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Leggett SE, Brennan MC, Martinez S, Tien J, Nelson CM. Relatively Rare Populations of Invasive Cells Drive Progression of Heterogeneous Tumors. Cell Mol Bioeng 2024; 17:7-24. [PMID: 38435793 PMCID: PMC10902221 DOI: 10.1007/s12195-023-00792-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024] Open
Abstract
Introduction Breast tumors often display an astonishing degree of spatial and temporal heterogeneity, which are associated with cancer progression, drug resistance, and relapse. Triple-negative breast cancer (TNBC) is a particularly aggressive and heterogeneous subtype for which targeted therapies are scarce. Consequently, patients with TNBC have a poorer overall prognosis compared to other breast cancer patients. Within heterogeneous tumors, individual clonal subpopulations may exhibit differences in their rates of growth and degrees of invasiveness. We hypothesized that such phenotypic heterogeneity at the single-cell level may accelerate tumor progression by enhancing the overall growth and invasion of the entire tumor. Methods To test this hypothesis, we isolated and characterized clonal subpopulations with distinct morphologies and biomarker expression from the inherently heterogeneous 4T1 mouse mammary carcinoma cell line. We then leveraged a 3D microfluidic tumor model to reverse-engineer intratumoral heterogeneity and thus investigate how interactions between phenotypically distinct subpopulations affect tumor growth and invasion. Results We found that the growth and invasion of multiclonal tumors were largely dictated by the presence of cells with epithelial and mesenchymal traits, respectively. The latter accelerated overall tumor invasion, even when these cells comprised less than 1% of the initial population. Consistently, tumor progression was delayed by selectively targeting the mesenchymal subpopulation. Discussion This work reveals that highly invasive cells can dominate tumor phenotype and that specifically targeting these cells can slow the progression of heterogeneous tumors, which may help inform therapeutic approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s12195-023-00792-w.
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Affiliation(s)
- Susan E. Leggett
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Molly C. Brennan
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
| | - Sophia Martinez
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
| | - Joe Tien
- Department of Biomedical Engineering, Boston University, Boston, MA 02215 USA
| | - Celeste M. Nelson
- Department of Chemical & Biological Engineering, Princeton University, 303 Hoyt Laboratory, 25 William Street, Princeton, NJ 08544 USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544 USA
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2
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Bhatia S, Gunter JH, Burgess JT, Adams MN, O'Byrne K, Thompson EW, Duijf PH. Stochastic epithelial-mesenchymal transitions diversify non-cancerous lung cell behaviours. Transl Oncol 2023; 37:101760. [PMID: 37611490 PMCID: PMC10466920 DOI: 10.1016/j.tranon.2023.101760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) is a hallmark of cancer. By enabling cells to shift between different morphological and functional states, EMP promotes invasion, metastasis and therapy resistance. We report that near-diploid non-cancerous human epithelial lung cells spontaneously shift along the EMP spectrum without genetic changes. Strikingly, more than half of single cell-derived clones adopt a mesenchymal morphology. We independently characterise epithelial-like and mesenchymal-like clones. Mesenchymal clones lose epithelial markers, display larger cell aspect ratios and lower motility, with mostly unaltered proliferation rates. Stemness marker expression and metabolic rewiring diverge independently of phenotypes. In 3D culture, more epithelial clones become mesenchymal-like. Thus, non-cancerous epithelial cells may acquire cancer metastasis-associated features prior to genetic alterations and cancerous transformation.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia.
| | - Jennifer H Gunter
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Queensland University of Technology, Woolloongabba 4102, Australia
| | - Joshua T Burgess
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Mark N Adams
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Kenneth O'Byrne
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Princess Alexandra Hospital, Woolloongabba 4102, QLD, Australia
| | - Erik W Thompson
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Pascal Hg Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide SA, 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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3
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He Z, Wilson A, Rich F, Kenwright D, Stevens A, Low YS, Thunders M. Chromosomal instability and its effect on cell lines. Cancer Rep (Hoboken) 2023:e1822. [PMID: 37095005 DOI: 10.1002/cnr2.1822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Cancer cell lines are invaluable model systems for biomedical research because they provide an almost unlimited supply of biological materials. However, there is considerable skepticism regarding the reproducibility of data derived from these in vitro models. RECENT FINDINGS Chromosomal instability (CIN) is one of the primary issues associated with cell lines, which can cause genetic heterogeneity and unstable cell properties within a cell population. Many of these problems can be avoided with some precautions. Here we review the underlying causes of CIN, including merotelic attachment, telomere dysfunction, DNA damage response defects, mitotic checkpoint defects and cell cycle disturbances. CONCLUSION In this review we summarize studies highlighting the consequences of CIN in various cell lines and provide suggestions on monitoring and controlling CIN during cell culture.
