Hepatocellular carcinoma (HCC) is an inflammation-associated cancer arising from viral and non-viral etiologies. Expansion of suppressive myeloid cells is a hallmark of chronic inflammation and cancer, but their heterogeneity in HCC is not fully resolved and might underlie immunotherapy resistance in the steatohepatitis setting. Here, we present a high resolution atlas of hepatic innate immune cells from patients with HCC that unravels a steatohepatitis contexture characterized by influx of inflammatory and immunosuppressive myeloid cells. A discrete myeloid cell population identified by selective expression of TREM1 and CD163 expands in steatohepatitis-HCC. We refer to this population as TREM1+ regulatory myeloid cells (Mreg), as it potently suppresses T cell effector functions, highly expresses TGFB1 and IL13RA1 and localizes to HCC fibrotic lesions.
from sddb import Catalog
cohort = Catalog().collection("geo-gse245908")
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-gse245908")
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-gse245908 --dest data/Licenses: 2 NCBI GEO policy
@article{Giraud_2024,
title = {THBS1+ myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1},
volume = {43},
ISSN = {2211-1247},
url = {http://dx.doi.org/10.1016/j.celrep.2024.113773},
DOI = {10.1016/j.celrep.2024.113773},
number = {2},
journal = {Cell Reports},
publisher = {Elsevier BV},
author = {Giraud, Julie and Chalopin, Domitille and Ramel, Eloïse and Boyer, Thomas and Zouine, Atika and Derieppe, Marie-Alix and Larmonier, Nicolas and Adotevi, Olivier and Le Bail, Brigitte and Blanc, Jean-Frédéric and Laurent, Christophe and Chiche, Laurence and Derive, Marc and Nikolski, Macha and Saleh, Maya},
year = {2024},
month = Feb,
pages = {113773}
}