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Wu L, Jin W, Yu H, Liu B. Modulating autophagy to treat diseases: A revisited review on in silico methods. J Adv Res 2024; 58:175-191. [PMID: 37192730 PMCID: PMC10982871 DOI: 10.1016/j.jare.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Autophagy refers to the conserved cellular catabolic process relevant to lysosome activity and plays a vital role in maintaining the dynamic equilibrium of intracellular matter by degrading harmful and abnormally accumulated cellular components. Accumulating evidence has recently revealed that dysregulation of autophagy by genetic and exogenous interventions may disrupt cellular homeostasis in human diseases. In silico approaches as powerful aids to experiments have also been extensively reported to play their critical roles in the storage, prediction, and analysis of massive amounts of experimental data. Thus, modulating autophagy to treat diseases by in silico methods would be anticipated. AIM OF REVIEW Here, we focus on summarizing the updated in silico approaches including databases, systems biology network approaches, omics-based analyses, mathematical models, and artificial intelligence (AI) methods that sought to modulate autophagy for potential therapeutic purposes, which will provide a new insight into more promising therapeutic strategies. KEY SCIENTIFIC CONCEPTS OF REVIEW Autophagy-related databases are the data basis of the in silico method, storing a large amount of information about DNA, RNA, proteins, small molecules and diseases. The systems biology approach is a method to systematically study the interrelationships among biological processes including autophagy from a macroscopic perspective. Omics-based analyses are based on high-throughput data to analyze gene expression at different levels of biological processes involving autophagy. mathematical models are visualization methods to describe the dynamic process of autophagy, and its accuracy is related to the selection of parameters. AI methods use big data related to autophagy to predict autophagy targets, design targeted small molecules, and classify diverse human diseases for potential therapeutic applications.
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Affiliation(s)
- Lifeng Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenke Jin
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haiyang Yu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Bo Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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2
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Allen TA, Cullen MM, Hawkey N, Mochizuki H, Nguyen L, Schechter E, Borst L, Yoder JA, Freedman JA, Patierno SR, Cheng K, Eward WC, Somarelli JA. A Zebrafish Model of Metastatic Colonization Pinpoints Cellular Mechanisms of Circulating Tumor Cell Extravasation. Front Oncol 2021; 11:641187. [PMID: 34631514 PMCID: PMC8495265 DOI: 10.3389/fonc.2021.641187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 08/31/2021] [Indexed: 01/18/2023] Open
Abstract
Metastasis is a multistep process in which cells must detach, migrate/invade local structures, intravasate, circulate, extravasate, and colonize. A full understanding of the complexity of this process has been limited by the lack of ability to study these steps in isolation with detailed molecular analyses. Leveraging a comparative oncology approach, we injected canine osteosarcoma cells into the circulation of transgenic zebrafish with fluorescent blood vessels in a biologically dynamic metastasis extravasation model. Circulating tumor cell clusters that successfully extravasated the vasculature as multicellular units were isolated under intravital imaging (n = 6). These extravasation-positive tumor cell clusters sublines were then molecularly profiled by RNA-Seq. Using a systems-level analysis, we pinpointed the downregulation of KRAS signaling, immune pathways, and extracellular matrix (ECM) organization as enriched in extravasated cells (p < 0.05). Within the extracellular matrix remodeling pathway, we identified versican (VCAN) as consistently upregulated and central to the ECM gene regulatory network (p < 0.05). Versican expression is prognostic for a poorer metastasis-free and overall survival in patients with osteosarcoma. Together, our results provide a novel experimental framework to study discrete steps in the metastatic process. Using this system, we identify the versican/ECM network dysregulation as a potential contributor to osteosarcoma circulating tumor cell metastasis.