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Affiliation(s)
- Zichen He
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Andrew Wilson
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Fenella Rich
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Diane Kenwright
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Aaron Stevens
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Yee Syuen Low
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Michelle Thunders
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
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4
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"Pulsed Hypoxia" Gradually Reprograms Breast Cancer Fibroblasts into Pro-Tumorigenic Cells via Mesenchymal-Epithelial Transition. Int J Mol Sci 2023; 24:ijms24032494. [PMID: 36768815 PMCID: PMC9916667 DOI: 10.3390/ijms24032494] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Hypoxia arises in most growing solid tumors and can lead to pleotropic effects that potentially increase tumor aggressiveness and resistance to therapy through regulation of the expression of genes associated with the epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET). The main goal of the current work was to obtain and investigate the intermediate phenotype of tumor cells undergoing the hypoxia-dependent transition from fibroblast to epithelial morphology. Primary breast cancer fibroblasts BrC4f, being cancer-associated fibroblasts, were subjected to one or two rounds of "pulsed hypoxia" (PH). PH induced transformation of fibroblast-shaped cells to semi-epithelial cells. Western blot analysis, fluorescent microscopy and flow cytometry of transformed cells demonstrated the decrease in the mesenchymal markers vimentin and N-cad and an increase in the epithelial marker E-cad. These cells kept mesenchymal markers αSMA and S100A4 and high ALDH activity. Real-time PCR data of the cells after one (BrC4f_Hyp1) and two (BrC4f_Hyp2) rounds of PH showed consistent up-regulation of TWIST1 gene as an early response and ZEB1/2 and SLUG transcriptional activity as a subsequent response. Reversion of BrC4f_Hyp2 cells to normoxia conditions converted them to epithelial-like cells (BrC4e) with decreased expression of EMT genes and up-regulation of MET-related OVOL2 and c-MYC genes. Transplantation of BrC4f and BrC4f_Hyp2 cells into SCID mice showed the acceleration of tumor growth up to 61.6% for BrC4f_Hyp2 cells. To summarize, rounds of PH imitate the MET process of tumorigenesis in which cancer-associated fibroblasts pass through intermediate stages and become more aggressive epithelial-like tumor cells.
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5
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Jain P, Corbo S, Mohammad K, Sahoo S, Ranganathan S, George JT, Levine H, Taube J, Toneff M, Jolly MK. Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state. J R Soc Interface 2023; 20:20220627. [PMID: 36628532 PMCID: PMC9832289 DOI: 10.1098/rsif.2022.0627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) and its reverse mesenchymal-epithelial transition (MET) are critical during embryonic development, wound healing and cancer metastasis. While phenotypic changes during short-term EMT induction are reversible, long-term EMT induction has been often associated with irreversibility. Here, we show that phenotypic changes seen in MCF10A cells upon long-term EMT induction by TGFβ need not be irreversible, but have relatively longer time scales of reversibility than those seen in short-term induction. Next, using a phenomenological mathematical model to account for the chromatin-mediated epigenetic silencing of the miR-200 family by ZEB family, we highlight how the epigenetic memory gained during long-term EMT induction can slow the recovery to the epithelial state post-TGFβ withdrawal. Our results suggest that epigenetic modifiers can govern the extent and time scale of EMT reversibility and advise caution against labelling phenotypic changes seen in long-term EMT induction as 'irreversible'.
