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Single-cell and spatial profiling reveal cDC2A-CXCL13+ CD8+ T-epithelial cell crosstalk and cytotoxicity through TNFRSF9 in cutaneous and mucosal lichen planus

GSE317789 Homo sapiens (human) Single-cell RNA-seq 42 samples Submitted 2026/02/06 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 42 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
42 samples: 14 × 10546-JF vs 14 × 10547-JF vs 14 × 10687-JFGroups 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.
Paper
Single-cell and spatial profiling reveal cDC2A-CXCL13(+)CD8(+) T-epithelial cell crosstalk and cytotoxicity through TNFRSF9 in cutaneous and mucosal lichen planusNature communications · 2026
Summary (written by the submitters)
Lichen planus (LP) is a chronic inflammatory disease of the skin and mucous membranes, marked by T cell infiltration and keratinocyte apoptosis. However, its immune microenvironment remains poorly understood. Using single-cell RNA sequencing, spatial transcriptomics, and proteomics on samples from 28 patients and 18 healthy controls, we identify elevated interferon (IFN) and cytotoxic signatures in CXCL13+CD8+ T cells in both cutaneous and mucosal LP, but not in lichen planopilaris.
Read the full summary ↓
T cells expressing TNF and IFNG are spatially linked to epithelial cells through ligand-receptor interactions, correlating with inflammation. We identify cDC2A cells as key contributors, proximal to CXCL13+CD8+ T cells, serving as a major source of IL-15. CXCL13+CD8+ T cells express TNFRSF9 (4-1BB), which enhances their cytotoxic responses in the skin. In summary, our data reveal a critical role for cDC2A in driving CXCL13+CD8+ T –epithelial cytotoxicity in cutaneous and mucosal LP through TNFRSF9.
Published in
Single-cell and spatial profiling reveal cDC2A-CXCL13(+)CD8(+) T-epithelial cell crosstalk and cytotoxicity through TNFRSF9 in cutaneous and mucosal lichen planus
Jiang R, Bogle R, Xing X et al. · Nature communications 2026 · PMID 41832141 · doi:10.1038/s41467-026-70506-z
This dataset
Open GSE317789 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 GSE317789_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1415256 and SRA study SRP667978. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41832141) ↗
Study design
14 × 10546-JF vs 14 × 10547-JF vs 14 × 10687-JF

Supports a between-group comparison across 42 samples.

How we read this: 3 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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