Non-Hodgkin Lymphoma (NHL) is the main cancer-related mortality for people living with HIV (PLWH), who have elevated risk for lymphoma relative to the general population. NHL genetic and molecular classifications have been intensely studied and correlated with clinical outcomes, but critical unanswered questions relevant to malignancy persist. For example, tumors positive for Epstein-Barr virus (EBV) account for 30-50% of HIV-associated NHLs, are particularly aggressive, and have poorer clinical outcomes – yet insights on the nature of EBV in NHL pathogenesis or potential therapeutic vulnerabilities have been limited. Here, we examined HIV-associated NHLs stratified by cell of origin (COO), molecular subtype, and EBV status using genome-wide spatial transcriptomic analyses.
from sddb import Catalog
cohort = Catalog().collection("geo-gse274051")
cohort.members # the 10 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-gse274051")
coll.ordered_artifacts.to_dataframe() # the 10 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-gse274051 --dest data/Licenses: 10 NCBI GEO policy
@article{Chadburn_2025,
title = {HIV-associated non-Hodgkin lymphoma tumor-microenvironment axes differ by EBV status across cellular origins},
url = {http://dx.doi.org/10.1101/2025.10.15.682084},
DOI = {10.1101/2025.10.15.682084},
publisher = {openRxiv},
author = {Chadburn, Amy and Aguilar Hernandez, Maria Montserrat and Dai, Joanne and Harrison, Mitra and Reinoso-Vizcaino, Nicolas M. and Barry, Ashley P. and Hocke, Emily and Abramson, Karen and Jain, Vaibhav and Chan, Cliburn and Cesarman, Ethel and Luftig, Micah A. and SoRelle, Elliott D.},
year = {2025},
month = Oct
}