HCA Data Explorer

Single cell transcriptomics of human epidermis identifies basal stem cell transition states.

Updated October 1, 2022

How stem cells give rise to epidermis is unclear despite the crucial role the epidermis plays in barrier and appendage formation. Here we use single cell-RNA sequencing to interrogate basal stem cell heterogeneity of human interfollicular epidermis and find four spatially distinct stem cell populations at the top and bottom of rete ridges and transitional positions between the basal and suprabasal epidermal layers. Cell-cell communication modeling suggests that basal cell populations serve as crucial signaling hubs to maintain epidermal communication. Combining pseudotime, RNA velocity, and cellular entropy analyses point to a hierarchical differentiation lineage supporting multi-stem cell interfollicular epidermal homeostasis models and suggest that transitional basal stem cells are stable states essential for proper stratification. Finally, alterations in differentially expressed transitional basal stem cell genes result in severe thinning of human skin equivalents, validating their essential role in epidermal homeostasis and reinforcing the critical nature of basal stem cell heterogeneity.

Qing NieDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.qnie@uci.edu
Scott X AtwoodDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.satwood@uci.edu
Shuxiong Wang1
Michael L Drummond1
Christian F Guerrero-Juarez1
Eric Tarapore1
Adam L MacLean2
Adam R Stabell1
Stephanie C Wu1
Guadalupe Gutierrez1
Bao T That1
Claudia A Benavente1
Qing Nie1
Scott X Atwood1
1Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.
2Department of Mathematics, University of California, Irvine, Irvine, CA, 92697, USA.
Ami Day

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/66d7d92a-d6c5-492c-815b-f81c7c93c984

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1.https://github.com/WangShuxiong/Human_Epi
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Analysis Portals

None

Project Label

HumanNeonatalForeskin

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

skin of body

Organ Part

skin of prepuce of penis

Selected Cell Types

Unspecified

Disease Status (Specimen)

normal

Disease Status (Donor)

normal

Development Stage

infant stage

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End

false

Analysis Protocol

analysis_protocol

File Format

4 file formats

Cell Count Estimate

17.6k

Donor Count

5
fastq.gz14 file(s)mtx.gz5 file(s)tsv.gz10 file(s)xlsx1 file(s)