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Affiliation(s)
- Tyler A Allen
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Mark M Cullen
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Nathan Hawkey
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Hiroyuki Mochizuki
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Lan Nguyen
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Elyse Schechter
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States
| | - Luke Borst
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States
| | - Jennifer A Freedman
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, NC, United States
| | - Steven R Patierno
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, NC, United States
| | - Ke Cheng
- Department of Molecular Biomedical Sciences and Comparative Medicine Institute, North Carolina State University, Raleigh, NC, United States.,Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, United States
| | - William C Eward
- Department of Orthopedics, Duke University Medical Center, Durham, NC, United States
| | - Jason A Somarelli
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, NC, United States
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3
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Quiros-Fernandez I, Figueroa-Protti L, Arias-Arias JL, Brenes-Cordero N, Siles F, Mora J, Mora-Rodríguez RA. Perturbation-Based Modeling Unveils the Autophagic Modulation of Chemosensitivity and Immunogenicity in Breast Cancer Cells. Metabolites 2021; 11:637. [PMID: 34564453 PMCID: PMC8469554 DOI: 10.3390/metabo11090637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 01/18/2023] Open
Abstract
In the absence of new therapeutic strategies, chemotherapeutic drugs are the most widely used strategy against metastatic breast cancer, in spite of eliciting multiple adverse effects and having low responses with an average 5-year patient survival rate. Among the new therapeutic targets that are currently in clinical trials, here, we addressed the association between the regulation of the metabolic process of autophagy and the exposure of damage-associated molecular patterns associated (DAMPs) to immunogenic cell death (ICD), which has not been previously studied. After validating an mCHR-GFP tandem LC3 sensor capacity to report dynamic changes of the autophagic metabolic flux in response to external stimuli and demonstrating that both basal autophagy levels and response to diverse autophagy regulators fluctuate among different cell lines, we explored the interaction between autophagy modulators and chemotherapeutic agents in regards of cytotoxicity and ICD using three different breast cancer cell lines. Since these interactions are very complex and variable throughout different cell lines, we designed a perturbation-based model in which we propose specific modes of action of chemotherapeutic agents on the autophagic flux and the corresponding strategies of modulation to enhance the response to chemotherapy. Our results point towards a promising therapeutic potential of the metabolic regulation of autophagy to overcome chemotherapy resistance by eliciting ICD.
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Affiliation(s)
- Isaac Quiros-Fernandez
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Master’s Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Lucía Figueroa-Protti
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Jorge L. Arias-Arias
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- Dulbecco Laboratory Studio, Residencial Lisboa 2G, Alajuela 20102, Costa Rica
| | - Norman Brenes-Cordero
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
| | - Francisco Siles
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Pattern Recognition and Intelligent Systems Laboratory (PRIS-Lab), Department of Electrical Engineering and Postgraduate Studies in Electrical Engineering, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Javier Mora
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
| | - Rodrigo Antonio Mora-Rodríguez
- Research Center for Tropical Diseases (CIET), Laboratory of Tumor Chemosensitivity (LQT), Faculty of Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica; (I.Q.-F.); (L.F.-P.); (J.L.A.-A.); (N.B.-C.); (F.S.); (J.M.)
- DC Laboratory, Laboratory of Surgery and Cancer, University of Costa Rica, San José 11501-2060, Costa Rica
- Master’s Program in Microbiology, University of Costa Rica, San José 11501-2060, Costa Rica
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4
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Abstract
Ecological fitness is the ability of individuals in a population to survive and reproduce. Individuals with increased fitness are better equipped to withstand the selective pressures of their environments. This paradigm pertains to all organismal life as we know it; however, it is also becoming increasingly clear that within multicellular organisms exist highly complex, competitive, and cooperative populations of cells under many of the same ecological and evolutionary constraints as populations of individuals in nature. In this review I discuss the parallels between populations of cancer cells and populations of individuals in the wild, highlighting how individuals in either context are constrained by their environments to converge on a small number of critical phenotypes to ensure survival and future reproductive success. I argue that the hallmarks of cancer can be distilled into key phenotypes necessary for cancer cell fitness: survival and reproduction. I posit that for therapeutic strategies to be maximally beneficial, they should seek to subvert these ecologically driven phenotypic responses.
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A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2. Cancers (Basel) 2021; 13:cancers13071609. [PMID: 33807227 PMCID: PMC8037024 DOI: 10.3390/cancers13071609] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/12/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Epithelial-mesenchymal transition (EMT) is a key process in cancer progression through which cells weaken their cell-cell adhesion and gain mobility and invasive traits. Besides chemical signaling, recent studies have established the connection of EMT to mechanical microenvironment, such as the stiffness of extracellular matrix (ECM). LOXL2 is representative of a family of enzymes that promotes fiber cross-linking in ECM. With increased cross-linking comes increased stiffness, which induces EMT that can, in turn, elevate LOXL2 levels. As such, a positive feedback loop among EMT, LOXL2, and ECM stiffness can be formed. We built a mathematical model on a core biochemical reaction network featuring this feedback loop, and showed how strongly it drives EMT. We also illustrated mechanistically how cross-linking connects with stiffness, using a mechanical model of collagen (a major component of ECM). Using this theoretical framework, we demonstrated the heterogeneity of LOXL2/stiffness and its implications on migrating cancer cells that could seed metastasis, the growth of secondary malignant tumors. This framework can inspire experimental studies of more fine-grained mechanotransduction and biomechanical heterogeneity in cancers. Abstract The epithelial-mesenchymal transition (EMT) plays a critical role in cancer progression, being responsible in many cases for the onset of the metastatic cascade and being integral in the ability of cells to resist drug treatment. Most studies of EMT focus on its induction via chemical signals such as TGF-β or Notch ligands, but it has become increasingly clear that biomechanical features of the microenvironment such as extracellular matrix (ECM) stiffness can be equally important. Here, we introduce a coupled feedback loop connecting stiffness to the EMT transcription factor ZEB1, which acts via increasing the secretion of LOXL2 that leads to increased cross-linking of collagen fibers in the ECM. This increased cross-linking can effectively increase ECM stiffness and increase ZEB1 levels, thus setting a positive feedback loop between ZEB1 and ECM stiffness. To investigate the impact of this non-cell-autonomous effect, we introduce a computational approach capable of connecting LOXL2 concentration to increased stiffness and thereby to higher ZEB1 levels. Our results indicate that this positive feedback loop, once activated, can effectively lock the cells in a mesenchymal state. The spatial-temporal heterogeneity of the LOXL2 concentration and thus the mechanical stiffness also has direct implications for migrating cells that attempt to escape the primary tumor.
