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Amniotic Fluid Reduces Liver Fibrosis By Attenuating Hepatic Stellate Cell Activation

GSE290015 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2025/03/17 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 7 conditions, mostly in triplicateGroups 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
Amniotic Fluid Reduces Liver Fibrosis By Attenuating Hepatic Stellate Cell ActivationbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Background & Aims: Persistent activation of hepatic stellate cells (HSCs) drives liver fibrosis, marked by myofibroblast activation (MFA) and epithelial-mesenchymal transition (EMT). Strategies to prevent or reverse this will be critical to treat liver fibrosis successfully. We previously showed that full-term, cell-free human amniotic fluid (cfAF) inhibits MFA and EMT in fibroblasts in vitro.
Read the full summary ↓
We hypothesize that cfAF treatment can attenuate HSC activation and limit liver fibrosis. Methods: HSC activation was assessed using murine models of acute (DMN) and chronic (CCl4) liver damage, three-dimensional hepatic spheroids, and HSC cultures. EMT and MFA were induced in vitro using ethanol (spheroids) or TGFβ (HSCs) and evaluated via scratch assays, multi-omics approaches, and RNA/protein analyses. Results: cfAF treatment prevented weight loss in mice with chronic liver damage without adverse events. Histological analysis revealed a modest reduction in fibrosis with preserved liver architecture in both chronic and acute murine liver damage models. Gene expression profiling and immunostaining indicated cfAF administration to CCl4-treated mice led to reduced EMT- and MFA-related biomarkers along with changes in transcripts associated with liver metabolism, immune regulatory pathways, and cell signaling. In hepatic spheroids exposed to ethanol cfAF treatment lowered COL1A1 protein levels and smooth muscle actin (SMA) RNA abundance in a dose-dependent manner. Treating primary or LX2 hepatic stellate cells with cfAF strongly represses EMT, and multi-omics analyses revealed that it also attenuates TGFβ-induced MFA and the inflammatory phenotype. Thus cfAF treatment prevents liver fibrosis by safeguarding hepatic stellate cell activation. Conclusions: cfAF treatment limits liver fibrosis by repressing HSC activation in liver fibrosis models. These findings suggest cfAF may be a safe and effective therapy for reducing liver fibrosis and preventing the development of cirrhosis and/or hepatocellular carcinoma.
Published in
Amniotic Fluid Reduces Liver Fibrosis By Attenuating Hepatic Stellate Cell Activation
Bowen CM, Ditmars F, Liu N et al. · bioRxiv : the preprint server for biology 2025 · PMID 40027749 · doi:10.1101/2025.02.20.639215
This dataset
Open GSE290015 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 GSE290015_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 PRJNA1225741 and SRA study SRP565073. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40027749) ↗
Study design
7 conditions, mostly in triplicate
LX2 cells; control DMEM only; biol ×3 LX2 cells; DMEM + 25% cell-free amniotic flui… ×3 DMEM + 1 uM A-83-01; biol ×3 DMEM + 10 ng/ml TGF-beta; biol ×3 DMEM + 10 ng/ml TGF-beta then + 1 uM A-83-01;… ×3 DMEM + 10 ng/ml TGF-beta then + 25% cell-free… ×3 DMEM + 10 ng/ml TGF-beta then + DMEM; biol ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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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