from sddb import Catalog
cohort = Catalog().collection("doi-10-1038-s41467-022-34581-2")
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="doi-10.1038/s41467-022-34581-2")
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 doi-10-1038-s41467-022-34581-2 --dest data/Licenses: 4 CC BY-NC-SA 4.0
The microenvironment of lymph node metastasized tumors (LNMT) determines tumor progression and response to therapy, but a systematic study of LNMT is lacking. Here, we generate single-cell maps of primary tumors (PTs) and paired LNMTs in 8 breast cancer patients. We demonstrate that the activation, cytotoxicity, and proliferation of T cells are suppressed in LNMT compared with PT. CD4<sup>+</sup>CXCL13<sup>+</sup> T cells in LNMT are more likely to differentiate into an exhausted state. Interestingly, LAMP3<sup>+</sup> dendritic cells in LNMT display lower T cell priming and activating ability than in PT. Additionally, we identify a subtype of PLA2G2A<sup>+</sup> cancer-associated fibroblasts enriched in HER2<sup>+</sup> breast cancer patients that promotes immune infiltration. We also show that the antigen-presentation pathway is downregulated in malignant cells of the metastatic lymph node. Altogether, we characterize the microenvironment of LNMT and PT, which may shed light on the individualized therapeutic strategies for breast cancer patients with lymph node metastasis.
@article{Liu_2022,
title = {Single cell profiling of primary and paired metastatic lymph node tumors in breast cancer patients},
volume = {13},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-022-34581-2},
DOI = {10.1038/s41467-022-34581-2},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Liu, Tong and Liu, Cheng and Yan, Meisi and Zhang, Lei and Zhang, Jing and Xiao, Min and Li, Zhigao and Wei, Xiaofan and Zhang, Hongquan},
year = {2022},
month = Nov
}