating factor that, due to its coupling with miR-200/ZEB/LIN28/let-7 circuit, fine-tunes the EMT-stemness interplay. Coupling OVOL can inhibit the stemness likelihood of M and elevate that of the hybrid E/M (partial EMT) phenotype, thereby pulling the ‘stemness window’ away from the M end of ‘EMT axis’. Our results unify various apparently contradictory experimental findings regarding the interconnection between EMT and stemness, corroborate the emerging notion that partial EMT associates with stemness, and offer new testable predictions.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Department of Bioengineering, Rice University, Houston, TX 77005-1827, USA
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005-1827, USA
| | - Marcelo Boareto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Institute of Physics, University of Sao Paulo, Sao Paulo 05508, Brazil
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, and Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth J Pienta
- The James Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.,Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Department of Biosciences, Rice University, Houston, TX 77005-1827, USA.,School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Department of Bioengineering, Rice University, Houston, TX 77005-1827, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA.,Department of Biosciences, Rice University, Houston, TX 77005-1827, USA
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90
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Le DJ, Chung DWD, Frausto RF, Kim MJ, Aldave AJ. Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus. PLoS One 2016; 11:e0158467. [PMID: 27355326 PMCID: PMC4927100 DOI: 10.1371/journal.pone.0158467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 06/16/2016] [Indexed: 12/13/2022] Open
Abstract
Posterior polymorphous corneal dystrophy 1 (PPCD1) is a genetic disorder that affects corneal endothelial cell function and leads to loss of visual acuity. PPCD1 has been linked to a locus on chromosome 20 in multiple families; however, Sanger sequencing of protein-coding genes in the consensus region failed to identify any causative missense mutations. In this study, custom capture probes were utilized for targeted next-generation sequencing of the linked region in a previously reported family with PPCD1. Variants were detected through two bioinformatics pipelines and filtered according to multiple criteria. Additionally, a high-resolution microarray was used to detect copy number variations. No non-synonymous variants in the protein-coding region of annotated genes were identified. However, 12 single nucleotide variants in 10 genes, and 9 indels in 7 genes met the filtering criteria and were considered candidate variants for PPCD1. Eleven single nucleotide variants were confirmed by Sanger sequencing, including 2 synonymous variants and 9 non-coding variants, in 9 genes. One microdeletion was detected in an intron of OVOL2 by microarray but was subsequently not identified by PCR. Using a comprehensive next-generation sequencing approach, a total of 16 genes containing single nucleotide variants or indels that segregated with the affected phenotype in an affected family previously mapped to the PPCD1 locus were identified. Screening of these candidate genes in other families previously mapped to the PPCD1 locus will likely result in the identification of the genetic basis of PPCD1.
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Affiliation(s)
- Derek J. Le
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Duk-Won D. Chung
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Ricardo F. Frausto
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Michelle J. Kim
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Anthony J. Aldave
- Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- * E-mail:
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91
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Kulkarni P, Getzenberg RH. Disorder, Promiscuous Interactions, and Stochasticity Regulate State Switching in the Unstable Prostate. J Cell Biochem 2016; 117:2235-40. [PMID: 27152744 DOI: 10.1002/jcb.25578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 12/12/2022]
Abstract
A causal link between benign prostatic hyperplasia (BPH) and prostate cancer has long been suspected but not widely accepted. A new model is proposed that supports such a connection. In contrast to the prevailing wisdom, our model, that draws on dynamical systems theory, suggests that in response to stress, epithelial cells in the unstable gland can give rise to both types of diseases via a phenotypic switching mechanism. The central idea is that phenotypic switching is a stochastic process which exploits the plasticity of the epithelial cell. It is driven by 'noise' contributed by the conformational dynamics of proteins that are intrinsically disordered. In a system that is noisy when stressed, disorder promotes promiscuity, unmasks latent information, and rewires the network to cause phenotypic switching. Cells with newly acquired phenotypes can transcend the traditional zonal boundaries to give rise to BPH or prostate cancer depending on the microenvironment. Establishing causality between the two diseases may provide us with an opportunity to better understand their etiology and guide prevention and treatment strategies. J. Cell. Biochem. 117: 2235-2240, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Prakash Kulkarni
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
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92
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Grigore AD, Jolly MK, Jia D, Farach-Carson MC, Levine H. Tumor Budding: The Name is EMT. Partial EMT. J Clin Med 2016; 5:jcm5050051. [PMID: 27136592 PMCID: PMC4882480 DOI: 10.3390/jcm5050051] [Citation(s) in RCA: 319] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 04/22/2016] [Indexed: 12/11/2022] Open
Abstract
Tumor budding is a histological phenomenon encountered in various cancers, whereby individual malignant cells and/or small clusters of malignant cells are seen in the tumor stroma. Postulated to be mirror epithelial-mesenchymal transition, tumor budding has been associated with poor cancer outcomes. However, the vast heterogeneity in its exact definition, methodology of assessment, and patient stratification need to be resolved before it can be routinely used as a standardized prognostic feature. Here, we discuss the heterogeneity in defining and assessing tumor budding, its clinical significance across multiple cancer types, and its prospective implementation in clinical practice. Next, we review the emerging evidence about partial, rather than complete, epithelial-mesenchymal phenotype at the tumor bud level, and its connection with tumor proliferation, quiescence, and stemness. Finally, based on recent literature, indicating a co-expression of epithelial and mesenchymal markers in many tumor buds, we posit tumor budding to be a manifestation of this hybrid epithelial/mesenchymal phenotype displaying collective cell migration.
