GEO series

RNA sequencing identifies MAP1A and PTTG1 as predictive genes of aging CD264+ human mesenchymal stem cells at early passage

GSE247950 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/02/22 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 10 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: 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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: RNA sequencing identifies MAP1A and PTTG1 as predictive genes of aging CD264(+) human mesenchymal stem cells at an early passageCytotechnology · 2025

Summary (written by the submitters)

Molecular profiles of mesenchymal stem cells (MSCs) are critically needed to standardize the composition and effectiveness of MSC therapeutics. This study employs RNA sequencing to identify genes to be used in concert with CD264 as a molecular profile of aging MSCs at a clinically relevant culture passage. CD264- and CD264+ populations were isolated by fluorescence-activated cell sorting from passage 4 MSC cultures.

Read the full summary ↓

Donor-matched CD264-/+ mRNA samples from 5 donors were subjected to pair-ended, next-generation sequencing. An independent set of 5 donor MSCs was used to validate differential expression of select genes with quantitative reverse transcription PCR. CD264+ cells accounted for 15% to 60% of the cells in MSC cultures and exhibited an aging phenotype. Pairwise differential expression analysis identified 2,322 downregulated genes and 2,695 upregulated genes in CD264+ MSCs relative to donor-matched CD264- MSCs with a Benjamini-Hochberg adjusted p-value (BH padj) < 0.1. Nearly 25% of these genes were unique to CD264-/+MSCs and not differentially expressed at a significance level of BH padj < 0.1 in previous RNA sequencing studies of early- vs. late-passage MSCs. Kyoto Encylopedia of Genes and Genomes pathways for DNA replication, cell cycle, spliceosome, RNA transport and ribosome biogenesis were downregulated in CD264+ MSCs and extracellular matrix-receptor interactions was upregulated (BH padj < 0.1). Pathway results were confirmed by Database for Annotation, Visualization, and Integrated Discovery gene set enrichment analysis. Least Absolute Shrinkage and Selection Operator regression was performed on the most significant genes and pathways and identified microtubule-associated protein 1A (MAP1A) and pituitary tumor-transforming gene 1 (PTTG1) as signature genes of CD264+ MSCs. For both the sequencing and validation sets, the combination of MAP1A and PTTG1 expression clustered MSC samples into distinct groups that had the correct CD264 classification with an accuracy of 100% (p ≤ 0.01). This study provides the first linkage of MAP1A upregulation to aging, CD264, and stem cells, and confirms previous reports of PTTG1 downregulation in aging MSCs. Our findings have application as quality metrics to standardize the composition of MSC therapies and as molecular targets to slow/reverse cellular aging.

Published in

RNA sequencing identifies MAP1A and PTTG1 as predictive genes of aging CD264(+) human mesenchymal stem cells at an early passage

Giler MK, Tucker HA, Foote AK et al. · Cytotechnology 2025 · PMID 39980838 · doi:10.1007/s10616-025-00724-8

This dataset

Open GSE247950 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 GSE247950_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 PRJNA1040958 and SRA study SRP472244. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39980838) ↗

Study design

10 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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

GSM7903667 donor 1, patient ID 7043, CD264 negative
GSM7903668 donor 1, patient ID 7043, CD264 positive
GSM7903669 donor 2, patient ID 7038, CD264 negative
GSM7903670 donor 2, patient ID 7038, CD264 postive
GSM7903671 donor 3, patient ID 7015, CD264 negative
GSM7903672 donor 3, patient ID 7015, CD264 positive
GSM7903673 donor 4, patient ID 7042, CD264 negative
GSM7903674 donor 4, patient ID 7042, CD264 positive
GSM7903675 donor 5, patient ID 7068, CD264 negative
GSM7903676 donor 5, patient ID 7068, CD264 positive

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