IDEAS home Printed from https://ideas.repec.org/a/plo/pcbi00/1004635.html
   My bibliography  Save this article

Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation

Author

Listed:
  • Brenda N Vo
  • Christopher C Drovandi
  • Anthony N Pettitt
  • Graeme J Pettet

Abstract

In vitro studies and mathematical models are now being widely used to study the underlying mechanisms driving the expansion of cell colonies. This can improve our understanding of cancer formation and progression. Although much progress has been made in terms of developing and analysing mathematical models, far less progress has been made in terms of understanding how to estimate model parameters using experimental in vitro image-based data. To address this issue, a new approximate Bayesian computation (ABC) algorithm is proposed to estimate key parameters governing the expansion of melanoma cell (MM127) colonies, including cell diffusivity, D, cell proliferation rate, λ, and cell-to-cell adhesion, q, in two experimental scenarios, namely with and without a chemical treatment to suppress cell proliferation. Even when little prior biological knowledge about the parameters is assumed, all parameters are precisely inferred with a small posterior coefficient of variation, approximately 2–12%. The ABC analyses reveal that the posterior distributions of D and q depend on the experimental elapsed time, whereas the posterior distribution of λ does not. The posterior mean values of D and q are in the ranges 226–268 µm2h−1, 311–351 µm2h−1 and 0.23–0.39, 0.32–0.61 for the experimental periods of 0–24 h and 24–48 h, respectively. Furthermore, we found that the posterior distribution of q also depends on the initial cell density, whereas the posterior distributions of D and λ do not. The ABC approach also enables information from the two experiments to be combined, resulting in greater precision for all estimates of D and λ.Author Summary: Quantifying the underlying parameters that drive the expansion of melanoma cell colonies such as the cell diffusivity, cell proliferation rate and cell-to-cell adhesion strength can improve our understanding of melanoma biology and its response to treatment. We combine a simulation-based model of collective cell spreading with a novel Bayesian computational algorithm to estimate these parameters from carefully chosen summaries of collective cell image data and to quantify their associated uncertainty across different experimental conditions. Our summarisation of the image data leads to precise estimates for all parameters. Our analysis reveals that the cell diffusivity and the cell-to-cell adhesion strength estimates depend on experimental elapsed time. Furthermore, the cell-to-cell adhesion strength estimate appears to depend on the initial cell density, whereas the cell proliferation rate estimate is approximately the same over different experimental conditions.

Suggested Citation

  • Brenda N Vo & Christopher C Drovandi & Anthony N Pettitt & Graeme J Pettet, 2015. "Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation," PLOS Computational Biology, Public Library of Science, vol. 11(12), pages 1-22, December.
  • Handle: RePEc:plo:pcbi00:1004635
    DOI: 10.1371/journal.pcbi.1004635
    as

    Download full text from publisher

    File URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004635
    Download Restriction: no

