GEO series
Single-cell transcriptome reveals keratinocyte subclusters that contribute to altered differentiation and inflammatory responses in atopic dermatitis
GSE328048
Homo sapiens
Expression profiling by high throughput sequencing
116 samples
Submitted 2026/06/01
Platform GPL24676
Summary
Atopic dermatitis (AD) is a common chronic inflammatory skin disease with complex, poorly understood pathogenesis due to its mechanistic heterogeneity. To investigate underlying mechanisms, we performed single-cell RNA sequencing (scRNA-seq) on lesional (LAD) and non-lesional (NAD) skin from 42 AD patients and skin from 23 healthy controls (HC). Keratinocytes (KCs) were the most abundant cell type identified. In healthy skin, KC differentiation followed a linear trajectory from basal KCs (BKs) through seven differentiated stages (DK1–DK7) to terminal keratinized cells (KK1 and KK2). In LAD, this process was disrupted, showing a reversed transition from KK2 to KK1, mainly driven by DK7. APOD and LYZ were identified as LAD-specific regulators of this aberrant keratinization, linked to IL-13- and IL-22-driven responses involving endoplasmic reticulum (ER) stress and oxidative damage. Mitochondrial and ER dysfunction were specifically enriched in LAD DK6 cells, suggesting this subcluster as a key pathogenic compartment associated with cytokine activation. Further, cell-cell interaction analysis (validated through Xenium spatial transcriptomics and immunohistochemistry) highlighted TWEAK, derived from IL13+ Th2 and cycling T cells acting on FN14+ basal and differentiated KCs, as a key contributor to AD-associated epidermal responses. These findings reveal how disrupted KC differentiation and specific immune pathways contribute to AD pathogenesis, identifying distinct cellular compartments and inflammatory circuits as potential therapeutic targets.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE328048_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 116 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1453562 and SRA study SRP691918. Searching any of these in the dataset finder brings you back here.
Study design
13 conditions, mostly in duplicate
6138-AB ×4
6726-JF ×3
6788-JF ×3
6178-AB ×2
6359-AB ×2
6372-AB ×2
6458-JF ×2
6636-JF ×2
+15 more
Supports a between-group comparison across 30 samples.
13 replicated groups read from the first 40 of 116 sample titles; they account for 30 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9670989 5917-AB-2
- GSM9670990 5941-AB-1
- GSM9670991 5995-AB-2
- GSM9670992 6138-AB-1
- GSM9670993 6138-AB-2
- GSM9670994 6138-AB-4
- GSM9670995 6138-AB-5
- GSM9670996 6178-AB-8
- GSM9670997 6178-AB-9
- GSM9670998 6201-AB-1
- GSM9670999 6359-AB-1
- GSM9671000 6359-AB-2
- GSM9671001 6372-AB-1
- GSM9671002 6372-AB-2
- GSM9671003 6425-JF-1
- GSM9671004 6458-JF-1
- GSM9671005 6458-JF-2
- GSM9671006 6636-JF-1
- GSM9671007 6636-JF-2
- GSM9671008 6673-JF-1
- GSM9671009 6673-JF-2
- GSM9671010 6726-JF-1
- GSM9671011 6726-JF-2
- GSM9671012 6726-JF-4
- GSM9671013 6733-JF-1
- GSM9671014 6766-JF-1
- GSM9671015 6766-JF-2
- GSM9671016 6788-JF-1
- GSM9671017 6788-JF-2
- GSM9671018 6788-JF-4
- GSM9671019 6830-AB-1
- GSM9671020 6830-AB-2
- GSM9671021 6835-AB-1
- GSM9671022 6835-AB-2
- GSM9671023 6883-JF-1
- GSM9671024 6883-JF-2
- GSM9671025 6911-JF-1
- GSM9671026 6919-JF-2
- GSM9671027 6929-JF-1
- GSM9671028 6938-JF-1
+ 76 more — browse all 116 samples with per-sample file links →
Similar datasets
- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples
- GSE303346 Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses 16 samples
- GSE282122 A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease 216 samples
- GSE273700 Whole transcriptome analysis reveals T cell signaling activation in septic patients with thrombocytopenia 104 samples
- GSE324131 A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis 38 samples
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples
- GSE198315 Multiregional single-cell profiling reveals extensive field cancerization and an immunosuppressive microenvironment in oral squamous cell carcinoma 36 samples
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples
Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.