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Affiliation(s)
- Alexandru Dan Grigore
- Departments of BioSciences, Rice University, Houston, TX 77005-1827, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
| | - Mohit Kumar Jolly
- Departments of Bioengineering, Rice University, Houston, TX 77005-1827, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
- Graduate Program in Systems, Synthetic and Physical Biology, Rice University, Houston, TX 77005-1827, USA.
| | - Mary C Farach-Carson
- Departments of BioSciences, Rice University, Houston, TX 77005-1827, USA.
- Departments of Bioengineering, Rice University, Houston, TX 77005-1827, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
| | - Herbert Levine
- Departments of BioSciences, Rice University, Houston, TX 77005-1827, USA.
- Departments of Bioengineering, Rice University, Houston, TX 77005-1827, USA.
- Departments of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA.
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
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93
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Mandal M, Ghosh B, Anura A, Mitra P, Pathak T, Chatterjee J. Modeling continuum of epithelial mesenchymal transition plasticity. Integr Biol (Camb) 2016; 8:167-76. [PMID: 26762753 DOI: 10.1039/c5ib00219b] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Living systems respond to ambient pathophysiological changes by altering their phenotype, a phenomenon called 'phenotypic plasticity'. This program contains information about adaptive biological dynamism. Epithelial-mesenchymal transition (EMT) is one such process found to be crucial in development, wound healing, and cancer wherein the epithelial cells with restricted migratory potential develop motile functions by acquiring mesenchymal characteristics. In the present study, phase contrast microscopy images of EMT induced HaCaT cells were acquired at 24 h intervals for 96 h. The expression study of relevant pivotal molecules viz. F-actin, vimentin, fibronectin and N-cadherin was carried out to confirm the EMT process. Cells were intuitively categorized into five distinct morphological phenotypes. A population of 500 cells for each temporal point was selected to quantify their frequency of occurrence. The plastic interplay of cell phenotypes from the observations was described as a Markovian process. A model was formulated empirically using simple linear algebra, to depict the possible mechanisms of cellular transformation among the five phenotypes. This work employed qualitative, semi-quantitative and quantitative tools towards illustration and establishment of the EMT continuum. Thus, it provides a newer perspective to understand the embedded plasticity across the EMT spectrum.
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Affiliation(s)
- Mousumi Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India.
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94
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Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Sci Rep 2015; 5:17379. [PMID: 26627083 PMCID: PMC4667179 DOI: 10.1038/srep17379] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/06/2015] [Indexed: 12/19/2022] Open
Abstract
Cellular plasticity during cancer metastasis is a major clinical challenge. Two key cellular plasticity mechanisms —Epithelial-to-Mesenchymal Transition (EMT) and Mesenchymal-to-Amoeboid Transition (MAT) – have been carefully investigated individually, yet a comprehensive understanding of their interconnections remains elusive. Previously, we have modeled the dynamics of the core regulatory circuits for both EMT (miR-200/ZEB/miR-34/SNAIL) and MAT (Rac1/RhoA). We now extend our previous work to study the coupling between these two core circuits by considering the two microRNAs (miR-200 and miR-34) as external signals to the core MAT circuit. We show that this coupled circuit enables four different stable steady states (phenotypes) that correspond to hybrid epithelial/mesenchymal (E/M), mesenchymal (M), amoeboid (A) and hybrid amoeboid/mesenchymal (A/M) phenotypes. Our model recapitulates the metastasis-suppressing role of the microRNAs even in the presence of EMT-inducing signals like Hepatocyte Growth Factor (HGF). It also enables mapping the microRNA levels to the transitions among various cell migration phenotypes. Finally, it offers a mechanistic understanding for the observed phenotypic transitions among different cell migration phenotypes, specifically the Collective-to-Amoeboid Transition (CAT).
