The identification of molecular characteristics that define metastatic disease is a primary research focus across numerous types of malignancies. Understanding the mechanisms that drive metastatic foci, which diverge significantly from the biology of primary tumors, and identifying new biomarkers specifically associated with metastatic disease, is of critical importance in oncology. Consequently, the characterization of the stroma associated with metastatic foci has been largely unexplored and remains an area requiring significant investigation. We identified a detailed transcriptional profile of the stromal compartment within primary tumors and corresponding metastatic foci using spatially resolved approaches. The identified stromal Met signature may serve as a prognostic biomarker and provide insights into the molecular mechanisms underlying the metastatic potential of the tumor microenvironment.
from sddb import Catalog
cohort = Catalog().collection("geo-gse273439")
cohort.members # the 4 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-gse273439")
coll.ordered_artifacts.to_dataframe() # the 4 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-gse273439 --dest data/Licenses: 4 NCBI GEO policy
@article{Bertolazzi_2025,
title = {Extraction of a stromal metastatic gene signature in breast cancer via spatial profiling},
volume = {44},
ISSN = {1756-9966},
url = {http://dx.doi.org/10.1186/s13046-025-03353-3},
DOI = {10.1186/s13046-025-03353-3},
number = {1},
journal = {Journal of Experimental & Clinical Cancer Research},
publisher = {Springer Science and Business Media LLC},
author = {Bertolazzi, Giorgio and Cancila, Valeria and Vacca, Davide and Belmonte, Beatrice and Lecis, Daniele and Moghaddam, Parsa Sirati and Di Napoli, Arianna and Colombo, Mario Paolo and Pruneri, Giancarlo and Del Sal, Giannino and Scita, Giorgio and Fassan, Matteo and Vecchione, Andrea and Bicciato, Silvio and Tripodo, Claudio},
year = {2025},
month = Mar
}