Methylation profiling of the aging epidermis [450k]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Nicholas Holzscheck
PROVIDER: E-MTAB-8992 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:DNA methylation array data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. DNA was extracted from suction blisters taken from the volar forearms of each subject, bisulfite converted, and profiled using Illumina Infinium MethylationEPIC BeadChip arrrays.
2020-07-24 | E-MTAB-8993 | biostudies-arrayexpress
Project description:Whole transcriptome sequencing data generated from epidermal samples (suction blister roofs) of healthy female subjects between 21 and 76 years. Aim of the project was the investigation of non-linearities in the human aging progression using an integrative multi-omics analysis. RNA was extracted from suction blisters taken from the volar forearms of each subject, cDNA converted and then sequenced on an Illumina HiSeq 2500 (single-end, 50 bp) to an approximate sequencing depth of 100 million reads per sample.
2020-07-24 | E-MTAB-8995 | biostudies-arrayexpress
Project description:DNA methylation data generated from epidermal samples (suction blister roofs) of healthy female subjects after repetitive irradiation on three consecutive days using a full spectrum solar simulator. DNA was extracted from suction blisters taken from irradiated and control sites on the lower backs of each subject 24 hours after the final irradiation. DNA was bisulfite converted and then profiled using Illumina Infinium MethylationEPIC BeadChip arrays.
2020-09-02 | E-MTAB-9249 | biostudies-arrayexpress
Project description:Whole transcriptome sequencing data generated from epidermal samples (suction blister roofs) of healthy female subjects after repetitive irradiation on three consecutive days using a full spectrum solar simulator. RNA was extracted from suction blisters taken from irradiated and control sites on the lower backs of each subject 24 hours after the final irradiation. RNA was cDNA converted and then sequenced on an Illumina HiSeq 2500 (single-end, 50 bp) to an approximate sequencing depth of 100 million reads per sample.
2020-09-02 | E-MTAB-9251 | biostudies-arrayexpress
Project description:Gold nanoparticles (GNPs) have been used in the development of novel therapies as a way of delivery of both stimulatory and tolerogenic peptide cargoes. Here we report that intradermal injection of GNPs loaded with the proinsulin peptide C19-A3, in patients with type 1 diabetes, results in recruitment and retention of immune cells in the skin. These include large numbers of clonally expanded T-cells sharing the same paired T-cell receptors (TCRs) with activated phenotypes, half of which, when the TCRs were re-expressed in a cell-based system, were confirmed to be specific for either GNP or proinsulin. All the identified gold-specific clones were CD8+, whilst proinsulin-specific clones were both CD8+ and CD4+. Proinsulin-specific CD8+ clones had a distinctive cytotoxic phenotype with overexpression of granulysin (GNLY) and KIR receptors. Clonally expanded antigen-specific T cells remained in situ for months to years, with a spectrum of tissue resident memory and effector memory phenotypes. As the T-cell response is divided between targeting the gold core and the antigenic cargo, this offers a route to improving resident memory T-cells formation in response to vaccines. In addition, our scRNAseq data indicate that focusing on clonally expanded skin infiltrating T-cells recruited to intradermally injected antigen is a highly efficient method to enrich and identify antigen-specific cells. This approach has the potential to be used to monitor the intradermal delivery of antigens and nanoparticles for immune modulation in humans the Enhanced Epidermal Antigen Specific Immunotherapy Trial -1 (EEASI) study was a two-centre, open-label, uncontrolled, single-group first-in-human Phase 1A safety study of C19-A3 GNP peptide in individuals with T1D (https://clinicaltrials.gov/ct2/show/NCT02837094). The investigational medicinal product (IMP) was C19-A3 GNP (Midacore™), which comprises Midacore™ GNPs (Midatech Pharma Plc, Cardiff, UK)(1, 20) of a size of less than 5 nm, covalently coupled to