From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells
Abstract With the significant challenges in using human embryonic stem cells (ESCs) for research and clinical applications, there is a growing impetus to seek alternative pluripotent cell sources. Embryonic stem-like (ES-like) cells emerge as a promising avenue in this pursuit. Our research demonstr...
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BMC
2025-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11612-y |
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| author | Nima Ghasemi Hossein Azizi Ali Qorbanee Thomas Skutella |
| author_facet | Nima Ghasemi Hossein Azizi Ali Qorbanee Thomas Skutella |
| author_sort | Nima Ghasemi |
| collection | DOAJ |
| description | Abstract With the significant challenges in using human embryonic stem cells (ESCs) for research and clinical applications, there is a growing impetus to seek alternative pluripotent cell sources. Embryonic stem-like (ES-like) cells emerge as a promising avenue in this pursuit. Our research demonstrates the potential for deriving ES-like cells from spermatogonial stem cells (SSCs) in a time-dependent manner under defined culture conditions. To better understand this process, we investigated the gene expression dynamics and underlying pathways associated with ES-like cell generation from SSCs. A deeper understanding of the signaling pathways underlying this biological process can lead us to refine protocols for ES-like cell generation, which could catalyze the development of more efficient and expedited methodologies inspired by the derivation pathway for future research in regenerative medicine. To identify differentially expressed genes (DEGs), we analyzed publicly available microarray data from murine cells obtained from the Gene Expression Omnibus (GEO). This analysis enabled the prediction of protein–protein interactions (PPIs), which were subsequently used for pathway enrichment analysis to identify biologically relevant pathways. Complementing these computational findings, we conducted in vitro experiments, including Fluidigm qPCR and immunostaining. These experiments serve as validation for our microarray data and the DEGs identified, providing reassurance about the reliability of our research. Among the identified enriched pathways in our investigation are the Toll-like receptor (TLR), GDNF/RET, interleukins (ILs), FGF/FGFR, and SMAD signaling pathway, along with the activation of NIMA kinases. Additionally, miR-410-3p, miRNA let-7e, Miat, and Xist are among some of the predicted non-coding RNAs. |
| format | Article |
| id | doaj-art-b6b01b09f8324a56ae81c63e8d2be9e0 |
| institution | DOAJ |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-b6b01b09f8324a56ae81c63e8d2be9e02025-08-20T02:55:31ZengBMCBMC Genomics1471-21642025-04-0126111610.1186/s12864-025-11612-yFrom unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cellsNima Ghasemi0Hossein Azizi1Ali Qorbanee2Thomas Skutella3Department of Applied Biotechnology and System Biology, College of Biotechnology, Amol University of Special Modern TechnologiesDepartment of Stem Cells and Cancer, College of Biotechnology, Amol University of Special Modern TechnologiesDepartment of Surgery, Faculty of General of Medicine, Koya UniversityInstitute for Anatomy and Cell Biology, Medical Faculty, University of HeidelbergAbstract With the significant challenges in using human embryonic stem cells (ESCs) for research and clinical applications, there is a growing impetus to seek alternative pluripotent cell sources. Embryonic stem-like (ES-like) cells emerge as a promising avenue in this pursuit. Our research demonstrates the potential for deriving ES-like cells from spermatogonial stem cells (SSCs) in a time-dependent manner under defined culture conditions. To better understand this process, we investigated the gene expression dynamics and underlying pathways associated with ES-like cell generation from SSCs. A deeper understanding of the signaling pathways underlying this biological process can lead us to refine protocols for ES-like cell generation, which could catalyze the development of more efficient and expedited methodologies inspired by the derivation pathway for future research in regenerative medicine. To identify differentially expressed genes (DEGs), we analyzed publicly available microarray data from murine cells obtained from the Gene Expression Omnibus (GEO). This analysis enabled the prediction of protein–protein interactions (PPIs), which were subsequently used for pathway enrichment analysis to identify biologically relevant pathways. Complementing these computational findings, we conducted in vitro experiments, including Fluidigm qPCR and immunostaining. These experiments serve as validation for our microarray data and the DEGs identified, providing reassurance about the reliability of our research. Among the identified enriched pathways in our investigation are the Toll-like receptor (TLR), GDNF/RET, interleukins (ILs), FGF/FGFR, and SMAD signaling pathway, along with the activation of NIMA kinases. Additionally, miR-410-3p, miRNA let-7e, Miat, and Xist are among some of the predicted non-coding RNAs.https://doi.org/10.1186/s12864-025-11612-ySpermatogonial stem cellsEmbryonic stem-like cellsMicroarray analysisPPI networkSignaling pathwaysmiRNA and lncRNA |
| spellingShingle | Nima Ghasemi Hossein Azizi Ali Qorbanee Thomas Skutella From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells BMC Genomics Spermatogonial stem cells Embryonic stem-like cells Microarray analysis PPI network Signaling pathways miRNA and lncRNA |
| title | From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells |
| title_full | From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells |
| title_fullStr | From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells |
| title_full_unstemmed | From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells |
| title_short | From unipotency to pluripotency: deciphering protein networks and signaling pathways in the generation of embryonic stem-like cells from murine spermatogonial stem cells |
| title_sort | from unipotency to pluripotency deciphering protein networks and signaling pathways in the generation of embryonic stem like cells from murine spermatogonial stem cells |
| topic | Spermatogonial stem cells Embryonic stem-like cells Microarray analysis PPI network Signaling pathways miRNA and lncRNA |
| url | https://doi.org/10.1186/s12864-025-11612-y |
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