SavedAdd your journal

Journals / Afyon Kocatepe Üniversitesi Fen ve Mühendislik Bilimleri Dergisi / 2026 / Cilt: 26 Sayı: 4

Comparative Bioinformatics Analysis of Transcriptomic Signatures and Regulatory Networks in BM-MSCs and UCB-MSCs: Molecular Insights for Regenerative Medicine

Kİ-MKH’ler ve GKK-MKH’lerdeki Transkriptomik İmzaların ve Düzenleyici Ağların Karşılaştırmalı Biyoinformatik Analizi: Rejeneratif Tıp İçin Moleküler Çıkarımlar

Ahmet Karakuş(BARTIN ÜNİVERSİTESİ)0000-0003-1458-808X
Pages
803–813
Publication Date
2026-08-03
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

This study provides a strategic framework for resource selection and emphasizes that MSC selection should be tailored to the specific pathological requirements of clinical practice.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Mesenchymal stem cells (MSCs) play a crucial role in regenerative medicine due to their multifaceted potential and immunomodulatory effects.
📊
Key Findings & Data:This study investigates molecular heterogeneity between bone marrow-derived (BM-MSC) and umbilical cord blood-derived (UCB-MSC) sources using an integrative bioinformatics approach on the GSE6029 dataset.
💡
Conclusion & Impact:This study provides a strategic framework for resource selection and emphasizes that MSC selection should be tailored to the specific pathological requirements of clinical practice.
🔬Design:Araştırma Makalesi
📍Scope:Comprehensive Sample
⚙️Variables:Mezenkimal kök hücre · Transkriptomik · Biyoinformatik analiz

Abstract

Mesenchymal stem cells (MSCs) play a crucial role in regenerative medicine due to their multifaceted potential and immunomodulatory effects. This study investigates molecular heterogeneity between bone marrow-derived (BM-MSC) and umbilical cord blood-derived (UCB-MSC) sources using an integrative bioinformatics approach on the GSE6029 dataset. The analysis identified 739 differentially expressed genes (DEGs); 374 of these were upregulated in UCB-MSCs and 365 in BM-MSCs. UCB-MSCs exhibited a rich transcriptomic profile in terms of RNA processing, proteasome, and spliceosome pathways, controlled by key genes such as MYC and HSPA4. In contrast, BM-MSCs showed significant enrichment in PI3K-Akt signaling, ECM-receptor interactions, and constitutive development. At the heart of this enrichment were the COL4A1 and MET genes. Post-transcriptional mapping identified miR-20b-5p as a key regulator in UCB-MSCs, while miR-15a-5p and miR-26a-5p were dominant in the BM-MSC regulatory network. These findings demonstrate that UCB-MSCs are molecularly specialized for rapid proliferation and immunomodulation, while BM-MSCs are optimized for structural integration and orthopedic repair. This study provides a strategic framework for resource selection and emphasizes that MSC selection should be tailored to the specific pathological requirements of clinical practice.

Özet

Mezenkimal kök hücreler (MSC'ler), çok yönlü potansiyelleri ve immünomodülatör etkileri nedeniyle rejeneratif tıpta çok önemli bir role sahiptir.Bu çalışma, GSE6029 veri kümesi üzerinde bütünleyici bir biyoinformatik yaklaşım kullanarak kemik iliğinden elde edilen (BM-MSC) ve göbek kordonu kanından elde edilen (UCB-MSC) kaynaklar arasındaki moleküler heterojenliği araştırmaktadır. Analiz sonucunda 739 farklı şekilde ifade edilen gen (DEG) belirlendi; bunlardan 374'ü UCB-MSC'lerde, 365'i ise BM-MSC'lerde yukarı doğru düzenlenmişti. UCB-MSC'ler, MYC ve HSPA4 gibi anahtar genler tarafından kontrol edilen, RNA işleme, proteazom ve splaysom yolları açısından zengin bir transkriptomik profil sergiledi. Bunun aksine, BM-MSC'ler PI3K-Akt yolağında, ECM-reseptör etkileşimlerinde ve yapısal gelişimde önemli ölçüde zenginleşme gösterdi; bu zenginleşmenin merkezinde COL4A1 ve MET genleri yer alıyordu. Transkripsiyon sonrası haritalama, UCB-MSC'lerde miR-20b-5p'yi kilit bir düzenleyici olarak tanımlarken, BM-MSC’lerde miR-15a-5p ve miR-26a-5p baskın konumdaydı. Bulgular, UCB-MSC'lerin hızlı çoğalma ve immünomodülasyon için moleküler olarak özelleşmiş olduğunu, BM-MSC'lerin ise yapısal entegrasyon ve ortopedik onarım için optimize edildiğini göstermektedir. Bu çalışma, kaynak seçimi için stratejik bir çerçeve sunmakta ve MSC seçiminin klinikte spesifik patolojik gereksinimlerine göre uyarlanması gerektiğini vurgulamaktadır.