an 18-amino acid human peptide, the sequence of which is identical to the residues from position 19 in the C-peptide of proinsulin through to position 3 on the A-chain of the same molecule (GSLQPLALEGSLQKRGIV). The peptide is synthesised with a linker to facilitate binding to the GNPs: 3-mercaptopropionyl-SLQPLALEGSLQKRGIV 2 acetate salt (disulfide bond). The chemical composition of the IMP contained a ratio of 4 C19-A3 peptides: 11 glucose C2: 29 glutathione ligands as determined by 1H-NMR (proton nuclear magnetic resonance). A typical batch contained: [C19-A3 peptide] = 1.33 mg/ml; [gold] = 5.5 mg/ml; [glucose linker] = 0.6 mg/ml; [glutathione linker] = 1.79 mg/ml. As the drug substance was diluted 1:7 to 1:10, depending on the content of C19-A3 peptide per particle, and as 50 μl of the diluted solution was administered to the study participants, this corresponded to C19-A3 peptide: 10 μg; gold: 39 μg; glucose linker: 4.3 μg; glutathione: 12.7 μg. Participants diagnosed with T1D and confirmed to possess the HLA-DRB1∗0401 genotype, were given three doses of C19-A3 GNP at 4-weekly intervals (weeks 0, 4, and 8) in the deltoid region of alternate arms (2 doses in one arm and 1 dose in the other arm) via CE-marked 600 μm length MicronJet600™ hollow microneedles (NanoPass Technologies Ltd. Israel) attached to a standard Luer-lock syringe. The single-dose given in 50 μl volume was equivalent to 10 μg of C19-A3 peptide Skin suction blisters were raised: Briefly, suction cups were applied to the deltoid region of participants’ arms, at the site of previous injection. Skin suction blisters were performed by gradually applying negative pressure (up to 60 kPa) from a suction pump machine VP25 (Eschmann, Lancing, UK) through a suction blister cup with a 15-mm hole in the base (UHBristol NHS Foundation Trust Medical Engineering Department, Bristol, UK) for 2–4 hr until a unilocular blister had formed within the cup. The cup was left in place for a further 30-60 minutes to encourage migration of lymphocytes into the blister fluid. The cup was then removed, and the blister fluid aspirated using a needle and syringe. Blister fluid was immediately suspended in 10ml heparinised RPMI (Gibco)+ 5% foetal calf serum Cells were counted then washed once and resuspended in an appropriate volume for scRNAseq. Samples were used fresh on the day of the collection. Samples were processed using a 10xGenomics V1 human 5’GEX kit and libraries were constructed following standard 10xGenomics protocols. Samples were pooled and sequenced on Illumina NextSeq and MiSeq scRNAseq libraries were sequenced aiming for 20,000 reads per cell for GEX and 5,000 reads/cell for VDJ.
2023-10-06 | E-MTAB-13388 | biostudies-arrayexpress
Project description:Epidermal keratinocytes are continuously dividing cells which, upon differentiation establish the outer skin barrier, the stratum corneum. In older age the epidermis becomes thinner, papillary protrusions flatten and the capacity for skin barrier repair decreases. Here we performed single-cell RNA sequencing of epidermal keratinocytes obtained by suction blisters from the volar forearm of younger (20-30) and older (65-70) healthy female individuals.
2024-08-28 | GSE275846 | GEO
Project description:To detect time of day dependent gene expression in human epidermis suction blister samples from 20 healthy subjects were obtained at three different time points throughout the day. RNA from 20 subjects were used to perform whole genome microarray analysis. Microarrays from 19 subjects showed sufficient quality to perform analysis for differential gene expression. We detected significant differential expression levels for several canonical clock genes such as Per1, Per2, Per3, Bmal1 and Rev-Erb_alpha throughout the day. In total we identified 294 genes that showed significant circadian gene expression including several transcription factors and rate limiting enzymes. To our knowledge this is the first study to investigate genome wide circadian gene expression in human epidermis. Suction blisters of human epidermis were obtained by applying a vacuum for approximately 2.5 h. Suction blisters for each subject (19 subjects in total) were harvested at 9.30 am, 2.30 pm and 7.30 pm.
