RNA-seq of WNT16-treated and Wild Type Human Limbal Epithelial Stem Cells
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ABSTRACT:
PROVIDER: PRJNA749250 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15224100_1.fastq.gz | Fastqsanger.gz | |||
| SRR15224100_2.fastq.gz | Fastqsanger.gz | |||
| SRR15224095_1.fastq.gz | Fastqsanger.gz | |||
| SRR15224095_2.fastq.gz | Fastqsanger.gz | |||
| SRR15224096_1.fastq.gz | Fastqsanger.gz |
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Project description:We first reported that WNT16 has the advanced effect on the proliferation and stemness maintenance of human limbal epithelial stem cells. To investigte the potential mechanism of WNT16 regulation, RNA-seq was used to analyze the differential expressed genes and relative cellular pathways between WNT16-treated and wild type human limbal epithelial stem cells.
2021-07-30 | GSE180698 | GEO
Project description:ABCB5 is marker for Limbal epithilal stem cells. A comparison between ABCB5+ versus ABCB5- cultured human limbal epithelial cells was carried out to evaluate the properties of the limbal stem cell ABCB5+ with a special focus on their role in inflammation and angiogenesis.
2023-10-24 | PXD041004 | Pride
Project description:Limbal epithelial stem cell (LESC) deficiency represents a significant clinical problem especially in bilateral cases. Induced pluripotent stem cells (iPSC) may be a promising source of LESC, allowing standardized and continual propagation and banking. The objective of this study was to generate iPSC from human limbal epithelial cultures and differentiate them back into limbal epithelial cells using substrata mimicking the natural LESC niche. Using Yamanaka’s episomal vectors limbal-derived iPSC were reprogrammed from LESC cultured from donor corneoscleral rims and from human skin fibroblasts. A clone from limbal-derived iPSC expressed stemness markers, had a diploid karyotype, and produced teratomas in nude mice representing three germ layers. Compared to parental LESC, this clone had fewer specific gene methylation changes revealed using the Illumina Infinium Methylation 450k Beadchips than compared to skin fibroblasts. The expression of putative LESC markers was examined by quantitative RT-PCR and immunostaining in limbal-derived and fibroblast-derived iPSC cultured on denuded human amniotic membrane or denuded cornea. Limbal-derived iPSC had markedly stronger expression of PAX6, ABCG2, Np63, keratins 14, 15, 17, and N-cadherin than fibroblast-derived iPSC. On denuded corneas, limbal-derived iPSC showed the expression of differentiated corneal keratins 3 and 12. The data suggest that iPSC differentiation to a desired lineage may be facilitated by their generation from the same tissue. This may be related to preservation of parental tissue epigenetic methylation signatures in iPSC and use of biological substrata similar to the natural niche of parental cells. The data pave the way for generating transplantable LESC from limbal-derived iPSC. Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2014-06-30 | E-GEOD-53918 | biostudies-arrayexpress
Project description:Limbal stem cells including epithelial and stromal/Mesenchymal stem cells that contribute to sustained corneal homeostasis, maintain their ability to act as self-renewal progenitor cells by virtue of their limbal niche and intercellular communication. Extracellular vehicles (EVs), including exosomes (Exos), are important paracrine mediators through their cargo transfer for intercellular communication in various stem cell niches. Previously we have shown the differential cargos and regulatory roles of limbal stromal cell (LSC)-derived Exos, in limbal epithelial cells (LEC) in normal (N) and diabetic (DM) limbal niche. In the present study, to have a comprehensive knowledge of reciprocal LEC-LSC crosstalk, we investigated the proteomics and miRNA profile of exosomes derived from LEC and their regulatory roles in LSC in N and DM limbus. Our study showed wound healing and proliferation rates in primary N-LSC were significantly enhanced upon treatment by normal LEC-derived Exos (N-Exos), but not by diabetic Exos (DM-Exos). Further, N-Exos treated LSC showed downregulation of keratocyte markers, ALDH3A1 and lumican, but not keratocan, and upregulation of MSC markers, CD105, CD90, and CD73 compared to the DM-Exos treated LSC. Using next generation sequencing (NGS) and proteomics analysis, we revealed some miRNAs and proteins in the Exos that affect the cellular crosstalk and the function of the cornea. We also documented differences in DM vs. normal LEC-derived Exo’s cargos. Overall, DM-Exos have less effect on LSC proliferation, wound healing, and stem cell maintenance than N-Exos, likely by transferring their cargo proteins and/or regulatory miRNAs targeting cell cycle, ERK/MAPK, TGF-β, EMT, PI3K-Akt-mTOR signaling molecules. This suggests that the small RNA and protein cargo differences in DM vs. N LEC-derived Exos could contribute to the disease state. Our study revealed a complex contribution of Exos to health and diabetic state of corneal homeostasis and suggests the potential of EV therapeutics for diabetic cornea regenerative medicine