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Subbalakshmi AR, Sahoo S, Biswas K, Jolly MK. A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT). Cells Tissues Organs 2021; 211:689-702. [PMID: 33567424 DOI: 10.1159/000512520] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity comprises reversible transitions among epithelial, hybrid epithelial/mesenchymal (E/M) and mesenchymal phenotypes, and underlies various aspects of aggressive tumor progression such as metastasis, therapy resistance, and immune evasion. The process of cells attaining one or more hybrid E/M phenotypes is termed as partial epithelial mesenchymal transition (EMT). Cells in hybrid E/M phenotype(s) can be more aggressive than those in either fully epithelial or mesenchymal state. Thus, identifying regulators of hybrid E/M phenotypes is essential to decipher the rheostats of phenotypic plasticity and consequent accelerators of metastasis. Here, using a computational systems biology approach, we demonstrate that SLUG (SNAIL2) - an EMT-inducing transcription factor - can inhibit cells from undergoing a complete EMT and thus stabilize them in hybrid E/M phenotype(s). It expands the parametric range enabling the existence of a hybrid E/M phenotype, thereby behaving as a phenotypic stability factor. Our simulations suggest that this specific property of SLUG emerges from the topology of the regulatory network it forms with other key regulators of epithelial-mesenchymal plasticity. Clinical data suggest that SLUG associates with worse patient prognosis across multiple carcinomas. Together, our results indicate that SLUG can stabilize hybrid E/M phenotype(s).
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Affiliation(s)
- Ayalur R Subbalakshmi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Kuheli Biswas
- Department of Physical Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India,
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7
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Pasani S, Sahoo S, Jolly MK. Hybrid E/M Phenotype(s) and Stemness: A Mechanistic Connection Embedded in Network Topology. J Clin Med 2020; 10:E60. [PMID: 33375334 PMCID: PMC7794989 DOI: 10.3390/jcm10010060] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/20/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
Metastasis remains an unsolved clinical challenge. Two crucial features of metastasizing cancer cells are (a) their ability to dynamically move along the epithelial-hybrid-mesenchymal spectrum and (b) their tumor initiation potential or stemness. With increasing functional characterization of hybrid epithelial/mesenchymal (E/M) phenotypes along the spectrum, recent in vitro and in vivo studies have suggested an increasing association of hybrid E/M phenotypes with stemness. However, the mechanistic underpinnings enabling this association remain unclear. Here, we develop a mechanism-based mathematical modeling framework that interrogates the emergent nonlinear dynamics of the coupled network modules regulating E/M plasticity (miR-200/ZEB) and stemness (LIN28/let-7). Simulating the dynamics of this coupled network across a large ensemble of parameter sets, we observe that hybrid E/M phenotype(s) are more likely to acquire stemness relative to "pure" epithelial or mesenchymal states. We also integrate multiple "phenotypic stability factors" (PSFs) that have been shown to stabilize hybrid E/M phenotypes both in silico and in vitro-such as OVOL1/2, GRHL2, and NRF2-with this network, and demonstrate that the enrichment of hybrid E/M phenotype(s) with stemness is largely conserved in the presence of these PSFs. Thus, our results offer mechanistic insights into recent experimental observations of hybrid E/M phenotype(s) that are essential for tumor initiation and highlight how this feature is embedded in the underlying topology of interconnected EMT (Epithelial-Mesenchymal Transition) and stemness networks.
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Affiliation(s)
- Satwik Pasani
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (S.P.); (S.S.)
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (S.P.); (S.S.)
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India; (S.P.); (S.S.)
