title: Computational investigation of epithelial cell dynamic phenotype in vitro.
abstract: BACKGROUND
  When grown in three-dimensional (3D) cultures, epithelial cells typically form cystic organoids that recapitulate cardinal features of in vivo epithelial structures. Characterizing essential cell actions and their roles, which constitute the system's dynamic phenotype, is critical to gaining deeper insight into the cystogenesis phenomena.
  
  
  METHODS
  Starting with an earlier in silico epithelial analogue (ISEA1) that validated for several Madin-Darby canine kidney (MDCK) epithelial cell culture attributes, we built a revised analogue (ISEA2) to increase overlap between analogue and cell culture traits. Both analogues used agent-based, discrete event methods. A set of axioms determined ISEA behaviors; together, they specified the analogue's operating principles. A new experimentation framework enabled tracking relative axiom use and roles during simulated cystogenesis along with establishment of the consequences of their disruption.
  
  
  RESULTS
  ISEA2 consistently produced convex cystic structures in a simulated embedded culture. Axiom use measures provided detailed descriptions of the analogue's dynamic phenotype. Dysregulating key cell death and division axioms led to disorganized structures. Adhering to either axiom less than 80% of the time caused ISEA1 to form easily identified morphological changes. ISEA2 was more robust to identical dysregulation. Both dysregulated analogues exhibited characteristics that resembled those associated with an in vitro model of early glandular epithelial cancer.
  
  
  CONCLUSIONS
  We documented the causal chains of events, and their relative roles, responsible for simulated cystogenesis. The results stand as an early hypothesis--a theory--of how individual MDCK cell actions give rise to consistently roundish, cystic organoids.
authors.affiliation: UCSF/UC Berkeley Joint Graduate Group in Bioengineering, University of California, Berkeley, California 94720, USA. seanhjk@berkeley.edu
authors.forename: Sean H J
authors.initials: SH
authors.lastname: Kim
authors.forename: Sunwoo
authors.initials: S
authors.lastname: Park
authors.forename: Keith
authors.initials: K
authors.lastname: Mostov
authors.forename: Jayanta
authors.initials: J
authors.lastname: Debnath
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Hunt
mesh_terms: D000818:Animals; D015984:Causality; D018929:Cell Culture Techniques; D002460:Cell Line; D003198:Computer Simulation; D004285:Dogs; D004847:Epithelial Cells / Q000166:cytology*; D008954:Models, Biological; D010641:Phenotype; D023822:Tissue Engineering