Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes [RNA-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA649536 | ENA |
REPOSITORIES: ENA
Dataset's files
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| SRR12344580.fastq.gz | Fastqsanger.gz | |||
| SRR12344581.fastq.gz | Fastqsanger.gz | |||
| SRR12344582.fastq.gz | Fastqsanger.gz | |||
| SRR12344583.fastq.gz | Fastqsanger.gz | |||
| SRR12344584.fastq.gz | Fastqsanger.gz |
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Project description:Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes
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Project description:Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes [DNA-Seq]
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Project description:Senescent cells are one source of the chronic inflammation that contributes to the diseases and debilities of aging. Whereas cellular senescence in fibroblasts is well documented, how this process is orchestrated in epithelial cells, the origin of human carcinomas, is much less understood. We used normal primary human oral keratinocytes (NOKs) to elucidate senescence programs in a prototype mucosal epithelial cell that undergoes senescence spontaneously. We employed widely-accepted assays to characterize senescence phenotypes in these cells and found that p21WAF1/CIP1 is not a reliable marker of senescence for NOKs, as it is for fibroblasts. We performed transcriptome analysis by RNA-seq and proteomic analysis of secreted proteins, both non-vesicular and those associated with extracellular vesicles (EVs). NOKs, while sharing with fibroblasts certain important aspects of inflammation, such as upregulation of the NF-κB, interferon, and p38MAPK pathways, also exhibit novel senescence associated characteristics. In two of the donors, we observed an expected repression of DNA repair genes, correlating with downregulation of E2F1 mRNA and protein, but saw a divergent result for the third donor. We were able to highlight potential senolytic targets. Our secretome analysis led us to propose additions to the senescence associated secretory phenotype, including HSP60, which we found on the surface of EVs. Moreover, EVs from senescent NOKs can create inflammation by stimulating interferon pathway signaling in THP-1 monocytes in culture. Our results highlight important senescence changes in epithelial cells in terms of how these cells contribute to chronic inflammation, aging, and age-related diseases.
2023-07-19 | GSE164780 | GEO
Project description:Senescent cells are one source of the chronic inflammation that contributes to the diseases and debilities of aging. Whereas cellular senescence in fibroblasts is well documented, how this process is orchestrated in epithelial cells, the origin of human carcinomas, is much less understood. We used normal primary human oral keratinocytes (NOKs) to elucidate senescence programs in a prototype mucosal epithelial cell that undergoes senescence spontaneously. We employed widely-accepted assays to characterize senescence phenotypes in these cells and found that p21WAF1/CIP1 is not a reliable marker of senescence for NOKs, as it is for fibroblasts. We performed transcriptome analysis by RNA-seq and proteomic analysis of secreted proteins, both non-vesicular and those associated with extracellular vesicles (EVs). NOKs, while sharing with fibroblasts certain important aspects of inflammation, such as upregulation of the NF-κB, interferon, and p38MAPK pathways, also exhibit novel senescence associated characteristics. In two of the donors, we observed an expected repression of DNA repair genes, correlating with downregulation of E2F1 mRNA and protein, but saw a divergent result for the third donor. We were able to highlight potential senolytic targets. Our secretome analysis led us to propose additions to the senescence associated secretory phenotype, including HSP60, which we found on the surface of EVs. Moreover, EVs from senescent NOKs can create inflammation by stimulating interferon pathway signaling in THP-1 monocytes in culture. Our results highlight important senescence changes in epithelial cells in terms of how these cells contribute to chronic inflammation, aging, and age-related diseases.
2021-03-18 | GSE155371 | GEO
Project description:Compared to skin wounds, oral mucosal wounds heal more rapidly with less inflammation, faster re-epithelialization, and minimal scarring. One cell type that may be a differentiating factor is keratinocytes. Using immortalized skin and oral keratinocytes, HaCaT and TIGK, respectively, we found that oral keratinocytes have an enhanced migratory and proliferative capacity. To examine the transcriptomic differences that underlie the improved healing abilities of oral keratinocytes, we generated an RNA-sequencing (RNA-seq) gene expression dataset utilizing HaCaT and TIGK. Differentially expressed genes (DEGs) were identified between HaCaT and TIGK at baseline and throughout the injury response. Gene Ontology (GO) or Reactome enrichment analysis was performed to understand the biological significance of DEGs. Processes related to inflammation and migration were uniquely enriched in TIGK. Additionally, TIGK retained its enhanced migratory capacity when grown on various basement membrane (BM) and extracellular matrix (ECM) substrates. This may be due to the differential expression of matrix metalloproteinases (MMPs) and integrins between HaCaT and TIGK. We also identified genes differentially over or under-expressed in HaCaT and TIGK following injury when compared to each respective cell type’s unwounded gene expression levels. Lastly, we showed that the post-injury secretome of TIGK promotes keratinocyte migration. Our comparative analyses suggest specific transcriptomic differences between oral and skin keratinocytes at unwounded baseline and in response to injury may underlie the distinct wound healing phenotypes seen in these two tissues. This work also provides a source of HaCaT and TIGK gene expression data over healing that can be used for future analyses.
