Collections / Single Cell Spatial Transcriptomics Redefines the Borderzone induced by Myocardial Infarction and Mechanical Injury

Single Cell Spatial Transcriptomics Redefines the Borderzone induced by Myocardial Infarction and Mechanical Injury

The ischemic borderzone (BZ) is a geographically complex and biologically enigmatic interface separating poorly perfused infarct zones (IZ) from comparatively healthy remote zones (RZ).  BZ cellular and molecular mechanisms are not well understood because efforts to dissect it inevitably include RZ and IZ in uncontrolled proportions. Here, we use single-cell/nuclei RNA-sequencing, spatial transcriptomics, and multiplexed RNA fluorescence in situ hybridization (mFISH) to identify BZ cardiomyocytes (CMs) subsets. BZ1 (Nppa+Xirp2­-) forms a hundreds-of-microns-thick transitional layer adjacent to RZ, while BZ2 (Nppa+Xirp2­+) forms a tens-of-microns-thick layer that the IZ edge. BZ2 CMs have reduced CM cell contact; colocalize with matricellular-protein-expressing myofibroblasts; and upregulate focal adhesion-, sarcomere-, and cytoskeletal-genes.  Surprisingly, the transcriptional BZ emerges within an hour of injury and is inducible by non-ischemic fine-needle-trauma. We suggest that mechanical instability and “loss of neighbor” at the BZ edge are the dominant inducers of the BZ transcriptional response.

Datasets14
Size~389 MB
AssayVisium
Samplemouse · heart
KindComparison
Flag a data issue
PMID:39086770 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse214611")
cohort.members        # the 14 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/")
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-gse214611")
coll.ordered_artifacts.to_dataframe()   # the 14 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse214611 --dest data/

Licenses: 14 NCBI GEO policy

Open in Vitessce
Visium
Mouse heart
GSM6613080
mouse heart 34.0 MB 3,540 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size34.0 MB
Spots3,540
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613081
mouse heart 28.3 MB 2,696 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size28.3 MB
Spots2,696
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613089
mouse heart myocardial infarction 54.5 MB 2,363 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size54.5 MB
Spots2,363
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613083
mouse heart myocardial infarction 21.0 MB 2,578 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size21.0 MB
Spots2,578
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613078
mouse heart 30.9 MB 3,057 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size30.9 MB
Spots3,057
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613087
mouse heart myocardial infarction 29.6 MB 2,325 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size29.6 MB
Spots2,325
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613090
mouse heart myocardial infarction 10.9 MB 1,551 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size10.9 MB
Spots1,551
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613086
mouse heart myocardial infarction 32.2 MB 2,438 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size32.2 MB
Spots2,438
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613084
mouse heart myocardial infarction 36.1 MB 2,251 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size36.1 MB
Spots2,251
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613088
mouse heart myocardial infarction 28.0 MB 2,428 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size28.0 MB
Spots2,428
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613079
mouse heart 23.7 MB 3,123 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size23.7 MB
Spots3,123
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613082
mouse heart myocardial infarction 24.9 MB 2,468 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size24.9 MB
Spots2,468
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613077
mouse heart 17.7 MB 1,917 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size17.7 MB
Spots1,917
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613085
mouse heart myocardial infarction 17.1 MB 2,461 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size17.1 MB
Spots2,461
silver H&E NCBI GEO policy Open in Vitessce

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