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Open Access Research article

A computational approach to resolve cell level contributions to early glandular epithelial cancer progression

Sean HJ Kim1, Jayanta Debnath2, Keith Mostov3, Sunwoo Park4 and C Anthony Hunt14*

Author Affiliations

1 UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California, 94720, USA

2 Department of Pathology, University of California, San Francisco, California 94143, USA

3 Department of Anatomy, University of California, San Francisco, California 94143, USA

4 Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA

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BMC Systems Biology 2009, 3:122  doi:10.1186/1752-0509-3-122

Published: 31 December 2009



Three-dimensional (3D) embedded cell cultures provide an appropriate physiological environment to reconstruct features of early glandular epithelial cancer. Although these are orders of magnitude simpler than tissues, they too are complex systems that have proven challenging to understand. We used agent-based, discrete event simulation modeling methods to build working hypotheses of mechanisms of epithelial 3D culture phenotype and early cancer progression. Starting with an earlier software analogue, we validated an improved in silico epithelial analogue (ISEA) for cardinal features of a normally developed MDCK cyst. A set of axiomatic operating principles defined simulated cell actions. We explored selective disruption of individual simulated cell actions. New framework features enabled recording detailed measures of ISEA cell activities and morphology.


Enabled by a small set of cell operating principles, ISEA cells multiplied and self-organized into cyst-like structures that mimicked those of MDCK cells in a 3D embedded cell culture. Selective disruption of "anoikis" or directional cell division caused the ISEA to develop phenotypic features resembling those of in vitro tumor reconstruction models and cancerous tissues in vivo. Disrupting either process, or both, altered cell activity patterns that resulted in morphologically similar outcomes. Increased disruption led to a prolonged presence of intraluminal cells.


ISEA mechanisms, behaviors, and morphological properties may have biological counterparts. To the extent that in silico-to-in vitro mappings are valid, the results suggest plausible, additional mechanisms of in vitro cancer reconstruction or reversion, and raise potentially significant implications for early cancer diagnosis based on histology. Further ISEA development and use are expected to provide a viable platform to complement in vitro methods for unraveling the mechanistic basis of epithelial morphogenesis and cancer progression.