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Hong T, Xing J. Data- and theory-driven approaches for understanding paths of epithelial-mesenchymal transition. Genesis 2024; 62:e23591. [PMID: 38553870 PMCID: PMC11017362 DOI: 10.1002/dvg.23591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/16/2024] [Accepted: 03/16/2024] [Indexed: 04/02/2024]
Abstract
Reversible transitions between epithelial and mesenchymal cell states are a crucial form of epithelial plasticity for development and disease progression. Recent experimental data and mechanistic models showed multiple intermediate epithelial-mesenchymal transition (EMT) states as well as trajectories of EMT underpinned by complex gene regulatory networks. In this review, we summarize recent progress in quantifying EMT and characterizing EMT paths with computational methods and quantitative experiments including omics-level measurements. We provide perspectives on how these studies can help relating fundamental cell biology to physiological and pathological outcomes of EMT.
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Affiliation(s)
- Tian Hong
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville TN, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Du J, Fan L, Razal JM, Chen S, Zhang H, Yang H, Li H, Li J. Strontium-doped mesoporous bioglass nanoparticles for enhanced wound healing with rapid vascularization. J Mater Chem B 2023; 11:7364-7377. [PMID: 37431606 DOI: 10.1039/d3tb01256e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Tissue engineered skin and its substitutes have a promising future in wound healing. However, enabling fast formation of blood vessels during the wound healing process is still a huge challenge to the currently available wound substitutes. In this work, active mesoporous bioglass nanoparticles with a high specific surface area and doped with strontium (Sr) were fabricated for rapid microvascularization and wound healing. The as-prepared bioglass nanoparticles with Sr ions significantly promoted the proliferation of fibroblasts and microvascularization of human umbilical vein endothelial cells in vitro. Silk fibroin sponges encapsulating the nanoparticles accelerated wound healing by promoting the formation of blood vessels and epithelium in vivo. This work provides a strategy for the design and development of active biomaterials for enhancing wound healing by rapid vascularization and epithelial reconstruction.
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Affiliation(s)
- Juan Du
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia.
| | - Linpeng Fan
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia.
| | - Joselito M Razal
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia.
| | - Sihao Chen
- School of Chemistry and Chemical Engineering, Multidisciplinary Center for Advanced Materials, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai University of Engineering Science, Shanghai 201620, P. R. China.
| | - Hongmei Zhang
- School of Chemistry and Chemical Engineering, Multidisciplinary Center for Advanced Materials, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai University of Engineering Science, Shanghai 201620, P. R. China.
| | - Hongjun Yang
- Key Laboratory of Green Processing and Functional New Textile Materials of Ministry of Education, Wuhan Textile University, Wuhan 430200, P. R. China
| | - Haiyan Li
- Chemical and Environment Engineering Department, School of Engineering, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Jingliang Li
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia.
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3
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Subhadarshini S, Markus J, Sahoo S, Jolly MK. Dynamics of Epithelial-Mesenchymal Plasticity: What Have Single-Cell Investigations Elucidated So Far? ACS OMEGA 2023; 8:11665-11673. [PMID: 37033874 PMCID: PMC10077445 DOI: 10.1021/acsomega.2c07989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Epithelial-mesenchymal plasticity (EMP) is a key driver of cancer metastasis and therapeutic resistance, through which cancer cells can reversibly and dynamically alter their molecular and functional traits along the epithelial-mesenchymal spectrum. While cells in the epithelial phenotype are usually tightly adherent, less metastatic, and drug-sensitive, those in the hybrid epithelial/mesenchymal and/or mesenchymal state are more invasive, migratory, drug-resistant, and immune-evasive. Single-cell studies have emerged as a powerful tool in gaining new insights into the dynamics of EMP across various cancer types. Here, we review many recent studies that employ single-cell analysis techniques to better understand the dynamics of EMP in cancer both in vitro and in vivo. These single-cell studies have underlined the plurality of trajectories cells can traverse during EMP and the consequent heterogeneity of hybrid epithelial/mesenchymal phenotypes seen at both preclinical and clinical levels. They also demonstrate how diverse EMP trajectories may exhibit hysteretic behavior and how the rate of such cell-state transitions depends on the genetic/epigenetic background of recipient cells, as well as the dose and/or duration of EMP-inducing growth factors. Finally, we discuss the relationship between EMP and patient survival across many cancer types. We also present a next set of questions related to EMP that could benefit much from single-cell observations and pave the way to better tackle phenotypic switching and heterogeneity in clinic.
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Affiliation(s)
| | - Joel Markus
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sarthak Sahoo
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre
for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
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Chakraborty K, Biswas A, Mishra S, Mallick AM, Tripathi A, Jan S, Sinha Roy R. Harnessing Peptide-Functionalized Multivalent Gold Nanorods for Promoting Enhanced Gene Silencing and Managing Breast Cancer Metastasis. ACS APPLIED BIO MATERIALS 2023; 6:458-472. [PMID: 36651932 DOI: 10.1021/acsabm.2c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Small interfering RNA (siRNA) has become the cornerstone against undruggable targets and for managing metastatic breast cancer. However, an effective gene silencing approach is faced with a major challenge due to the delivery problem. In our present study, we have demonstrated efficient siRNA delivery, superior gene silencing, and inhibition of metastasis in triple-negative breast cancer cells (MDA-MB-231) using rod-shaped (aspect ratio: 4) multivalent peptide-functionalized gold nanoparticles and compared them to monovalent free peptide doses. Multivalency is a new concept in biology, and tuning the physical parameters of multivalent nanoparticles can enhance gene silencing and antitumor efficacy. We explored the effect of the multivalency of shape- and size-dependent peptide-functionalized gold nanoparticles in siRNA delivery. Our study demonstrates that peptide functionalization leads to reduced toxicity of the nanoparticles. Such designed peptide-functionalized nanorods also demonstrate antimetastatic efficacy in Notch1-silenced cells by preventing EMT progression in vitro. We have shown siRNA delivery in the hard-to-transfect primary cell line HUVEC and also demonstrated that the Notch1-silenced MDA-MB-231 cell line has failed to form nanobridge-mediated foci with the HUVEC in the co-culture of HUVEC and MDA-MB-231, which promote metastasis. This antimetastatic effect is further checked in a xenotransplant in vivo zebrafish model. In vivo studies also suggest that our designed nanoparticles mediated inhibition of micrometastasis due to silencing of the Notch1 gene. The outcome of our study highlights that the structure-activity relationship of multifunctional nanoparticles can be harnessed to modulate their biological activity.
