GEO series

Epithelial-derived IL-23 promotes oral mucosal immunopathology

GSE243173 Homo sapiens (human) RNA-seq (gene expression) 17 samples Submitted 2024/05/08 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 17 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: 17 samples: 8 × Perio vs 5 × LAD vs 4 × HealthyGroups 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: Epithelial-derived interleukin-23 promotes oral mucosal immunopathologyImmunity · 2024

Summary (written by the submitters)

At mucosal surfaces, epithelial cells provide a structural barrier and an immune defense system. However, dysregulated epithelial responses can contribute to disease states. Here, we demonstrate that epithelial intrinsic production of IL-23 triggers an inflammatory loop in the prevalent oral disease, periodontitis. Epithelial IL-23 expression localized to areas proximal to the disease-associated microbiome, is evident both in experimental models and in patients with common and genetic forms of disease.

Read the full summary ↓

Mechanistically, flagellated microbial species of the periodontitis microbiome, trigger epithelial IL-23 induction in a TLR5-dependent manner. Intriguingly, unlike other Th17-driven diseases, here non-hematopoietic cell-derived IL-23 serves as an initiator of pathogenic inflammation. Beyond periodontitis, analysis of publicly available datasets reveals expression of epithelial IL-23 in settings of infection, malignancy, and autoimmunity, suggesting a broader role for epithelial-intrinsic IL-23 in human disease. Collectively, this work highlights an unappreciated role for the barrier epithelium in the induction of IL-23-mediated inflammation.

Published in

Epithelial-derived interleukin-23 promotes oral mucosal immunopathology

Kim TS, Ikeuchi T, Theofilou VI et al. · Immunity 2024 · PMID 38513665 · doi:10.1016/j.immuni.2024.02.020

This dataset

Open GSE243173 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 GSE243173_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 PRJNA1016477 and SRA study SRP460361. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38513665) ↗

Study design

8 × Perio vs 5 × LAD vs 4 × Healthy

Supports a between-group comparison across 17 samples.

How we read this: 3 replicated groups read from 17 sample titles; they account for 17 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

GSM7780224 Healthy 1 Healthy
GSM7780225 Healthy 2 Healthy
GSM7780226 Healthy 3 Healthy
GSM7780227 Healthy 4 Healthy
GSM7780228 Perio 1 Perio
GSM7780229 Perio 2 Perio
GSM7780230 Perio 3 Perio
GSM7780231 Perio 4 Perio
GSM7780232 Perio 5 Perio
GSM7780233 Perio 6 Perio
GSM7780234 Perio 7 Perio
GSM7780235 Perio 8 Perio
GSM7780236 LAD 1 LAD
GSM7780237 LAD 2 LAD
GSM7780238 LAD 3 LAD
GSM7780239 LAD 4 LAD
GSM7780240 LAD 5 LAD

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