Collections / In situ targeted gene expression analysis of healing skin on SD0 post-wounding in Wildtype and Rnasel knock out wounds

In situ targeted gene expression analysis of healing skin on SD0 post-wounding in Wildtype and Rnasel knock out wounds

We generated a spatial transcriptomics dataset of wildtype (C57BL/6, n = 3)and Rnasel knockout (Rnaseltm1Slvm, n =3) mice at scab detachment day 0, to investigate specific type of cell populations and their gene expressions.

Datasets6
Size~2.8 GB
Assay10x Xenium
Samplemouse · hair follicle
KindComparison
10.1172/JCI172595 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse278431")
coll.ordered_artifacts.df()                 # the 6 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()}

RNase L represses hair follicle regeneration through altered innate immune signaling.

Mammalian injury responses are predominantly characterized by fibrosis and scarring rather than functional regeneration. This limited regenerative capacity in mammals could reflect a loss of proregeneration programs or active suppression by genes functioning akin to tumor suppressors. To uncover programs governing regeneration in mammals, we screened transcripts in human participants following laser rejuvenation treatment and compared them with mice with enhanced wound-induced hair neogenesis (WIHN), a rare example of mammalian organogenesis. We found that Rnasel-/- mice exhibit an increased regenerative capacity, with elevated WIHN through enhanced IL-36α. Consistent with RNase L's known role to stimulate caspase-1, we found that pharmacologic inhibition of caspases promoted regeneration in an IL-36-dependent manner in multiple epithelial tissues. We identified a negative feedback loop, where RNase L-activated caspase-1 restrains the proregenerative dsRNA-TLR3 signaling cascade through the cleavage of toll-like adaptor protein TRIF. Through integrated single-cell RNA-seq and spatial transcriptomic profiling, we confirmed OAS & IL-36 genes to be highly expressed at the site of wounding and elevated in Rnasel-/- mouse wounds. This work suggests that RNase L functions as a regeneration repressor gene, in a functional trade off that tempers immune hyperactivation during viral infection at the cost of inhibiting regeneration.

Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546227
mouse hair follicle injury 422 MB 24,144 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size422 MB
Obs24,144
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546224
mouse hair follicle injury 689 MB 32,760 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size689 MB
Obs32,760
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546225
mouse hair follicle injury 602 MB 30,901 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size602 MB
Obs30,901
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546228
mouse hair follicle injury 338 MB 16,368 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size338 MB
Obs16,368
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546226
mouse hair follicle injury 415 MB 18,612 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size415 MB
Obs18,612
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546229
mouse hair follicle injury 392 MB 19,985 obs bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size392 MB
Obs19,985
bronze NCBI GEO policy Open in Vitessce

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