The single and same cell 3D atlas of epigenome and transcriptome of the lower urinary tract

In response to RFA-DK-20-013 “GenitoUrinary Development Molecular Anatomy Project (GUDMAP) - Atlas Projects”, this proposal aims “to generate data to visualize the developing urinary tract, to identify new functional and anatomical domains, and cell types”. The embryonic hindgut or cloaca progresses from a single hollow organ to two separate entities – the urinary tract and anorectal tract. The urinary tract further differentiates into the bladder rostrally and the genital urethra caudally. Guided by tissue-specific gene expression patterns, we show that several selected transcription factors and signaling molecules are critical for urinary tract development and, are responsible for some of the most complex human birth defects. However, these low-throughput and isolated case studies offer limited information; and it is difficult integrate these findings to discern gene-gene and gene-cell relationships in development and in disease. Resources including spatial annotation of all genes in all cells are needed. Using innovative technologies including single cell Multi-omics and Spatial Transcriptome, this application aims to 1) create a series of digital libraries from all cells of mouse lower urinary tract, in which every cell is annotated based on its' own transcriptomic and epigenomic profiles; 2) generate ultrahigh-density tissue- specific spatial transcriptomic map of the lower urinary tract; and 3) display spatial transcriptome at near single cell resolution onto the 3D digitalized mouse and human embryos. These resources will serve the research community to establish a comprehensive understanding of urinary tract development, including but not limited to cloaca septation and urinary tract differentiation.