Leptomeningeal disease (LMD) remains a rapidly lethal complication for late-stage melanoma patients. The inaccessible nature of the disease site and lack of understanding of the biology of this unique metastatic site are major barriers to developing efficacious therapies for patients with melanoma LMD. This study aims to characterize the tumor microenvironment of the leptomeningeal tissues and patient-matched extra-cranial metastatic sites using spatial transcriptomic analyses.
from sddb import Catalog
cohort = Catalog().collection("geo-gse250636")
cohort.members # the 9 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-gse250636")
coll.ordered_artifacts.to_dataframe() # the 9 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-gse250636 --dest data/Licenses: 9 NCBI GEO policy
@article{Alhaddad_2024,
title = {Spatial transcriptomics analysis identifies a tumor-promoting function of the meningeal stroma in melanoma leptomeningeal disease},
volume = {5},
ISSN = {2666-3791},
url = {http://dx.doi.org/10.1016/j.xcrm.2024.101606},
DOI = {10.1016/j.xcrm.2024.101606},
number = {6},
journal = {Cell Reports Medicine},
publisher = {Elsevier BV},
author = {Alhaddad, Hasan and Ospina, Oscar E. and Khaled, Mariam Lotfy and Ren, Yuan and Vallebuona, Ethan and Boozo, Mohammad Baraa and Forsyth, Peter A. and Pina, Yolanda and Macaulay, Robert and Law, Vincent and Tsai, Kenneth Y. and Cress, W. Douglas and Fridley, Brooke and Smalley, Inna},
year = {2024},
month = June,
pages = {101606}
}