Preserving chromatin nano-structure to enhance chondrocyte therapeutic potential for cartilage repair

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Summary There is a gap in the knowledge about how chondrocytes lose their phenotype and matrix production capacity during in vitro expansion. This gap in knowledge stems from the paucity of studies that directly interrogate chondrocyte genome architecture and transcriptional profiles in single cells to capture the inherent heterogeneity of cell differentiation. To fill this unmet gap, we will use state-of-the-art super-resolution imaging, single cell RNA Sequencing (RNA-Seq), high-throughput RNA-FISH (MERFISH) and metabolic labeling (FUNCAT) technologies to relate, on a cell-by-cell level, the chromatin nano-structure, transcriptional output, epigenetic modifications and matrix production capacity of single chondrocytes expanded in culture under different epigenetic and chemo-physical cues. We will further develop machine learning models to predict chondrocyte phenotype using super-resolution images of chondrocyte chromatin nano-structure. Our central hypothesis is that there are distinct chromatin nano-structural arrangements and transcriptional signatures associated with chondrocytes that have high matrix production capacity, and that chromatin nano-structure can be manipulated in a predictive manner via the combination of epigenetic and chemo-physical cues to improve chondrocyte therapeutic potential. The basis for this hypothesis is our preliminary super-resolution data of chromatin nano-structure in in vitro expanded chondrocytes and mesenchymal stem cells grown on substrates of varying stiffness and subjected to various chemical cues. The proposed work is significant as it will generate new knowledge about how chromatin nano-structure and epigenetic landscape regulates matrix production capacity of chondrocytes and how this capacity can be enhanced through manipulation of chromatin and epigenetic states. Our Aims are: matrix whether chromatin nano-structure and transcription are predictive of chondrocyte production capacity Aim 1: Determine Aim 2: Determine how chemo-physical and epigenetic cues impact transitions in chromatin nano- structure and matrix production in chondrocytes Aim 3: Determine whether predicted cues improve chondrocyte therapeutic efficacy In summary, we expect to contribute to the identification of new in vitro expansion conditions that maintain naïve chondrocyte phenotype and enhance their therapeutic potential. The proposed research is innovative as it represents a drastic departure from the status quo by applying multi-faceted, single-cell based imaging and sequencing technologies to determine the relationship between chondrocyte chromatin and epigenetic state, transcriptional activities, and matrix production. If successful, this work may change clinical practice by providing improved cell populations for cartilage repair.