HCA Data Explorer

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

Updated June 10, 2022

Tissue engineering offers a promising treatment strategy for ureteral strictures. Successful ureter engineering is necessitated by detailed understanding of the tissue architecture, cellular heterogeneity, and signaling pathways underlying regeneration. We define and spatially map cell populations within the human ureter by using a combinatorial approach: single-cell RNA sequencing, 10X Visium spatial transciptomics, and immunofluorescence. The stromal and urothelial cell populations are analyzed in detail, and we infer potential cell-cell communication networks underpinning the bi-directional crosstalk between these compartments. Specifically, we analyze and experimentally validate the importance of Sonic Hedgehog (SHH) signaling pathway in adult stem cell maintenance. The SHH-expressing basal cells support organoid generation in vitro, and accurately predict the differentiation trajectory of basal stem cells, to terminally differentiated umbrella cells, in vivo. Our results highlight essential processes involved in adult ureter tissue homeostasis, and provide a toolkit for guiding ureter tissue engineering. Overall design: Two normal human ureters each were subjected to spatial transcriptomics using 10X Genomics Spatial Gene Expression. Data was processed using Spaceranger 1.3.0 and anayzed using Seurat v4.0.4 to better understand the architecture and cellular heterogeneity of the ureter. These samples have matching single cell RNAseq data, which were used to enhance and validate the Spatial Gene Expression data.

Angela H TingLerner Research Institutetinga@ccf.org
Angela H Ting (Experimental Scientist)1
Byron H Lee1
Matthew Bradley1
Pierre-Emmanuel Desprez2
1Lerner Research Institute
2Cleveland Clinic
William G Sullivan
Brittney D Wick

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/9833669b-d694-4b93-a3d0-6b6f9dbcfc10
None
INSDC Project Accessions:
SRP337049, SRP337050
GEO Series Accessions:INSDC Study Accessions:

For information regarding data sharing and data use, please see our Data Access Policy.

Analysis Portals

None

Project Label

humanAdultUreter

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

ureter

Organ Part

Unspecified

Selected Cell Types

Unspecified

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

human adult stage

Library Construction Method

2 library construction methods

Nucleic Acid Source

2 nucleic acid sources

Paired End

false

Analysis Protocol

analysis_protocol_1, analysis_protocol_2

File Format

3 file formats

Cell Count Estimate

30.9k

Donor Count

10
csv.gz2 file(s)fastq.gz148 file(s)txt.gz2 file(s)