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Affiliation(s)
- Paras Jain
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Sophia Corbo
- Department of Biology, Widener University, Chester, PA 19013, USA
| | - Kulsoom Mohammad
- Department of Biology, Widener University, Chester, PA 19013, USA
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | | | - Jason T. George
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 76798, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics and Departments of Physics and Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Joseph Taube
- Department of Biology, Baylor University, Waco, TX 76706, USA
| | - Michael Toneff
- Department of Biology, Widener University, Chester, PA 19013, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
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6
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Growth dynamics of breast cancer stem cells: effects of self-feedback and EMT mechanisms. Theory Biosci 2022; 141:297-311. [PMID: 35921025 DOI: 10.1007/s12064-022-00374-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/06/2022] [Indexed: 10/16/2022]
Abstract
Breast cancer stem cells (BCSCs) with the ability to self-renew and differentiate have been identified in primary breast cancer tissues and cell lines. The BCSCs are often resistant to traditional radiation and/or chemotherapies. Previous studies have also shown that successful therapy must eradicate cancer stem cells. The purpose of this paper is to develop a mathematical model with self-feedback mechanism to illustrate the issues regarding the difficulties of absolutely eliminating a breast cancer. In addition, we introduce the mechanism of the epithelial-mesenchymal transition (EMT) to investigate the influence of EMT on the effects of breast cancer growth and treatment. Results indicate that the EMT mechanism facilitates the growth of breast cancer and makes breast cancer more difficult to be cured. Therefore, targeting the signals involved in EMT can halt tumor progression in breast cancer. Finally, we apply the experimental data to carry out numerical simulations and validate our theoretical conclusions.
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7
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Cioce M, Sacconi A, Donzelli S, Bonomo C, Perracchio L, Carosi M, Telera S, Fazio VM, Botti C, Strano S, Blandino G. Breast cancer metastasis: is it a matter of OMICS and proper ex-vivo models? Comput Struct Biotechnol J 2022; 20:4003-4008. [PMID: 35983233 PMCID: PMC9355905 DOI: 10.1016/j.csbj.2022.07.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Genomics has greatly increased the understanding of the study of breast cancer (BC) and has shaped the concept of intra-tumor heterogeneity, currently recognized as a propelling force for cancer progression. In this context, knowledge and understanding of metastatic breast cancer (mBC) has somehow lagged behind that of primary breast cancer. This may be explained by the relative scarcity of matched mBC samples, however it is possible that the mutation spectrum obtained from primary BC does not capture the full complexity of the metastatic disease. Here, we provide a few examples supporting this possibility, from public databases. We evoke the need to perform an integrated multi-OMICS characterization of mBC, to obtain a broad understanding of this complex disease, whose evolution cannot be explained solely by genomics. Pertinent to this, we suggest that rather an infrequent use of Patient-Derived –Tumor-Organoids (PDTOs) may be influenced by assuming that the metastatic conditions of PDTOs growth (mPDTOs) should be similar to those of the tissue of origin. We challenge this view by suggesting that the use of “target-organ inspired” growth conditions for mPDTOs, may better fit the emerging knowledge of metastatic disease. Thus, the integrated use of multi-OMICS and of clinically relevant mPDTOs may allow a further understanding of such disease and foster therapeutically relevant advances. We believe that our points may be valid for other solid cancers.
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Affiliation(s)
- Mario Cioce
- Laboratory of Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
| | - Andrea Sacconi
- Clinical Trial Center, Biostatistics and Bioinformatics Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudia Bonomo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Letizia Perracchio
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mariantonia Carosi
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Stefano Telera
- Neurosurgery Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Vito Michele Fazio
- Laboratory of Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Claudio Botti
- Breast Surgery Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Sabrina Strano
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
- Corresponding author at: Translational Oncology Research UnitItalian National Cancer Institute Regina Elena Rome, Italy.