2023-10-23 | PXD040918 | Pride
Project description:Compared to stem cells in other tissues, relatively little is known about the limbal niche, which is believed to play a pivotal role in regulating self-renewal and fate decision of limbal epithelial stem cells. Here we comprehensively investigated the human limbal niche with single-cell RNA sequencing. On analysis, all 47,627 cells located at human Limbus was classified into 14 clusters, and 8 types of cells were annotated. Specifically, we depicted the heterogeneity and hierarchy of limbal epithelial cells, and revealed a consecutive differentiation trajectory from limbal stem/progenitor cells by RNA velocity and pseudotime analyses. Besides, representative signaling pathway components and cell-cell communications engaged in limbal niche regulation were deciphered, suggesting a tightly regulation of the microenvironment around limbal stem/progenitor cells. Finally, comparative analysis revealed conservational and divergent transcriptional signals across species. Overall, this study provides an unbiased and systematic view of transcriptional organization of human Limbus, and dissected cell-contact-dependent regulations of limbal niche, providing foundations for investigating the cellular and molecular mechanisms, pathogenesis of related disease and potential interventions.
2021-06-14 | GSE157474 | GEO
Project description:Characterization of the Limbal Epithelial Stem Cell Niche
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Project description:Corneal epithelial stem cells reside in the limbus that is the transitional zone between the cornea and conjunctiva, and are essential to maintain the homeostasis of corneal epithelium. However, their characterization is poorly understood. Therefore, we constructed gene expression profiles of limbal epithelial SP and non-SP cell using RNA-sequencing. As a result, limbal epithelial SP cells have immature cell phenotypes with endothelial/mesenchymal cell markers, while limbal epithelial non-SP cells have epithelial progenitor cell markers.
2016-04-18 | GSE79620 | GEO
Project description:Limbal epithelial stem cell (LESC) deficiency represents a significant clinical problem especially in bilateral cases. Induced pluripotent stem cells (iPSC) may be a promising source of LESC, allowing standardized and continual propagation and banking. The objective of this study was to generate iPSC from human limbal epithelial cultures and differentiate them back into limbal epithelial cells using substrata mimicking the natural LESC niche. Using Yamanaka’s episomal vectors limbal-derived iPSC were reprogrammed from LESC cultured from donor corneoscleral rims and from human skin fibroblasts. A clone from limbal-derived iPSC expressed stemness markers, had a diploid karyotype, and produced teratomas in nude mice representing three germ layers. Compared to parental LESC, this clone had fewer specific gene methylation changes revealed using the Illumina Infinium Methylation 450k Beadchips than compared to skin fibroblasts. The expression of putative LESC markers was examined by quantitative RT-PCR and immunostaining in limbal-derived and fibroblast-derived iPSC cultured on denuded human amniotic membrane or denuded cornea. Limbal-derived iPSC had markedly stronger expression of PAX6, ABCG2, Np63, keratins 14, 15, 17, and N-cadherin than fibroblast-derived iPSC. On denuded corneas, limbal-derived iPSC showed the expression of differentiated corneal keratins 3 and 12. The data suggest that iPSC differentiation to a desired lineage may be facilitated by their generation from the same tissue. This may be related to preservation of parental tissue epigenetic methylation signatures in iPSC and use of biological substrata similar to the natural niche of parental cells. The data pave the way for generating transplantable LESC from limbal-derived iPSC.
2014-06-30 | GSE53918 | GEO
Project description:Limbal vs. corneal epithelial basal cell gene expression patterns were identified and compared Keywords: repeat
2006-01-27 | GSE4098 | GEO
Project description: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.
2020-09-24 | GSE158454 | GEO