Cancerous cells arise in the spatial context of human tissues giving rise to a collection of interacting host and disease cells termed the tumor microenvironment. Recent focus has been given to adaptive immune cells in the tumor microenvironment, as their frequency has been seen to be prognostic of patient survival in certain cancers, and novel therapies activate these cells against tumors to great effect. Unfortunately, ?there are a dearth of methods available to characterize the immune repertoire while maintaining spatial information??. The current tradeoff is either (1) spatial resolution and low dimensionality data, such as tissue staining or fluorescence in situ hybridization, or (2) high dimensionality data on dissociated cells, such as single cell RNA sequencing, that no longer contain spatial information. Here we propose ?Celltower?, a novel technique to categorize cell position and associated RNA expression in intact tissue sections. ?Celltower? yields high-resolution spatially resolved RNA sequencing data that will allow researchers and physicians to investigate cell patterning in health and disease. A strong motivating application of ?Celltower? is in situ sequencing of tumor infiltrating lymphocytes to characterize T cell and B cell clonal expansion in the tumor microenvironment. This project will be undertaken at Stanford University with the mentorship of Dr. Julia Salzman of Biochemistry, and Dr. Ed Engleman of Pathology. The principle investigator is Rob Bierman who will learn to manage a collaborative technique development project and will gain a mixture of experimental and computational skills and domain expertise in tumor immunology.
With the increasing affordability of single cell sequencing, we propose ?Celltower?, a novel technique to categorize cell position and associated RNA expression in intact tissues. ?Celltower yields high-resolution spatially resolved RNA sequencing data that will allow researchers and physicians to investigate cell patterning in health and disease. A strong motivating application of Celltower? is in situ sequencing of tumor infiltrating lymphocytes to characterize T cell and B cell clonal expansion in the tumor microenvironment.
