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Transcriptome Response and Protein Abundance are Correlated with Split Formation and Cell Detachment as Secondary Effects to Autoantibodies in Human Skin Organ Culture Models for Pemphgus Vulgaris

GSE285008 Homo sapiens (human) RNA-seq (gene expression) 78 samples Submitted 2025/02/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 78 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
78 samples: 13 conditions, mostly with about 6 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Pemphigus vulgaris (PV) is an autoimmune disease caused by autoantibodies (AAbs) targeting Desmoglein 1 (DSG1) or Desmoglein 3 (DSG3) on keratinocytes, leading to disrupted cell-cell adhesion and epidermal blistering. To investigate the early signaling events triggered by AAb binding, we examined transcriptomic and proteomic responses in a human skin organ culture (HSOC) model for PV.
Read the full summary ↓
After injecting the single-chain variable fragment (scFv) PX43, which targets DSG1 and DSG3, or the mouse-derived DSG3 AAb AK23, we quantified transcriptome changes at 0, 5, 10, and 24 hours and proteome responses at 0 and 24 hours, using human or murine IgG as controls. Differential pathway regulation was analyzed over time using gene set variation and enrichment analysis, with pathway responses compared to in vitro and in situ responses of normal human epithelial keratinocytes (NHEKs) under conditions such as stretching, differentiation, migration, detachment, and acute wounding. Only PX43 induced split formation in the HSOC model, which was associated with significant transcriptomic and proteomic changes, while AK23 did not alter gene expression or protein levels. Enriched pathways in response to split formation included TNFα, Interferon α/γ, IL2-STAT5, and IL5-STAT3 signaling across all time points. The transcriptomic response closely resembled that of acute skin wounding and keratinocyte detachment, with an inverse correlation to cell stretching and differentiation and no correlation to keratinocyte migration. These findings indicate that AAbs targeting DSG1 and/or DSG3 alone do not drive broad transcriptomic or proteomic changes; rather, observed changes result from split formation, resembling the response to wounding and inflammation.
This dataset
Open GSE285008 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE285008_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1200800 and SRA study SRP552841. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
13 conditions, mostly with about 6 replicates each
NA_0h ×6 AK23_5h ×6 PX43_5h ×6 mIgG_5h ×6 hIgG_5h ×6 AK23_10h ×6 PX43_10h ×6 mIgG_10h ×6 +5 more

Supports a between-group comparison across 78 samples.

How we read this: 13 replicated groups read from 78 sample titles; they account for 78 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 38 more — browse all 78 samples with per-sample file links →

Datasets on a similar topic

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