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Single-cell RNA transcriptome helps define the limbal/corneal epithelial stem/early transit amplifying cells and how autophagy affects this population in cornea

ABSTRACT: Purpose: Single-cell RNA-sequencing (scRNA-seq) was used to interrogate the relatively rare stem (SC) and early transit amplifying (TA) cell populations in limbal/corneal epithelia from wild-type and autophagy-compromised mice. Results: Unbiased clustering detected 10 distinct populations: three clusters of mesenchymal and seven clusters of epithelial cells, based on their unique molecular signatures. A discrete group of mesenchymal cells expressed genes associated with corneal stromal SCs. We identified three limbal/corneal epithelial cell subpopulations designated as stem/early TA, mature TA, and differentiated corneal epithelial cells. Thioredoxin-interacting protein and PDZ-binding kinase (PBK) were identified as novel regulators of stem/early TA cell quiescence. PBK arrested corneal epithelial cells in G2/M phase of the cell cycle. Beclin1+/− mice displayed a decrease in proliferation-associated (Ki67, Lrig1) and stress-response (H2ax) genes. The most increased gene in beclin1+/− mice was transcription factor ATF3, which negatively regulates limbal epithelial cell proliferation. Conclusions: Establishment of a comprehensive atlas of genes expressed by stromal and epithelial cells from limbus and cornea forms the foundation for unraveling regulatory networks among these distinct tissues. Similarly, scRNA-seq profiling of the anterior segmental epithelia from wild-type and autophagy-deficient mice provides new insights into how autophagy influences proliferation in these tissues.

ORGANISM(S): Mus musculus

PROVIDER: GSE158454 | GEO | 2020/09/24

REPOSITORIES: GEO

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Project description:For decades, it has been well accepted that corneal epithelial stem cells and their immediate progeny, the early transit amplifying (eTA) cells, reside in the limbal epithelial basal layer. Activation of quiescent stem/eTA cells is required for proper re-epithelialization during wound healing. The molecular profile of activated stem/eTA cells remains unclear because of difficulties in obtaining discrete cell populations for analyses. Single cell RNA sequencing (scRNA-seq) technology can profile the transcriptome at a single cell level, providing information on how stem/eTA cell activation is regulated. Using this technology, we report that ACE2, a key component in the renin-angiotensin system (RAS), functions as a negative regulator of stem/eTA activation. Methods: Mouse corneal epithelium was exposed to 1M NaOH for 30s or mechanically removed with a diamond burr. Corneas were processed for scRNA-seq and data was analyzed using R with a Seurat package. Limbal epithelial cell proliferation was assessed using BrdU incorporation. RT-qPCR, western blotting and immunostaining were conducted to determine the change of gene expression. Results: ACE2 was predominantly expressed in the stem cell-enriched limbal basal epithelium. scRNA-seq combined with GO analysis suggested that ACE2 was involved in limbal stem/eTA cell proliferation. Interestingly, immunostaining and RT-qPCR indicated that ACE2 expression was reduced following corneal injuries. Reduction in ACE2 promoted proliferation in human limbal epithelial cell culture as well as in mouse limbal epithelium after corneal epithelial debridement. Significantly, the negative effect of ACE2 on proliferation was not reversed following treatment with the angiotensin II receptor blocker losartan, indicating that the function of ACE2 in limbal epithelium is independent of RAS. scRNA-seq also revealed that reduction of ACE2 caused activation of the TGFA/EGFR pathway, which reduced expression of Lcn2. Lcn2 is a negative regulator of proliferation in a variety of cells. Inhibition of EGFR or overexpression of Lcn2 reversed the increased proliferation in limbal epithelial cells lacking ACE2. Conclusion: Our findings strongly support the idea that in response to corneal injury, ACE2 is downregulated, which results in the activation of stem/eTA cell proliferation via a novel TGFA/EGFR/Lcn2 signaling pathway in an angiotensin-independent way.

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Single-cell RNA transcriptome helps define the limbal/corneal epithelial stem/early transit amplifying cells and how autophagy affects this population in cornea

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