RECODE: Non-invasive cell patterning and monitoring to generate data-guided computational models that inform synthetic gene circuit-guided cartilage development

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Efforts to develop stem-cell based regeneration strategies have yet to be clinically usable especially for difficult to repair tissues like muscle and cartilage. The goal of this Reproducible Cells and Organoids via Directed-Differentiation Encoding (RECODE) project is to understand how adult human stem cells transform into chondrocytes, the cells in cartilage. Ultimately, these engineered cells could be used to repair traumatic and debilitating cartilage injuries. This project will generate new knowledge about the regulators of stem cell-based cartilage formation that can be used to develop new regeneration strategies. The results will also be broadly applicable to the tissue regeneration field in cases where tissue functionality requires long-term stability. This work offers a unique opportunity to train teams of undergraduate and graduate scientists and engineers in methods that enhance the translation of fundamental studies of biology into sophisticated engineering systems.This RECODE project aims to employ innovative methods that combine biophysical techniques, data-guided algorithms, and synthetic gene circuit engineering for the cell state–specific perturbation of the drivers controlling differentiation of adult human mesenchymal stem cells (hMSCs) into chondrocytes. Specifically, this project focuses on conditions that drive maturation of the hMSC derived chondrocyte (hMdCh) phenotype into either stable articular cartilage chondrocytes or hypertrophic chondrocytes. The influence of the biophysical conditions on long-term hMdCh phenotype will be monitored using high-throughput methods to dynamically and non-destructively measure the secretome and the evolving stiffness of the nascent tissues. The regulatory pathways associated with transitions in phenotype will be identified by correlating RNA- and microRNA-sequencing and genome-wide chromatin architectural data with the secretomic markers of phenotype transitions. A mathematical model of phenotype transitions will be generated to pinpoint transcriptional and translational regulators that drive phenotype changes under specific environmental conditions. A flexible synthetic gene circuit platform will be used to engineer gene circuits that simultaneously activate and/or repress the genomic regulators found to maintain articular or hypertrophic chondrocyte phenotypes. Finally, the efficacy of these gene circuits to maintain hMdCh phenotype and produce functional cartilage tissues will be tested. The outcomes of this work will demonstrate the utility of data-driven models to inform the design of synthetic gene circuits to improve tissue regeneration strategies.This RECODE project is jointly funded by the Engineering Biology and Health Cluster in the Division of Chemical, Bioengineering, Environmental, and Transport Systems, the Biomechanics and Mechanobiology Program in the Division of Civil, Mechanical, and Manufacturing Innovation, and the Systems and Synthetic Biology Program in the Division of Molecular and Cellular Biosciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.