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Serotonin attenuates tumor-necrosis-factor-alpha-induced intestinal inflammation by interacting with human mucosal tissue

GSE269175 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/03/12 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 14 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
14 samples: 4 × Control intestinal organoid, TNFa treated, vs 4 × Control intestinal organoid, serotonin hydrochloride treated, vs 3 × Control intestinal organoid, untreated, vs 3 × Control intestinal organoid, TNFa+serotonin hydrochloride treated,Groups 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
Serotonin attenuates tumor necrosis factor-induced intestinal inflammation by interacting with human mucosal tissueExperimental & molecular medicine · 2025
Summary (written by the submitters)
The intestine houses the largest immune system and is serviced by the largest and most complex peripheral nervous system in the human body. The gut-brain axis orchestrates communication between the central and enteric nervous systems, playing a pivotal role in regulating overall body function and intestinal homeostasis. Using a human 3D in vitro model, we investigated the effect of serotonin, a neuromodulator produced in the gut, on immune cell and intestinal tissue interactions.
Read the full summary ↓
Our findings revealed that serotonin attenuates the tumor-necrosis-factor-alpha-induced pro-inflammatory response, mostly by affecting the expression of chemokines. Serotonin was found to impact tissue-migrating monocytes’ phenotype and distribution, without direct contact with the cells, by remodeling the intestinal tissue. Collectively, using fully human model of intestine, our results show that serotonin has a crucial role in communication among gut-brain axis components and regulates monocyte migration and plasticity, thereby contributing to gut homeostasis and the progression of intestinal inflammation. In vivo studies focused on role of neuromodulators in gut homeostasis and inflammation have shown controversial results, highlighting importance of development of human experimental models. Moreover, our results emphasize importance of human health research in human-cell-based models and suggests serotonin signaling pathway as new therapeutic target for inflammatory bowel disease.
Published in
Serotonin attenuates tumor necrosis factor-induced intestinal inflammation by interacting with human mucosal tissue
Bosáková V, Papatheodorou I, Kafka F et al. · Experimental & molecular medicine 2025 · PMID 39894823 · doi:10.1038/s12276-025-01397-1
This dataset
Open GSE269175 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 GSE269175_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 PRJNA1120458 and SRA study SRP512023. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39894823) ↗
Study design
4 × Control intestinal organoid, TNFa treated, vs 4 × Control intestinal organoid, serotonin hydrochloride treated, vs 3 × Control intestinal organoid, untreated, vs 3 × Control intestinal organoid, TNFa+serotonin hydrochloride treated,

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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
Datasets on a similar topic

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