Ureter single-cell and spatial mapping reveal cell types, architecture, and signaling networks

Abstract

Tissue engineering offers a promising treatment strategy for ureteral strictures, but its success requires an in-depth understanding of the architecture, cellular heterogeneity, and signaling pathways underlying tissue regeneration. Here we define and spatially map cell populations within the human ureter using single-cell RNA sequencing, spatial gene expression, and immunofluorescence approaches. We focused on the stromal and urothelial cell populations to enumerate distinct cell types composing the human ureter and inferred potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Furthermore, we analyzed and experimentally validated the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells supported organoid generation in vitro and accurately predicted the differentiation trajectory from basal stem cells to terminally differentiated umbrella cells. Our results highlight essential processes involved in adult ureter tissue homeostasis and provide a blueprint for guiding ureter tissue engineering.

Erasure of Biologically Meaningful Signal by Unsupervised scRNAseq Batch-correction Methods

“…To differentiate the effects of our specific implementations of these algorithms from what is seen in practice, we performed TOWCAB analyses on a recent release of human urinary bladder cells (30,942 cells; 10 donors, aligned using Seurat’s MCCA), based on their released UMAP coordinates 38 . Indeed, we found that different cell-types were merged across batches including B- and urothelial-cells ( ED Fig.…”