    File URL: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004635&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pcbi.1004635?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. C. C. Drovandi & A. N. Pettitt, 2011. "Estimation of Parameters for Macroparasite Population Evolution Using Approximate Bayesian Computation," Biometrics, The International Biometric Society, vol. 67(1), pages 225-233, March.
    2. Maxime Lenormand & Franck Jabot & Guillaume Deffuant, 2013. "Adaptive approximate Bayesian computation for complex models," Computational Statistics, Springer, vol. 28(6), pages 2777-2796, December.
    3. Bortot, P. & Coles, S.G. & Sisson, S.A., 2007. "Inference for Stereological Extremes," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 84-92, March.
    4. Paul Fearnhead & Dennis Prangle, 2012. "Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 74(3), pages 419-474, June.
    5. Simpson, Matthew J. & Landman, Kerry A. & Hughes, Barry D., 2010. "Cell invasion with proliferation mechanisms motivated by time-lapse data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(18), pages 3779-3790.
    6. Mark A. Beaumont & Jean-Marie Cornuet & Jean-Michel Marin & Christian P. Robert, 2009. "Adaptive approximate Bayesian computation," Biometrika, Biometrika Trust, vol. 96(4), pages 983-990.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Chen, C.C.-M. & Drovandi, C.C. & Keith, J.M. & Anthony, K. & Caley, M.J. & Mengersen, K.L., 2017. "Bayesian semi-individual based model with approximate Bayesian computation for parameters calibration: Modelling Crown-of-Thorns populations on the Great Barrier Reef," Ecological Modelling, Elsevier, vol. 364(C), pages 113-123.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Li, J. & Nott, D.J. & Fan, Y. & Sisson, S.A., 2017. "Extending approximate Bayesian computation methods to high dimensions via a Gaussian copula model," Computational Statistics & Data Analysis, Elsevier, vol. 106(C), pages 77-89.
    2. Lee, Xing Ju & Hainy, Markus & McKeone, James P. & Drovandi, Christopher C. & Pettitt, Anthony N., 2018. "ABC model selection for spatial extremes models applied to South Australian maximum temperature data," Computational Statistics & Data Analysis, Elsevier, vol. 128(C), pages 128-144.
    3. Xing Ju Lee & Christopher C. Drovandi & Anthony N. Pettitt, 2015. "Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets," Biometrics, The International Biometric Society, vol. 71(1), pages 198-207, March.
    4. Henri Pesonen & Umberto Simola & Alvaro Köhn‐Luque & Henri Vuollekoski & Xiaoran Lai & Arnoldo Frigessi & Samuel Kaski & David T. Frazier & Worapree Maneesoonthorn & Gael M. Martin & Jukka Corander, 2023. "ABC of the future," International Statistical Review, International Statistical Institute, vol. 91(2), pages 243-268, August.
    5. Gael M. Martin & David T. Frazier & Christian P. Robert, 2021. "Approximating Bayes in the 21st Century," Monash Econometrics and Business Statistics Working Papers 24/21, Monash University, Department of Econometrics and Business Statistics.
    6. Genya Kobayashi & Kazuhiko Kakamu, 2019. "Approximate Bayesian computation for Lorenz curves from grouped data," Computational Statistics, Springer, vol. 34(1), pages 253-279, March.
    7. Warne, David J. & Baker, Ruth E. & Simpson, Matthew J., 2018. "Multilevel rejection sampling for approximate Bayesian computation," Computational Statistics & Data Analysis, Elsevier, vol. 124(C), pages 71-86.
    8. Creel, Michael & Kristensen, Dennis, 2016. "On selection of statistics for approximate Bayesian computing (or the method of simulated moments)," Computational Statistics & Data Analysis, Elsevier, vol. 100(C), pages 99-114.
    9. Lorenzo Pacchiardi & Pierre Künzli & Marcel Schöngens & Bastien Chopard & Ritabrata Dutta, 2021. "Distance-learning For Approximate Bayesian Computation To Model a Volcanic Eruption," Sankhya B: The Indian Journal of Statistics, Springer;Indian Statistical Institute, vol. 83(1), pages 288-317, May.
    10. Silk Daniel & Filippi Sarah & Stumpf Michael P. H., 2013. "Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(5), pages 603-618, October.
    11. Filippi Sarah & Barnes Chris P. & Cornebise Julien & Stumpf Michael P.H., 2013. "On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(1), pages 87-107, March.
    12. Francois Olivier & Laval Guillaume, 2011. "Deviance Information Criteria for Model Selection in Approximate Bayesian Computation," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-25, July.
    13. McKinley, Trevelyan J. & Ross, Joshua V. & Deardon, Rob & Cook, Alex R., 2014. "Simulation-based Bayesian inference for epidemic models," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 434-447.
    14. Gael M. Martin & David T. Frazier & Christian P. Robert, 2020. "Computing Bayes: Bayesian Computation from 1763 to the 21st Century," Monash Econometrics and Business Statistics Working Papers 14/20, Monash University, Department of Econometrics and Business Statistics.
    15. Pierre-Olivier Goffard & Patrick Laub, 2021. "Approximate Bayesian Computations to fit and compare insurance loss models," Working Papers hal-02891046, HAL.
    16. Bertl Johanna & Ewing Gregory & Kosiol Carolin & Futschik Andreas, 2017. "Approximate maximum likelihood estimation for population genetic inference," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 16(5-6), pages 291-312, December.
    17. Jung Hsuan & Marjoram Paul, 2011. "Choice of Summary Statistic Weights in Approximate Bayesian Computation," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-23, September.
    18. Anthony Ebert & Ritabrata Dutta & Kerrie Mengersen & Antonietta Mira & Fabrizio Ruggeri & Paul Wu, 2021. "Likelihood‐free parameter estimation for dynamic queueing networks: Case study of passenger flow in an international airport terminal," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(3), pages 770-792, June.
    19. Stefano Cabras & María Castellanos & Erlis Ruli, 2014. "A Quasi likelihood approximation of posterior distributions for likelihood-intractable complex models," METRON, Springer;Sapienza Università di Roma, vol. 72(2), pages 153-167, August.
    20. Zhang, Jingjing & Dennis, Todd E. & Landers, Todd J. & Bell, Elizabeth & Perry, George L.W., 2017. "Linking individual-based and statistical inferential models in movement ecology: A case study with black petrels (Procellaria parkinsoni)," Ecological Modelling, Elsevier, vol. 360(C), pages 425-436.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1004635. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.