Integration of Systems and Synthetic Biology to Advance Development of Human Tissues In Vitro

Project summary/ abstract: Organoids reproduce the complex differentiation, cell sorting and self-organization of organogenesis, enabling the study of tissue development and modeling of organ physiology and disease ex vivo. The induced human Pluripotent stem cell (ihPSC) derived organoids are on their way to revolutionizing the future of human cell/organ transplantations. However, a major challenge is centered around the limited ability to control and direct the dynamic process of self-organization at the cellular population level. This drawback diminishes our engineering efforts to build reliable human tissues by mimicking natural biological processes. As such, currently, human organoids exhibit (a) aberrant cell types and (b) stalled developmental stages (immaturity) (c) limited robustness and reproducibility during multilineage tissue formation. In this proposal, we will harness the power of synthetic and system biology and provide a framework to build next-generation organoids with augmented performance and robustness for regenerative medicine. Our method is guided by computational models and genetic technologies. We have recently discovered that in our liver organoids, GATA6-engineered circuits can dictate final cell fates based on the initial GATA6 expression level. Here in Aim 1, we will establish a clonally resolved engineering approach to build human organoids. We will use our library of genetically engineered clones to rationally design mixtures of clones that exhibit specific quantitatively defined outcomes at the tissue level and use this to augment and reconstitute mesodermal niche important for liver maturation. The successful completion of this aim enables us to build human organoids with a high degree of reproducibility. In Aim 2, we devise a computational platform to design and build organoid variants with defined hepatic functions. The successful completion of this study will result in a hypothesis-driven framework for rational engineering and advancement of stem cell-derived tissues ex vivo. Our study will also generate liver tissues with close proximity to adult human liver and reduces dependence on animal experiments and increases access to refined human tissues.