1
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Jain P, Kizhuttil R, Nair MB, Bhatia S, Thompson EW, George JT, Jolly MK. Cell-state transitions and density-dependent interactions together explain the dynamics of spontaneous epithelial-mesenchymal heterogeneity. iScience 2024; 27:110310. [PMID: 39055927 PMCID: PMC11269952 DOI: 10.1016/j.isci.2024.110310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/21/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer cell populations comprise phenotypes distributed among the epithelial-mesenchymal (E-M) spectrum. However, it remains unclear which population-level processes give rise to the observed experimental distribution and dynamical changes in E-M heterogeneity, including (1) differential growth, (2) cell-state switching, and (3) population density-dependent growth or state-transition rates. Here, we analyze the necessity of these three processes in explaining the dynamics of E-M population distributions as observed in PMC42-LA and HCC38 breast cancer cells. We find that, while cell-state transition is necessary to reproduce experimental observations of dynamical changes in E-M fractions, including density-dependent growth interactions (cooperation or suppression) better explains the data. Further, our models predict that treatment of HCC38 cells with transforming growth factor β (TGF-β) signaling and Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/3) inhibitors enhances the rate of mesenchymal-epithelial transition (MET) instead of lowering that of E-M transition (EMT). Overall, our study identifies the population-level processes shaping the dynamics of spontaneous E-M heterogeneity in breast cancer cells.
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Affiliation(s)
- Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Madhav B. Nair
- Indian Institute of Science Education and Research, Kolkata, India
| | - Sugandha Bhatia
- School of Biomedical Science, Queensland University of Technology (QUT) at Translational Research Institute, Woolloongabba QLD 4102, Australia
| | - Erik W. Thompson
- Diamantina Institute, The University of Queensland, Brisbane QLD, Australia
| | - Jason T. George
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, India
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2
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Baumgartner A, Robinson M, Golde T, Jaydev S, Huang S, Hadlock J, Funk C. Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer's pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599924. [PMID: 38979220 PMCID: PMC11230164 DOI: 10.1101/2024.06.21.599924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
The identification of microglia subtypes is important for understanding the role of innate immunity in neurodegenerative diseases. Current methods of unsupervised cell type identification assume a small noise-to-signal ratio of transcriptome measurements that would produce well-separated cell clusters. However, identification of subtypes is obscured by gene expression noise, diminishing the distances in transcriptome space between distinct cell types and blurring boundaries. Here we use Fokker-Planck (FP) diffusion maps to model cellular differentiation as a stochastic process whereby cells settle into local minima, corresponding to cell subtypes, in a potential landscape constructed from transcriptome data using a nearest neighbor graph approach. By applying critical transition fields, we identify individual cells on the verge of transitioning between subtypes, revealing microglial cells in inactivated, homeostatic state before radially transitioning into various specialized subtypes. Specifically, we show that cells from Alzheimer's disease patients are enriched in a microglia subtype associated to antigen presentation and T-cell recruitment.
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Affiliation(s)
| | | | - Todd Golde
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Institute Emory Brain Health, Emory University School of Medicine, Atlanta, GA, USA
| | - Suman Jaydev
- Department of Neurology, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA
| | - Jennifer Hadlock
- Institute for Systems Biology, Seattle, WA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA
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3
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Junior MGV, Côrtes AMDA, Carneiro FRG, Carels N, da Silva FAB. Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity. Int J Mol Sci 2024; 25:4894. [PMID: 38732140 PMCID: PMC11084314 DOI: 10.3390/ijms25094894] [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: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Glioblastoma Multiforme is a brain tumor distinguished by its aggressiveness. We suggested that this aggressiveness leads single-cell RNA-sequence data (scRNA-seq) to span a representative portion of the cancer attractors domain. This conjecture allowed us to interpret the scRNA-seq heterogeneity as reflecting a representative trajectory within the attractor's domain. We considered factors such as genomic instability to characterize the cancer dynamics through stochastic fixed points. The fixed points were derived from centroids obtained through various clustering methods to verify our method sensitivity. This methodological foundation is based upon sample and time average equivalence, assigning an interpretative value to the data cluster centroids and supporting parameters estimation. We used stochastic simulations to reproduce the dynamics, and our results showed an alignment between experimental and simulated dataset centroids. We also computed the Waddington landscape, which provided a visual framework for validating the centroids and standard deviations as characterizations of cancer attractors. Additionally, we examined the stability and transitions between attractors and revealed a potential interplay between subtypes. These transitions might be related to cancer recurrence and progression, connecting the molecular mechanisms of cancer heterogeneity with statistical properties of gene expression dynamics. Our work advances the modeling of gene expression dynamics and paves the way for personalized therapeutic interventions.
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Affiliation(s)
- Marcos Guilherme Vieira Junior
- Graduate Program in Computational and Systems Biology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Adriano Maurício de Almeida Côrtes
- Department of Applied Mathematics, Institute of Mathematics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, Brazil;
- Systems Engineering and Computer Science Program, Coordination of Postgraduate Programs in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, Brazil
| | - Flávia Raquel Gonçalves Carneiro
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil;
- Laboratório Interdisciplinar de Pesquisas Médicas, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, Brazil
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-361, Brazil
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4
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Shah A. Rethinking cancer initiation: The role of large-scale mutational events. Genes Chromosomes Cancer 2024; 63:e23213. [PMID: 37950638 DOI: 10.1002/gcc.23213] [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: 06/08/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Cancer initiation is revisited in light of recent discoveries in cancer pathogenesis. Of note is the detection of mutated cancer genes in benign conditions. More significantly, somatic clones, which harbor mutations in cancer genes, arise in normal tissues from early development through adulthood, but seldom do they transform into cancer. Further, clustered mutational events-kataegis, chromothripsis and chromoplexy-are widespread in cancer, generating point mutations and chromosomal rearrangements in a single cellular catastrophe. These observations are contrary to the prevailing somatic mutation theory, which states that a cancer is caused by the gradual accumulation of mutations over time. A different perspective is proposed within the framework of Waddington's epigenetic landscape wherein tumorigenesis is viewed primarily as a disruption of cell development. Cell types are defined by their specific gene-expression profiles, determined by the gene regulatory network, and can be regarded as attractor states of the network dynamics: they represent specific, self-stabilizing patterns of gene activities across the genome. However, large-scale mutational events reshape the landscape topology, creating abnormal "unphysiological" attractors. This is the crux of the process of initiation. Initiation primes the cell for conversion into a tumor phenotype by oncogenes and tumor suppressor genes, which drive cell proliferation and clonal diversification. This view of tumorigenesis calls for a different approach to therapy.
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Affiliation(s)
- Amil Shah
- Department of Medicine, University of British Columbia, Vancouver, Canada
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5
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Jiang H, Liu J, Song Y, Lei J. Quantitative Modeling of Stemness in Single-Cell RNA Sequencing Data: A Nonlinear One-Class Support Vector Machine Method. J Comput Biol 2024; 31:41-57. [PMID: 38010500 DOI: 10.1089/cmb.2022.0484] [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] [Indexed: 11/29/2023] Open
Abstract
Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemness of individual cells for assessing the potential for self-renewal and differentiation from the cell of origin can define a measurement for quantifying different cell states, which is important in understanding the dynamics of cancer evolution, and might further provide possible targeted therapies aimed at tumor stem cells. Nevertheless, it is usually difficult to quantify the stemness of a cell based on molecular information associated with the cell. In this study, we proposed a stemness definition method with one-class Hadamard kernel support vector machine (OCHSVM) based on single-cell RNA sequencing (scRNA-seq) data. Applications of the proposed OCHSVM stemness are assessed by various data sets, including preimplantation embryo cells, induced pluripotent stem cells, or tumor cells. We further compared the OCHSVM model with state-of-the-art methods CytoTRACE, one-class logistic regression, or one-class SVM methods with different kernels. The computational results demonstrate that the OCHSVM method is more suitable for stemness identification using scRNA-seq data.
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Affiliation(s)
- Hao Jiang
- School of Mathematics, Renmin University of China, Beijing, China
| | - Jingxin Liu
- School of Software, Beihang University, Beijing, China
| | - You Song
- School of Software, Beihang University, Beijing, China
| | - Jinzhi Lei
- School of Mathematical Sciences, Center for Applied Mathematics, Tiangong University, Tianjin, China
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6
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Nakamura YT, Himeoka Y, Saito N, Furusawa C. Evolution of hierarchy and irreversibility in theoretical cell differentiation model. PNAS NEXUS 2024; 3:pgad454. [PMID: 38205032 PMCID: PMC10776358 DOI: 10.1093/pnasnexus/pgad454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
The process of cell differentiation in multicellular organisms is characterized by hierarchy and irreversibility in many cases. However, the conditions and selection pressures that give rise to these characteristics remain poorly understood. By using a mathematical model, here we show that the network of differentiation potency (differentiation diagram) becomes necessarily hierarchical and irreversible by increasing the number of terminally differentiated states under certain conditions. The mechanisms generating these characteristics are clarified using geometry in the cell state space. The results demonstrate that the hierarchical organization and irreversibility can manifest independently of direct selection pressures associated with these characteristics, instead they appear to evolve as byproducts of selective forces favoring a diversity of differentiated cell types. The study also provides a new perspective on the structure of gene regulatory networks that produce hierarchical and irreversible differentiation diagrams. These results indicate some constraints on cell differentiation, which are expected to provide a starting point for theoretical discussion of the implicit limits and directions of evolution in multicellular organisms.
