Collections / Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]

Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma [Spatial Transcriptomics]

To functionally assess the role of pericytes in glioma development and progression, we study the effects of pericyte depletion in orthotopic and transgenic mouse models of high-grade glioma using single-cell and spatial transcriptomics. We present evidence that pericytes mitigate glioma development by orchestrating a tumor-suppressive microenvironment, challenging the concept of pericytes as merely pro-oncogenic cells, and underscoring the importance of pericyte preservation in future GBM therapies.

Datasets8
Size~334 MB
AssayVisium
Samplemouse · brain
KindComparison
Flag a data issue
PMID:41339360 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse272236")
cohort.members        # the 8 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/")
Install (Python 3.12+) Docs →
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="geo-gse272236")
coll.ordered_artifacts.to_dataframe()   # the 8 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse272236 --dest data/
Install (Python 3.12+) Docs →

Licenses: 8 NCBI GEO policy

Member datasets · 8
Open in Vitessce
Visium
Mouse brain
GSM8396159
mouse brain glioma 25.3 MB 1,462 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size25.3 MB
Spots1,462
Magnificationother · 3.577 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396166
mouse brain glioma 56.8 MB 2,887 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size56.8 MB
Spots2,887
Magnificationother · 3.583 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396161
mouse brain glioma 55.3 MB 2,723 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size55.3 MB
Spots2,723
Magnificationother · 3.581 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396160
mouse brain glioma 25.2 MB 1,398 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size25.2 MB
Spots1,398
Magnificationother · 3.595 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396163
mouse brain glioma 35.9 MB 2,301 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size35.9 MB
Spots2,301
Magnificationother · 3.581 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396162
mouse brain glioma 36.3 MB 1,921 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size36.3 MB
Spots1,921
Magnificationother · 3.575 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396165
mouse brain glioma 53.0 MB 2,725 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size53.0 MB
Spots2,725
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8396164
mouse brain glioma 45.7 MB 2,383 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size45.7 MB
Spots2,383
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s41467-025-66985-1 ↗
BibTeX 
@article{Braun_2025,
  title = {Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma},
  volume = {16},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-025-66985-1},
  DOI = {10.1038/s41467-025-66985-1},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Braun, Sebastian and Bolivar, Paulina and Oudenaarden, Clara and Sjölund, Jonas and Bocci, Matteo and Harbst, Katja and Talkhoncheh, Mehrnaz Safaee and Phung, Bengt and Cordero, Eugenia and Rosberg, Rebecca and Johansson, Elinn and Jönsson, Göran B. and Pietras, Alexander and Pietras, Kristian},
  year = {2025},
  month = Dec
}