Dataset Information

Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls

ABSTRACT: Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls

PROVIDER: PRJNA790997 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17283423_1.fastq.gz	Fastqsanger.gz
	SRR17283423_2.fastq.gz	Fastqsanger.gz
	SRR17283424_1.fastq.gz	Fastqsanger.gz
	SRR17283424_2.fastq.gz	Fastqsanger.gz
	SRR17283425_1.fastq.gz	Fastqsanger.gz

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Project description:Although most cutaneous squamous cell carcinomas (cSCC) develop from actinic keratoses (AK), the key events for this evolution remain unclear. We have combined the results of different genomic and expression array platforms on matched samples of sun-exposed skin, AK and cSCC from ten immunocompetent patients, with the objective of better understanding the mechanisms involved in this progression. Gene expression analysis and copy number alterations were assessed using GeneChip Human Gene 2.0 ST Array® (Affymetrix ) and CytoScan HD Cytogenetics Solution® (Affymetrix) platforms, respectively. Integration of genome and transcriptome results was evaluated using the DR-Integrator tool. Additional studies (qPCR, immunohistochemistry and Western blot) were performed for selected genes. Twenty-two genes showed a progressive expression spectrum from clinically normal sun-exposed skin samples to cSCC. FOSL1 and BNC1 encode transcription factors whose expression was increased in cSCC in the expression array and the qPCR. By immunohistochemistry, FOSL1 showed an intense staining at the invasive front of cSCC samples and BNC1 expression varied from a nuclear location (sun-exposed skin) to a cytoplasmic location (cSCC). Western blot analyses confirmed the enhancement of FOSL1 and BNC1 expression. Additionally, the smallest overlapping regions of genomic imbalance (SORIs) involving at least 3 of the samples of each group (sun-exposed skin, AK or cSCC) were selected. One of the SORIs was a deletion in the p24.1 band of chromosome 3, shared by 7 of the cSCC. A strong correlation in the integration analysis was found for NEK10, a gene contained in the previously mentioned SORI. Loss of NEK10 expression in cSCC was confirmed by immunohistochemistry and western blot analyses. In conclusion, our findings suggest that FOSL1 may play a role in promoting the cSCC invasion ability. We have also identified two additional genes, NEK10 and BNC1, which could also act as tumor drivers.

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Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls

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