2012-07-30 | E-GEOD-35635 | biostudies-arrayexpress
Project description:Acute compartment syndrome (ACS) is a disease in which local circulation is affected due to increased pressure within the compartment. We previously found in patients with calf fractures, the pressure of fascial compartment could be sharply reduced upon the appearance of tension blisters. Deep fascia, as the important structure for compartment, might play key role in this process. Therefore, the aim of the present study was to examine the differences in gene profile in deep fascia tissue in fracture patients of the calf with or without tension blisters, and to explore the role of fascia in pressure improvement in ACS. Patients with lower leg fracture were enrolled and divided into without tension blister control group (CON group, n=10), and with tension blister group (TB group, n=10). Deep fascia tissues were collected and LC-MS/MS label-free quantitative proteomics were performed. Genes involved in fascia structure and fibroblast function were further validated by Western blot. The differentially expressed proteins were found to be mainly enriched in pathways related to protein synthesis and processing, stress fiber assembly, cell-substrate adhesion, leukocyte mediated cytotoxicity, and cellular response to stress. Compared with the CON group, the expression of Peroxidasin homolog (PXDN), which promotes the function of fibroblasts, and Leukocyte differentiation antigen 74 (CD74), which enhances the proliferation of fibroblasts, were significantly upregulated, while the expression of Matrix metalloproteinase-9 (MMP9), which is involved in collagen hydrolysis, and Neutrophil elastase (ELANE), which is involved in elastin hydrolysis, were significantly reduced in the TB group (p all <0.05), indicating fascia tissue underwent microenvironment reconstruction during ACS.In summary, the ACS accompanied by blisters is associated with the enhanced function and proliferation of fibroblasts and reduced hydrolysis of collagen and elastin. The adaptive alterations in the stiffness and elasticity of the deep fascia might be crucial for pressure release of ACS.
2024-05-30 | PXD044022 | Pride
Project description:Allergic and irritant contact dermatitis can be challenging to distinguish. We used single cell RNA sequencing (scRNA-seq) and insterstitial fluid proteomic analysis to compare suction blister biopsy skin samples from human volunteers with induced allergic and irritant contact dermatitis reactions.
2024-09-15 | GSE267929 | GEO
Project description:To probe the phenotype of the cDC compartment during pathology, we developed a simplified human experimental skin blister model to sample infiltrating cells in order to examine the function and kinetics of DC populations in response to a bacterial insult in healthy individuals. ASDC were recruited to the inflammatory site, displaying a distinctive effector signature. Human Skin Blister 1.5 x 107 UV killed E.coli (Strain: NCTC 10418, Source: Public Health England, UK) in 100 µl sterile saline was intradermally injected into the forearm approximately 7 cm from the cubital fossa. For the suction blister, a 10 mm diameter suction blister was induced at 24 hours post challenge over the injection site by a negative pressure instrument. Once a blister formed, blister exudate was collected, cells were isolated. Next, Blister cells were stained for DC subsets and index sorted on FACS ARIA III (BD Biosciences) into 96 well plate containing lysis buffer, one cell/well - using the gating strategy in Supplementary Figure 1a. Plates were sealed and stored at -80°C. Single-cell cDNA libraries were prepared using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: (i) 1 mg/mL BSA Lysis buffer (Ambionâ Thermo Fisher Scientific); and (ii) 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA), with 300 samples/lane. Pre-processing, quality assessment and control and analysis of SMARTseq2 single cell transcriptome data. Paired-end raw reads were aligned to the human reference genome (GRCh38 version 25 release: Gencode) using RSEM version 1.3.0. Transcript Per Million read (TPM) values were calculated using RSEM and used for downstream analysis. Quality control, selection of highly variable genes, PCA, and differential gene analysis was performed using the Seurat R package. The expression levels of key signature genes by known cell types was used to annotate the cell clusters accordingly.
2024-09-24 | E-MTAB-14451 | biostudies-arrayexpress