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~3.0 GB
Assay10x Xenium
Samplemouse · hair follicle
KindComparison
Flag a data issue
10.1172/JCI172595 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse278431")
cohort.members        # the 6 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-gse278431")
coll.ordered_artifacts.to_dataframe()   # the 6 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-gse278431 --dest data/

Licenses: 6 NCBI GEO policy

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 443 MB 24,144 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size443 MB
Cells24,144
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546224
mouse hair follicle injury 723 MB 32,760 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size723 MB
Cells32,760
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546225
mouse hair follicle injury 631 MB 30,901 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size631 MB
Cells30,901
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546228
mouse hair follicle injury 355 MB 16,368 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size355 MB
Cells16,368
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546226
mouse hair follicle injury 435 MB 18,612 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size435 MB
Cells18,612
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse hair follicle
GSM8546229
mouse hair follicle injury 411 MB 19,985 cells bronze NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuehair follicle
Conditioninjury
Size411 MB
Cells19,985
bronze NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1172/jci172595 ↗
BibTeX
@article{Kirby_2025,
  title = {RNase L represses hair follicle regeneration through altered innate immune signaling},
  volume = {135},
  ISSN = {1558-8238},
  url = {http://dx.doi.org/10.1172/jci172595},
  DOI = {10.1172/jci172595},
  number = {6},
  journal = {Journal of Clinical Investigation},
  publisher = {American Society for Clinical Investigation},
  author = {Kirby, Charles S. and Islam, Nasif and Wier, Eric and Alphonse, Martin P. and Sweren, Evan and Wang, Gaofeng and Liu, Haiyun and Kim, Dongwon and Li, Ang and Lee, Sam S. and Overmiller, Andrew M. and Xue, Yingchao and Reddy, Sashank and Archer, Nathan K. and Miller, Lloyd S. and Yu, Jianshi and Huang, Weiliang and Jones, Jace W. and Kim, Sooah and Kane, Maureen A. and Silverman, Robert H. and Garza, Luis A.},
  year = {2025},
  month = Feb
}