Fibrotic colorectal cancers (CRC) are characterized by immune exclusion driven by activated stroma, particularly by cancer-associated fibroblasts (CAFs). This study aims to describe characteristics of spatial immune landscape of CRCs, which are subtyped by transcriptomic signatures and microsatellite instability.
from sddb import Catalog
cohort = Catalog().collection("geo-gse285505")
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-gse285505")
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-gse285505 --dest data/Licenses: 4 NCBI GEO policy
@article{Iwane_2025,
title = {Targeting fibroblast derived thrombospondin 2 disrupts an immune-exclusionary environment at the tumor front in colorectal cancer},
volume = {16},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-025-66485-2},
DOI = {10.1038/s41467-025-66485-2},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Iwane, Kosuke and Nakanishi, Yuki and Muta, Yu and Chen, Jiayu and Yasumura, Kento and Omatsu, Mayuki and Aoyama, Naoki and Ikeda, Munehiro and Masui, Yoko and Cai, Liyang and Yamakawa, Go and Hamada, Kensuke and Mizukoshi, Kenta and Kawai, Munenori and Iimori, Kei and Nakayama, Shinnosuke and Agatsuma, Nobukazu and Utsumi, Takahiro and Nagao, Munemasa and Maruno, Takahisa and Hiramatsu, Yukiko and Kakiuchi, Nobuyuki and Nakagawa, Masahiro M. and Fukui, Yasuhiro and Kusunoki, Yukina and Kasashima, Hiroaki and Fujimoto, Masakazu and Itatani, Yoshiro and Kogame, Toshiaki and Fukuda, Akihisa and Yashiro, Masakazu and Maeda, Kiyoshi and Kabashima, Kenji and Obama, Kazutaka and Ogawa, Seishi and Diaz-Meco, Maria T. and Moscat, Jorge and Seno, Hiroshi},
year = {2025},
month = Nov
}