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Affiliation(s)
- Yoshiyuki T Nakamura
- Department of Physics, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Center for Biosystems Dynamics Research, RIKEN, Suita 565-0874, Japan
| | - Yusuke Himeoka
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
| | - Nen Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8526, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Chikara Furusawa
- Department of Physics, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Universal Biology Institute, The University of Tokyo, Bunkyo-ku 113-0033, Japan
- Center for Biosystems Dynamics Research, RIKEN, Suita 565-0874, Japan
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7
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Weisman CM. The permissive binding theory of cancer. Front Oncol 2023; 13:1272981. [PMID: 38023252 PMCID: PMC10666763 DOI: 10.3389/fonc.2023.1272981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The later stages of cancer, including the invasion and colonization of new tissues, are actively mysterious compared to earlier stages like primary tumor formation. While we lack many details about both, we do have an apparently successful explanatory framework for the earlier stages: one in which genetic mutations hold ultimate causal and explanatory power. By contrast, on both empirical and conceptual grounds, it is not currently clear that mutations alone can explain the later stages of cancer. Can a different type of molecular change do better? Here, I introduce the "permissive binding theory" of cancer, which proposes that novel protein binding interactions are the key causal and explanatory entity in invasion and metastasis. It posits that binding is more abundant at baseline than we observe because it is restricted in normal physiology; that any large perturbation to physiological state revives this baseline abundance, unleashing many new binding interactions; and that a subset of these cause the cellular functions at the heart of oncogenesis, especially invasion and metastasis. Significant physiological perturbations occur in cancer cells in very early stages, and generally become more extreme with progression, providing interactions that continually fuel invasion and metastasis. The theory is compatible with, but not limited to, causal roles for the diverse molecular changes observed in cancer (e.g. gene expression or epigenetic changes), as these generally act causally upstream of proteins, and so may exert their effects by changing the protein binding interactions that occur in the cell. This admits the possibility that molecular changes that appear quite different may actually converge in creating the same few protein complexes, simplifying our picture of invasion and metastasis. If correct, the theory offers a concrete therapeutic strategy: targeting the key novel complexes. The theory is straightforwardly testable by large-scale identification of protein interactions in different cancers.
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Affiliation(s)
- Caroline M. Weisman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
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8
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Carels N, Sgariglia D, Junior MGV, Lima CR, Carneiro FRG, da Silva GF, da Silva FAB, Scardini R, Tuszynski JA, de Andrade CV, Monteiro AC, Martins MG, da Silva TG, Ferraz H, Finotelli PV, Balbino TA, Pinto JC. A Strategy Utilizing Protein-Protein Interaction Hubs for the Treatment of Cancer Diseases. Int J Mol Sci 2023; 24:16098. [PMID: 38003288 PMCID: PMC10671768 DOI: 10.3390/ijms242216098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 11/26/2023] Open
Abstract
We describe a strategy for the development of a rational approach of neoplastic disease therapy based on the demonstration that scale-free networks are susceptible to specific attacks directed against its connective hubs. This strategy involves the (i) selection of up-regulated hubs of connectivity in the tumors interactome, (ii) drug repurposing of these hubs, (iii) RNA silencing of non-druggable hubs, (iv) in vitro hub validation, (v) tumor-on-a-chip, (vi) in vivo validation, and (vii) clinical trial. Hubs are protein targets that are assessed as targets for rational therapy of cancer in the context of personalized oncology. We confirmed the existence of a negative correlation between malignant cell aggressivity and the target number needed for specific drugs or RNA interference (RNAi) to maximize the benefit to the patient's overall survival. Interestingly, we found that some additional proteins not generally targeted by drug treatments might justify the addition of inhibitors designed against them in order to improve therapeutic outcomes. However, many proteins are not druggable, or the available pharmacopeia for these targets is limited, which justifies a therapy based on encapsulated RNAi.
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Affiliation(s)
- Nicolas Carels
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Domenico Sgariglia
- Engenharia de Sistemas e Computação, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, RJ, Brazil;
| | - Marcos Guilherme Vieira Junior
- Computational Modeling of Biological Systems, Scientific Computing Program (PROCC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil or (M.G.V.J.); (F.A.B.d.S.)
| | - Carlyle Ribeiro Lima
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Flávia Raquel Gonçalves Carneiro
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (F.R.G.C.); (R.S.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, RJ, Brazil
| | - Gilberto Ferreira da Silva
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Fabricio Alves Barbosa da Silva
- Computational Modeling of Biological Systems, Scientific Computing Program (PROCC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil or (M.G.V.J.); (F.A.B.d.S.)
| | - Rafaela Scardini
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (F.R.G.C.); (R.S.)
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, RJ, Brazil
- Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro 22290-255, RJ, Brazil
| | - Jack Adam Tuszynski
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, 10129 Turin, Italy;
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
- Department of Physics, University of Alberta, Edmonton, AB T6G 2J1, Canada
| | - Cecilia Vianna de Andrade
- Department of Pathology, Instituto Fernandes Figueira, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 22250-020, RJ, Brazil;
| | - Ana Carolina Monteiro
- Laboratory of Osteo and Tumor Immunology, Department of Immunobiology, Fluminense Federal University, Rio de Janeiro 24210-201, RJ, Brazil;
| | - Marcel Guimarães Martins
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Talita Goulart da Silva
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Helen Ferraz
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Priscilla Vanessa Finotelli
- Laboratório de Nanotecnologia Biofuncional, Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil;
| | - Tiago Albertini Balbino
- Nanotechnology Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil;
| | - José Carlos Pinto
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
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9
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Wang Y, Zhou JX, Pedrini E, Rubin I, Khalil M, Taramelli R, Qian H, Huang S. Cell population growth kinetics in the presence of stochastic heterogeneity of cell phenotype. J Theor Biol 2023; 575:111645. [PMID: 37863423 DOI: 10.1016/j.jtbi.2023.111645] [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: 03/03/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform exponential growth of the cell population. Here we measured the stochastic time courses of growth of an ensemble of populations of HL60 leukemia cells in cultures, starting with distinct initial cell numbers to capture a departure from the uniform exponential growth model for the initial growth ("take-off"). Despite being derived from the same cell clone, we observed significant variations in the early growth patterns of individual cultures with statistically significant differences in growth dynamics, which could be explained by the presence of inter-converting subpopulations with different growth rates, and which could last for many generations. Based on the hypothesis of existence of multiple subpopulations, we developed a branching process model that was consistent with the experimental observations.
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Affiliation(s)
- Yue Wang
- Department of Computational Medicine, University of California, Los Angeles, CA, United States of America; Department of Applied Mathematics, University of Washington, Seattle, WA, United States of America
| | - Joseph X Zhou
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Edoardo Pedrini
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Irit Rubin
- Institute for Systems Biology, Seattle, WA, United States of America
| | - May Khalil
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Roberto Taramelli
- Department of Theoretical and Applied Science, University of Insubria, Italy
| | - Hong Qian
- Department of Applied Mathematics, University of Washington, Seattle, WA, United States of America
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA, United States of America.
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10
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Jain P, Pillai M, Duddu AS, Somarelli JA, Goyal Y, Jolly MK. Dynamical hallmarks of cancer: Phenotypic switching in melanoma and epithelial-mesenchymal plasticity. Semin Cancer Biol 2023; 96:48-63. [PMID: 37788736 DOI: 10.1016/j.semcancer.2023.09.007] [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: 04/19/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023]
Abstract
Phenotypic plasticity was recently incorporated as a hallmark of cancer. This plasticity can manifest along many interconnected axes, such as stemness and differentiation, drug-sensitive and drug-resistant states, and between epithelial and mesenchymal cell-states. Despite growing acceptance for phenotypic plasticity as a hallmark of cancer, the dynamics of this process remains poorly understood. In particular, the knowledge necessary for a predictive understanding of how individual cancer cells and populations of cells dynamically switch their phenotypes in response to the intensity and/or duration of their current and past environmental stimuli remains far from complete. Here, we present recent investigations of phenotypic plasticity from a systems-level perspective using two exemplars: epithelial-mesenchymal plasticity in carcinomas and phenotypic switching in melanoma. We highlight how an integrated computational-experimental approach has helped unravel insights into specific dynamical hallmarks of phenotypic plasticity in different cancers to address the following questions: a) how many distinct cell-states or phenotypes exist?; b) how reversible are transitions among these cell-states, and what factors control the extent of reversibility?; and c) how might cell-cell communication be able to alter rates of cell-state switching and enable diverse patterns of phenotypic heterogeneity? Understanding these dynamic features of phenotypic plasticity may be a key component in shifting the paradigm of cancer treatment from reactionary to a more predictive, proactive approach.
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Affiliation(s)
- Paras Jain
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Jason A Somarelli
- Department of Medicine, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Synthetic Biology, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India.
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11
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Wang Y, Zhou JX, Pedrini E, Rubin I, Khalil M, Taramelli R, Qian H, Huang S. Cell Population Growth Kinetics in the Presence of Stochastic Heterogeneity of Cell Phenotype. ARXIV 2023:arXiv:2301.03782v2. [PMID: 37904742 PMCID: PMC10614996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform exponential growth of the cell population. Here we measured the stochastic time courses of growth of an ensemble of populations of HL60 leukemia cells in cultures, starting with distinct initial cell numbers to capture a departure from the uniform exponential growth model for the initial growth ("take-off"). Despite being derived from the same cell clone, we observed significant variations in the early growth patterns of individual cultures with statistically significant differences in growth dynamics, which could be explained by the presence of inter-converting subpopulations with different growth rates, and which could last for many generations. Based on the hypothesis of existence of multiple subpopulations, we developed a branching process model that was consistent with the experimental observations.
