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HMGA2 overexpression induces plasticity in myometrial cells and a transcriptomic profile more similar to that of uterine fibroids

GSE268710 Homo sapiens (human) RNA-seq (gene expression) 61 samples Submitted 2024/08/14 Platform GPL24676Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 61 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
61 samples: 32 × Myometrium from fibroid-free patient (MyoN), patient MP vs 22 × HMGA2 fibroid (HMGA2F), patient MP vs 3 × TERT immortalized myometrium cells depleted for CRIP1 transduced with a control lentivirus passage vs 3 × TERT immortalized myometrium cells depleted for CRIP1 transduced with an HMGA2 lentivirus passageGroups 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
HMGA2 overexpression induces plasticity in myometrial cells and a transcriptomic profile more similar to that of uterine fibroidsF&S science · 2024
Summary (written by the submitters)
Objective: To study the possible role for HMGA2 overexpression in differentiated myometrial cells and its potential to induce a stem cell-like or dedifferentiating phenotype and drive fibroid development. Design: Myometrial cells were immortalized and transduced with an HMGA2 lentivirus to produce HMGA2hi cells. In vitro stem cell assays were conducted, and ribonucleic acid from HMGA2hi and control cells as well as fibroid-free myometrial and HMGA2 fibroid (HMGA2F) tissues were submitted for ribonucleic acid sequencing.
Read the full summary ↓
Setting: University research laboratory. Patient(s): Women who underwent hysterectomy for symptomatic uterine fibroids or other gynecological conditions. Intervention(s): Not applicable. Main Outcome Measure(s): In vitro stem cell-like properties from myometrial cell lines. Ribonucleic acid sequencing and collagen production of HMGA2-overexpressing primary leiomyoma tissue and cell lines. Result(s): HMGA2hicellshadenhancedself-renewalcapacity,decreasedproliferation,andagreaterabilitytodifferentiateintoother mesenchymal cell types. HMGA2hi cells exhibited a stem cell-like signature and shared transcriptomic similarities with HMGA2F. Moreover, dysregulated extracellular matrix pathways were observed in both HMGA2hi cells and HMGA2F. Conclusion(s): Our findings show that HMGA2 overexpression may drive myometrial cells to dedifferentiate into a more plastic phenotype and provide evidence for an alternative mechanism for fibroid etiology, suggesting that fibroids arise not only from a mutated stem cell but also from a mutated differentiated myometrial cell.
Published in
HMGA2 overexpression induces plasticity in myometrial cells and a transcriptomic profile more similar to that of uterine fibroids
Paul EN, Carpenter TJ, Pavliscak LA et al. · F&S science 2024 · PMID 39025326 · doi:10.1016/j.xfss.2024.07.006
This dataset
Open GSE268710 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 GSE268710_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 PRJNA1118308. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39025326) ↗
Study design
32 × Myometrium from fibroid-free patient (MyoN), patient MP vs 22 × HMGA2 fibroid (HMGA2F), patient MP vs 3 × TERT immortalized myometrium cells depleted for CRIP1 transduced with a control lentivirus passage vs 3 × TERT immortalized myometrium cells depleted for CRIP1 transduced with an HMGA2 lentivirus passage

Supports a case/control comparison: 55 samples read as cases, 3 as controls.

How we read this: 4 replicated groups read from 61 sample titles; they account for 60 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

+ 21 more — browse all 61 samples with per-sample file links →

Datasets on a similar topic

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