Collections / Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [Visium]

Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction [Visium]

Fibrosis is important pathogenesis in heart failure with preserved ejection fraction (HFpEF). We previously reported that the overexpression of cardiac transcription factors, Mef2c/Gata4/Tbx5/Hand2 (MGTH) could directly reprogram cardiac fibroblasts (CFs) into induced CMs (iCMs) and reduce fibrosis. Here we show that in vivo cardiac reprogramming generated iCMs from resident CFs, improved cardiac function, and reversed fibrosis in HFpEF model using a novel transgenic mouse system. Visium revealed spatial information on changes in gene expression in HFpEF.

Datasets3
Size~88.0 MB
AssayVisium
Samplemouse · heart
KindComparison
Flag a data issue
PMID:39673349 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse218759")
cohort.members        # the 3 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/")
Install (Python 3.12+) Docs →
Python · lamindb

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-gse218759")
coll.ordered_artifacts.to_dataframe()   # the 3 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse218759 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Visium
Mouse heart
GSM6756178
mouse heart 27.1 MB 1,935 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size27.1 MB
Spots1,935
Magnificationother · 3.619 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6756180
mouse heart diastolic heart failure 37.7 MB 2,994 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditiondiastolic heart failure
Size37.7 MB
Spots2,994
Magnificationother · 3.617 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6756179
mouse heart diastolic heart failure 23.2 MB 2,157 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditiondiastolic heart failure
Size23.2 MB
Spots2,157
Magnificationother · 3.618 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1161/circulationaha.123.067504 ↗
BibTeX 
@article{Yamada_2025,
  title = {Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction},
  volume = {151},
  ISSN = {1524-4539},
  url = {http://dx.doi.org/10.1161/circulationaha.123.067504},
  DOI = {10.1161/circulationaha.123.067504},
  number = {6},
  journal = {Circulation},
  publisher = {Ovid Technologies (Wolters Kluwer Health)},
  author = {Yamada, Yu and Sadahiro, Taketaro and Nakano, Koji and Honda, Seiichiro and Abe, Yuto and Akiyama, Tatsuya and Fujita, Ryo and Nakamura, Masashi and Maeda, Takashi and Kuze, Yuta and Onishi, Masaya and Seki, Masahide and Suzuki, Yutaka and Takeuchi, Chikara and Iwasaki, Yuka W. and Murano, Kensaku and Sakata-Yanagimoto, Mamiko and Chiba, Shigeru and Kato, Hideyuki and Sakamoto, Hiroaki and Hiramatsu, Yuji and Ieda, Masaki},
  year = {2025},
  month = Feb,
  pages = {379–395}
}