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Affiliation(s)
- Yue Wang
- Department of Computational Medicine, University of California, Los Angeles, California, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Joseph X. Zhou
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Edoardo Pedrini
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Irit Rubin
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - May Khalil
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Roberto Taramelli
- Department of Theoretical and Applied Science, University of Insubria, Italy
| | - Hong Qian
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Sui Huang
- Institute for Systems Biology, Seattle, Washington, United States of America
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12
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Gopalan V, Hannenhalli S. Towards a Synthesis of the Non-Genetic and Genetic Views of Cancer in Understanding Pancreatic Ductal Adenocarcinoma Initiation and Prevention. Cancers (Basel) 2023; 15:cancers15072159. [PMID: 37046820 PMCID: PMC10093726 DOI: 10.3390/cancers15072159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
While much of the research in oncogenesis and cancer therapy has focused on mutations in key cancer driver genes, more recent work suggests a complementary non-genetic paradigm. This paradigm focuses on how transcriptional and phenotypic heterogeneity, even in clonally derived cells, can create sub-populations associated with oncogenesis, metastasis, and therapy resistance. We discuss this complementary paradigm in the context of pancreatic ductal adenocarcinoma. A better understanding of cellular transcriptional heterogeneity and its association with oncogenesis can lead to more effective therapies that prevent tumor initiation and slow progression.
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Affiliation(s)
- Vishaka Gopalan
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
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13
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Pillai M, Hojel E, Jolly MK, Goyal Y. Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools. NATURE COMPUTATIONAL SCIENCE 2023; 3:301-313. [PMID: 38177938 DOI: 10.1038/s43588-023-00427-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/03/2023] [Indexed: 01/06/2024]
Abstract
Individual cells within an otherwise genetically homogenous population constantly undergo fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity is being increasingly implicated in cancer therapy resistance and metastasis. Identifying the origins of non-genetic heterogeneity is therefore crucial for making clinical breakthroughs. We discuss with examples how dynamical models and computational tools have provided critical multiscale insights into the nature and consequences of non-genetic heterogeneity in cancer. We demonstrate how mechanistic modeling has been pivotal in establishing key concepts underlying non-genetic diversity at various biological scales, from population dynamics to gene regulatory networks. We discuss advances in single-cell longitudinal profiling techniques to reveal patterns of non-genetic heterogeneity, highlighting the ongoing efforts and challenges in statistical frameworks to robustly interpret such multimodal datasets. Moving forward, we stress the need for data-driven statistical and mechanistically motivated dynamical frameworks to come together to develop predictive cancer models and inform therapeutic strategies.
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Affiliation(s)
- Maalavika Pillai
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | - Emilia Hojel
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India.
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Department of Biomedical Engineering, Northwestern University McCormick School of Engineering, Evanston, IL, USA.
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14
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Luo W. Nasopharyngeal carcinoma ecology theory: cancer as multidimensional spatiotemporal "unity of ecology and evolution" pathological ecosystem. Theranostics 2023; 13:1607-1631. [PMID: 37056571 PMCID: PMC10086202 DOI: 10.7150/thno.82690] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/26/2023] [Indexed: 03/14/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a particular entity of head neck cancer that is generally regarded as a genetic disease with diverse intertumor and intratumor heterogeneity. This perspective review mainly outlines the up-to-date knowledge of cancer ecology and NPC progression, and presents a number of conceptual stepping-stones. At the beginning, I explicitly advocate that the nature of NPC (cancer) is not a genetic disease but an ecological disease: a multidimensional spatiotemporal "unity of ecology and evolution" pathological ecosystem. The hallmarks of cancer is proposed to act as ecological factors of population fitness. Subsequently, NPC cells are described as invasive species and its metastasis as a multidirectional ecological dispersal. The foundational ecological principles include intraspecific relationship (e.g. communication) and interspecific relationship (e.g. competition, predation, parasitism and mutualism) are interpreted to understand NPC progression. "Mulberry-fish-ponds" model can well illustrate the dynamic reciprocity of cancer ecosystem. Tumor-host interface is the ecological transition zone of cancer, and tumor buddings should be recognized as ecological islands separated from the mainland. It should be noted that tumor-host interface has a significantly molecular and functional edge effect because of its curvature and irregularity. Selection driving factors and ecological therapy including hyperthermia for NPC patients, and future perspectives in such field as "ecological pathology", "multidimensional tumoriecology" are also discussed. I advance that "nothing in cancer evolution or ecology makes sense except in the light of the other". The cancer ecology tree is constructed to comprehensively point out the future research direction. Taken together, the establishment of NPC ecology theory and cancer ecology tree might provide a novel conceptual framework and paradigm for our understanding of cancer complex causal process and potential preventive and therapeutic applications for patients.
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Affiliation(s)
- Weiren Luo
- Cancer Research Institute, Department of Pathology, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen Third People's Hospital, National Clinical Research Center for Infectious Diseases, Shenzhen, China
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15
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Wang Y, Zhou JX, Pedrini E, Rubin I, Khalil M, Qian H, Huang S. Cell Population Growth Kinetics in the Presence of Stochastic Heterogeneity of Cell Phenotype. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527773. [PMID: 36824755 PMCID: PMC9948979 DOI: 10.1101/2023.02.08.527773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized exponential growth. Here we measured the stochastic time courses of growth of an ensemble of populations of HL60 leukemia cells in cultures, starting with distinct initial cell numbers to capture the departure from the exponential growth model in the initial growth phase. Despite being derived from the same cell clone, we observed significant variations in the early growth patterns of individual cultures with statistically significant differences in growth kinetics and the presence of subpopulations with different growth rates that endured for many generations. Based on the hypothesis of existence of multiple inter-converting subpopulations, we developed a branching process model that captures the experimental observations.
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Affiliation(s)
- Yue Wang
- Department of Computational Medicine, University of California, Los Angeles, California, United States of America
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Joseph X. Zhou
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Edoardo Pedrini
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Irit Rubin
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - May Khalil
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Hong Qian
- Department of Applied Mathematics, University of Washington, Seattle, Washington, United States of America
| | - Sui Huang
- Institute for Systems Biology, Seattle, Washington, United States of America
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16
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Feinberg AP, Levchenko A. Epigenetics as a mediator of plasticity in cancer. Science 2023; 379:eaaw3835. [PMID: 36758093 PMCID: PMC10249049 DOI: 10.1126/science.aaw3835] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/22/2022] [Indexed: 02/11/2023]
Abstract
The concept of an epigenetic landscape describing potential cellular fates arising from pluripotent cells, first advanced by Conrad Waddington, has evolved in light of experiments showing nondeterministic outcomes of regulatory processes and mathematical methods for quantifying stochasticity. In this Review, we discuss modern approaches to epigenetic and gene regulation landscapes and the associated ideas of entropy and attractor states, illustrating how their definitions are both more precise and relevant to understanding cancer etiology and the plasticity of cancerous states. We address the interplay between different types of regulatory landscapes and how their changes underlie cancer progression. We also consider the roles of cellular aging and intrinsic and extrinsic stimuli in modulating cellular states and how landscape alterations can be quantitatively mapped onto phenotypic outcomes and thereby used in therapy development.
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Affiliation(s)
- Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University Schools of Medicine, Biomedical Engineering, and Public Health, Baltimore, MD 21205, USA
| | - Andre Levchenko
- Yale Systems Biology Institute and Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
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17
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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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18
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Toh K, Saunders D, Verd B, Steventon B. Zebrafish neuromesodermal progenitors undergo a critical state transition in vivo. iScience 2022; 25:105216. [PMID: 36274939 PMCID: PMC9579027 DOI: 10.1016/j.isci.2022.105216] [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: 02/25/2022] [Revised: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. Here, we assess this theoretical model in zebrafish neuromesodermal progenitors (NMps) in vivo during late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) before their differentiation into spinal cord and paraxial mesoderm. Analysis of a published 18ss scRNA-seq dataset showed that the NMp population is noisier than its derivatives. By building in silico composite gene expression maps from image data, we assigned an 'NM index' to in silico NMps based on the expression of neural and mesodermal markers and demonstrated that cell population heterogeneity peaked at 24ss. Further examination revealed cells with gene expression profiles incongruent with their prospective fate. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.