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8
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Jain P, Bhatia S, Thompson EW, Jolly MK. Population Dynamics of Epithelial-Mesenchymal Heterogeneity in Cancer Cells. Biomolecules 2022; 12:biom12030348. [PMID: 35327538 PMCID: PMC8945776 DOI: 10.3390/biom12030348] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/16/2022] Open
Abstract
Phenotypic heterogeneity is a hallmark of aggressive cancer behaviour and a clinical challenge. Despite much characterisation of this heterogeneity at a multi-omics level in many cancers, we have a limited understanding of how this heterogeneity emerges spontaneously in an isogenic cell population. Some longitudinal observations of dynamics in epithelial-mesenchymal heterogeneity, a canonical example of phenotypic heterogeneity, have offered us opportunities to quantify the rates of phenotypic switching that may drive such heterogeneity. Here, we offer a mathematical modeling framework that explains the salient features of population dynamics noted in PMC42-LA cells: (a) predominance of EpCAMhigh subpopulation, (b) re-establishment of parental distributions from the EpCAMhigh and EpCAMlow subpopulations, and (c) enhanced heterogeneity in clonal populations established from individual cells. Our framework proposes that fluctuations or noise in content duplication and partitioning of SNAIL—an EMT-inducing transcription factor—during cell division can explain spontaneous phenotypic switching and consequent dynamic heterogeneity in PMC42-LA cells observed experimentally at both single-cell and bulk level analysis. Together, we propose that asymmetric cell division can be a potential mechanism for phenotypic heterogeneity.
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Affiliation(s)
- Paras Jain
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
| | - Sugandha Bhatia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane 4000, Australia;
- The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba 4102, Australia
- Translational Research Institute, Woolloongabba 4102, Australia
| | - Erik W. Thompson
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane 4000, Australia;
- Translational Research Institute, Woolloongabba 4102, Australia
- Correspondence: (E.W.T.); (M.K.J.)
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India;
- Correspondence: (E.W.T.); (M.K.J.)
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9
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Wang Q, Karvelsson ST, Johannsson F, Vilhjalmsson AI, Hagen L, de Miranda Fonseca D, Sharma A, Slupphaug G, Rolfsson O. UDP-glucose dehydrogenase expression is upregulated following EMT and differentially affects intracellular glycerophosphocholine and acetylaspartate levels in breast mesenchymal cell lines. Mol Oncol 2021; 16:1816-1840. [PMID: 34942055 PMCID: PMC9067156 DOI: 10.1002/1878-0261.13172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/04/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022] Open
Abstract
Metabolic rewiring is one of the indispensable drivers of epithelial-mesenchymal transition (EMT) involved in breast cancer metastasis. In this study, we explored the metabolic changes during spontaneous EMT in three separately established breast EMT cell models using a proteomics approach supported by metabolomic analysis. We identified common proteomic changes, including in the expression of CDH1, CDH2, VIM, LGALS1, SERPINE1, PKP3, ATP2A2, JUP, MTCH2, RPL26L1 and PLOD2. Consistently altered metabolic enzymes included: FDFT1, SORD, TSTA3 and UDP-glucose dehydrogenase (UGDH). Of these, UGDH was most prominently altered and has previously been associated with breast cancer patient survival. siRNA-mediated knockdown of UGDH resulted in delayed cell proliferation and dampened invasive potential of mesenchymal cells, and downregulated expression of the EMT transcription factor SNAI1. Metabolomic analysis revealed that siRNA-mediated knockdown of UGDH decreased intracellular glycerophosphocholine (GPC), whereas levels of acetylaspartate (NAA) increased. Finally, our data suggested that platelet-derived growth factor receptor beta (PDGFRB) signaling was activated in mesenchymal cells. siRNA-mediated knockdown of PDGFRB downregulated UGDH expression, potentially via NFkB-p65. Our results support an unexplored relationship between UGDH and GPC, both of which have previously been independently associated with breast cancer progression.
