GEO series

Functional Dynamics of Dendritic Cells in Response to Cutibacterium acnes Strains Associated with Healthy and Acne-prone Skin

GSE255918 Homo sapiens (human) RNA-seq (gene expression) 68 samples Submitted 2025/02/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 68 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: 68 samples: 24 conditions, mostly in duplicateGroups 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: Functional Dynamics of Dendritic Cells in Response to Cutibacteriumacnes Strains Associated with Healthy and Acne-Prone SkinThe Journal of investigative dermatology · 2025

Summary (written by the submitters)

The pathogenesis of acne vulgaris is multifactorial and is influenced by the presence of Cutibacterium acnes. This study investigated how different strains of C. acnes, associated with either healthy skin (CH) or acne-prone skin (CA), selectively modulate the function of three dendritic cell (DC) subtypes: Langerhans cell-derived (LCDC), monocyte-derived (moDCs), and myeloid (mDCs).

Read the full summary ↓

Our findings revealed that all DC subtypes secreted varying levels of TGF-β, IL-1β, IL-6, IL-12p70, and IL-23 in response to C. acnes stimulation. Notably, moDCs exhibited the highest cytokine secretion in response to CA-ribotypes, indicating their potent immune responsiveness. Conversely, LCDCs were the least responsive, regardless of the ribotypes. Principal component (PCA) and gene ontology (GO) analysis of bulk RNA sequencing data of DCs exposed to C. acnes identified extensive transcriptional changes, particularly in immune response pathways. moDCs showed the most pronounced transcriptional changes, aligning with their high cytokine secretion levels. Additionally, we identified specific genes upregulated by CA-ribotypes, with notable differences among the DC types, highlighting the unique contributions of each DC subtype to the skin's immune defense mechanisms against C. acnes. Overall, our study underscores the complexity of DC responses in the skin's immune environment and provides valuable insights into their roles in acne.

Published in

Functional Dynamics of Dendritic Cells in Response to Cutibacteriumacnes Strains Associated with Healthy and Acne-Prone Skin

Del Vecchio G, Nguyen NPN, Ouyang K et al. · The Journal of investigative dermatology 2025 · PMID 40020992 · doi:10.1016/j.jid.2025.02.132

This dataset

Open GSE255918 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 GSE255918_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 PRJNA1077240 and SRA study SRP489975. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40020992) ↗

Study design

24 conditions, mostly in duplicate

LCDC cell type, cells alone, ×4 moDC cell type, cells alone, ×4 LCDC cell type, 43PA1, ×3 mDC cell type, cells alone, ×3 LCDC cell type, 110PA ×2 LCDC cell type, 110PA3, ×2 LCDC cell type, 110PA4, ×2 LCDC cell type, 42PA3, ×2 +30 more

Supports a between-group comparison across 54 samples.

How we read this: 24 replicated groups read from 68 sample titles; they account for 54 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

GSM8082554 LCDC cell type, cells alone
GSM8082555 LCDC cell type, cells alone, replicate 2 LCDC cell type, cells a…
GSM8082556 LCDC cell type, cells alone, replicate 3 LCDC cell type, cells a…
GSM8082557 LCDC cell type, cells alone, replicate 4 LCDC cell type, cells a…
GSM8082558 LCDC cell type, cells alone, replicate 5 LCDC cell type, cells a…
GSM8082559 LCDC cell type, 110PA3 LCDC cell type, 110PA
GSM8082560 LCDC cell type, 110PA3, replicate 2 LCDC cell type, 110PA3,
GSM8082561 LCDC cell type, 110PA3, replicate 3 LCDC cell type, 110PA3,
GSM8082562 LCDC cell type, 110PA4 LCDC cell type, 110PA
GSM8082563 LCDC cell type, 110PA4, replicate 2 LCDC cell type, 110PA4,
GSM8082564 LCDC cell type, 110PA4, replicate 3 LCDC cell type, 110PA4,
GSM8082565 LCDC cell type, 42PA3
GSM8082566 LCDC cell type, 42PA3, replicate 2 LCDC cell type, 42PA3,
GSM8082567 LCDC cell type, 42PA3, replicate 3 LCDC cell type, 42PA3,
GSM8082568 LCDC cell type, 43PA1, LCDC cell type, 43PA1,
GSM8082569 LCDC cell type, 43PA1, replicate 2 LCDC cell type, 43PA1,
GSM8082570 LCDC cell type, 43PA1, replicate 3 LCDC cell type, 43PA1,
GSM8082571 LCDC cell type, 5PA1
GSM8082572 LCDC cell type, 5PA1, replicate 2 LCDC cell type, 5PA1,
GSM8082573 LCDC cell type, 5PA1, replicate 3 LCDC cell type, 5PA1,
GSM8082574 LCDC cell type, 96PA1
GSM8082575 LCDC cell type, 96PA1, replicate 2 LCDC cell type, 96PA1,
GSM8082576 LCDC cell type, 96PA1, replicate 3 LCDC cell type, 96PA1,
GSM8082577 mDC cell type, cells alone
GSM8082578 mDC cell type, cells alone, replicate 2 mDC cell type, cells al…
GSM8082579 mDC cell type, cells alone, replicate 3 mDC cell type, cells al…
GSM8082580 mDC cell type, cells alone, replicate 4 mDC cell type, cells al…
GSM8082581 mDC cell type, 110PA3 mDC cell type, 110PA
GSM8082582 mDC cell type, 110PA3, replicate 2 mDC cell type, 110PA3,
GSM8082583 mDC cell type, 110PA3, replicate 3 mDC cell type, 110PA3,
GSM8082584 mDC cell type, 110PA4 mDC cell type, 110PA
GSM8082585 mDC cell type, 110PA4, replicate 2 mDC cell type, 110PA4,
GSM8082586 mDC cell type, 110PA4, replicate 3 mDC cell type, 110PA4,
GSM8082587 mDC cell type, 42PA3
GSM8082588 mDC cell type, 42PA3, replicate 2 mDC cell type, 42PA3,
GSM8082589 mDC cell type, 42PA3, replicate 3 mDC cell type, 42PA3,
GSM8082590 mDC cell type, 43PA1
GSM8082591 mDC cell type, 43PA1, replicate 2 mDC cell type, 43PA1,
GSM8082592 mDC cell type, 43PA1, replicate 3 mDC cell type, 43PA1,
GSM8082593 mDC cell type, 5PA1

+ 28 more — browse all 68 samples with per-sample file links →

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