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MacAulay C, Keyes M, Hayes M, Lo A, Wang G, Guillaud M, Gleave M, Fazli L, Korbelik J, Collins C, Keyes S, Palcic B. Quantification of large scale DNA organization for predicting prostate cancer recurrence. Cytometry A 2017; 91:1164-1174. [PMID: 29194951 DOI: 10.1002/cyto.a.23287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/06/2017] [Accepted: 10/31/2017] [Indexed: 11/09/2022]
Abstract
This study investigates whether Genomic Organization at Large Scales (which we propose to call GOALS) as quantified via nuclear phenotype characteristics and cell sociology features (describing cell organization within tissue) collected from prostate tissue microarrays (TMAs) can separate biochemical failure from biochemical nonevidence of disease (BNED) after radical prostatectomy (RP). Of the 78 prostate cancer tissue cores collected from patients treated with RP, 16 who developed biochemical relapse (failure group) and 16 who were BNED patients (nonfailure group) were included in the analyses (36 cores from 32 patients). A section from this TMA was stained stoichiometrically for DNA using the Feulgen-Thionin methodology, and scanned with a Pannoramic MIDI scanner. Approximately 110 nuclear phenotypic features, predominately quantifying large scale DNA organization (GOALS), were extracted from each segmented nuclei. In addition, the centers of these segmented nuclei defined a Voronoi tessellation and subsequent architectural analysis. Prostate TMA core classification as biochemical failure or BNED after RP using GOALS features was conducted (a) based on cell type and cell position within the epithelium (all cells, all epithelial cells, epithelial >2 cell layers away from basement membrane) from all cores, and (b) based on epithelial cells more than two cell layers from the basement membrane using a Classifier trained on Gleason 6, 8, 9 (16 cores) only and applied to a Test set consisting of the Gleason 7 cores (20 cores). Successful core classification as biochemical failure or BNED after RP by a linear classifier was 75% using all cells, 83% using all epithelial cells, and 86% using epithelial >2 layers. Overall success of predicted classification by the linear Classifier of (b) was 87.5% using the Training Set and 80% using the Test Set. Overall success of predicted progression using Gleason score alone was 75% for Gleason >7 as failures and 69% for Gleason >6 as failures. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Calum MacAulay
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Mira Keyes
- BC Cancer Agency, Department of Radiation Oncology, Vancouver, BC, Canada
| | - Malcolm Hayes
- BC Cancer Agency, Department of Pathology, Vancouver, BC, Canada
| | - Andrea Lo
- BC Cancer Agency, Department of Radiation Oncology, Vancouver, BC, Canada
| | - Gang Wang
- BC Cancer Agency, Department of Pathology, Vancouver, BC, Canada
| | - Martial Guillaud
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urology, Vancouver, BC, Canada
| | - Laden Fazli
- Vancouver Prostate Centre, Department of Pathology, Vancouver, BC, Canada
| | - Jagoda Korbelik
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urology, Vancouver, BC, Canada
| | - Sarah Keyes
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
| | - Branko Palcic
- BC Cancer Research Centre, Department of Integrative Oncology, Vancouver, BC, Canada
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Ulman V, Svoboda D, Nykter M, Kozubek M, Ruusuvuori P. Virtual cell imaging: A review on simulation methods employed in image cytometry. Cytometry A 2016; 89:1057-1072. [PMID: 27922735 DOI: 10.1002/cyto.a.23031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/20/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
The simulations of cells and microscope images thereof have been used to facilitate the development, selection, and validation of image analysis algorithms employed in cytometry as well as for modeling and understanding cell structure and dynamics beyond what is visible in the eyepiece. The simulation approaches vary from simple parametric models of specific cell components-especially shapes of cells and cell nuclei-to learning-based synthesis and multi-stage simulation models for complex scenes that simultaneously visualize multiple object types and incorporate various properties of the imaged objects and laws of image formation. This review covers advances in artificial digital cell generation at scales ranging from particles up to tissue synthesis and microscope image simulation methods, provides examples of the use of simulated images for various purposes ranging from subcellular object detection to cell tracking, and discusses how such simulators have been validated. Finally, the future possibilities and limitations of simulation-based validation are considered. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Vladimír Ulman
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - David Svoboda
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Matti Nykter
- Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere, Tampere, Finland
| | - Michal Kozubek
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Pekka Ruusuvuori
- Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere, Tampere, Finland.,Pori Campus, Tampere University of Technology, Pori, Finland
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Gardiner BS, Wong KKL, Joldes GR, Rich AJ, Tan CW, Burgess AW, Smith DW. Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components. PLoS Comput Biol 2015; 11:e1004544. [PMID: 26452000 PMCID: PMC4599884 DOI: 10.1371/journal.pcbi.1004544] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023] Open
Abstract
This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an ‘agent’, meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory. Modelling is an important tool in understanding the behaviour of biological tissues. In this paper we advocate a new modelling framework in which cells and tissues are represented by a collection of particles with associated properties. The particles interact with each other and can change their behaviour in response to changes in their environment. We demonstrate how the propose framework can be used to represent the mechanical behaviour of different tissues with much greater flexibility as compared to traditional continuum based methods.
