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.
from sddb import Catalog
cohort = Catalog().collection("geo-gse322883")
cohort.members # the 4 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/") 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-gse322883")
coll.ordered_artifacts.to_dataframe() # the 4 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] # sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse322883 --dest data/ Licenses: 4 NCBI GEO policy
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