Collections / Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps

Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps

Diagnostic protocols in endodontics rely heavily on subjective pain assessments and sensibility testing, which often fail to reflect the true histopathological and molecular state of the pulp. This limitation can result in misdiagnosis of reversible pulpitis as irreversible, leading to unnecessary devitalization of teeth that might otherwise respond to vital pulp therapy (VPT). Improved understanding of pulp biology is essential to refine case selection and enhance VPT outcomes. We aim to investigate the transcriptomic profiles of pulpitis, identify inflammation subtypes, and improve classification beyond the traditional reversible/irreversible framework. Methods: Spatial transcriptomics (Visium-CytAssist-V2) was used to analyze four dental pulp tissues. Cell deconvolution and differential gene expression analyses were performed to characterize transcriptomic signatures of healthy pulp (HL), reversible pulpitis (RP), and irreversible pulpitis (IP), with specific attention to coronal regions adjacent to carious lesions.

Datasets4
Size~94 MB
AssayVisium
Samplehuman · dental pulp
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE322883 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse322883")
coll.ordered_artifacts.df()                 # the 4 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
Human dental pulp
GSM9560414
human dental pulp pulpitis 25 MB 1,170 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuedental pulp
Conditionpulpitis
Size25 MB
Obs1,170
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human dental pulp
GSM9560412
human dental pulp pulpitis 24 MB 1,496 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuedental pulp
Conditionpulpitis
Size24 MB
Obs1,496
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human dental pulp
GSM9560413
human dental pulp pulpitis 22 MB 1,091 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuedental pulp
Conditionpulpitis
Size22 MB
Obs1,091
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human dental pulp
GSM9560411
human dental pulp 23 MB 759 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuedental pulp
Size23 MB
Obs759
silver H&E NCBI GEO policy Open in Vitessce

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