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8
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Somarelli JA, Rupprecht G, Altunel E, Flamant EM, Rao S, Sivaraj D, Lazarides AL, Hoskinson SM, Sheth MU, Cheng S, Kim SY, Ware KE, Agarwal A, Cullen MM, Selmic LE, Everitt JI, McCall SJ, Eward C, Eward WC, Hsu DS. A Comparative Oncology Drug Discovery Pipeline to Identify and Validate New Treatments for Osteosarcoma. Cancers (Basel) 2020; 12:cancers12113335. [PMID: 33187254 PMCID: PMC7696249 DOI: 10.3390/cancers12113335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Osteosarcoma is a rare bone cancer that occurs primarily in children. The discovery of new treatments for osteosarcoma and other rare cancer types has been severely limited by access to patient samples to study these often-complex diseases. Here we capitalize on naturally-occurring cancers in pet dogs to study the biology of these rare cancers. Using living cells from canine and human patients to test thousands of drugs simultaneously, we identify a unique combination of drugs that disrupts protein degradation and protein trafficking in cancer cells. This drug combination represents a promising new treatment to treat both dogs and people with osteosarcoma. Abstract Background: Osteosarcoma is a rare but aggressive bone cancer that occurs primarily in children. Like other rare cancers, treatment advances for osteosarcoma have stagnated, with little improvement in survival for the past several decades. Developing new treatments has been hampered by extensive genomic heterogeneity and limited access to patient samples to study the biology of this complex disease. Methods: To overcome these barriers, we combined the power of comparative oncology with patient-derived models of cancer and high-throughput chemical screens in a cross-species drug discovery pipeline. Results: Coupling in vitro high-throughput drug screens on low-passage and established cell lines with in vivo validation in patient-derived xenografts we identify the proteasome and CRM1 nuclear export pathways as therapeutic sensitivities in osteosarcoma, with dual inhibition of these pathways inducing synergistic cytotoxicity. Conclusions: These collective efforts provide an experimental framework and set of new tools for osteosarcoma and other rare cancers to identify and study new therapeutic vulnerabilities.
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Affiliation(s)
- Jason A. Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Correspondence:
| | - Gabrielle Rupprecht
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Erdem Altunel
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Etienne M. Flamant
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Sneha Rao
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Dharshan Sivaraj
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Alexander L. Lazarides
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Sarah M. Hoskinson
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Maya U. Sheth
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Serene Cheng
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Kathryn E. Ware
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Anika Agarwal
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
| | - Mark M. Cullen
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - Laura E. Selmic
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Jeffrey I. Everitt
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shannon J. McCall
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cindy Eward
- Surgery Service, Triangle Veterinary Referral Hospital, Durham, NC 27710, USA;
| | - William C. Eward
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA; (S.R.); (A.L.L.); (S.M.H.); (M.M.C.)
| | - David S. Hsu
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; (G.R.); (E.A.); (E.M.F.); (D.S.); (M.U.S.); (S.C.); (K.E.W.); (A.A.); (D.S.H.)
- Duke Cancer Institute, Durham, NC 27710, USA; (J.I.E.); (S.J.M.); (W.C.E.)
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Jia W, Tripathi S, Chakraborty P, Chedere A, Rangarajan A, Levine H, Jolly MK. Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. Oncotarget 2020; 11:2611-2624. [PMID: 32676163 PMCID: PMC7343638 DOI: 10.18632/oncotarget.27651] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/01/2020] [Indexed: 12/12/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reverse process mesenchymal-epithelial transition (MET) are central to metastatic aggressiveness and therapy resistance in solid tumors. While molecular determinants of both processes have been extensively characterized, the heterogeneity in the response of tumor cells to EMT and MET inducers has come into focus recently, and has been implicated in the failure of anti-cancer therapies. Recent experimental studies have shown that some cells can undergo an irreversible EMT depending on the duration of exposure to EMT-inducing signals. While the irreversibility of MET, or equivalently, resistance to EMT, has not been studied in as much detail, evidence supporting such behavior is slowly emerging. Here, we identify two possible mechanisms that can underlie resistance of cells to undergo EMT: epigenetic feedback in ZEB1/GRHL2 feedback loop and stochastic partitioning of biomolecules during cell division. Identifying the ZEB1/GRHL2 axis as a key determinant of epithelial-mesenchymal plasticity across many cancer types, we use mechanistic mathematical models to show how GRHL2 can be involved in both the abovementioned processes, thus driving an irreversible MET. Our study highlights how an isogenic population may contain subpopulation with varying degrees of susceptibility or resistance to EMT, and proposes a next set of questions for detailed experimental studies characterizing the irreversibility of MET/resistance to EMT.
