Cellular plasticity is a hallmark of rare Claudin-low (CL) and metaplastic (MBC) breast cancer subtypes, with a documented overlap whose exact extent is yet unknown, and which are associated to resistance and poor survival. We used spatial transcriptomics to further characterise these plastic subtypes, respectively defined molecularly and histopathologically. We identified 3 putative CL tumours (CL-like) and 4 genomically unstable TNBC samples via molecular analyses, combined with 4 MBCs identified by a breast pathologist. High resolution images are available on Zenodo https://zenodo.org/records/20727406
from sddb import Catalog
cohort = Catalog().collection("geo-gse213688")
cohort.members # the 14 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-gse213688")
coll.ordered_artifacts.to_dataframe() # the 14 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-gse213688 --dest data/Licenses: 14 NCBI GEO policy
@article{Coutant_2023,
title = {Spatial Transcriptomics Reveal Pitfalls and Opportunities for the Detection of Rare High-Plasticity Breast Cancer Subtypes},
volume = {103},
ISSN = {0023-6837},
url = {http://dx.doi.org/10.1016/j.labinv.2023.100258},
DOI = {10.1016/j.labinv.2023.100258},
number = {12},
journal = {Laboratory Investigation},
publisher = {Elsevier BV},
author = {Coutant, Angèle and Cockenpot, Vincent and Muller, Lauriane and Degletagne, Cyril and Pommier, Roxane and Tonon, Laurie and Ardin, Maude and Michallet, Marie-Cécile and Caux, Christophe and Laurent, Marie and Morel, Anne-Pierre and Saintigny, Pierre and Puisieux, Alain and Ouzounova, Maria and Martinez, Pierre},
year = {2023},
month = Dec,
pages = {100258}
}