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Affiliation(s)
- Kane Toh
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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19
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Kulkarni P, Mohanty A, Bhattacharya S, Singhal S, Guo L, Ramisetty S, Mirzapoiazova T, Mambetsariev B, Mittan S, Malhotra J, Gupta N, Kim P, Babikian R, Rajurkar S, Subbiah S, Tan T, Nguyen D, Merla A, Kollimuttathuillam SV, Phillips T, Baik P, Tan B, Vashi P, Shrestha S, Leach B, Garg R, Rich PL, Stewart FM, Pisick E, Salgia R. Addressing Drug Resistance in Cancer: A Team Medicine Approach. J Clin Med 2022; 11:5701. [PMID: 36233569 PMCID: PMC9572909 DOI: 10.3390/jcm11195701] [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: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 12/04/2022] Open
Abstract
Drug resistance remains one of the major impediments to treating cancer. Although many patients respond well initially, resistance to therapy typically ensues. Several confounding factors appear to contribute to this challenge. Here, we first discuss some of the challenges associated with drug resistance. We then discuss how a 'Team Medicine' approach, involving an interdisciplinary team of basic scientists working together with clinicians, has uncovered new therapeutic strategies. These strategies, referred to as intermittent or 'adaptive' therapy, which are based on eco-evolutionary principles, have met with remarkable success in potentially precluding or delaying the emergence of drug resistance in several cancers. Incorporating such treatment strategies into clinical protocols could potentially enhance the precision of delivering personalized medicine to patients. Furthermore, reaching out to patients in the network of hospitals affiliated with leading academic centers could help them benefit from such innovative treatment options. Finally, lowering the dose of the drug and its frequency (because of intermittent rather than continuous therapy) can also have a significant impact on lowering the toxicity and undesirable side effects of the drugs while lowering the financial burden carried by the patient and insurance providers.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sharad Singhal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Linlin Guo
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sravani Ramisetty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Tamara Mirzapoiazova
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Bolot Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Sandeep Mittan
- Montefiore Medical Center, The University Hospital for Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Jyoti Malhotra
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1000 FivePoint, Irvine, CA 92618, USA
| | - Naveen Gupta
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1100 San Bernardino Road, Suite 1100, Upland, CA 91786, USA
| | - Pauline Kim
- Department of Pharmacy, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Razmig Babikian
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Swapnil Rajurkar
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1100 San Bernardino Road, Suite 1100, Upland, CA 91786, USA
| | - Shanmuga Subbiah
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1250 S. Sunset Ave., Suite 303, West Covina, CA 91790, USA
| | - Tingting Tan
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 1601 Avocado Ave., Newport Beach, CA 92660, USA
| | - Danny Nguyen
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 19671 Beach Blvd. #315, Huntington Beach, CA 92648, USA
| | - Amartej Merla
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 38660 Medical Center Dr, Suite A380, Palmdale, CA 93551, USA
| | - Sudarsan V. Kollimuttathuillam
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 16300 Sand Canyon Ave., Suite 207, Irvine, CA 92618, USA
| | - Tanyanika Phillips
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 44151 15th St. West, Lancaster, CA 93534, USA
| | - Peter Baik
- Cancer Treatment Centers of America, CTCA Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA
| | - Bradford Tan
- Cancer Treatment Centers of America, CTCA Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA
| | - Pankaj Vashi
- Cancer Treatment Centers of America, CTCA Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA
| | - Sagun Shrestha
- Cancer Treatment Centers of America, CTCA Phoenix, 14200 West Celebrate Life Way, Goodyear, AZ 85338, USA
| | - Benjamin Leach
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, 15031 Rinaldi St., Suite 150, Mission Hills, CA 91345, USA
| | - Ruchi Garg
- Cancer Treatment Centers of America, CTCA Atlanta, 600 Celebrate Life Parkway, Newnan, GA 30265, USA
| | - Patricia L. Rich
- Cancer Treatment Centers of America, CTCA Atlanta, 600 Celebrate Life Parkway, Newnan, GA 30265, USA
| | - F. Marc Stewart
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Evan Pisick
- Cancer Treatment Centers of America, CTCA Chicago, 2520 Elisha Avenue, Zion, IL 60099, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA 91010, USA
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20
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Stochastic population dynamics of cancer stemness and adaptive response to therapies. Essays Biochem 2022; 66:387-398. [PMID: 36073715 DOI: 10.1042/ebc20220038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023]
Abstract
Intratumoral heterogeneity can exist along multiple axes: Cancer stem cells (CSCs)/non-CSCs, drug-sensitive/drug-tolerant states, and a spectrum of epithelial-hybrid-mesenchymal phenotypes. Further, these diverse cell-states can switch reversibly among one another, thereby posing a major challenge to therapeutic efficacy. Therefore, understanding the origins of phenotypic plasticity and heterogeneity remains an active area of investigation. While genomic components (mutations, chromosomal instability) driving heterogeneity have been well-studied, recent reports highlight the role of non-genetic mechanisms in enabling both phenotypic plasticity and heterogeneity. Here, we discuss various processes underlying phenotypic plasticity such as stochastic gene expression, chromatin reprogramming, asymmetric cell division and the presence of multiple stable gene expression patterns ('attractors'). These processes can facilitate a dynamically evolving cell population such that a subpopulation of (drug-tolerant) cells can survive lethal drug exposure and recapitulate population heterogeneity on drug withdrawal, leading to relapse. These drug-tolerant cells can be both pre-existing and also induced by the drug itself through cell-state reprogramming. The dynamics of cell-state transitions both in absence and presence of the drug can be quantified through mathematical models. Such a dynamical systems approach to elucidating patterns of intratumoral heterogeneity by integrating longitudinal experimental data with mathematical models can help design effective combinatorial and/or sequential therapies for better clinical outcomes.
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21
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Fields C, Levin M. Competency in Navigating Arbitrary Spaces as an Invariant for Analyzing Cognition in Diverse Embodiments. ENTROPY (BASEL, SWITZERLAND) 2022; 24:819. [PMID: 35741540 PMCID: PMC9222757 DOI: 10.3390/e24060819] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 06/08/2022] [Indexed: 12/20/2022]
Abstract
One of the most salient features of life is its capacity to handle novelty and namely to thrive and adapt to new circumstances and changes in both the environment and internal components. An understanding of this capacity is central to several fields: the evolution of form and function, the design of effective strategies for biomedicine, and the creation of novel life forms via chimeric and bioengineering technologies. Here, we review instructive examples of living organisms solving diverse problems and propose competent navigation in arbitrary spaces as an invariant for thinking about the scaling of cognition during evolution. We argue that our innate capacity to recognize agency and intelligence in unfamiliar guises lags far behind our ability to detect it in familiar behavioral contexts. The multi-scale competency of life is essential to adaptive function, potentiating evolution and providing strategies for top-down control (not micromanagement) to address complex disease and injury. We propose an observer-focused viewpoint that is agnostic about scale and implementation, illustrating how evolution pivoted similar strategies to explore and exploit metabolic, transcriptional, morphological, and finally 3D motion spaces. By generalizing the concept of behavior, we gain novel perspectives on evolution, strategies for system-level biomedical interventions, and the construction of bioengineered intelligences. This framework is a first step toward relating to intelligence in highly unfamiliar embodiments, which will be essential for progress in artificial intelligence and regenerative medicine and for thriving in a world increasingly populated by synthetic, bio-robotic, and hybrid beings.
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Affiliation(s)
- Chris Fields
- Allen Discovery Center at Tufts University, Science and Engineering Complex, 200 College Ave., Medford, MA 02155, USA;
| | - Michael Levin
- Allen Discovery Center at Tufts University, Science and Engineering Complex, 200 College Ave., Medford, MA 02155, USA;
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
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22
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Zhao G, Zhou H, Jin G, Jin B, Geng S, Luo Z, Ge Z, Xu F. Rational Design of Electrically Conductive Biomaterials toward Excitable Tissues Regeneration. Prog Polym Sci 2022. [DOI: 10.1016/j.progpolymsci.2022.101573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time. Sci Rep 2022; 12:5518. [PMID: 35365706 PMCID: PMC8976067 DOI: 10.1038/s41598-022-09438-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/23/2022] [Indexed: 12/26/2022] Open
Abstract
Genetic mutations have long been recognized as drivers of cancer drug resistance, but recent work has defined additional non-genetic mechanisms of plasticity, wherein cancer cells assume a drug resistant phenotype marked by altered epigenetic and transcriptional states. Currently, little is known about the real-time, dynamic nature of this phenotypic shift. Using a bladder cancer model of nongenetic plasticity, we discovered that rapid transition to drug resistance entails upregulation of mitochondrial gene expression and a corresponding metabolic shift towards the tricarboxylic acid cycle and oxidative phosphorylation. Based on this distinction, we were able to track cancer cell metabolic profiles in real time using fluorescence lifetime microscopy (FLIM). We observed single cells transitioning spontaneously to an oxidative phosphorylation state over hours to days, a trend that intensified with exposure to cisplatin chemotherapy. Conversely, pharmacological inhibition of oxidative phosphorylation significantly reversed the FLIM metabolic signature and reduced cisplatin resistance. These rapid, spontaneous metabolic shifts offer a new means of tracking nongenetic cancer plasticity and forestalling the emergence of drug resistance.
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24
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Wu S, Zhou T, Tian T. A robust method for designing multistable systems by embedding bistable subsystems. NPJ Syst Biol Appl 2022; 8:10. [PMID: 35338169 PMCID: PMC8956579 DOI: 10.1038/s41540-022-00220-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
Although multistability is an important dynamic property of a wide range of complex systems, it is still a challenge to develop mathematical models for realising high order multistability using realistic regulatory mechanisms. To address this issue, we propose a robust method to develop multistable mathematical models by embedding bistable models together. Using the GATA1-GATA2-PU.1 module in hematopoiesis as the test system, we first develop a tristable model based on two bistable models without any high cooperative coefficients, and then modify the tristable model based on experimentally determined mechanisms. The modified model successfully realises four stable steady states and accurately reflects a recent experimental observation showing four transcriptional states. In addition, we develop a stochastic model, and stochastic simulations successfully realise the experimental observations in single cells. These results suggest that the proposed method is a general approach to develop mathematical models for realising multistability and heterogeneity in complex systems.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Melbourne, VIC, Australia
| | - Tianshou Zhou
- School of Mathematics and Statistics, Sun Yet-Sen University, Guangzhou, China
| | - Tianhai Tian
- School of Mathematics, Monash University, Melbourne, VIC, Australia.
