ABSTRACT Mesenchymal stem cells (MSCs) have broad-based potential in regenerative medicine cell therapies and can be isolated from a variety of different tissues. Though MSCs from different tissues are phenotypically similar, a barrier to their clinical use is the high variability of their trophic and regenerative properties. This variability suggests that inherent differences exist in the molecular machinery guiding MSC properties between different MSC populations, yet, to date, these differences are ill-defined. To this end, we have preliminary evidence that MSC phenotypes correlate to their regenerative outcomes. In this study, we aim to elucidate how the molecular and cellular properties of distinct MSC populations determine their regenerative properties. Our hypothesis is that MSCs from different tissues have different regenerative properties which correlate to specific molecular profiles defined by gene expression and transcriptional activity. To test this hypothesis, the project proposed has three Specific Aims (SAs). In SA1, we will determine how tissue-specificity dictates gene expression and dynamic transcription factor activity of distinct MSCs. SA2 will determine how differences in the cellular and molecular properties of MSCs correlate to MSC phenotype. Finally, in SA3, we will determine how the molecular profiles and cellular activities of MSCs dictate their regenerative properties. Findings of the proposed study will provide novel insights about how the distinct molecular profiles of MSCs dictate their biological and physiological properties. In a therapeutic context, this would enable the development of innovative screening technologies for MSC therapies to identify and enrich for the most appropriate MSC for the specific therapeutic application.