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Affiliation(s)
- Qiong Wang
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Sigurdur Trausti Karvelsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Freyr Johannsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Arnar Ingi Vilhjalmsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Davi de Miranda Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, N-7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Norway
| | - Ottar Rolfsson
- Center for Systems Biology, Biomedical Center, Faculty of Medicine, School of Health Sciences, University of Iceland, Sturlugata 8, 101, Reykjavik, Iceland
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10
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Wang P, Zhou R, Thomas P, Zhao L, Zhou R, Mandal S, Jolly MK, Richard DJ, Rehm BHA, Ostrikov K(K, Dai X, Williams ED, Thompson EW. Epithelial-to-Mesenchymal Transition Enhances Cancer Cell Sensitivity to Cytotoxic Effects of Cold Atmospheric Plasmas in Breast and Bladder Cancer Systems. Cancers (Basel) 2021; 13:2889. [PMID: 34207708 PMCID: PMC8226878 DOI: 10.3390/cancers13122889] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
Cold atmospheric plasma (CAP) has emerged as a highly selective anticancer agent, most recently in the form of plasma-activated medium (PAM). Since epithelial-mesenchymal transition (EMT) has been implicated in resistance to various cancer therapies, we assessed whether EMT status is associated with PAM response. Mesenchymal breast cancer cell lines, as well as the mesenchymal variant in an isogenic EMT/MET human breast cancer cell system (PMC42-ET/LA), were more sensitive to PAM treatment than their epithelial counterparts, contrary to their responses to other therapies. The same trend was seen in luminal muscle-invasive bladder cancer model (TSU-Pr1/B1/B2) and the non-muscle-invasive basal 5637 bladder cancer cell line. Three-dimensional spheroid cultures of the bladder cancer cell lines were less sensitive to the PAM treatment compared to their two-dimensional counterparts; however, incrementally better responses were again seen in more mesenchymally-shifted cell lines. This study provides evidence that PAM preferentially inhibits mesenchymally-shifted carcinoma cells, which have been associated with resistance to other therapies. Thus, PAM may represent a novel treatment that can selectively inhibit triple-negative breast cancers and a subset of aggressive bladder cancers, which tend to be more mesenchymal. Our approach may potentially be utilized for other aggressive cancers exhibiting EMT and opens new opportunities for CAP and PAM as a promising new onco-therapy.
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Affiliation(s)
- Peiyu Wang
- Queensland University of Technology (QUT), School of Biomedical Sciences, Brisbane 4059, Australia; (P.W.); (P.T.)
- Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Renwu Zhou
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney 2006, Australia; (R.Z.)
| | - Patrick Thomas
- Queensland University of Technology (QUT), School of Biomedical Sciences, Brisbane 4059, Australia; (P.W.); (P.T.)
- Translational Research Institute, Woolloongabba, Queensland 4102, Australia
- Queensland Bladder Cancer Initiative (QBCI), Woolloongabba, Queensland 4102, Australia
| | - Liqian Zhao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Rusen Zhou
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney 2006, Australia; (R.Z.)
| | - Susmita Mandal
- 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
| | - Derek J. Richard
- Queensland University of Technology (QUT), School of Biomedical Sciences, Brisbane 4059, Australia; (P.W.); (P.T.)
- Translational Research Institute, Woolloongabba, Queensland 4102, Australia
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Kostya (Ken) Ostrikov
- School of Chemistry and Physics, Queensland University of Technology, Brisbane 4000, Australia
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Elizabeth D. Williams
- Queensland University of Technology (QUT), School of Biomedical Sciences, Brisbane 4059, Australia; (P.W.); (P.T.)
- Translational Research Institute, Woolloongabba, Queensland 4102, Australia
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney 2006, Australia; (R.Z.)
| | - Erik W. Thompson
- Queensland University of Technology (QUT), School of Biomedical Sciences, Brisbane 4059, Australia; (P.W.); (P.T.)
- Translational Research Institute, Woolloongabba, Queensland 4102, Australia
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11
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Kane LE, Mellotte GS, Conlon KC, Ryan BM, Maher SG. Multi-Omic Biomarkers as Potential Tools for the Characterisation of Pancreatic Cystic Lesions and Cancer: Innovative Patient Data Integration. Cancers (Basel) 2021; 13:769. [PMID: 33673153 PMCID: PMC7918773 DOI: 10.3390/cancers13040769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/27/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer (PC) is regarded as one of the most lethal malignant diseases in the world, with GLOBOCAN 2020 estimates indicating that PC was responsible for almost half a million deaths worldwide in 2020. Pancreatic cystic lesions (PCLs) are fluid-filled structures found within or on the surface of the pancreas, which can either be pre-malignant or have no malignant potential. While some PCLs are found in symptomatic patients, nowadays many PCLs are found incidentally in patients undergoing cross-sectional imaging for other reasons-so called 'incidentalomas'. Current methods of characterising PCLs are imperfect and vary hugely between institutions and countries. As such, there is a profound need for improved diagnostic algorithms. This could facilitate more accurate risk stratification of those PCLs that have malignant potential and reduce unnecessary surveillance. As PC continues to have such a poor prognosis, earlier recognition and risk stratification of PCLs may lead to better treatment protocols. This review will focus on the importance of biomarkers in the context of PCLs and PCand outline how current 'omics'-related work could contribute to the identification of a novel integrated biomarker profile for the risk stratification of patients with PCLs and PC.
