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Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomas

GSE309174 Homo sapiens (human) RNA-seq (gene expression) 25 samples Submitted 2026/05/11 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 25 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
25 samples: 7 conditions, mostly with about 4 replicates eachGroups 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
Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomasFrontiers in cell and developmental biology · 2026
Summary (written by the submitters)
Background and objective: Uterine leiomyomas may arise from somatic stem or progenitor cells, leading to abnormal activation, proliferation, and clonal expansion. In organ cultures of myometrium and leiomyoma, differentiated cells decline after 7 days, whereas resident stem cells may persist within their niches and subsequently become activated, proliferate, and repopulate tissue slices.
Read the full summary ↓
This study investigated gene expression programs that regulate the proliferation and differentiation of myometrial and MED12-mutant leiomyoma stem cells during long-term organ culture. Results: Comparison of normal and tumor tissues at baseline and after culture revealed several fibroid transcriptional signatures that were preserved during prolonged ex vivo culture. The MED12 mutation persisted in the repopulated fibroid slices, supporting the hypothesis that fibroids originate from stem or progenitor cells harboring MED12 mutation. Both tissues activated hypoxia and stemness-associated programs, including robust induction of HMGA1, HMGA2, and PLAG1. Myometrium induced KITLG/KIT expression, a limited number of CD49b (ITGA2)-stem-positive and Ki67-positive proliferating cells, indicating restrained proliferation, likely mediated by upregulation of ITGA2-AS1. Additionally, myometrial slice cultures were enriched for immune and endothelial/vascular programs, including several SOX family members. In contrast, leiomyoma cultures exhibited widespread CD24/CD73 expression, focal CD49b clusters, high Ki67 positivity, metabolic reprogramming toward complex carbohydrate degradation, SLC-mediated transport, and a low-PLIN2/high-ACLY signature. Uterine leiomyoma cultures repressed genes involved in vascular homeostasis (e.g., PLPP3) and preferentially activated pathways related to smooth muscle excitability and vesicle secretion. Extracellular matrix (ECM) remodeling was strongly pro-fibrotic in leiomyomas, with significant upregulation of several TGFB-regulated and related genes, a disrupted balance of KLF regulators, including loss of the anti-fibrotic repressor KLF10 and induction of the pro-fibrotic KLF5 factor, and broad upregulation of integrins. Differential expression of multiple HOX genes further distinguished ECM regulation between tissues. From niche survival to pro-fibrotic expansion, the study delineates checkpoints primed for intervention, highlighting potential therapeutic opportunities targeting profibrotic signaling, metabolic dependencies, and integrin-mediated ECM interactions. Conclusion: Long-term organ culture recapitulates key molecular features of fibroids and reveals tissue-specific mechanisms governing stem cell activation and differentiation. These findings identify potential therapeutic opportunities and establish long-term organ culture as a robust, physiologically relevant platform for investigating normal and tumor biology.
Published in
Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomas
Vázquez P, Salas A, Beltrán-Flores S et al. · Frontiers in cell and developmental biology 2026 · PMID 42099382 · doi:10.3389/fcell.2026.1804196
This dataset
Open GSE309174 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 GSE309174_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 PRJNA1334273 and SRA study SRP627176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42099382) ↗
Study design
7 conditions, mostly with about 4 replicates each
MED12-mutated leiomyoma, freshly collected, d… ×4 MED12-mutated leiomyoma, cultured in long-ter… ×4 paired myometrium, freshly collected, day 0, ×4 paired myometrium, cultured in long-term orga… ×4 paired myometrium, cultured in long-term orga… ×3 paired myometrium, cultured in long-term orga… ×2 paired myometrium, cultured in long-term orga… ×2 MED12-mutated leiomyoma, cultured in long-ter… ×1 +1 more

Supports a between-group comparison across 23 samples.

How we read this: 7 replicated groups read from 25 sample titles; they account for 23 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
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