from sddb import Catalog
cohort = Catalog().collection("geo-gse304669")
cohort.members # the 1 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-gse304669")
coll.ordered_artifacts.to_dataframe() # the 1 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-gse304669 --dest data/Licenses: 1 NCBI GEO policy
<h4>Introduction</h4>Kidney transplant rejections are classified as active antibody mediated rejection (AMR) and cell mediated rejection (TCMR), with AMR primarily driven by antibodies produced by B cells, whereas TCMR is mediated by T lymphocytes that orchestrate cellular immune responses against the graft. Emerging evidence highlights the essential roles of innate immune cells in rejections, especially monocytes/macrophages and natural killer (NK) cells. However, the roles of specific innate immune cell subpopulations in kidney allograft rejection remain incompletely understood.<h4>Methods</h4>We performed the spatial transcriptomics using the formalin-fixed paraffin-embedded (FFPE) core needle biopsies from human kidney allografts.<h4>Results</h4>We demonstrated that non-rejection, AMR, acute TCMR and chronic active AMR have distinct transcriptomic features. Subclusters of monocytes/macrophages with high <i>Fc gamma receptor IIIA</i> (<i>FCGR3A</i>) expression were identified in C4d-positive active AMR and acute TCMR, and the spatial distribution of these cells corresponded to the characteristic histopathological features. Key markers related to monocyte/macrophage activation and innate alloantigen recognition were upregulated, along with metabolic pathways associated with trained immunity in AMR and TCMR.<h4>Discussion</h4>Taking together, these findings revealed that intragraft monocytes/macrophages with high <i>FCGR3A</i> expression play a critical role in kidney transplant rejections.
@article{Chen_Wongworawat_2025,
title = {Spatial transcriptomics reveals distinct role of monocytes/macrophages with high FCGR3A expression in kidney transplant rejections},
volume = {16},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2025.1654741},
DOI = {10.3389/fimmu.2025.1654741},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Chen Wongworawat, Yan and Nepal, Chirag and Duhon, Mark and Chen, Wanqiu and Nguyen, Minh-Tri and Godzik, Adam and Qiu, Xinru and Li, Wei Vivian and Yu, Gary and Villicana, Rafael and Zuppan, Craig and De Vera, Michael and Eadon, Michael T. and Haas, Mark and Wang, Charles},
year = {2025},
month = Sept
}