Previous studies have highlighted the capacity of brain cancer cells to functionally interact with the tumor microenvironment (TME). This TME-cancer crosstalk crucially contributes to tumor cell invasion and disease progression. In this study, we performed spatial transcriptomic sequencing analysis of a complete annotated DIPG tumor-infiltrated patient brainstem. We identified four distinct tumor subpopulations and assessed respective ligand-receptor pairs that actively promote DIPG tumor progression via crosstalk with endothelial, neuronal and immune cell communities. These interactions might promote DIPG tumor progression and represent novel therapeutic targets.
from sddb import Catalog
cohort = Catalog().collection("geo-gse280990")
cohort.members # the 10 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/")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-gse280990")
coll.ordered_artifacts.to_dataframe() # the 10 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse280990 --dest data/Licenses: 10 NCBI GEO policy
@article{Kordowski_2025,
title = {Spatial analysis of a complete DIPG-infiltrated brainstem reveals novel ligand-receptor mediators of tumour-to-TME crosstalk},
volume = {13},
ISSN = {2051-5960},
url = {http://dx.doi.org/10.1186/s40478-025-01952-x},
DOI = {10.1186/s40478-025-01952-x},
number = {1},
journal = {Acta Neuropathologica Communications},
publisher = {Springer Science and Business Media LLC},
author = {Kordowski, Anja and Mulay, Onkar and Tan, Xiao and Vo, Tuan and Baumgartner, Ulrich and Maybury, Mellissa K. and Hassall, Timothy and Harris, Lachlan and Nguyen, Quan and Day, Bryan W.},
year = {2025},
month = Feb
}