Myocardial infarctions (MI) affect 805,000 people per year in the United States. To mitigate the pathological effects of MI, we have developed and investigated pro-reparative decellularized extracellular matrix (ECM) biomaterials: an intravascularly infusible ECM (iECM). However, no one has ever utilized single cell and spatially resolved transcriptomics to further probe how systemically administered infusible ECM can elicit pro-repair in an MI model. Thus, we utilize spatial transcriptomics and single nucleus RNA sequencing (snRNAseq) to further measure pro-repair in various cell types, and thus validate these findings with spectral flow cytometry.With iECM, we found pro-reparative macrophage activation, fibroblast remodeling, increased vasculature development, and cardioprotection. Thus, we depict the pro-reparative nature of decellularized ECM biomaterials on cardiac cell types and elucidate previously undiscovered therapeutic pathways, further demonstrating infusible ECM’s potential as an MI therapy.
from sddb import Catalog
cohort = Catalog().collection("geo-gse299772")
cohort.members # the 12 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-gse299772")
coll.ordered_artifacts.to_dataframe() # the 12 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-gse299772 --dest data/Licenses: 12 NCBI GEO policy
@article{Mesfin_2025,
title = {Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction},
url = {http://dx.doi.org/10.1101/2025.11.08.687255},
DOI = {10.1101/2025.11.08.687255},
publisher = {openRxiv},
author = {Mesfin, Joshua M. and Chen, Alexander and Lyons, Quincy P. and Nguyen, Michael B. and Karkanitsa, Maria L. and Yu, Justin and Ninh, Van K. and Gardner, Emily and Wong, Elyse G. and Paleti, Sriya N. and Cheng, Julian and Bridgelal, Benjamin D. and Reimold, Kate E. and Cao, Selena and Uhre, Connor and Luo, Colin G. and Fu, Zhenxing and King, Kevin R. and Christman, Karen L.},
year = {2025},
month = Nov
}