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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of the gene expression profile in normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines

ABSTRACT: The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. We used microarrays to characterize gene expression profile in normal human epidermal keratinocytes (NHEK) and cSCC cell lines. Total RNAs from normal human epidermal keratinocytes (n=5) and cSCC cell lines (n=8) were extracted. The samples were processed for Affymetrix 3´ IVT Express Kit according to manufacture’s protocol.

ORGANISM(S): Homo sapiens

SUBMITTER: Liisa Nissinen

PROVIDER: E-GEOD-66359 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EphB2 Promotes Progression of Cutaneous Squamous Cell Carcinoma.

Farshchian Mehdi M Nissinen Liisa L Siljamäki Elina E Riihilä Pilvi P Toriseva Mervi M Kivisaari Atte A Ala-Aho Risto R Kallajoki Markku M Veräjänkorva Esko E Honkanen Hanne-Kaisa HK Heljasvaara Ritva R Pihlajaniemi Taina T Grénman Reidar R Peltonen Juha J Peltonen Sirkku S Kähäri Veli-Matti VM

The Journal of investigative dermatology 20150319 7

Keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC), is the most common metastatic skin cancer. We have examined the role of Eph/ephrin signaling in the progression of cSCC. Analysis of the expression of EPH and EFN families in cSCC cells and normal epidermal keratinocytes revealed overexpression of EPHB2 mRNA in cSCC cells and cSCC tumors in vivo. Tumor cell-specific overexpression of EphB2 was detected in human cSCCs and in chemically induced mouse cSCCs with immunohisto ...[more]

PMID: 25789706

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Analysis of the gene expression profile in cutaneous squamous cell carcinoma cells after EphB2 knockdown

Project description:The role of Eph/ephrin signaling in numerous biological processes has been established. However, Eph/ephrin signaling has been shown to have complex role in tumor progression. The role of EphB2 receptor in the progression of cutaneous squamous cell carcinoma (cSCC) has not been studied before. EphB2 is significantly overexpressed in cSCC cells compared with normal human epidermal keratinocytes (NHEKs). We used microarray based global gene expression profiling to study the effect of EphB2 knockdown on the expression of different genes in cSCC cells. cSCC cell lines (n=3) were transfected with either control or EphB2 siRNA (75 nM) and incubated for 72 hours. Total RNA was extracted and processed expression profiling with GeneChip 3’ IVT Express Kit according to manufacturer’s protocol.

2015-08-27 | E-GEOD-66361 | biostudies-arrayexpress

EphB2 promotes progression of cutaneous squamous cell carcinoma

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-27 | E-GEOD-66368 | biostudies-arrayexpress

RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.

Project description:The incidence of keratinocyte-derived skin cancer, cutaneous squamous cell carcinoma (cSCC) is increasing worldwide making it the second most common metastatic skin cancer. In this project we used SOLiD next generation sequencing to characterize gene expression profiles in normal human epidermal keratinocytes (NHEKs) and cSCC cell lines. Total RNAs from normal human epidermal keratinocytes (NHEKs) (n=4) and cSCC cell lines (n=8) were extracted. The samples were sequenced using SOLiD next generation sequencing.

2015-08-27 | E-GEOD-66412 | biostudies-arrayexpress

Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses

Project description:Keratinocyte cancers (KC) are the most prevalent malignancies in fair-skinned populations, posing a significant medical and economic burden to health systems. KC originate in the epidermis and mainly comprise basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cSCC). Here, we combined single-cell transcriptomics, methylomics and multi-omics to investigate the epigenomic dynamics during epidermal differentiation. We identified ~4,000 differentially accessible regions between undifferentiated and differentiated keratinocytes, corresponding to regulatory regions associated with key transcription factors. DNA methylation at these regions defined AK/cSCC subtypes with epidermal stem cell- or keratinocyte-like features. Using cell type deconvolution tools and integration of bulk and single-cell methylomes, we demonstrate that these subclasses are consistent with distinct cells-of-origin. Further characterization of the subclasses with an epigenetic mitotic-like clock, and the study of other unstratified KC entities uncovered distinct phenotypic and clinical features for the subclasses, linking invasive and metastatic KC cases with undifferentiated cells-of-origin. Our study provides a thorough characterization of the epigenomic dynamics underlying human keratinocyte differentiation and uncovers novel links between KC cells-of-origin and their prognosis

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Analysis of the gene expression profile in normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines

2015-08-27 | GSE66359 | GEO

RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of AIM2.

