Collections / Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation

Spatial transcriptomic profiling of human saphenous vein grafts reveals molecular remodeling and smooth muscle cell phenotypic transition during early neointima proliferation

Vein graft failure is driven by early neointima l proliferation involving vascular smooth muscle cell (VSMC) proliferation, inflammation, and extracellular matrix remodeling. To elucidate the spatial and transcriptional landscape of this process, we performed spatial transcriptomic profiling of ex vivo cultured human saphenous vein segments at baseline (Day 0) and after 7 days in organ culture. Integration of spatial gene expression with histological features revealed distinct zones of VSMC transdifferentiation, inflammatory activation, and extracellular matrix reorganization. This dataset provides a resource for investigating molecular mechanisms underlying early human vein graft adaptation and neointimal proliferation.

Datasets6
Size~37.5 MB
AssayVisium
Samplehuman · saphenous vein
KindTime course
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PMID:41569144 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse310351")
cohort.members        # the 6 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-gse310351")
coll.ordered_artifacts.to_dataframe()   # the 6 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-gse310351 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Human saphenous vein
GSM9294395
human saphenous vein 4.0 MB 4,965 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size4.0 MB
Spots4,965
Magnificationother · 3.183 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294393
human saphenous vein 9.5 MB 4,964 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size9.5 MB
Spots4,964
Magnificationother · 3.191 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294396
human saphenous vein 3.9 MB 4,990 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size3.9 MB
Spots4,990
Magnificationother · 3.831 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294397
human saphenous vein 4.1 MB 4,975 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size4.1 MB
Spots4,975
Magnificationother · 3.835 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294398
human saphenous vein 6.1 MB 4,941 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size6.1 MB
Spots4,941
Magnificationother · 3.916 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human saphenous vein
GSM9294394
human saphenous vein 9.9 MB 4,583 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuesaphenous vein
Size9.9 MB
Spots4,583
Magnificationother · 3.910 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1152/ajpheart.00653.2025 ↗
BibTeX 
@article{Kim_2026,
  title = {Comprehensive transcriptomics and proteomics analysis of neointima formation in human saphenous vein: implications for bypass graft disease},
  volume = {330},
  ISSN = {1522-1539},
  url = {http://dx.doi.org/10.1152/ajpheart.00653.2025},
  DOI = {10.1152/ajpheart.00653.2025},
  number = {2},
  journal = {American Journal of Physiology-Heart and Circulatory Physiology},
  publisher = {American Physiological Society},
  author = {Kim, David S. and Goo, Brandee and Shi, Hong and Dong, Shuilin and Weintraub, Daniel S. and Coffey, Philip and Veerapaneni, Praneet and Chouhaita, Ronnie and Guduru, Medha and Cyriac, Nicole and Aboud, Ghaith and Ong, Vy and Cave, Stephen and Greenway, Jacob and Mundkur, Rohan and Ahmadieh, Samah and Harb, Ragheb and Ogbi, Mourad and Fulton, David J. and Huo, Yuqing and Zhang, Wei and Long, Xiaochun and Guha, Avirup and Kim, Ha Won and Shi, Yang and Rice, Robert D. and Zhou, Jiang and Chiang, Austin W. T. and Gallo, Dominic R. and Patel, Vijay S. and Lee, Richard and Weintraub, Neal L.},
  year = {2026},
  month = Feb,
  pages = {H620–H641}
}