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25
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Kulkarni P, Bhattacharya S, Achuthan S, Behal A, Jolly MK, Kotnala S, Mohanty A, Rangarajan G, Salgia R, Uversky V. Intrinsically Disordered Proteins: Critical Components of the Wetware. Chem Rev 2022; 122:6614-6633. [PMID: 35170314 PMCID: PMC9250291 DOI: 10.1021/acs.chemrev.1c00848] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the wealth of knowledge gained about intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and, hence, poorly understood. A living cell is a complex adaptive system that can be described as a wetware─a metaphor used to describe the cell as a computer comprising both hardware and software and attuned to logic gates─capable of "making" decisions. In this focused Review, we discuss how IDPs, as critical components of the wetware, influence cell-fate decisions by wiring protein interaction networks to keep them minimally frustrated. Because IDPs lie between order and chaos, we explore the possibility that they can be modeled as attractors. Further, we discuss how the conformational dynamics of IDPs manifests itself as conformational noise, which can potentially amplify transcriptional noise to stochastically switch cellular phenotypes. Finally, we explore the potential role of IDPs in prebiotic evolution, in forming proteinaceous membrane-less organelles, in the origin of multicellularity, and in protein conformation-based transgenerational inheritance of acquired characteristics. Together, these ideas provide a new conceptual framework to discern how IDPs may perform critical biological functions despite their lack of structure.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Supriyo Bhattacharya
- Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Division of Research Informatics, Center for Informatics, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Amita Behal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sourabh Kotnala
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
- Center for Neuroscience, Indian Institute of Science, Bangalore 560012, India
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Vladimir Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow region 141700, Russia
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26
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Bose I. Tipping the Balance: A Criticality Perspective. ENTROPY 2022; 24:e24030405. [PMID: 35327916 PMCID: PMC8947304 DOI: 10.3390/e24030405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 01/02/2023]
Abstract
Cell populations are often characterised by phenotypic heterogeneity in the form of two distinct subpopulations. We consider a model of tumour cells consisting of two subpopulations: non-cancer promoting (NCP) and cancer-promoting (CP). Under steady state conditions, the model has similarities with a well-known model of population genetics which exhibits a purely noise-induced transition from unimodality to bimodality at a critical value of the noise intensity σ2. The noise is associated with the parameter λ representing the system-environment coupling. In the case of the tumour model, λ has a natural interpretation in terms of the tissue microenvironment which has considerable influence on the phenotypic composition of the tumour. Oncogenic transformations give rise to considerable fluctuations in the parameter. We compute the λ−σ2 phase diagram in a stochastic setting, drawing analogies between bifurcations and phase transitions. In the region of bimodality, a transition from a state of balance to a state of dominance, in terms of the competing subpopulations, occurs at λ = 0. Away from this point, the NCP (CP) subpopulation becomes dominant as λ changes towards positive (negative) values. The variance of the steady state probability density function as well as two entropic measures provide characteristic signatures at the transition point.
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Affiliation(s)
- Indrani Bose
- Department of Physics, Bose Institute, 93/1, A. P. C. Road, Kolkata 700009, India
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27
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Lee J, Lee H, Kim HJ, Yun J, Lee T, Lee G, Kim HS, Hong Y. Quantification of doping state of redox sensitive nanoparticles for probing the invasiveness of cancer cells using surface enhanced Raman scattering. Mater Today Bio 2022; 14:100241. [PMID: 35313446 PMCID: PMC8933517 DOI: 10.1016/j.mtbio.2022.100241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 12/19/2022] Open
Abstract
Redox activity is known to regulate migration, invasion, metastasis, proliferation, and vascularization of cancer. Because cancer is heterogeneous, the role of redox activity in different cancers and cancer-related processes vary widely. In this study, water soluble, Tween 80-coated polyaniline (TPAni) nanoparticles were synthesized and used as nano-agents for sensing the redox activities of various cancer cells. To identify the relationship between the redox activity and the aggressiveness of cancer cells, two different cancer cell lines, derived from the same tissue but different with regards to aggressiveness, were selected for study. First, the cancer cell lines were incubated with TPAni nanoparticles, and an absorbance ratio obtained from the cell culture media was used as a colorimetric indicator of the redox activities of the cells. Simultaneously, hydrophobically modified filter papers coated with silver nanosnowflakes (SNSF) were used as sensing substrates for surface enhanced Raman scattering (SERS). SERS spectra obtained from varying concentrations of rhodamine 6G were used to confirm the detection limit of the SNSF-based SERS substrate. Cell culture media containing TPAni nanoparticles were treated with the SNSF-containing SERS substrates to examine the redox activities of the various cancer cell lines.The redox activities of cancer cell lines were confirmed by absorbance spectral analysis, and these redox activities were better identified via an SERS analysis method. A SNSF-containing SERS substrate, fabricated from SNSF and filter paper, was used to sense redox activity in cancer cell lines and to further identify correlations between redox activity and cancer cell line aggressiveness, as indicated by the use of EpCAM as a biomarker. Finally, potential of in vivo redox activity sensing was also confirmed.
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Affiliation(s)
- Jaehun Lee
- Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea
| | - Hwunjae Lee
- Department of Radiology, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
- YUHS-KRIBB Medical Convergence Research Institute, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
- Graduate Program of Nanoscience and Technology, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyun Jung Kim
- Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Jongsu Yun
- Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Hyun Soo Kim
- Department of Electronic Engineering, Kwangwoon University, Seoul, 01897, Republic of Korea
- Corresponding author.
| | - Yoochan Hong
- Department of Medical Device, Korea Institute of Machinery and Materials (KIMM), Daegu, 42994, Republic of Korea
- Corresponding author.
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28
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Chen L, Wang Y, Liu J, Wang H. Coloured noise induces phenotypic diversity with energy dissipation. Biosystems 2022; 214:104648. [PMID: 35218875 DOI: 10.1016/j.biosystems.2022.104648] [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: 07/16/2021] [Revised: 02/17/2022] [Accepted: 02/20/2022] [Indexed: 11/02/2022]
Abstract
Genes integrate many different sources of noise to adapt their survival strategy with energy costs, but how this noise impacts gene phenotype switching is not fully understood. Here, we refine a mechanistic model with multiplicative and additive coloured noise and analyse the influence of noise strength (NS) and autocorrelation time (AT) on gene phenotypic diversity. Different from white noise, we found that in the autocorrelation time-scale plane, increasing the multiplicative noise will broaden the bimodal region of the gene product, and additive noise will induce bimodal region drift from the lower level to the higher level, while the AT will promote this transition. Specifically, the effect of AT on gene expression is similar to a feedback loop; that is, the AT of multiplicative noise will elongate the mean first passage time (MFPT) from the low stable state to the high stable state, but it will reduce the MFPT from the high stable state to the low stable state, and the opposite is true for additive noise. Moreover, these transitions will violate the detailed equilibrium and then consume energy. By effective topology network reconstruction, we found that when the NS is small, the more obvious the bimodality is, the lower the energy dissipation; however, when the NS is large, it will consume more energy with a tendency for bimodality. The overall analysis implies that living organisms will utilize noise strength and its autocorrelation time for better survival in complex and fluctuating environments.
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Affiliation(s)
- Leiyan Chen
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Yan Wang
- Department of Neurology, The First Affiliated Hospital, University of South China, HengYang, 421001, Hunan, People's Republic of China
| | - Jinrong Liu
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China
| | - Haohua Wang
- School of Sciences, Hainan University, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Coll Forestry, Key Laboratory of Genetics & Germplasm Innovation Tropical Special Fo, Ministry of Education, Haikou, 570228, Hainan, People's Republic of China; Hainan University, Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, Haikou, 570228, Hainan, People's Republic of China.
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29
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Abstract
Viral infection is an indisputable causal factor for nearly 17% of all human cancers. However, the diversity and complexity of oncogenic mechanisms raises new questions as to the mechanistic role of viruses in cancer. Classical viral oncogenes have been identified for all tumor-associated viruses. These oncogenes can have multiple oncogenic activities that may or may not be utilized in a particular tumor cell. In addition, stochastic events, like viral mutation and integration, as well as heritable host susceptibilities and immune deficiencies are also implicated in tumorigenesis. A more contemporary view of tumor biology highlights the importance of evolutionary forces that select for phenotypes better adapted to a complex and changing environment. Given the challenges of prioritizing singular mechanistic causes, it may be necessary to integrate concepts from evolutionary theory and systems biology to better understand viral cancer-driving forces. Here, we propose that viral infection provides a biological “entropy” that increases genetic variation and phenotypic plasticity, accelerating the main driving forces of cancer cell evolution. Viruses can also influence the evolutionary selection criteria by altering the tumor microenvironment and immune signaling. Utilizing concepts from cancer cell evolution, population genetics, thermodynamics, and systems biology may provide new perspectives on viral oncogenesis and identify novel therapeutic strategies for treating viruses and cancer.
