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

## TL;DR

This study uses RNA sequencing to identify genes that predict aging in CD264+ human mesenchymal stem cells, offering potential for improving stem cell therapies.

## Contribution

The study identifies MAP1A and PTTG1 as novel predictive genes for aging CD264+ mesenchymal stem cells.

## Key findings

- CD264+ MSCs showed an aging phenotype compared to CD264− MSCs.
- MAP1A and PTTG1 accurately classified CD264 status with 100% accuracy.
- MAP1A is newly linked to CD264, aging, and senescence.

## Abstract

Molecular profiles of mesenchymal stem cells (MSCs) are 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. CD264+ MSCs exhibited an aging phenotype relative to their CD264− counterpart. 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. 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. Least Absolute Shrinkage and Selection Operator regression identified microtubule-associated protein 1A (MAP1A) and pituitary tumor-transforming gene 1 (PTTG1) as predictive genes of CD264+ MSCs. Combined MAP1A and PTTG1 expression correctly classified CD264 status of MSC samples with an accuracy of 100%. Differential expression and predictive ability of MAP1A and PTTG1 compared favorably with that of existing senescence markers expressed in early passage CD264−/+ MSCs. This study provides the first linkage of MAP1A to CD264, aging and senescence. Our findings have application as quality metrics to standardize the composition of MSC therapies and as molecular targets to slow/reverse cellular aging.

The online version contains supplementary material available at 10.1007/s10616-025-00724-8.