Human kidney
NCBI566
human kidney nephrolithiasis 204 MB 939 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots939
silver H&E
Collections / A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease
A Spatial Transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease
Datasets7
Size~1.6 GB
AssayVisium
Samplehuman · kidney
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("doi-10-1038-s41467-023-38975-8")
cohort.members # the 7 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/") Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="doi-10.1038/s41467-023-38975-8")
coll.ordered_artifacts.to_dataframe() # the 7 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1038-s41467-023-38975-8 --dest data/Licenses: 7 CC BY-NC-SA 4.0
About the study
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease.
Kidney stone disease causes significant morbidity and increases health care utilization. In this work, we decipher the cellular and molecular niche of the human renal papilla in patients with calcium oxalate (CaOx) stone disease and healthy subjects. In addition to identifying cell types important in papillary physiology, we characterize collecting duct cell subtypes and an undifferentiated epithelial cell type that was more prevalent in stone patients. Despite the focal nature of mineral deposition in nephrolithiasis, we uncover a global injury signature characterized by immune activation, oxidative stress and extracellular matrix remodeling. We also identify the association of MMP7 and MMP9 expression with stone disease and mineral deposition, respectively. MMP7 and MMP9 are significantly increased in the urine of patients with CaOx stone disease, and their levels correlate with disease activity. Our results define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human papilla and identify associated urinary biomarkers.
Member datasets · 7
Human kidney
NCBI568
human kidney 242 MB 2,438 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Spots2,438
silver H&E
Human kidney
NCBI565
human kidney nephrolithiasis 209 MB 1,085 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots1,085
silver H&E
Human kidney
NCBI567
human kidney nephrolithiasis 211 MB 817 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots817
silver H&E
Human kidney
NCBI564
human kidney nephrolithiasis 210 MB 262 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots262
silver H&E
Human kidney
NCBI563
human kidney nephrolithiasis 247 MB 1,376 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots1,376
silver H&E
Human kidney
NCBI562
human kidney nephrolithiasis 256 MB 2,468 spots silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Spots2,468
silver H&E
Cite this collection
doi.org/10.1038/s41467-023-38975-8 ↗ BibTeX
@article{Canela_2023,
title = {A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease},
volume = {14},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-023-38975-8},
DOI = {10.1038/s41467-023-38975-8},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Canela, Victor Hugo and Bowen, William S. and Ferreira, Ricardo Melo and Syed, Farooq and Lingeman, James E. and Sabo, Angela R. and Barwinska, Daria and Winfree, Seth and Lake, Blue B. and Cheng, Ying-Hua and Gaut, Joseph P. and Ferkowicz, Michael and LaFavers, Kaice A. and Zhang, Kun and Coe, Fredric L. and Worcester, Elaine and Jain, Sanjay and Eadon, Michael T. and Williams, James C. and El-Achkar, Tarek M.},
year = {2023},
month = July
}