The study of epithelial morphogenesis is fundamental to increasing our understanding of organ function and disease. Great progress has been made through study of culture systems such as EMT6/Ro mouse mammary tumor spheroids and Madin-Darby canine kidney (MDCK) cells, but many aspects of even simple morphogenesis remain unclear. For example, are specific cell actions tightly coupled to the characteristics cell environment or are they more often cell state dependent? Our objective was to discover plausible representations of the operating principles realized during characteristic growth of EMT6/Ro mouse mammary tumor spheroids and MDCK cells in culture. To reach that objective we engineered and iteratively falsified agent-oriented analogues of EMT6 spheroid growth (Chapter 2) and MDCK cystogenesis (Chapters 3 and 4). An approach to understanding how individual cell behaviors contribute to system behaviors is to discover a set of principles that enable abstract agents to exhibit closely analogous behaviors using only information available in an agent's immediate environment. EMT6 spheroids and MDCK cysts display consistent and predictable growth characteristics, implying that individual cell behaviors are tightly controlled and regulated. We listed key attributes of EMT6 spheroid growth and MDCK cystogenesis, which became our behavioral targets.

To understand the in vitro systems we created analogues made up of quasi-autonomous software agents and an abstract environment in which they could operate. The EMT6 analogue was designed so that upon execution it could mimic EMT6 cells forming spheroids in culture. Each agent used an identical set of axiomatic operating principles. In sequence, we used the list of targeted attributes to falsify and revise these axioms, until the analogue exhibited behaviors and attributes that were within prespecified ranges of those targeted, thereby achieving a level of validation. For the analogue of MDCK cystogenesis we tested our hypotheses through in vitro experimentation and quantitative validation. We observed novel growth patterns, including a cell behavior shift that began around day five of growth.

We posit that the validated analogues' operating principles are reasonable representations of those utilized by EMT6/Ro and MDCK cells during morphogenesis. Simulations provide an observable theory for cystogenesis based on hypothesized, cell-level operating principles.