Project description:Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Chronic inflammation has been recognized as a risk factor for cSCC and inflammation is a typical feature of the progression of actinic keratosis lesions to invasive and metastatic cSCC. Inflammasomes are important components of the innate immune response involved in onset of inflammation. Inflammasome component AIM2 serves as a sensor for cytoplasmic double-strand DNA, and this way plays a key role in response to bacterial and viral colonization. Activation of inflammasome by cytoplasmic DNA in epidermal keratinocytes can promote the initiation of inflammation in autoimmune and autoinflammatory skin diseases. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) and oligonucleotide array-based expression analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=5) revealed overexpression of AIM2 in cSCC cells (GSE66412 and GSE66368, respectively). We wanted to futher study the RNA expression profile of AIM2 knockdown cSCC cells.

2017-08-18 | GSE94270 | GEO

RNA-Seq whole transcriptome analysis of normal human epidermal keratinocytes and cutaneous squamous cell carcinoma cell lines.

2015-08-27 | GSE66412 | GEO

Transcription profiling of human keratinocytes used in a small molecule screen to identify inducers of epidermal keratinocyte differentiation

Project description:An essential function of the human epidermis is the maintenance of a protective barrier against the environment. As a consequence, keratinocytes, which make up this layer of the skin, undergo an elaborate process of self-renewal, terminal differentiation and cell death. Misregulation of these processes can lead to several human diseases including psoriasis and basal cell and squamous cell carcinomas. To identify novel regulators of keratinocyte differentiation, a cell-based screen of small molecule libraries was carried out for molecules that induce terminal differentiation of normal human epidermal keratinocytes (NHEKs). One class of molecules was identified, the 2-(3,4,5-trimethoxy-phenylamino)-pyrrolo[2,3-d]pyrimidines, which were shown to induce differentiation of epidermal progenitor cells to terminally differentiated keratinocytes. These molecules serve as useful mechanistic probes of the cellular differentiation programs that regulate the formation and homeostasis of the epidermis, and may lead to novel therapeutic approaches for the treatment of skin hyperproliferative disorders. Experiment Overall Design: samples were taken from duplicate treatments of cells with DMSO or PP-2 (compound 9) at various time points

2009-04-10 | E-GEOD-6932 | biostudies-arrayexpress

Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cell types of origin

Project description:Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer type and arises from keratinocytes. Most cSCC progress from a UV-induced precancerous lesion termed actinic keratosis (AK). Despite various efforts to characterize these lesions molecularly, the etiology of AK and its progression to cSCC remain only partially understood. Here we have used Infinium MethylationEPIC BeadChips to interrogate the DNA methylation status of about 850.000 CpGs in epidermal preparations from healthy skin, AK and cSCC. Importantly, we found that the premalignant AK samples displayed classical features of cancer methylomes and were highly similar to cSCC methylomes. Further analysis identified typical features of stem cell methylomes, such as a reduced DNA methylation age, non-CpG methylation and stem cell-related keratin and enhancer methylation patterns. Interestingly, this signature was detected only in one half of the AK and cSCC samples, while the other half showed methylation patterns that were more closely related to the control epidermis. These findings suggest the existence of two distinct subclasses of AK and cSCC that originate from distinct keratinocyte differentiation stages.

2017-12-19 | E-MTAB-5738 | biostudies-arrayexpress

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2022-08-29 | GSE205981 | GEO

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