2025-04-04 | GSE270877 | GEO
Project description:NAD+ metabolism governs proinflammatory senescence secretome
| PRJNA438344 | ENA
Project description:Senescent cells produce chronic inflammation that contributes to the diseases and debilities of aging. How this process is orchestrated in epithelial cells, the origin of human carcinomas, is poorly understood. We used human normal oral keratinocytes (NOKs) to elucidate senescence programs in a prototype primary mucosal epithelial cell that senesces spontaneously. While NOKs exhibit several typical facets of senescence, they also display distinct characteristics. These include expression of p21WAF1/CIP1 at early passages, making this common marker of senescence unreliable in NOKs. Transcriptome analysis by RNA-seq revealed specific commonalities with and differences from cancer cells, explicating the tumor avoidance role of senescence. Repression of DNA repair genes that correlated with downregulation of E2F1 mRNA and protein was observed for two donors; a divergent result was seen for the third. Using proteomic profiling of soluble (non-vesicular) and extracellular vesicle (EV) associated secretions, we propose additions to the senescence associated secretory phenotype, including HSP60, which localizes to the surface of EVs. Finally, EVs from senescent NOKs activate interferon pathway signaling in THP-1 monocytes in a STING-dependent manner and associate with mitochondrial and nuclear DNA. Our results highlight senescence changes in epithelial cells and how they might contribute to chronic inflammation and age-related diseases.
| S-EPMC7950289 | biostudies-literature
Project description:Shisha smoking is widely believed to be a hazard-free habit. Studies have reported shisha smoking to be associated with oral lesions as well ascarcinomas of the lung, esophagus, bladder, and pancreas. A better understanding of the underlying mechanism may contribute to the identification of biomarkers for targeted therapy and better prognosis of the disease. In this study, we have established a chronic model of shisha-exposed oral keratinocytes to study the effect of shisha smoking on oral cells. Normal oral keratinocytes (non-transformed and immortalised), OKF/TERT1, were chronically treated with shisha extract for 8 months. In vitro cellular assays as well as total proteomic analysis were performed using the OKF6/TERT1-Parental and shisha-exposed cells (OKF6/TERT1-Shisha) to understand the effect of shisha smoking on cellular transformation. Chronic exposure of OKF6/TERT1 cells with shisha resulted in a significant increase in cellular proliferation and cell invasion compared to the OKF6/TERT1-Parental cells. Quantitative proteomic analysis of OKF6/TERT1-Parental and OKF6/TERT1-Shisha cells resulted in the identification of more than 5,515 proteins. Of these 5,515 proteins, 82, 77, 106, 110 proteins were found to be differentially expressed (1.5-fold) in OKF6/TERT1 cells chronically treated with shisha extract for 2M, 4M, 6M and 8M, respectively when compared with OKF6/TERT1-Parental. Pathway and gene ontology-based analysis revealed dysregulation of interferon pathway, upregulation of proteins involved in cell growth and downregulation of immune processes. This study reveals that chronic treatment of normal oral keratinocytes with shisha leads to cellular transformation. Elucidation of dysregulated proteins in shisha smoke-exposed cells will provide insights into the effect of shisha smoking on oral cells and aid in identification of therapeutic targets.
2019-02-21 | PXD011106 | Pride
Project description:The morphology and the behavior of skin and oral tissue keratinocytes are different. One significant dissimilarity between the two sites is the response to injury. Oral and skin keratinocytes have intrinsic differences in the response to injury and such differences are reflected in gene expression profiles. We used microarrays to investigate differences in global gene expression patterns between baseline skin and oral epithelium sheets without their underlying connective tissue.
2014-06-15 | GSE56135 | GEO
Project description:This was a hypothesis generating experiment to look at miR expression in a range of oral keratinocytes, including normal, precancer and oral cancer samples. The cells were cultures as per standard protocols (duplicate cultures) before assessment on the Affy miRNA array (1.0) one normal oral keratinocyte, one precancer, and 2 cancer samples, all in duplicate
2013-11-28 | E-GEOD-52811 | biostudies-arrayexpress