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Affiliation(s)
- Laura E. Kane
- Department of Surgery, Trinity St. James’s Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland;
| | - Gregory S. Mellotte
- Department of Gastroenterology, Tallaght University Hospital, Dublin D24 NR0A, Ireland; (G.S.M.); (B.M.R.)
| | - Kevin C. Conlon
- Discipline of Surgery, School of Medicine, Trinity College Dublin, Dublin D02 PN40, Ireland;
| | - Barbara M. Ryan
- Department of Gastroenterology, Tallaght University Hospital, Dublin D24 NR0A, Ireland; (G.S.M.); (B.M.R.)
| | - Stephen G. Maher
- Department of Surgery, Trinity St. James’s Cancer Institute, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland;
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Bhat M, Pasini E, Pastrello C, Rahmati S, Angeli M, Kotlyar M, Ghanekar A, Jurisica I. Integrative analysis of layers of data in hepatocellular carcinoma reveals pathway dependencies. World J Hepatol 2021; 13:94-108. [PMID: 33584989 PMCID: PMC7856865 DOI: 10.4254/wjh.v13.i1.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/19/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The broader use of high-throughput technologies has led to improved molecular characterization of hepatocellular carcinoma (HCC).
AIM To comprehensively analyze and characterize all publicly available genomic, gene expression, methylation, miRNA and proteomic data in HCC, covering 85 studies and 3355 patient sample profiles, to identify the key dysregulated genes and pathways they affect.
METHODS We collected and curated all well-annotated and publicly available high-throughput datasets from PubMed and Gene Expression Omnibus derived from human HCC tissue. Comprehensive pathway enrichment analysis was performed using pathDIP for each data type (genomic, gene expression, methylation, miRNA and proteomic), and the overlap of pathways was assessed to elucidate pathway dependencies in HCC.
RESULTS We identified a total of 8733 abstracts retrieved by the search on PubMed on HCC for the different layers of data on human HCC samples, published until December 2016. The common key dysregulated pathways in HCC tissue across different layers of data included epidermal growth factor (EGFR) and β1-integrin pathways. Genes along these pathways were significantly and consistently dysregulated across the different types of high-throughput data and had prognostic value with respect to overall survival. Using CTD database, estradiol would best modulate and revert these genes appropriately.
CONCLUSION By analyzing and integrating all available high-throughput genomic, transcriptomic, miRNA, methylation and proteomic data from human HCC tissue, we identified EGFR, β1-integrin and axon guidance as pathway dependencies in HCC. These are master regulators of key pathways in HCC, such as the mTOR, Ras/Raf/MAPK and p53 pathways. The genes implicated in these pathways had prognostic value in HCC, with Netrin and Slit3 being novel proteins of prognostic importance to HCC. Based on this integrative analysis, EGFR, and β1-integrin are master regulators that could serve as potential therapeutic targets in HCC.
