Improved understanding of both the respiratory and the urinary systems at a high-resolution, high content multiscale level and the parenchymal-extracellular space interactions will provide remarkable insight into morphogenesis, homeostasis and injury/repair of the body’s principal barriers. Characterizing the identities of all the cell types and their spatial organization is the first step towards understanding the functions and malfunctions of these organs.

This group seeks to build spatial multi-omics maps of respiratory system (RS) and urinary system (US) barrier organs at single-cell resolution, using a combination of highly efficient sequencing approaches on dissociated cells, and highly multiplexed in situ mapping of RNA and proteins with fluorescent imaging. There are three main goals to this project. Aim 1 is to establish an experimental and computation pipeline for generating and analyzing 3D multi- omics maps for human tissues. This pipeline will include single-nucleus RNA sequencing and chromatin accessibility mapping, highly multiplexed in situ imaging of RNA, and a computational framework to integrate different types of data to create coherent spatial maps of RNA and chromatin status. Aim 2. In one Organ Specific Project (OSP), create a Lung Airways and Parenchymal Map (LAPMAP), covering the entire intrathoracic human airway, as well as three critical niches of the human lung for both sexes. Aim 3. In a second OSP, create the Bladder Ureter and Kidney Maps (BUKMAP), covering the human kidney and lower urinary tract.