Osteosarcoma is the most common malignant bone tumor in children, characterized by a high degree of genomic instability, resulting in copy-number alterations and genomic rearrangements without disease-defining recurrent mutations. Clinical trials based on molecular characterization have failed to find new effective therapies or improve outcomes over the last 40 years. To better understand the immune microenvironment of osteosarcoma, we performed single-cell RNA sequencing on six tumor biopsy samples, combined with a previously-published cohort of six samples. Additional osteosarcoma samples were profiled using spatial transcriptomics for validation of discovered subtypes and to add spatial context. Analysis revealed immunosuppressive cells, including myeloid-derived suppressor cells (MDSCs), regulatory and exhausted T-cells, and LAMP3+ dendritic cells. Using cell-cell communication modeling, we identified robust interactions between MDSCs and other cells, leading to NF-κB upregulation and an immunosuppressive microenvironment, as well as interactions involving regulatory T-cells and osteosarcoma cells that promoted tumor progression and a proangiogenic niche.
from sddb import Catalog
cohort = Catalog().collection("geo-gse299025")
cohort.members # the 2 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-gse299025")
coll.ordered_artifacts.to_dataframe() # the 2 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-gse299025 --dest data/Licenses: 2 NCBI GEO policy
@article{Taylor_2025,
title = {Immunosuppressive Tumor Microenvironment of Osteosarcoma},
volume = {17},
ISSN = {2072-6694},
url = {http://dx.doi.org/10.3390/cancers17132117},
DOI = {10.3390/cancers17132117},
number = {13},
journal = {Cancers},
publisher = {MDPI AG},
author = {Taylor, Aaron Michael and Sheng, Jianting and Ng, Patrick Kwok Shing and Harder, Jeffrey M. and Kumar, Parveen and Ahn, Ju Young and Cao, Yuliang and Dzis, Alissa M. and Jillette, Nathaniel L. and Goodspeed, Andrew and Bodlak, Avery and Wu, Qian and Isakoff, Michael S. and George, Joshy and Grassmann, Jessica D. S. and Luo, Diane and Flynn, William F. and Courtois, Elise T. and Robson, Paul and Hayashi, Masanori and Paolillo, Alini Trujillo and Petrilli, Antonio Sergio and Caminada de Toledo, Silvia Regina and Balarezo, Fabiola Sara and Lindsay, Adam D. and Hoang, Bang and Wong, Stephen T. C. and Lau, Ching C.},
year = {2025},
month = June,
pages = {2117}
}