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Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

ABSTRACT: 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. Bisulphite converted DNA from the 78 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

ORGANISM(S): Homo sapiens

SUBMITTER: Andrew Feinberg

PROVIDER: E-GEOD-51954 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Vandiver Amy R AR Irizarry Rafael A RA Hansen Kasper D KD Garza Luis A LA Runarsson Arni A Li Xin X Chien Anna L AL Wang Timothy S TS Leung Sherry G SG Kang Sewon S Feinberg Andrew P AP

Genome biology 20150416

<h4>Background</h4>Aging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging and/or chronic sun exposure in humans.<h4>Results</h4>We compare epidermis and dermis of both sun-protected and sun-exposed skin derived from younger subjects (under 35 ye ...[more]

PMID: 25886480

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Epigenome analysis of human epidermal and dermal samples with aging and sun exposure

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

Expression data from epidermal samples

Project description:Gene expression profiling of epidermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Affymetrix U133A plus 2.0 array was used to obtain gene expression data. Samples included 4 younger sun exposed epidermal samples, 4 older sun exposed epidermal samples, 3 younger sun protected epidermal samples, 5 older sun protected epidermal samples.

2015-03-23 | GSE67098 | GEO

Epigenome analysis of human epidermal samples with aging and sun exposure

Project description:Genome wide DNA methylation profiling of epidermal samples obtained from sum-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals.

2015-03-23 | GSE52972 | GEO

Epigenome analysis of human epidermal samples with aging and sun exposure

2015-03-23 | E-GEOD-52972 | biostudies-arrayexpress

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

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 | GSE220998 | GEO

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

2022-12-19 | GSE221000 | GEO

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.

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miRNA expression data from sun-exposed and sun- protected skin of young (18-25 years) and old (>70 years) females

Project description:In this study we explored the effects of chronological and photoageing on the miRNome of human skin. To this end, miRNA expression was analysed in biopsies collected from sun-exposed (outer arm) and sun-protected (inner arm) skin from fair-skinned (phototype II/III) healthy female volunteers of two age groups: young, 18-25 years and aged, >70 years. Strict inclusion criteria were used for photoageing scoring and for chronological ageing. Microarray analysis revealed that chronological ageing had minor effect on the human skin miRNome. In contrast, photoageing had a robust impact on miRNAs, and a set of miRNAs differentially expressed between sun-protected and sun-exposed skin of the young and aged groups was identified. We have performed miRNome analysis (using microarray) on RNA isolated from sun-exposed and sun-protected skin of young and old females

2018-08-31 | GSE114006 | GEO

Transcription profiling of human nevoid basal cell carcinoma syndrome primary fibroblasts with non-sense or miss-sense mutations in the tumor supressor gene PTCH1

Project description:Mutations in the tumor suppressor gene PTCH1 are responsible for Gorlin syndrome, or nevoid basal cell carcinoma syndrome (NBCCS). NBCCS causes predisposition to basal cell carcinoma (BCC), the commonest cancer in adult human. In the general population BCC develop almost exclusively in sun-exposed area of the skin (Buettner PG, Raasch BA (1998) Int J Cancer 78: 587-593). In contrast, and, intriguingly, NBCCS BCCs are observed in both sun-protected and sun-exposed areas. Interestingly, our previous studies have shown that both fibroblasts and keratinocytes from NBCCS patients exhibit normal nucleotide excision repair of UVB-induced DNA lesions and survival capacities following a single UVB irradiation (Brellier F, Valin A, et al. (2008) Br J Dermatol.). These data suggest that sun UV are far from being the only etiologic factor of BCC in NBCCS patients. In this study we aimed at documenting the possible role of NBCCS fibroblasts in BCC development in NBCCS patients. Thus, the genome expression of NBCCS primary fibroblasts cultured in a dermal equivalent was compared to the one of control fibroblasts under the same circumstances.

2009-03-19 | E-TABM-549 | biostudies-arrayexpress

Epigenetic patterns with aging and exercise are associated with indicators of healthspan in humans

Project description:Genome wise DNA methylation profiling of peripheral blood mononuclear cells (PBMCs) obtained from younger sedentary (Y-SED), older sedentary (O-SED) and older aerobically exercise trained (O-Ex) human subjects. The Illumina 450K methylation beadchip array was used to obtain DNA methylation profiles across approximately 450,000 CpG dinucleotide methylation loci in DNA isolated from PBMCs. Samples include 12 Y-SED subjects, 15 O-SED subjects and 11 O-Ex subjects.

2020-10-01 | GSE85311 | GEO

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