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Human myometrial transcriptome and DNA methylome of testosterone treated patients appear more similar to myometrium from fibroid patients

GSE288971 Homo sapiens (human) DNA methylation 105 samples Submitted 2025/06/01 Platform GPL24676Platform GPL18573
At a glance

DNA methylation · human · 105 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
105 samples: 43 × Myometrium from fibroid patient (MyoF), patient MP vs 33 × Myometrium from fibroid-free patient (MyoN), patient MP vs 19 × Myometrium from fibroid patient (MyoF), patient HF vs 7 × Myometrium from testosterone treated patient (MyoT), patient MPGroups 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
The Human Myometrial Transcriptome and the DNA Methylome of Testosterone-treated Patients Resemble the Myometria from Fibroid PatientsReproductive sciences (Thousand Oaks, Calif.) · 2025
Summary (written by the submitters)
Uterine fibroids, or leiomyomas, are noncancerous tumors of the myometrium and the most common reproductive tract tumors in women, with an incidence of up to 80% by age 50. Currently, hysterectomy is the only definitive cure, and effective non-hormonal therapeutics are lacking. Understanding the etiology of fibroids may lead to alternative, less invasive treatments.
Read the full summary ↓
Several obstetric disorders, including polycystic ovary syndrome (PCOS), have been linked to uterine fibroids, and women with PCOS often exhibit hormonal imbalances, particularly elevated serum testosterone levels. However, the impact of testosterone on the myometrium remains poorly understood. We hypothesize that elevated testosterone may increase the risk of developing uterine fibroids. Using RNA sequencing and MethylationEPIC array analysis, we compared myometrial tissue from women without fibroids (MyoN, n=33), with fibroids (MyoF, n=66), and after testosterone therapy (MyoT, n=7). The transcriptomic and methylation profiles of MyoT clustered with MyoF and were distinct from MyoN. We identified 1,321 differentially expressed protein-coding genes between MyoT and MyoN, while only 494 were found between MyoT and MyoF. Disease ontology analysis of MyoT vs. MyoN revealed enrichment of the fibroid tumor gene set. Fibroid associated genes including TGFβ3, CCND1, SERPINE1, and FGFR1 were upregulated in MyoT and MyoF samples compared to MyoN samples. The DNA methylation profiles of MyoT were closer to those of MyoF, but no correlation was observed between methylation status and gene expression. Our preliminary data suggest that testosterone induces transcriptional and methylation changes in the myometrium consistent with those observed in MyoF tissues. These findings suggest that elevated testosterone may be associated with an increased risk of developing uterine fibroids.
Published in
The Human Myometrial Transcriptome and the DNA Methylome of Testosterone-treated Patients Resemble the Myometria from Fibroid Patients
Paul EN, Carpenter TJ, Bossick A et al. · Reproductive sciences (Thousand Oaks, Calif.) 2025 · PMID 40474053 · doi:10.1007/s43032-025-01893-9
This dataset
Open GSE288971 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 GSE288971_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1220138 and SRA study SRP562054. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40474053) ↗
Study design
43 × Myometrium from fibroid patient (MyoF), patient MP vs 33 × Myometrium from fibroid-free patient (MyoN), patient MP vs 19 × Myometrium from fibroid patient (MyoF), patient HF vs 7 × Myometrium from testosterone treated patient (MyoT), patient MP

Supports a between-group comparison across 102 samples.

How we read this: 4 replicated groups read from 105 sample titles; they account for 102 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

+ 65 more — browse all 105 samples with per-sample file links →

Datasets on a similar topic

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