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Applied Sciences
Volume 15
Issue 18
10.3390/app15189881
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Exploratory Analysis of Differentially Expressed Genes for Distinguishing Adipose-Derived Mesenchymal Stroma/Stem Cells from Fibroblasts

by
Masami Kanawa
1,*,
Katsumi Fujimoto
2,
Tania Saskianti
3,
Ayumu Nakashima
4,5 and
Takeshi Kawamoto
1,6
1
Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima 734-8533, Japan
2
Department of Molecular Biology and Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8533, Japan
3
Department of Pediatric Dentistry, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
4
Department of Stem Cell Biology and Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8533, Japan
5
Department of Nephrology, Graduate School of Medicine, University of Yamanashi, Yamanashi 409-3898, Japan
6
Writing Center, Hiroshima University, Higashi-Hiroshima 739-8512, Japan
*
Author to whom correspondence should be addressed.
Appl. Sci. 2025, 15(18), 9881; https://doi.org/10.3390/app15189881 (registering DOI)
Submission received: 12 August 2025 / Revised: 3 September 2025 / Accepted: 8 September 2025 / Published: 9 September 2025
Versions Notes

Abstract

Adipose-derived mesenchymal stromal/stem cells (AT-MSCs) can be typically isolated from adipose tissue using a minimally invasive procedure. However, since AT-MSCs are usually obtained from subcutaneous tissue, there is a risk of contamination with fibroblasts (FBs), which can reduce the differentiation potential of AT-MSCs. To avoid this contamination, it is crucial to identify specific markers to effectively distinguish AT-MSCs from FBs. Analysis of microarray data obtained from three studies (GSE9451, GSE66084, GSE94667, and GSE38947) revealed 123 genes expressed at levels more than 1.5-fold higher in AT-MSCs compared to FBs. Using STRING, a protein–protein interaction (PPI) network consisting of 80 nodes and 197 edges was identified within the 123 genes. Further investigation using Molecular Complex Detection in Cytoscape identified a module of 12 genes: COL3A1, FBN1, COL4A1, COL5A2, POSTN, CTGF, SPARC, HSPG2, FSTL1, LAMA2, LAMC1, COL16A1. Gene Ontology analysis revealed that these genes were enriched in extracellular region (GO: 0005576). Additionally, these 12 genes corresponded to the top 12 of the 15 hub genes calculated using the Maximal Clique Centrality algorithm. The results of this study suggest that these 12 genes may serve as markers for distinguishing AT-MSCs from FBs, offering potential applications in regenerative medicine.
Keywords: adipose-derived mesenchymal stem cells; gene markers; extracellular matrix; fibroblasts; hub genes; protein–protein interaction (PPI) network adipose-derived mesenchymal stem cells; gene markers; extracellular matrix; fibroblasts; hub genes; protein–protein interaction (PPI) network

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MDPI and ACS Style

Kanawa, M.; Fujimoto, K.; Saskianti, T.; Nakashima, A.; Kawamoto, T. Exploratory Analysis of Differentially Expressed Genes for Distinguishing Adipose-Derived Mesenchymal Stroma/Stem Cells from Fibroblasts. Appl. Sci. 2025, 15, 9881. https://doi.org/10.3390/app15189881

AMA Style

Kanawa M, Fujimoto K, Saskianti T, Nakashima A, Kawamoto T. Exploratory Analysis of Differentially Expressed Genes for Distinguishing Adipose-Derived Mesenchymal Stroma/Stem Cells from Fibroblasts. Applied Sciences. 2025; 15(18):9881. https://doi.org/10.3390/app15189881

Chicago/Turabian Style

Kanawa, Masami, Katsumi Fujimoto, Tania Saskianti, Ayumu Nakashima, and Takeshi Kawamoto. 2025. "Exploratory Analysis of Differentially Expressed Genes for Distinguishing Adipose-Derived Mesenchymal Stroma/Stem Cells from Fibroblasts" Applied Sciences 15, no. 18: 9881. https://doi.org/10.3390/app15189881

APA Style

Kanawa, M., Fujimoto, K., Saskianti, T., Nakashima, A., & Kawamoto, T. (2025). Exploratory Analysis of Differentially Expressed Genes for Distinguishing Adipose-Derived Mesenchymal Stroma/Stem Cells from Fibroblasts. Applied Sciences, 15(18), 9881. https://doi.org/10.3390/app15189881

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