Comparative Transcriptomic Profiling of Mesenchymal Stem Cells from Distinct Tissue Origins and Isolation Methods Highlights the Stability and Immunomodulatory Signature of Umbilical Cord-Derived Smumf Cells

Nov 24, 2025Tissue engineering and regenerative medicine

Gene Activity Comparison of Stem Cells from Different Tissues and Isolation Methods Shows Stable Immune-Regulating Features in Umbilical Cord-Derived Stem Cells

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Regenerative Health on OpenScience ↗PubMed ↗DOI ↗OA ↗

Abstract

Fetal mesenchymal stem cells (MSCs) exhibited 2,208 upregulated and 2,594 downregulated genes compared to adult MSCs.

Distinct transcriptomic profiles were observed between fetal MSCs (from umbilical cord) and adult MSCs (from bone marrow and adipose tissue).
Key transcription factors such as E2F1 and NF-κB1 were enriched in fetal MSCs.
Fetal MSCs were associated with enhanced pathways related to glycolysis, cholesterol biosynthesis, and TNF-α signaling.
Transcriptomic stability was noted in smumf cells, with only 12 differentially expressed genes identified between early and late passages.
smumf cells demonstrated improved innate immune responses and cholesterol metabolism compared to enzymatically isolated umbilical cord MSCs.

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BACKGROUND: Mesenchymal stem cells (MSCs) derived from bone marrow (BM), adipose tissue (AD), and umbilical cord (UC) exhibit therapeutic potential in regenerative medicine. However, their properties, including transcriptomic profiles, vary based on tissue origin, passage stage, and isolation method, complicating their clinical standardization. Addressing these unresolved differences requires comprehensive approaches, such as RNA sequencing, to analyze transcriptomic profiles in detail.

METHODS: In this study, RNA-seq was employed to analyze MSC transcriptomes from BM, AD, and UC tissues. UC MSCs were isolated using enzymatic digestion or the Minimal Cube Explant (MCE) method (smumf cells), and transcriptomes of early (P3-4) and late (P10) passages of smumf cells were compared. Differentially expressed genes (DEGs) were identified, followed by transcription factor (TF) and pathway analyses.

RESULTS: Fetal MSCs (UC and smumf cells) exhibited distinct transcriptomic profiles compared to adult MSCs (BM and AD), with 2,208 upregulated and 2,594 downregulated DEGs. Key transcription factors, such as E2F1 and NF-κB1, and pathways, including glycolysis, cholesterol biosynthesis, and TNF-α signaling, were enriched in fetal MSCs. smumf cells demonstrated transcriptomic stability between early and late passages, with only 12 DEGs identified. Additionally, smumf cells showed enhanced innate immune responses and cholesterol metabolism compared to enzymatically isolated UC MSCs.

CONCLUSION: This study provides a comprehensive transcriptomic comparison of MSCs, highlighting the superior transcriptional stability, immunomodulatory capacity, and metabolic flexibility of fetal MSCs, particularly smumf cells. These findings underscore their potential as a reliable cell source for therapeutic applications and encourage further exploration of their clinical application.

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Comparative Transcriptomic Profiling of Mesenchymal Stem Cells from Distinct Tissue Origins and Isolation Methods Highlights the Stability and Immunomodulatory Signature of Umbilical Cord-Derived Smumf Cells

Abstract

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