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Affiliation(s)
- Bruce S. Gardiner
- School of Engineering and Information Technology, Murdoch University, Perth, Australia
- * E-mail:
| | - Kelvin K. L. Wong
- Engineering Computational Biology, School of Computer Science and Software Engineering, The University of Western Australia, Perth, Australia
| | - Grand R. Joldes
- Intelligent Systems for Medicine Laboratory, School of Mechanical and Chemical Engineering, The University of Western Australia, Perth, Australia
| | - Addison J. Rich
- Engineering Computational Biology, School of Computer Science and Software Engineering, The University of Western Australia, Perth, Australia
| | - Chin Wee Tan
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Antony W. Burgess
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Surgery, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David W. Smith
- Engineering Computational Biology, School of Computer Science and Software Engineering, The University of Western Australia, Perth, Australia
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Bensaci J, Chen ZY, Mack MC, Guillaud M, Stamatas GN. Geometrical and topological analysis of in vivo confocal microscopy images reveals dynamic maturation of epidermal structures during the first years of life. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:095004. [PMID: 26359808 DOI: 10.1117/1.jbo.20.9.095004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/31/2015] [Indexed: 06/05/2023]
Abstract
Reflectance confocal microscopy is successfully used in infant skin research. Infant skin structure, function, and composition are undergoing a maturation process. We aimed to uncover how the epidermal architecture and cellular topology change with time. Images were collected from three age groups of healthy infants between one and four years of age and adults. Cell centers were manually identified on the images at the stratum granulosum (SG) and stratum spinosum (SS) levels. Voronoi diagrams were used to calculate geometrical and topological parameters. Infant cell density is higher than that of adults and decreases with age. Projected cell area, cell perimeter, and average distance to the nearest neighbors increase with age but do so distinctly between the two layers. Structural entropy is different between the two strata, but remains constant with time. For all ages and layers, the distribution of the number of nearest neighbors is typical of a cooperator network architecture. The topological analysis provides evidence of the maturation process in infant skin. The differences between infant and adult are more pronounced in the SG than SS, while cell cooperation is evident in all cases of healthy skin examined.
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Affiliation(s)
- Jalil Bensaci
- Johnson & Johnson Santé Beauté France, 1 rue Camille Desmoulins, Issy-les-Moulineaux 92130, France
| | - Zhao Yang Chen
- British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - M Catherine Mack
- Johnson and Johnson Consumer Companies Inc., 199 Grandview Road, Skillman, New Jersey 08558, United States
| | - Martial Guillaud
- British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, British Columbia V5Z 1L3, Canada
| | - Georgios N Stamatas
- Johnson & Johnson Santé Beauté France, 1 rue Camille Desmoulins, Issy-les-Moulineaux 92130, France
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Berbegall AP, Villamón E, Tadeo I, Martinsson T, Cañete A, Castel V, Navarro S, Noguera R. Neuroblastoma after childhood: prognostic relevance of segmental chromosome aberrations, ATRX protein status, and immune cell infiltration. Neoplasia 2015; 16:471-80. [PMID: 25077701 PMCID: PMC4198743 DOI: 10.1016/j.neo.2014.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma (NB) is a common malignancy in children but rarely occurs during adolescence or adulthood. This subgroup is characterized by an indolent disease course, almost uniformly fatal, yet little is known about the biologic characteristics. The aim of this study was to identify differential features regarding DNA copy number alterations, α-thalassemia/mental retardation syndrome X-linked (ATRX) protein expression, and the presence of tumor-associated inflammatory cells. Thirty-one NB patients older than 10 years who were included in the Spanish NB Registry were considered for the current study; seven young and middle-aged adult patients (range 18-60 years) formed part of the cohort. We performed single nucleotide polymorphism arrays, immunohistochemistry for immune markers (CD4, CD8, CD20, CD11b, CD11c, and CD68), and ATRX protein expression. Assorted genetic profiles were found with a predominant presence of a segmental chromosome aberration (SCA) profile. Preadolescent and adolescent NB tumors showed a higher number of SCA, including 17q gain and 11q deletion. There was also a marked infiltration of immune cells, mainly high and heterogeneous, in young and middle-aged adult tumors. ATRX negative expression was present in the tumors. The characteristics of preadolescent, adolescent, young adult, and middle-aged adult NB tumors are different, not only from childhood NB tumors but also from each other. Similar examinations of a larger number of such tumor tissues from cooperative groups should lead to a better older age–dependent tumor pattern and to innovative, individual risk-adapted therapeutic approaches for these patients.
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Affiliation(s)
- Ana P Berbegall
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Eva Villamón
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Irene Tadeo
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain; Medical Research Foundation INCLIVA, Hospital Clínico, INCLIVA, Valencia, Spain
| | - Tommy Martinsson
- Department of Clinical Genetics, Göteborg University, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Adela Cañete
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Castel
- Pediatric Oncology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Samuel Navarro
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain
| | - Rosa Noguera
- Pathology Department, Medical School, University of Valencia, INCLIVA, Valencia, Spain.
