CAREER: Whole-tissue chemical and transcriptional profiling

The ability to probe the molecular state of biological samples at the single-cell level has drastically advanced our understanding of the complex network of cellular interactions in our organs and tissue. However, most single-cell genomic measurements require dissociating cells from their native environment, thereby destroying information about cellular context. The spatial and chemical context of a cell are critical parameters in both developmental and disease states as chemical and physical interactions with neighboring cells can influence signaling pathways that determine cell fate. This research aims to transition from cataloging cellular identity in tissues and organs to mapping cellular distributions by developing a platform to profile the chemical composition and transcriptional state of intact tissue specimens with single-cell resolution. The project involves combining advanced microscopy to image the position of cells in a tissue, and automated fluid handling to collect genomic material from single cells for analysis. This technology compliments international efforts to create a comprehensive human cell atlas by aiding in the production of cell-level maps of developing and diseased tissue for both fundamental and translational biological research. <br/><br/>This research will leverage recent advances in microfluidics, non-linear optical microscopy, and high-throughput DNA sequencing to develop a novel approach for spatial-transcriptomic analysis of unfixed tissue. Specifically, stimulated Raman scattering microscopy will be used to perform label-free histological imaging of tissue slices. A microfluidic platform will then be implemented to precisely and systematically capture individual cells from dissected tissue and molecularly encode RNA from each cell with its position of origin. High-throughput sequencing will then reveal both the transcriptional state and original location of each cell. High-resolution transcriptional maps of interrogated tissue samples will be accessible through a public database, providing a resource for developmental biologists and biomedical researchers. In addition to these research goals, the principal investigator of this project will also direct an undergraduate research program, focused on enhancing recruitment of historically underrepresented minority students and first-generation college students to the UC Berkeley Bioengineering department. This program will provide academic mentorship and fund early undergraduate research to strengthen the pipeline for a more diverse biological research community. Results of this project can be found at streetslab.berkeley.edu/publications.<br/><br/>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.