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~371 MB
AssayVisium
Samplemouse · heart
KindComparison
PMID:39086770 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse214611")
coll.ordered_artifacts.df()                 # the 14 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Open in Vitessce
Visium
Mouse heart
GSM6613080
mouse heart 32 MB 3,540 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size32 MB
Obs3,540
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613081
mouse heart 27 MB 2,696 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size27 MB
Obs2,696
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613089
mouse heart myocardial infarction 52 MB 2,363 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size52 MB
Obs2,363
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613083
mouse heart myocardial infarction 20 MB 2,578 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size20 MB
Obs2,578
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613078
mouse heart 29 MB 3,057 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size29 MB
Obs3,057
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613087
mouse heart myocardial infarction 28 MB 2,325 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size28 MB
Obs2,325
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613090
mouse heart myocardial infarction 10 MB 1,551 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size10 MB
Obs1,551
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613086
mouse heart myocardial infarction 31 MB 2,438 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size31 MB
Obs2,438
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613084
mouse heart myocardial infarction 34 MB 2,251 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size34 MB
Obs2,251
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613088
mouse heart myocardial infarction 27 MB 2,428 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size27 MB
Obs2,428
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613079
mouse heart 23 MB 3,123 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size23 MB
Obs3,123
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613082
mouse heart myocardial infarction 24 MB 2,468 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size24 MB
Obs2,468
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613077
mouse heart 17 MB 1,917 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Size17 MB
Obs1,917
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM6613085
mouse heart myocardial infarction 16 MB 2,461 obs silver H&E
TechnologyVisium
Organismmouse
Tissueheart
Conditionmyocardial infarction
Size16 MB
Obs2,461
silver H&E Open in Vitessce

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