This dataset comprises spatial transcriptomic profiles from 10 tissue samples of Diffuse Large B-cell Lymphoma (DLBCL) the most common subtype of non-Hodgkin’s lymphoma and secondary lymphoid organ controls (SLO). The diffuse nature of DLBCL challenges the analysis of cellular organization within the immune tumor microenvironment (TME). We employed spatial transcriptomics to map spatially-resolved gene expression patterns. The analysis led to the identification of six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This resource offers valuable insights into the spatial complexity of the DLBCL microenvironment and its potential prognostic significance.
from sddb import Catalog
cohort = Catalog().collection("geo-gse276542")
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-gse276542")
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-gse276542 --dest data/Licenses: 9 NCBI GEO policy
@article{Diaz_Herrero_2026,
title = {Spatial transcriptomics unveils immune cellular ecosystems associated with patient survival in diffuse large B-cell lymphoma},
volume = {15},
ISSN = {2162-402X},
url = {http://dx.doi.org/10.1080/2162402x.2026.2660418},
DOI = {10.1080/2162402x.2026.2660418},
number = {1},
journal = {OncoImmunology},
publisher = {Informa UK Limited},
author = {Diaz-Herrero, Alba and Pelaez-Prestel, Héctor Fernando and Massenet-Regad, Lucile and Veyssiere, Maëva and Calvani, Julien and Cristinelli, Caterina and Lehmann-Che, Jacqueline and Meignin, Véronique and Thieblemont, Catherine and Blanc, Véronique and Soumelis, Vassili and Tonnerre, Pierre},
year = {2026},
month = Apr
}