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Affiliation(s)
- Italo Tempera
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA, United States
| | - Paul M Lieberman
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA, United States
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30
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Gopalan V, Singh A, Rashidi Mehrabadi F, Wang L, Ruppin E, Arda HE, Hannenhalli S. A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC. Cancer Res 2021; 81:3958-3970. [PMID: 34049974 PMCID: PMC8338776 DOI: 10.1158/0008-5472.can-21-0427] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) tumors can originate either from acinar or ductal cells in the adult pancreas. We re-analyze multiple pancreas and PDAC single-cell RNA-seq datasets and find a subset of nonmalignant acinar cells, which we refer to as acinar edge (AE) cells, whose transcriptomes highly diverge from a typical acinar cell in each dataset. Genes upregulated among AE cells are enriched for transcriptomic signatures of pancreatic progenitors, acinar dedifferentiation, and several oncogenic programs. AE-upregulated genes are upregulated in human PDAC tumors, and consistently, their promoters are hypomethylated. High expression of these genes is associated with poor patient survival. The fraction of AE-like cells increases with age in healthy pancreatic tissue, which is not explained by clonal mutations, thus pointing to a nongenetic source of variation. The fraction of AE-like cells is also significantly higher in human pancreatitis samples. Finally, we find edge-like states in lung, liver, prostate, and colon tissues, suggesting that subpopulations of healthy cells across tissues can exist in pre-neoplastic states. SIGNIFICANCE: These findings show "edge" epithelial cell states with oncogenic transcriptional activity in human organs without oncogenic mutations. In the pancreas, the fraction of acinar cells increases with age.
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Affiliation(s)
- Vishaka Gopalan
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland.
| | - Arashdeep Singh
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - Farid Rashidi Mehrabadi
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
- Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland.
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31
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Global analysis of a cancer model with drug resistance due to Lamarckian induction and microvesicle transfer. J Theor Biol 2021; 527:110812. [PMID: 34129816 DOI: 10.1016/j.jtbi.2021.110812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 11/20/2022]
Abstract
Development of resistance to chemotherapy in cancer patients strongly effects the outcome of the treatment. Due to chemotherapeutic agents, resistance can emerge by Darwinian evolution. Besides this, acquired drug resistance may arise via changes in gene expression. A recent discovery in cancer research uncovered a third possibility, indicating that this phenotype conversion can occur through the transfer of microvesicles from resistant to sensitive cells, a mechanism resembling the spread of an infectious agent. We present a model describing the evolution of sensitive and resistant tumour cells considering Darwinian selection, Lamarckian induction and microvesicle transfer. We identify three threshold parameters which determine the existence and stability of the three possible equilibria. Using a simple Dulac function, we give a complete description of the dynamics of the model depending on the three threshold parameters. We also establish an agent based model as a spatial version of the ODE model and compare the outputs of the two models. We find that although the ODE model does not provide spatial information about the structure of the tumour, it is capable to determine the outcome in terms of tumour size and distribution of cell types. We demonstrate the possible effects of increasing drug concentration, and characterize the possible bifurcation sequences. Our results show that the presence of microvesicle transfer cannot ruin a therapy that otherwise leads to extinction, however it may doom a partially successful therapy to failure.
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32
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Rausch M, Blanc L, De Souza Silva O, Dormond O, Griffioen AW, Nowak-Sliwinska P. Characterization of Renal Cell Carcinoma Heterotypic 3D Co-Cultures with Immune Cell Subsets. Cancers (Basel) 2021; 13:2551. [PMID: 34067456 PMCID: PMC8197009 DOI: 10.3390/cancers13112551] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Two-dimensional cell culture-based platforms are easy and reproducible, however, they do not resemble the heterotypic cell-cell interactions or the complex tumor microenvironment. These parameters influence the treatment response and the cancer cell fate. Platforms to study the efficacy of anti-cancer treatments and their impact on the tumor microenvironment are currently being developed. In this study, we established robust, reproducible, and easy-to-use short-term spheroid cultures to mimic clear cell renal cell carcinoma (ccRCC). These 3D co-cultures included human endothelial cells, fibroblasts, immune cell subsets, and ccRCC cell lines, both parental and sunitinib-resistant. During spheroid formation, cells induce the production and secretion of the extracellular matrix. We monitored immune cell infiltration, surface protein expression, and the response to a treatment showing that the immune cells infiltrated the spheroid co-cultures within 6 h. Treatment with an optimized drug combination or the small molecule-based targeted drug sunitinib increased immune cell infiltration significantly. Assessing the therapeutic potential of this drug combination in this platform, we revealed that the expression of PD-L1 increased in 3D co-cultures. The cost- and time-effective establishment of our 3D co-culture model and its application as a pre-clinical drug screening platform can facilitate the treatment validation and clinical translation.
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Affiliation(s)
- Magdalena Rausch
- School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (L.B.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
| | - Léa Blanc
- School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (L.B.)
| | - Olga De Souza Silva
- Department of Visceral Surgery, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (O.D.S.S.); (O.D.)
| | - Olivier Dormond
- Department of Visceral Surgery, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (O.D.S.S.); (O.D.)
| | - Arjan W. Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Patrycja Nowak-Sliwinska
- School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, 1211 Geneva, Switzerland; (M.R.); (L.B.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1211 Geneva, Switzerland
- Translational Research Center in Oncohaematology, 1211 Geneva, Switzerland
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33
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Does Cancer Biology Rely on Parrondo's Principles? Cancers (Basel) 2021; 13:cancers13092197. [PMID: 34063648 PMCID: PMC8125342 DOI: 10.3390/cancers13092197] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Parrondo’s paradox, whereby losing strategies or deleterious effects can combine to provide a winning outcome, has been increasingly applied by biologists to explain complex adaptations in many living systems. Here, we suggest that considering this paradox in oncology, particularly in relation to the phenotypic diversity of malignant cells, could also be a promising approach to understand several puzzling aspects of cancer biology. For example, the high genetic and epigenetic instability of cancer cells, their metastatic behavior and their capacity to enter dormancy could be explained by Parrondo’s theory. We also discuss the relevance of Parrondo’s paradox in a therapeutical framework using different examples. This work provides a compelling argument that the traditional separation between medicine and other disciplines remains a fundamental limitation that needs to be overcome if complex processes, such as oncogenesis, are to be completely understood. Abstract Many aspects of cancer biology remain puzzling, including the proliferative and survival success of malignant cells in spite of their high genetic and epigenetic instability as well as their ability to express migrating phenotypes and/or enter dormancy despite possible fitness loss. Understanding the potential adaptive value of these phenotypic traits is confounded by the fact that, when considered separately, they seem to be rather detrimental at the cell level, at least in the short term. Here, we argue that cancer’s biology and success could frequently be governed by processes underlying Parrondo’s paradox, whereby combinations of intrinsically losing strategies may result in winning outcomes. Oncogenic selection would favor Parrondo’s dynamics because, given the environmental adversity in which malignant cells emerge and evolve, alternating between various less optimal strategies would represent the sole viable option to counteract the changing and deleterious environments cells are exposed to during tumorigenesis. We suggest that malignant processes could be viewed through this lens, and we discuss how Parrondo’s principles are also important when designing therapies against cancer.
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34
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Sherekar S, Viswanathan GA. Boolean dynamic modeling of cancer signaling networks: Prognosis, progression, and therapeutics. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Shubhank Sherekar
- Department of Chemical Engineering Indian Institute of Technology Bombay, Powai Mumbai India
| | - Ganesh A. Viswanathan
- Department of Chemical Engineering Indian Institute of Technology Bombay, Powai Mumbai India
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35
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Capp JP, DeGregori J, Nedelcu AM, Dujon AM, Boutry J, Pujol P, Alix-Panabières C, Hamede R, Roche B, Ujvari B, Marusyk A, Gatenby R, Thomas F. Group phenotypic composition in cancer. eLife 2021; 10:63518. [PMID: 33784238 PMCID: PMC8009660 DOI: 10.7554/elife.63518] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Although individual cancer cells are generally considered the Darwinian units of selection in malignant populations, they frequently act as members of groups where fitness of the group cannot be reduced to the average fitness of individual group members. A growing body of studies reveals limitations of reductionist approaches to explaining biological and clinical observations. For example, induction of angiogenesis, inhibition of the immune system, and niche engineering through environmental acidification and/or remodeling of extracellular matrix cannot be achieved by single tumor cells and require collective actions of groups of cells. Success or failure of such group activities depends on the phenotypic makeup of the individual group members. Conversely, these group activities affect the fitness of individual members of the group, ultimately affecting the composition of the group. This phenomenon, where phenotypic makeup of individual group members impacts the fitness of both members and groups, has been captured in the term 'group phenotypic composition' (GPC). We provide examples where considerations of GPC could help in understanding the evolution and clinical progression of cancers and argue that use of the GPC framework can facilitate new insights into cancer biology and assist with the development of new therapeutic strategies.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Aurora M Nedelcu
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Antoine M Dujon
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Justine Boutry
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Pascal Pujol
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Catherine Alix-Panabières
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France.,Laboratory of Rare Human Circulating Cells (LCCRH), University Medical Centre of Montpellier, Montpellier, France
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Australia.,School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Andriy Marusyk
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Robert Gatenby
- Department of Cancer Physiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, United States
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), University of Montpellier, CNRS, IRD, Montpellier, France
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36
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Jiménez-Sánchez J, Bosque JJ, Jiménez Londoño GA, Molina-García D, Martínez Á, Pérez-Beteta J, Ortega-Sabater C, Honguero Martínez AF, García Vicente AM, Calvo GF, Pérez-García VM. Evolutionary dynamics at the tumor edge reveal metabolic imaging biomarkers. Proc Natl Acad Sci U S A 2021; 118:e2018110118. [PMID: 33536339 PMCID: PMC8017959 DOI: 10.1073/pnas.2018110118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023] Open
Abstract
Human cancers are biologically and morphologically heterogeneous. A variety of clonal populations emerge within these neoplasms and their interaction leads to complex spatiotemporal dynamics during tumor growth. We studied the reshaping of metabolic activity in human cancers by means of continuous and discrete mathematical models and matched the results to positron emission tomography (PET) imaging data. Our models revealed that the location of increasingly active proliferative cellular spots progressively drifted from the center of the tumor to the periphery, as a result of the competition between gradually more aggressive phenotypes. This computational finding led to the development of a metric, normalized distance from 18F-fluorodeoxyglucose (18F-FDG) hotspot to centroid (NHOC), based on the separation from the location of the activity (proliferation) hotspot to the tumor centroid. The NHOC metric can be computed for patients using 18F-FDG PET-computed tomography (PET/CT) images where the voxel of maximum uptake (standardized uptake value [SUV]max) is taken as the activity hotspot. Two datasets of 18F-FDG PET/CT images were collected, one from 61 breast cancer patients and another from 161 non-small-cell lung cancer patients. In both cohorts, survival analyses were carried out for the NHOC and for other classical PET/CT-based biomarkers, finding that the former had a high prognostic value, outperforming the latter. In summary, our work offers additional insights into the evolutionary mechanisms behind tumor progression, provides a different PET/CT-based biomarker, and reveals that an activity hotspot closer to the tumor periphery is associated to a worst patient outcome.
