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| Status |
Public on Mar 31, 2022 |
| Title |
scRNA sequencing analysis for human ureters and patient derived ureter oragnoid |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
10 normal human ureters each were subjected to RNA sequencing at single cell resolution on Novaseq using 10X Gemonics library preparation platform. Data was processed using Cellranger 4.0.0 and anayzed using Seurat v3.2.1 to characterize various cell types and understand finer details of the regenrative pathways in the ureter urothelium. This was further explored by analyzing single cell RNA sequencing data from human ureter derived organoid (generated in the same manner as the 10 ureter samples). Freshly processed and thawed tissue sample from the same human subject was used as control to further understand the urothelial regenerative pathways.
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| Contributor(s) |
Ting AH, Lee BH, Fink EE, Sona S |
| Citation(s) |
35914526 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| K08 CA237842 |
Chromatin Modifier Gene Mutation and Enhancer Dysfunction in Bladder Cancer |
CLEVELAND CLINIC LERNER COLLEGE OF MEDICINE - CWRU |
Byron H Lee |
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| Submission date |
Sep 14, 2021 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Angela H Ting |
| E-mail(s) |
ahting@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Ting
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
Tx |
| ZIP/Postal code |
77054-1901 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE194129 |
Single-cell and spatial mapping identify cell types and signaling networks in the human ureter |
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| Relations |
| BioProject |
PRJNA763198 |
| SRA |
SRP337049 |
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