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Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis.

ABSTRACT: Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis.

PROVIDER: PRJNA912237 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR22742300_1.fastq.gz	Fastqsanger.gz
	SRR22742300_2.fastq.gz	Fastqsanger.gz
	SRR22742500_1.fastq.gz	Fastqsanger.gz
	SRR22742500_2.fastq.gz	Fastqsanger.gz
	SRR22742600_1.fastq.gz	Fastqsanger.gz

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Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. II[

Project description:Here we used a pan-cytokeratin antibody to differentiate the epidermal from dermal compartment and assayed over 18,000 RNA probes from multiple regions of interest (ROI) comparing sun protected skin, and two regions (edge and center) from AK/sun damaged skin. This allows for a trajectory from sun protected to sun damaged within an individual. Traditionally, cancer biology focusses on change within the tumor compartment for diagnosis and staging and current genetic profiling of actinic keratosis (the precursor lesion for cutaneous squamous cell carcinoma) has focused on analysis limited to whole skin or the epidermal compartment alone. Here we use spatial transcriptomics to compare and contrast the epidermal and stromal compartments from different regions of actinic keratosis and matched sun protected skin from six individuals. Our data show that the major changes in AK at the transcriptional level are evident in the dermal compartment. Sun protected skin (n=5-6 from 6 individuals for a total of 34 ROI), the center of an AK lesion (n=3 for a total of 18 ROI) and edge of the AK lesion (n=2-3 for a total of 17 ROI) representing sun-damaged skin, from six unrelated individuals, the center of an AK lesion (n=3 for a total of 18 ROI) and edge of the AK lesion (n=2-3 for a total of 17 ROI) representing sun-damaged skin, from six unrelated individuals.

2022-12-19 | GSE221000 | GEO

Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. [I]

2022-12-19 | GSE220998 | GEO

Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. II[

Project description:Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. II[

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Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. [I]

Project description:Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis. [I]

| PRJNA912241 | ENA

Characterizing dermal transcriptional change in the progression from sun-protected skin to actinic keratosis.

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-19 | GSE221001 | GEO

Identification of differentially expressed genes in actinic keratosis samples treated with ingenol mebutate gel

Project description:Actinic keratosis is a common skin disease that may progress to invasive squamous cell carcinoma. Ingenol mebutate has demonstrated efficacy in field treatment of actinic keratosis. However, molecular mechanisms on ingenol mebutate response are not yet fully understood.

2020-05-18 | GSE142108 | GEO

Transcription profiling of human normal skin, actinic keratosis and squamous cell carcinoma

Project description:normal skin (no), actinic keratosis (ak), and squamous cell carcinoma (scc) of the skin were examined:; BACKGROUND: Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. This study examined and identified differentially expressed genes in cutaneous squamous cell carcinoma (SCC). RESULTS: Three different biopsies of 5 immunosuppressed organ-transplanted recipients each normal skin (all were pooled), actinic keratosis (AK) (two were pooled), and invasive SCC and additionally 5 normal skin tissues from immunocompetent patients were analyzed. Thus, total RNA of 15 specimens were used for hybridization with Affymetrix HG-U133A microarray technology containing 22,283 genes. Data analyses were performed by prediction analysis of microarrays using nearest shrunken centroids with the threshold 3.5 and ANOVA analysis was independently performed in order to identify differentially expressed genes (p < 0.05). Verification of 13 up- or down-regulated genes was performed by quantitative real-time reverse transcription (RT)-PCR and genes were additionally confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. CONCLUSION: The majority of identified differentially expressed genes in cutaneous SCC were previously not described.

2007-10-02 | E-GEOD-2503 | biostudies-arrayexpress

RNAseq experiment of non-exposed skin, actinic keratosis, intraepidermal carcinoma and squamous cell carcinoma

Project description:The goal of the study is to compare the transcriptomic profile of patient-derived skin samples, Actinic Keratosis, Intraepidermal Carcinoma and Squamous Cell Carcinoma samples using next generation RNA Sequencing. We aim to identify perturbed pathways and similarities between the 4 conditions. Please note that detailed patients' information, such as gender and age, was withheld from this submission to protect the patients' identity.

2017-05-16 | E-MTAB-5678 | biostudies-arrayexpress

Cylindromas sun protected and exposed

Project description:The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.

| EGAS00001002521 | EGA

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Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples.

2015-03-23 | GSE51954 | GEO

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