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Affiliation(s)
- Mamatha Bhat
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Elisa Pasini
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Sara Rahmati
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Marc Angeli
- Multi Organ transplant Program, University Health Network, Toronto M5G2N2, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Anand Ghanekar
- Surgery, University Health Network, Toronto M5G 2C4, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health NetworkandKrembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto M5T 0S8, Canada
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Metabolic Constrains Rule Metastasis Progression. Cells 2020; 9:cells9092081. [PMID: 32932943 PMCID: PMC7563739 DOI: 10.3390/cells9092081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
Metastasis formation accounts for the majority of tumor-associated deaths and consists of different steps, each of them being characterized by a distinctive adaptive phenotype of the cancer cells. Metabolic reprogramming represents one of the main adaptive phenotypes exploited by cancer cells during all the main steps of tumor and metastatic progression. In particular, the metabolism of cancer cells evolves profoundly through all the main phases of metastasis formation, namely the metastatic dissemination, the metastatic colonization of distant organs, the metastatic dormancy, and ultimately the outgrowth into macroscopic lesions. However, the metabolic reprogramming of metastasizing cancer cells has only recently become the subject of intense study. From a clinical point of view, the latter steps of the metastatic process are very important, because patients often undergo surgical removal of the primary tumor when cancer cells have already left the primary tumor site, even though distant metastases are not clinically detectable yet. In this scenario, to precisely elucidate if and how metabolic reprogramming drives acquisition of cancer-specific adaptive phenotypes might pave the way to new therapeutic strategies by combining chemotherapy with metabolic drugs for better cancer eradication. In this review we discuss the latest evidence that claim the importance of metabolic adaptation for cancer progression.
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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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Dvorakova M, Lapcik P, Bouchalova P, Bouchal P. Transgelin Silencing Induces Different Processes in Different Breast Cancer Cell Lines. Proteomics 2020; 20:e1900383. [PMID: 32061197 DOI: 10.1002/pmic.201900383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/10/2020] [Indexed: 12/30/2022]
Abstract
Transgelin is a protein reported to be a marker of several cancers. However, previous studies have shown both up- and down-regulation of transgelin in tumors when compared with non-tumor tissues and the mechanisms whereby transgelin may affect the development of cancer remain largely unknown. Transgelin is especially abundant in smooth muscle cells and is associated with actin stress fibers. These contractile structures participate in cell motility, adhesion, and the maintenance of cell morphology. Here, the role of transgelin in breast cancer is focused on. Initially, the effects of transgelin on cell migration of the breast cancer cell lines, BT 549 and PMC 42, is studied. Interestingly, transgelin silencing increased the migration of PMC 42 cells, but decreased the migration of BT 549 cells. To clarify these contradictory results, the changes in protein abundances after transgelin silencing in these two cell lines are analyzed using quantitative proteomics. The results confirmed the role of transgelin in the migration of BT 549 cells and suggest the involvement of transgelin in apoptosis and small molecule biochemistry in PMC 42 cells. The context-dependent function of transgelin reflects the different molecular backgrounds of these cell lines, which differ in karyotypes, mutation statuses, and proteome profiles.
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Affiliation(s)
- Monika Dvorakova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, 61137, Czech Republic.,Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, 65653, Czech Republic
| | - Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, 61137, Czech Republic
| | - Pavla Bouchalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, 61137, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, 61137, Czech Republic
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Parsons J, Francavilla C. 'Omics Approaches to Explore the Breast Cancer Landscape. Front Cell Dev Biol 2020; 7:395. [PMID: 32039208 PMCID: PMC6987401 DOI: 10.3389/fcell.2019.00395] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer incidence is increasing worldwide with more than 600,000 deaths reported in 2018 alone. In current practice treatment options for breast cancer patients consists of surgery, chemotherapy, radiotherapy or targeting of classical markers of breast cancer subtype: estrogen receptor (ER) and HER2. However, these treatments fail to prevent recurrence and metastasis. Improved understanding of breast cancer and metastasis biology will help uncover novel biomarkers and therapeutic opportunities to improve patient stratification and treatment. We will first provide an overview of current methods and models used to study breast cancer biology, focusing on 2D and 3D cell culture, including organoids, and on in vivo models such as the MMTV mouse model and patient-derived xenografts (PDX). Next, genomic, transcriptomic, and proteomic approaches and their integration will be considered in the context of breast cancer susceptibility, breast cancer drivers, and therapeutic response and resistance to treatment. Finally, we will discuss how 'Omics datasets in combination with traditional breast cancer models are useful for generating insights into breast cancer biology, for suggesting individual treatments in precision oncology, and for creating data repositories to undergo further meta-analysis. System biology has the potential to catalyze the next great leap forward in treatment options for breast cancer patients.
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Affiliation(s)
- Joseph Parsons
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
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