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95
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Hong T, Watanabe K, Ta CH, Villarreal-Ponce A, Nie Q, Dai X. An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States. PLoS Comput Biol 2015; 11:e1004569. [PMID: 26554584 PMCID: PMC4640575 DOI: 10.1371/journal.pcbi.1004569] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022] Open
Abstract
Reversible epithelial-to-mesenchymal transition (EMT) is central to tissue development, epithelial stemness, and cancer metastasis. While many regulatory elements have been identified to induce EMT, the complex process underlying such cellular plasticity remains poorly understood. Utilizing a systems biology approach integrating modeling and experiments, we found multiple intermediate states contributing to EMT and that the robustness of the transitions is modulated by transcriptional factor Ovol2. In particular, we obtained evidence for a mutual inhibition relationship between Ovol2 and EMT inducer Zeb1, and observed that adding this regulation generates a novel four-state system consisting of two distinct intermediate phenotypes that differ in differentiation propensities and are favored in different environmental conditions. We identified epithelial cells that naturally exist in an intermediate state with bidirectional differentiation potential, and found the balance between EMT-promoting and -inhibiting factors to be critical in achieving and selecting between intermediate states. Our analysis suggests a new design principle in controlling cellular plasticity through multiple intermediate cell fates and underscores the critical involvement of Ovol2 and its associated molecular regulations. Cumulative evidence reveals remarkable lineage plasticity of somatic cells. Epithelial-to-mesenchymal transition (EMT) represents a prime example of such plasticity where an epithelial cell is converted into a mesenchymal cell. This process is used in normal development to generate crucial cell types, and is hijacked by cancer cells for invasion and metastasis. Recent studies also suggest the importance of EMT in generating stem cell properties. The reversibility of EMT and its sensitivity to varying environmental stimuli pose interesting challenges to understand the intricate regulatory networks that direct cellular state transitions and their dynamics. Here we use a systems biology approach to probe into the complexity of the EMT process. We report a new molecular regulation that expands the known regulatory network, and show that this new network is capable of generating multiple intermediate states, which we provide experimental evidence for. We present modeling and experimental results to highlight the significance of a delicate balance between EMT-promoting and -inhibiting factors for achieving and/or selecting an intermediate state, and to suggest the biological significance of the multiple intermediate states. This work further elucidates the complex strategies that control epithelial cell behavior and cancer/stem cell plasticity.
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Affiliation(s)
- Tian Hong
- Department of Mathematics, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Kazuhide Watanabe
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Catherine Ha Ta
- Department of Mathematics, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Alvaro Villarreal-Ponce
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California, United States of America
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- * E-mail: (QN); (XD)
| | - Xing Dai
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California, United States of America
- * E-mail: (QN); (XD)
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96
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Jolly MK, Boareto M, Huang B, Jia D, Lu M, Ben-Jacob E, Onuchic JN, Levine H. Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis. Front Oncol 2015; 5:155. [PMID: 26258068 PMCID: PMC4507461 DOI: 10.3389/fonc.2015.00155] [Citation(s) in RCA: 470] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
Transitions between epithelial and mesenchymal phenotypes – the epithelial to mesenchymal transition (EMT) and its reverse the mesenchymal to epithelial transition (MET) – are hallmarks of cancer metastasis. While transitioning between the epithelial and mesenchymal phenotypes, cells can also attain a hybrid epithelial/mesenchymal (E/M) (i.e., partial or intermediate EMT) phenotype. Cells in this phenotype have mixed epithelial (e.g., adhesion) and mesenchymal (e.g., migration) properties, thereby allowing them to move collectively as clusters. If these clusters reach the bloodstream intact, they can give rise to clusters of circulating tumor cells (CTCs), as have often been seen experimentally. Here, we review the operating principles of the core regulatory network for EMT/MET that acts as a “three-way” switch giving rise to three distinct phenotypes – E, M and hybrid E/M – and present a theoretical framework that can elucidate the role of many other players in regulating epithelial plasticity. Furthermore, we highlight recent studies on partial EMT and its association with drug resistance and tumor-initiating potential; and discuss how cell–cell communication between cells in a partial EMT phenotype can enable the formation of clusters of CTCs. These clusters can be more apoptosis-resistant and have more tumor-initiating potential than singly moving CTCs with a wholly mesenchymal (complete EMT) phenotype. Also, more such clusters can be formed under inflammatory conditions that are often generated by various therapies. Finally, we discuss the multiple advantages that the partial EMT or hybrid E/M phenotype have as compared to a complete EMT phenotype and argue that these collectively migrating cells are the primary “bad actors” of metastasis.
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Affiliation(s)
- Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Department of Bioengineering, Rice University , Houston, TX , USA
| | - Marcelo Boareto
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Institute of Physics, University of São Paulo , São Paulo , Brazil
| | - Bin Huang
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Department of Chemistry, Rice University , Houston, TX , USA
| | - Dongya Jia
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Graduate Program in Systems, Synthetic and Physical Biology, Rice University , Houston, TX , USA
| | - Mingyang Lu
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; School of Physics and Astronomy, and The Sagol School of Neuroscience, Tel-Aviv University , Tel-Aviv , Israel ; Department of Biosciences, Rice University , Houston, TX , USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Department of Chemistry, Rice University , Houston, TX , USA ; Department of Physics and Astronomy, Rice University , Houston, TX , USA ; Department of Biosciences, Rice University , Houston, TX , USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University , Houston, TX , USA ; Department of Bioengineering, Rice University , Houston, TX , USA ; Department of Physics and Astronomy, Rice University , Houston, TX , USA ; Department of Biosciences, Rice University , Houston, TX , USA
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