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Affiliation(s)
- Wen Jia
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics and Astronomy, Rice University, Houston, TX, USA
| | - Shubham Tripathi
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Adithya Chedere
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Annapoorni Rangarajan
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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Insights into the Multi-Dimensional Dynamic Landscape of Epithelial-Mesenchymal Plasticity through Inter-Disciplinary Approaches. J Clin Med 2020; 9:jcm9061624. [PMID: 32471235 PMCID: PMC7356048 DOI: 10.3390/jcm9061624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/31/2022] Open
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Tripathi S, Levine H, Jolly MK. The Physics of Cellular Decision Making During Epithelial-Mesenchymal Transition. Annu Rev Biophys 2020; 49:1-18. [PMID: 31913665 DOI: 10.1146/annurev-biophys-121219-081557] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is a process by which cells lose epithelial traits, such as cell-cell adhesion and apico-basal polarity, and acquire migratory and invasive traits. EMT is crucial to embryonic development and wound healing. Misregulated EMT has been implicated in processes associated with cancer aggressiveness, including metastasis. Recent experimental advances such as single-cell analysis and temporal phenotypic characterization have established that EMT is a multistable process wherein cells exhibit and switch among multiple phenotypic states. This is in contrast to the classical perception of EMT as leading to a binary choice. Mathematical modeling has been at the forefront of this transformation for the field, not only providing a conceptual framework to integrate and analyze experimental data, but also making testable predictions. In this article, we review the key features and characteristics of EMT dynamics, with a focus on the mathematical modeling approaches that have been instrumental to obtaining various useful insights.
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Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, USA.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA; .,Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA; .,Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India;
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12
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Anticipating critical transitions in epithelial-hybrid-mesenchymal cell-fate determination. Proc Natl Acad Sci U S A 2019; 116:26343-26352. [PMID: 31843939 DOI: 10.1073/pnas.1913773116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In the vicinity of a tipping point, critical transitions occur when small changes in an input condition cause sudden, large, and often irreversible changes in the state of a system. Many natural systems ranging from ecosystems to molecular biosystems are known to exhibit critical transitions in their response to stochastic perturbations. In diseases, an early prediction of upcoming critical transitions from a healthy to a disease state by using early-warning signals is of prime interest due to potential application in forecasting disease onset. Here, we analyze cell-fate transitions between different phenotypes (epithelial, hybrid-epithelial/mesenchymal [E/M], and mesenchymal states) that are implicated in cancer metastasis and chemoresistance. These transitions are mediated by a mutually inhibitory feedback loop-microRNA-200/ZEB-driven by the levels of transcription factor SNAIL. We find that the proximity to tipping points enabling these transitions among different phenotypes can be captured by critical slowing down-based early-warning signals, calculated from the trajectory of ZEB messenger RNA level. Further, the basin stability analysis reveals the unexpectedly large basin of attraction for a hybrid-E/M phenotype. Finally, we identified mechanisms that can potentially elude the transition to a hybrid-E/M phenotype. Overall, our results unravel the early-warning signals that can be used to anticipate upcoming epithelial-hybrid-mesenchymal transitions. With the emerging evidence about the hybrid-E/M phenotype being a key driver of metastasis, drug resistance, and tumor relapse, our results suggest ways to potentially evade these transitions, reducing the fitness of cancer cells and restricting tumor aggressiveness.
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Jolly MK, Celià-Terrassa T. Dynamics of Phenotypic Heterogeneity Associated with EMT and Stemness during Cancer Progression. J Clin Med 2019; 8:E1542. [PMID: 31557977 PMCID: PMC6832750 DOI: 10.3390/jcm8101542] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic and phenotypic heterogeneity contribute to the generation of diverse tumor cell populations, thus enhancing cancer aggressiveness and therapy resistance. Compared to genetic heterogeneity, a consequence of mutational events, phenotypic heterogeneity arises from dynamic, reversible cell state transitions in response to varying intracellular/extracellular signals. Such phenotypic plasticity enables rapid adaptive responses to various stressful conditions and can have a strong impact on cancer progression. Herein, we have reviewed relevant literature on mechanisms associated with dynamic phenotypic changes and cellular plasticity, such as epithelial-mesenchymal transition (EMT) and cancer stemness, which have been reported to facilitate cancer metastasis. We also discuss how non-cell-autonomous mechanisms such as cell-cell communication can lead to an emergent population-level response in tumors. The molecular mechanisms underlying the complexity of tumor systems are crucial for comprehending cancer progression, and may provide new avenues for designing therapeutic strategies.
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Affiliation(s)
- Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India.
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.
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