Spatiotemporal Profiling of the Tumor Immune Microenvironment

University Of Pennsylvania, Philadelphia PA

Investigators

Abstract

PROJECT SUMMARY The tumor immune microenvironment (TIME) is a complex system, composed of immune and cancer cells, tissues, and other biological components, that play an important role in the regulation and progression of cancer. Traditional methods like flow cytometry and scRNA-seq have frequently failed to capture the complex biology and mechanisms that drive immune cell interactions within this environment. However, advancements in spatial transcriptomics have transformed our understanding of cellular heterogeneity, enabling the identification of new cellular interactions and functional dynamics between different cell types and their microenvironments that were previously elusive. Spatial transcriptomics builds upon the principles of single-cell transcriptomics by preserving the spatial information of gene expression within tissue samples. This technology allows researchers to study gene expression in the context of tissue architecture, providing a more complete understanding of the cellular function and interactions between cells. Although this method preserves spatial molecular information, it only provides a snapshot of gene expression at a single point in time, limiting our ability to track molecular changes over time. To address this limitation, I propose developing a new method for spatiotemporal monitoring of live tissue transcriptomics, allowing us to capture how immune cells interact and respond to changes in the TIME during tumor development. In my predoctoral studies, I have engineered a nanostraw array with an electrophoresis setup for RNA extraction from live cells with high viability, and optimized a next-generation sequencing (NGS) spatial barcoding tool to preserve the spatial context of RNA molecules post-extraction, allowing for longitudinal cell tracking. For the F99 phase, I will further refine the nanostraw extraction setup and assess whether its integration with the NGS-based spatial barcoding platform can preserve extracted RNA molecules between individual cells. To validate the live spatiotemporal mapping technology's ability to monitor gene expression in the TIME over time, I will culture patient-derived tumor tissue on nanostraws and track transcriptional changes in cancer and immune cells over 2-3 weeks, while also examining spatial dynamics between these populations. This new technology will offer unprecedented insights into cellular behavior, revealing spatial distributions, cell-cell interactions, and disease processes, with transformative implications for cancer research. For the K00 phase, I will identify a combination of renowned bioengineering and immunotherapy labs to explore the evolution and rearrangement of the TIME during therapy and develop innovative tools at the intersection of synthetic and computational biology, integrating single-cell genomics with both spatial and temporal resolution. Completion of this project will successfully prepare me to launch an NIH-funded laboratory focused on designing novel sequencing platforms that bridge space and time to study TIME dynamics and tumor evolution, for therapeutic targeting and personalized medicine.