biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsHidde Smits M.methylation profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16746Skin‑homing CD4⁺CLA⁺ T cells are involved in chronic AD inflammation and may carry long‑lived disease-modifying effects through stable DNA methylation programs. By profiling the DNA methylome of healthy individuals and AD patients before and after one year of dupilumab or upadacitinib. This study tests whether these therapies facilitate epigenetic reprogramming. Using flow cytometry, CD4+CLA+ T cells were isolated from AD patients (n=12) at baseline and after 52 weeks of dupilumab (n=6) or upadacitinib (n=6) treatment. DNA methylome was conducted using the EPIC array. Non-atopic healthy controls (HC) (n=6) were included for comparison.biostudies-arrayexpressNucleic Acid Extraction - Skin-homing T cells were collected and stored in RLT plus lysis buffer. They were thawed on ice, followed by simultaneous isolation of RNA and DNA using AllPrep DNA/RNA Micro Kit (Qiagen) and following the manufacturer’s protocol. The quality of isolated DNA and RNA was checked on tapestation, using genomic DNA screentape analysis kit (Agilent) and high sensitivity RNA screentape analysis kit (Agilent) respectively. Samples with DIN score > 7 for DNA and RIN score > 7 for RNA were sent for subsequent analysis.Sample Collection - PBMCs were separated via Ficoll-Paque (GE Healthcare, Chicago, IL) density gradient centrifugation. Following isolation, PBMCs were cryopreserved in RPMI 1640 medium supplemented with 2mM L-glutamine, 100 IU/ml penicillin-streptomycin, 20% fetal bovine serum (FBS), and 10% DMSO (Sigma-Aldrich, St. Louis, MO), then stored at −170 °C until required for further analysis. PBMCs were thawed, counted and 1-2 × 106 cells were used for flow cytometry staining; 2.5-5 × 105 cells were seeded per well for each staining panel. The remaining PBMCs (6-10 × 106 cells) were used for CD3+CD4+CLA+ T cell flow cytometry sorting. For cells sorting; cells were washed with phosphate-buffered saline (PBS, Sigma-Aldrich), then incubated with eBioscience Fixable Viability Dye (Invitrogen) for 30 minutes at 4°C. Cells were then washed, and incubated with a surface antibody mix in FACS buffer for 25 minutes at 4°C, then washed and resuspended in FACS buffer (PBS, 2% FBS, 0.1% sodium azide). Following that, LD-CD19-CD3+CD4+CLA+ T cells were sorted (50,000 cells) on ARIA-III sorter. Sorted cells are centrifuged and lysed in RLT plus lysis buffer (AllPrep DNA/RNA Micro Kit; Qiagen). Samples were stored in -80C for future analysis.Hybridization - DNA methylation analysis using Illumina’s Infinium MethylationEPIC v2.0 935k BeadChip were performed by GenomeScan B.V. (Plesmanlaan 1d, 2333 BZ, Leiden, The Netherlands).Labeling - DNA methylation analysis using Illumina’s Infinium MethylationEPIC v2.0 935k BeadChip were performed by GenomeScan B.V. (Plesmanlaan 1d, 2333 BZ, Leiden, The Netherlands).Scaning - DNA methylation analysis using Illumina’s Infinium MethylationEPIC v2.0 935k BeadChip were performed by GenomeScan B.V. (Plesmanlaan 1d, 2333 BZ, Leiden, The Netherlands).MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsHidde Smits M.falseDNA methylome of human CD4⁺ CLA⁺ T cells in healthy controls and atopic dermatitis patients treated with dupilumab or upadacitinibSkin‑homing CD4⁺CLA⁺ T cells are involved in chronic AD inflammation and may carry long‑lived disease-modifying effects through stable DNA methylation programs. By profiling the DNA methylome of healthy individuals and AD patients before and after one year of dupilumab or upadacitinib. This study tests whether these therapies facilitate epigenetic reprogramming. Using flow cytometry, CD4+CLA+ T cells were isolated from AD patients (n=12) at baseline and after 52 weeks of dupilumab (n=6) or upadacitinib (n=6) treatment. DNA methylome was conducted using the EPIC array. Non-atopic healthy controls (HC) (n=6) were included for comparison.2026-04-30T00:00:00Z2026-05-01T13:19:42.535Z2026-03-11T15:44:32.496ZE-MTAB-16746ERP191200EFO_0002944EFO_0003814EFO_0003813EFO_0002759EFO_0005518EFO_0003815