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Affiliation(s)
- Kasturee Chakraborty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Abhijit Biswas
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Sukumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Argha Mario Mallick
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Archana Tripathi
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Somnath Jan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Rituparna Sinha Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India.,Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India.,Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
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Hirway SU, Hassan NT, Sofroniou M, Lemmon CA, Weinberg SH. Immunofluorescence Image Feature Analysis and Phenotype Scoring Pipeline for Distinguishing Epithelial-Mesenchymal Transition. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:849-859. [PMID: 34011419 PMCID: PMC8349798 DOI: 10.1017/s1431927621000428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Epithelial–mesenchymal transition (EMT) is an essential biological process, also implicated in pathological settings such as cancer metastasis, in which epithelial cells transdifferentiate into mesenchymal cells. We devised an image analysis pipeline to distinguish between tissues comprised of epithelial and mesenchymal cells, based on extracted features from immunofluorescence images of differing biochemical markers. Mammary epithelial cells were cultured with 0 (control), 2, 4, or 10 ng/mL TGF-β1, a well-established EMT-inducer. Cells were fixed, stained, and imaged for E-cadherin, actin, fibronectin, and nuclei via immunofluorescence microscopy. Feature selection was performed on different combinations of individual cell markers using a Bag-of-Features extraction. Control and high-dose images comprised the training data set, and the intermediate dose images comprised the testing data set. A feature distance analysis was performed to quantify differences between the treatment groups. The pipeline was successful in distinguishing between control (epithelial) and the high-dose (mesenchymal) groups, as well as demonstrating progress along the EMT process in the intermediate dose groups. Validation using quantitative PCR (qPCR) demonstrated that biomarker expression measurements were well-correlated with the feature distance analysis. Overall, we identified image pipeline characteristics for feature extraction and quantification of immunofluorescence images to distinguish progression of EMT.
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Affiliation(s)
- Shreyas U. Hirway
- Biomedical Engineering Department, The Ohio State University, Columbus, OH, USA
| | - Nadiah T. Hassan
- Biomedical Engineering Department, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael Sofroniou
- Biomedical Engineering Department, Virginia Commonwealth University, Richmond, VA, USA
| | - Christopher A. Lemmon
- Biomedical Engineering Department, Virginia Commonwealth University, Richmond, VA, USA
| | - Seth H. Weinberg
- Biomedical Engineering Department, The Ohio State University, Columbus, OH, USA
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Ghosh B, Chatterjee S, Dhakar R, Muley S, Mitra P, Chatterjee J. Arecanut-induced fibrosis display dual phases of reorganising glycans and amides in skin extracellular matrix. Int J Biol Macromol 2021; 185:251-263. [PMID: 34161821 DOI: 10.1016/j.ijbiomac.2021.06.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022]
Abstract
The habit of chewing arecanut leads to fibrosis in the oral tissues, which can lead to cancer. Despite high mortality, fibrosis has limited clinical success owing to organ-specific variations, genetic predispositions, and slow progression. Fibrosis is a progressive condition that is unresponsive to medications in the severe phase. To understand underlying macromolecular changes we studied the extracellular matrix's (ECM) key molecular modifications in the early and late phase of arecanut-induced fibrosis in skin. To study the fibrosis, we topically applied arecanut extract on the mice skin. We observed that the matrix changes observe early and late phases based on ECM characteristics including the matrix proteins and the glycans. A spike in the levels of proteoglycans and β-sheet structures are noted in the early phase. A significant drop in the proteoglycans and strengthening of amide covalent interactions is observed in the late phase. Although, almost no physical changes are noticeable only in the early phase; the late phase observes thick collagen bundling and a 4-fold stiffening of the skin tissue. The study indicates that the temporal interplay of proteins and glycans determine the matrix's severity state while opening avenues to research directed towards the phase-specific clinical discovery.
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Affiliation(s)
- Biswajoy Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
| | | | - Ramgopal Dhakar
- Department of Biotechnology, Mohanlal Sukhadia University, Rajasthan 313001, India
| | - Saylee Muley
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pabitra Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
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Jolly MK, Murphy RJ, Bhatia S, Whitfield HJ, Redfern A, Davis MJ, Thompson EW. Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications. Cells Tissues Organs 2021; 211:110-133. [PMID: 33902034 DOI: 10.1159/000515289] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 11/19/2022] Open
Abstract
The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.
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Affiliation(s)
- Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Ryan J Murphy
- Queensland University of Technology, School of Mathematical Sciences, Brisbane, Queensland, Australia
| | - Sugandha Bhatia
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia.,The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Redfern
- Department of Medicine, School of Medicine, University of Western Australia, Fiona Stanley Hospital Campus, Perth, Washington, Australia
| | - Melissa J Davis
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.,Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Erik W Thompson
- Queensland University of Technology, Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Brisbane, Queensland, Australia.,Queensland University of Technology, Translational Research Institute, Brisbane, Queensland, Australia
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