Simulation and Statistical Techniques to Explore Lymphoid Tissue Organogenesis

Secondary lymphoid organs have a key role in the initiation of adaptive immune responses to infection. Organogenesis occurs in foetal development, and the use of genetic tools, imaging technologies, and ex vivo culture systems has provided significant insights into the cellular components and associated signalling pathways that are involved. However such approaches tend to be reductionist and descriptive, focusing on the contribution of individual components, and cannot fully explain how lymphoid organs develop through interaction between biological components.

In this study, a set of simulation and statistical tools have been developed that provide further insights into the molecular and biophysical mechanisms of lymphoid tissue organogenesis. Specifically, the formation of Peyer’s Patches, gut-associated secondary lymphoid organs, is examined. In collaboration with experimental immunologists, a structured process in the design and calibration of a computer simulation of the biological process has been conducted, leading to the development of a publicly accessible scientific tool where cell behaviour emerges that is statistically similar to that observed in ex vivo culture. Robust biological hypotheses can be generated through use of the tool to perform in silico experimentation that simulates different physiological conditions. A lack of available statistical tools to analyse in silico simulation results has been addressed through the development and release of the spartan toolkit, a set of techniques that can suggest the influence that pathways and components have on simulation behaviour, offering valuable biological insight into the system being explored.

An analysis of simulation results using spartan suggests the influence of biological pathways on tissue formation changes during development, in contrast to hypotheses in
the literature that suggest the process is chemokine driven. Data presented suggests the development period is biphasic, with cell adhesion the key factor early in development, and chemokine expression influential at later point. Through novel application of the statistical tools in spartan to perform a time-lapse analysis of cell behaviour, it is suggested this change in phase occurs between hours 24 and 36. Novel in silico experimentation performed has suggested the key biological factors in causing cell aggregation, and suggested a role for LTin cells in limiting size and number of Peyer’s Patches. A range of potential laboratory investigations have been suggested that could validate whether these simulation derived hypotheses are valid.