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Affiliation(s)
- Juan Jiménez-Sánchez
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | - Jesús J Bosque
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | | | - David Molina-García
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | - Álvaro Martínez
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
- Nuclear Medicine Unit, Hospital General Universitario de Ciudad Real, Ciudad Real, 13005, Spain
| | - Julián Pérez-Beteta
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | - Carmen Ortega-Sabater
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain
| | | | - Ana M García Vicente
- Thoracic Surgery Unit, Hospital General Universitario de Albacete, Albacete, 02006, Spain
| | - Gabriel F Calvo
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain;
| | - Víctor M Pérez-García
- Mathematical Oncology Laboratory, Universidad de Castilla-La Mancha, Ciudad Real, 13071, Spain;
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37
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Groote JF, Larsen KG. Symbolic Coloured SCC Decomposition. TOOLS AND ALGORITHMS FOR THE CONSTRUCTION AND ANALYSIS OF SYSTEMS 2021. [PMCID: PMC7984532 DOI: 10.1007/978-3-030-72013-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Problems arising in many scientific disciplines are often modelled using edge-coloured directed graphs. These can be enormous in the number of both vertices and colours. Given such a graph, the original problem frequently translates to the detection of the graph’s strongly connected components, which is challenging at this scale. We propose a new, symbolic algorithm that computes all the monochromatic strongly connected components of an edge-coloured graph. In the worst case, the algorithm performs \documentclass[12pt]{minimal}
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\begin{document}$$O(p\cdot n\cdot \log n)$$\end{document}O(p·n·logn) symbolic steps, where p is the number of colours and n the number of vertices. We evaluate the algorithm using an experimental implementation based on Binary Decision Diagrams (BDDs) and large (up to \documentclass[12pt]{minimal}
\usepackage{amsmath}
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\begin{document}$$2^{48}$$\end{document}248) coloured graphs produced by models appearing in systems biology.
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38
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Kulkarni P. Intrinsically Disordered Proteins: Insights from Poincaré, Waddington, and Lamarck. Biomolecules 2020; 10:E1490. [PMID: 33126482 PMCID: PMC7692701 DOI: 10.3390/biom10111490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
The past quarter-century may justly be referred to as a period analogous to the "Cambrian explosion" in the history of proteins. This period is marked by the appearance of the intrinsically disordered proteins (IDPs) on the scene since their discovery in the mid-1990s. Here, I first reflect on how we accidentally stumbled on these fascinating molecules. Next, I describe our research on the IDPs over the past decade and identify six areas as important for future research in this field. In addition, I draw on discoveries others in the field have made to present a more comprehensive essay. More specifically, I discuss the role of IDPs in two fundamental aspects of life: in phenotypic switching, and in multicellularity that marks one of the major evolutionary transitions. I highlight how serendipity, imagination, and an interdisciplinary approach embodying empirical evidence and theoretical insights from the works of Poincaré, Waddington, and Lamarck, shaped our thinking, and how this led us to propose the MRK hypothesis, a conceptual framework addressing phenotypic switching, the emergence of new traits, and adaptive evolution via nongenetic and IDP conformation-based mechanisms. Finally, I present a perspective on the evolutionary link between phenotypic switching and the origin of multicellularity.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Experimental Therapeutics, City of Hope, National Medical Center, Duarte, CA 91010, USA
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39
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Abstract
Application of nonlinear dynamics to cancer ecosystems. Chemical turbulence and strange attractor models in tumor growth, invasion and pattern formation are investigated. Computational algorithms for detecting such structures are proposed. Complex systems applications to cancer dynamics.
Cancers are complex, adaptive ecosystems. They remain the leading cause of disease-related death among children in North America. As we approach computational oncology and Deep Learning Healthcare, our mathematical models of cancer dynamics must be revised. Recent findings support the perspective that cancer-microenvironment interactions may consist of chaotic gene expressions and turbulent protein flows during pattern formation. As such, cancer pattern formation, protein-folding and metastatic invasion are discussed herein as processes driven by chemical turbulence within the framework of complex systems theory. To conclude, cancer stem cells are presented as strange attractors of the Waddington landscape.
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40
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Topological analysis reveals state transitions in human gut and marine bacterial communities. NPJ Biofilms Microbiomes 2020; 6:41. [PMID: 33057043 PMCID: PMC7560872 DOI: 10.1038/s41522-020-00145-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/28/2020] [Indexed: 12/16/2022] Open
Abstract
Microbiome dynamics influence the health and functioning of human physiology and the environment and are driven in part by interactions between large numbers of microbial taxa, making large-scale prediction and modeling a challenge. Here, using topological data analysis, we identify states and dynamical features relevant to macroscopic processes. We show that gut disease processes and marine geochemical events are associated with transitions between community states, defined as topological features of the data density. We find a reproducible two-state succession during recovery from cholera in the gut microbiomes of multiple patients, evidence of dynamic stability in the gut microbiome of a healthy human after experiencing diarrhea during travel, and periodic state transitions in a marine Prochlorococcus community driven by water column cycling. Our approach bridges small-scale fluctuations in microbiome composition and large-scale changes in phenotype without details of underlying mechanisms, and provides an assessment of microbiome stability and its relation to human and environmental health.
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41
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Wu J, Xiao Y, Sun J, Sun H, Chen H, Zhu Y, Fu H, Yu C, E W, Lai S, Ma L, Li J, Fei L, Jiang M, Wang J, Ye F, Wang R, Zhou Z, Zhang G, Zhang T, Ding Q, Wang Z, Hao S, Liu L, Zheng W, He J, Huang W, Wang Y, Xie J, Li T, Cheng T, Han X, Huang H, Guo G. A single-cell survey of cellular hierarchy in acute myeloid leukemia. J Hematol Oncol 2020; 13:128. [PMID: 32977829 PMCID: PMC7517826 DOI: 10.1186/s13045-020-00941-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a fatal hematopoietic malignancy and has a prognosis that varies with its genetic complexity. However, there has been no appropriate integrative analysis on the hierarchy of different AML subtypes. Methods Using Microwell-seq, a high-throughput single-cell mRNA sequencing platform, we analyzed the cellular hierarchy of bone marrow samples from 40 patients and 3 healthy donors. We also used single-cell single-molecule real-time (SMRT) sequencing to investigate the clonal heterogeneity of AML cells. Results From the integrative analysis of 191727 AML cells, we established a single-cell AML landscape and identified an AML progenitor cell cluster with novel AML markers. Patients with ribosomal protein high progenitor cells had a low remission rate. We deduced two types of AML with diverse clinical outcomes. We traced mitochondrial mutations in the AML landscape by combining Microwell-seq with SMRT sequencing. We propose the existence of a phenotypic “cancer attractor” that might help to define a common phenotype for AML progenitor cells. Finally, we explored the potential drug targets by making comparisons between the AML landscape and the Human Cell Landscape. Conclusions We identified a key AML progenitor cell cluster. A high ribosomal protein gene level indicates the poor prognosis. We deduced two types of AML and explored the potential drug targets. Our results suggest the existence of a cancer attractor.