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Tadeo I, Berbegall AP, Escudero LM, Alvaro T, Noguera R. Biotensegrity of the extracellular matrix: physiology, dynamic mechanical balance, and implications in oncology and mechanotherapy. Front Oncol 2014; 4:39. [PMID: 24624363 PMCID: PMC3940942 DOI: 10.3389/fonc.2014.00039] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 02/15/2014] [Indexed: 01/25/2023] Open
Abstract
Cells have the capacity to convert mechanical stimuli into chemical changes. This process is based on the tensegrity principle, a mechanism of tensional integrity. To date, this principle has been demonstrated to act in physiological processes such as mechanotransduction and mechanosensing at different scales (from cell sensing through integrins to molecular mechanical interventions or even localized massage). The process involves intra- and extracellular components, including the participation of extracellular matrix (ECM) and microtubules that act as compression structures, and actin filaments which act as tension structures. The nucleus itself has its own tensegrity system which is implicated in cell proliferation, differentiation, and apoptosis. Despite present advances, only the tip of the iceberg has so far been uncovered regarding the role of ECM compounds in influencing biotensegrity in pathological processes. Groups of cells, together with the surrounding ground substance, are subject to different and specific forces that certainly influence biological processes. In this paper, we review the current knowledge on the role of ECM elements in determining biotensegrity in malignant processes and describe their implication in therapeutic response, resistance to chemo- and radiotherapy, and subsequent tumor progression. Original data based on the study of neuroblastic tumors will be provided.
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Affiliation(s)
- Irene Tadeo
- Foundation INCLIVA, Hospital Clínico de Valencia , Valencia , Spain
| | - Ana P Berbegall
- Foundation INCLIVA, Hospital Clínico de Valencia , Valencia , Spain ; Department of Pathology, Medical School, University of Valencia , Valencia , Spain
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Departamento de Biología Celular de la Universidad de Sevilla , Seville , Spain
| | - Tomás Alvaro
- Department of Pathology, Hospital de Tortosa, Verge de la Cinta, IISPV, URV , Tortosa , Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia , Valencia , Spain
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von Neubeck C, Shankaran H, Geniza MJ, Kauer PM, Robinson RJ, Chrisler WB, Sowa MB. Integrated experimental and computational approach to understand the effects of heavy ion radiation on skin homeostasis. Integr Biol (Camb) 2013; 5:1229-43. [DOI: 10.1039/c3ib40071a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Claere von Neubeck
- German Cancer Consortium (DKTK), OncoRay - National Center for Radiation Research in Oncology, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Harish Shankaran
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J. Geniza
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, USA
| | - Paula M. Kauer
- Systems Toxicology, Pacific Northwest National Laboratory, P.O. Box 999, MS J4-02, Richland, WA 99352, USA. Fax: +1 509-371-7304; Tel: +1 509-371-6898
| | - R. Joe Robinson
- Systems Toxicology, Pacific Northwest National Laboratory, P.O. Box 999, MS J4-02, Richland, WA 99352, USA. Fax: +1 509-371-7304; Tel: +1 509-371-6898
| | - William B. Chrisler
- Systems Toxicology, Pacific Northwest National Laboratory, P.O. Box 999, MS J4-02, Richland, WA 99352, USA. Fax: +1 509-371-7304; Tel: +1 509-371-6898
| | - Marianne B. Sowa
- Systems Toxicology, Pacific Northwest National Laboratory, P.O. Box 999, MS J4-02, Richland, WA 99352, USA. Fax: +1 509-371-7304; Tel: +1 509-371-6898
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Csikász-Nagy A, Escudero LM, Guillaud M, Sedwards S, Baum B, Cavaliere M. Cooperation and competition in the dynamics of tissue architecture during homeostasis and tumorigenesis. Semin Cancer Biol 2013; 23:293-8. [PMID: 23751796 DOI: 10.1016/j.semcancer.2013.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 05/28/2013] [Accepted: 05/30/2013] [Indexed: 01/26/2023]
Abstract
The construction of a network of cell-to-cell contacts makes it possible to characterize the patterns and spatial organization of tissues. Such networks are highly dynamic, depending on the changes of the tissue architecture caused by cell division, death and migration. Local competitive and cooperative cell-to-cell interactions influence the choices cells make. We review the literature on quantitative data of epithelial tissue topology and present a dynamical network model that can be used to explore the evolutionary dynamics of a two dimensional tissue architecture with arbitrary cell-to-cell interactions. In particular, we show that various forms of experimentally observed types of interactions can be modelled using game theory. We discuss a model of cooperative and non-cooperative cell-to-cell communication that can capture the interplay between cellular competition and tissue dynamics. We conclude with an outlook on the possible uses of this approach in modelling tumorigenesis and tissue homeostasis.
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Affiliation(s)
- Attila Csikász-Nagy
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige 38010, Italy.
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