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~1.5 GB
AssayVisium
Samplehuman · kidney
KindComparison
10.1038/s41467-023-38975-8 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1038/s41467-023-38975-8")
coll.ordered_artifacts.df()                 # the 7 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
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
Open in Vitessce
Visium
Human kidney
NCBI566
human kidney nephrolithiasis 195 MB 939 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size195 MB
Obs939
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI568
human kidney 231 MB 2,438 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Size231 MB
Obs2,438
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI565
human kidney nephrolithiasis 200 MB 1,085 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size200 MB
Obs1,085
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI567
human kidney nephrolithiasis 201 MB 817 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size201 MB
Obs817
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI564
human kidney nephrolithiasis 200 MB 262 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size200 MB
Obs262
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI563
human kidney nephrolithiasis 235 MB 1,376 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size235 MB
Obs1,376
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human kidney
NCBI562
human kidney nephrolithiasis 244 MB 2,468 obs silver H&E
TechnologyVisium
Organismhuman
Tissuekidney
Conditionnephrolithiasis
Size244 MB
Obs2,468
silver H&E Open in Vitessce

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
}