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Affiliation(s)
- Junqing Wu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yuanyuan Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huarui Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guodong Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tingyue Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiong Ding
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Zou Wang
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Sheng Hao
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Lizhen Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weiyan Zheng
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jingsong He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yungui Wang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jin Xie
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, 310058, China
| | - Tiefeng Li
- Institute of Applied Mechanics, Zhejiang University, Hangzhou, 310027, China
| | - Tao Cheng
- Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300000, China.,Alliance for Atlas of Blood Cells, Tianjin, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - He Huang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
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42
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Capp JP, Thomas F. A Similar Speciation Process Relying on Cellular Stochasticity in Microbial and Cancer Cell Populations. iScience 2020; 23:101531. [PMID: 33083761 PMCID: PMC7502340 DOI: 10.1016/j.isci.2020.101531] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Similarities between microbial and cancer cells were noticed in recent years and serve as a basis for an atavism theory of cancer. Cancer cells would rely on the reactivation of an ancestral "genetic program" that would have been repressed in metazoan cells. Here we argue that cancer cells resemble unicellular organisms mainly in their similar way to exploit cellular stochasticity to produce cell specialization and maximize proliferation. Indeed, the relationship between low stochasticity, specialization, and quiescence found in normal differentiated metazoan cells is lost in cancer. On the contrary, low stochasticity and specialization are associated with high proliferation among cancer cells, as it is observed for the "specialist" cells in microbial populations that fully exploit nutritional resources to maximize proliferation. Thus, we propose a model where the appearance of cancer phenotypes can be solely due to an adaptation and a speciation process based on initial increase in cellular stochasticity.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, 31077 Toulouse, France
| | - Frédéric Thomas
- CREEC, UMR IRD 224, CNRS 5290, University of Montpellier, 34394 Montpellier, France
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43
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Lei J. A general mathematical framework for understanding the behavior of heterogeneous stem cell regeneration. J Theor Biol 2020; 492:110196. [PMID: 32067937 DOI: 10.1016/j.jtbi.2020.110196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 12/28/2019] [Accepted: 02/11/2020] [Indexed: 11/21/2022]
Abstract
Stem cell heterogeneity is essential for homeostasis in tissue development. This paper establishes a general mathematical framework to model the dynamics of stem cell regeneration with cell heterogeneity and random transitions of epigenetic states. The framework generalizes the classical G0 cell cycle model and incorporates the epigenetic states of individual cells represented by a continuous multidimensional variable. In the model, the kinetic rates of cell behaviors, including proliferation, differentiation, and apoptosis, are dependent on their epigenetic states, and the random transitions of epigenetic states between cell cycles are represented by an inheritance probability function that describes the conditional probability of cell state changes. Moreover, the model can be extended to include genotypic changes and describe the process of gene mutation-induced tumor development. The proposed mathematical framework provides a generalized formula that helps us to understand various dynamic processes of stem cell regeneration, including tissue development, degeneration, and abnormal growth.
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Affiliation(s)
- Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.
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44
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Farmer CG. Parental Care, Destabilizing Selection, and the Evolution of Tetrapod Endothermy. Physiology (Bethesda) 2020; 35:160-176. [PMID: 32293231 DOI: 10.1152/physiol.00058.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Parental care has evolved convergently an extraordinary number of times among tetrapods that reproduce terrestrially, suggesting strong positive selection for this behavior in the terrestrial environment. This review speculates that destabilizing selection on parental care, and especially embryo incubation, drove the convergent evolution of many tetrapod traits, including endothermy.
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Affiliation(s)
- C G Farmer
- Trinity College Dublin, Dublin, Ireland; and University of Utah, Salt Lake City, Utah
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45
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Bhatia S, Wang P, Toh A, Thompson EW. New Insights Into the Role of Phenotypic Plasticity and EMT in Driving Cancer Progression. Front Mol Biosci 2020; 7:71. [PMID: 32391381 PMCID: PMC7190792 DOI: 10.3389/fmolb.2020.00071] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor cells demonstrate substantial plasticity in their genotypic and phenotypic characteristics. Epithelial-mesenchymal plasticity (EMP) can be characterized into dynamic intermediate states and can be orchestrated by many factors, either intercellularly via epigenetic reprograming, or extracellularly via growth factors, inflammation and/or hypoxia generated by the tumor stromal microenvironment. EMP has the capability to alter phenotype and produce heterogeneity, and thus by changing the whole cancer landscape can attenuate oncogenic signaling networks, invoke anti-apoptotic features, defend against chemotherapeutics and reprogram angiogenic and immune recognition functions. We discuss here the role of phenotypic plasticity in tumor initiation, progression and metastasis and provide an update of the modalities utilized for the molecular characterization of the EMT states and attributes of cellular behavior, including cellular metabolism, in the context of EMP. We also summarize recent findings in dynamic EMP studies that provide new insights into the phenotypic plasticity of EMP flux in cancer and propose therapeutic strategies to impede the metastatic outgrowth of phenotypically heterogeneous tumors.
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Affiliation(s)
- Sugandha Bhatia
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
| | - Peiyu Wang
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
| | - Alan Toh
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
| | - Erik W Thompson
- Institute of Health and Biomedical Innovation and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
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46
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Xu T, Li HT, Wei J, Li M, Hsieh TC, Lu YT, Lakshminarasimhan R, Xu R, Hodara E, Morrison G, Gujar H, Rhie SK, Siegmund K, Liang G, Goldkorn A. Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype. Int J Cancer 2020; 146:3065-3076. [PMID: 32017074 DOI: 10.1002/ijc.32904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
Highly tumorigenic, drug-resistant cancer stem-like cells drive cancer progression. These aggressive cells can arise repeatedly from bulk tumor cells independently of mutational events, suggesting an epigenetic mechanism. To test this possibility, we studied bladder cancer cells as they cyclically shifted to and from a cancer stem-like phenotype, and we discovered that these two states exhibit distinct DNA methylation and chromatin accessibility. Most differential chromatin accessibility was independent of methylation and affected the expression of driver genes such as E2F3, a cell cycle regulator associated with aggressive bladder cancer. Cancer stem-like cells exhibited increased E2F3 promoter accessibility and increased E2F3 expression that drove cell migration, invasiveness and drug resistance. Epigenetic interference using a DNA methylation inhibitor blocked the transition to a cancer stem-like state and reduced E2F3 expression. Our findings indicate that epigenetic plasticity plays a key role in the transition to and from an aggressive, drug-resistant phenotype.
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Affiliation(s)
- Tong Xu
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Hong-Tao Li
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jenny Wei
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Meng Li
- Norris Bioinformatics Core, Health Sciences Libraries, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Tien-Chan Hsieh
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Yi-Tsung Lu
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | | | - Rong Xu
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Emmanuelle Hodara
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Gareth Morrison
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Hemant Gujar
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Kimberly Siegmund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Internal Medicine, University of Southern California Keck School of Medicine and Norris Comprehensive Cancer Center, Los Angeles, CA
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47
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Serrano JJ, Delgado B, Medina MÁ. Control of tumor angiogenesis and metastasis through modulation of cell redox state. Biochim Biophys Acta Rev Cancer 2020; 1873:188352. [PMID: 32035101 DOI: 10.1016/j.bbcan.2020.188352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 12/14/2022]
Abstract
Redox reactions pervade all biology. The control of cellular redox state is essential for bioenergetics and for the proper functioning of many biological functions. This review traces a timeline of findings regarding the connections between redox and cancer. There is ample evidence of the involvement of cellular redox state on the different hallmarks of cancer. Evidence of the control of tumor angiogenesis and metastasis through modulation of cell redox state is reviewed and highlighted.
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Affiliation(s)
- José J Serrano
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain
| | - Belén Delgado
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain
| | - Miguel Ángel Medina
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071 Málaga, Spain; IBIMA (Biomedical Research Institute of Málaga), E-29071 Málaga, Spain; CIBER de Enfermedades Raras (CIBERER), E-29071 Málaga, Spain.
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48
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Disentangling a complex response in cell reprogramming and probing the Waddington landscape by automatic construction of Petri nets. Biosystems 2020; 189:104092. [PMID: 31917281 DOI: 10.1016/j.biosystems.2019.104092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/02/2019] [Accepted: 12/20/2019] [Indexed: 01/19/2023]
Abstract
We analyzed the developmental switch to sporulation of a multinucleate Physarum polycephalum plasmodial cell, a complex response to phytochrome photoreceptor activation. Automatic construction of Petri nets representing finite state machines assembled from trajectories of differential gene expression in single cells revealed alternative, genotype-dependent interconnected developmental routes and identified reversible steps, metastable states, commitment points, and subsequent irreversible steps together with molecular signatures associated with cell fate decision and differentiation. Formation of cyclic transits identified by transition invariants in mutants that are locked in a proliferative state is remarkable considering the view that oncogenic alterations may cause the formation of cancer attractors. We conclude that the Petri net approach is useful to probe the Waddington landscape of cellular reprogramming, to disentangle developmental routes for the reconstruction of the gene regulatory network, and to understand how genetic alterations or physiological conditions reshape the landscape eventually creating new basins of attraction. Unraveling the complexity of pathogenesis, disease progression, drug response or the analysis of attractor landscapes in other complex systems of uncertain structure might be additional fields of application.
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49
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Erenpreisa J, Giuliani A. Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics. Int J Mol Sci 2019; 21:E240. [PMID: 31905791 PMCID: PMC6981914 DOI: 10.3390/ijms21010240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/22/2019] [Accepted: 12/27/2019] [Indexed: 02/06/2023] Open
Abstract
The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.
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Affiliation(s)
- Jekaterina Erenpreisa
- Cancer Research Division, Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Alessandro Giuliani
- Environmental and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy;
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A systems approach to clinical oncology uses deep phenotyping to deliver personalized care. Nat Rev Clin Oncol 2019; 17:183-194. [DOI: 10.1038/s41571-019-0273-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 02/06/2023]
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