🔖

Cite This Article

Karakuş, A. (2026). Comparative Bioinformatics Analysis of Transcriptomic Signatures and Regulatory Networks in BM-MSCs and UCB-MSCs: Molecular Insights for Regenerative Medicine. Afyon Kocatepe Üniversitesi Fen ve Mühendislik Bilimleri Dergisi, Cilt: 26 Sayı: 4, 803–813. https://doi.org/10.35414/akufemubid.1850855

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (33)

  1. Andrzejewska, A., Lukomska, B. and Janowski, M., 2019. Concise review: Mesenchymal stem cells: from roots to boost. Stem Cells, 37(7), 855-864.
  2. Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., Marshall, K. A., Phillippy, K. H., Sherman, P. M., Holko, M., Yefanov, A., Lee, H., Zhang, N., Robertson, C. L., Serova, N., Davis, S. & Soboleva, A., 2013. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Research, 41(D1), D991-D995.
  3. Batsali, A. K., Kastrinaki, M. C., Papadaki, H. A. and Pontikoglou, C., 2019. Mesenchymal stem cells derived from Wharton's Jelly of the umbilical cord: biological properties and emerging clinical applications. Current Stem Cell Research & Therapy, 14, 58-71.
  4. Chang, L., Zhou, G., Soufan, O. and Xia, J., 2022. miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology. Nucleic Acids Research, 50, W217-W227.
  5. Chin, C. H., Chen, S. H., Wu, H. H., Ho, C. W., Ko, M. T. and Lin, C. Y., 2014. CytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Systems Biology, 8, S11.
  6. Ding, D. C., Chang, Y. H., Shyu, W. C. and Lin, S. Z., 2015. Human umbilical cord mesenchymal stem cells: a new era for stem cell therapy. Cell Transplantation, 24(3), 339-347.
  7. Dominici, M., Le Blanc, K., Mueller, I., Slaper-Cortenbach, I., Marini, F., Krause, D., Deans, R., Keating, A., Prockop, Dj. and Horwitz, E., 2006. Minimal criteria for defining multipotent mesenchymal stromal cells. The International Society for Cellular Therapy position statement. Cytotherapy, 8(4), 315-317.
  8. Ge, S. X., Jung, D. and Yao, R., 2020. ShinyGO: a graphical enrichment tool for animals and plants. Bioinformatics, 36, 2628-2629.
  9. Han, X. and Fan, Z., 2021. MicroRNAs regulation in osteogenic differentiation of mesenchymal stem cells. Frontiers in Dental Medicine, 2, 747068.
  10. Han, Y., Li, X., Zhang, Y., Han, Y., Chang, F. and Ding, J., 2019. Mesenchymal Stem Cells for Regenerative Medicine. Cells, 8(8), 886.
  11. Hass, R., Kasper, C., Böhm, S. and Jacobs, R., 2011. Different populations and sources of human mesenchymal stem cells (MSC): A comparison of adult and neonatal tissue-derived MSC. Cell Community Signaling, 9, 12.
  12. Heo, J. S., Choi, Y., Kim, H. O., 2016. Comparison of molecular profiles of human mesenchymal stem cells derived from bone marrow, umbilical cord blood, placenta, and adipose tissue. International Journal of Molecular Medicine, 37, 115-125.
  13. Hou, W., Duan, L., Huang, C., Li, X., Xu, X., Qin, P., Hong, N., Wang, D. and Jin, W., 2021. Cross-tissue characterization of heterogeneities of mesenchymal stem cells and their differentiation potentials. Frontiers in Cell and Developmental Biology, 9, 781021.
  14. Infante, A. and Rodriguez, C. I., 2018. Osteogenesis and aging: lessons from mesenchymal stem cells. Stem Cell Research & Therapy, 9(1), 244.
  15. Jones, E. and McGonagle, D., 2008. Human bone marrow mesenchymal stem cells in vivo. Rheumatology, 47, 126-131.
  16. Keenan, A. B., Torre, D., Lachmann, A., Leong, J., Wojciechowicz, K. and Ma'ayan, A., 2019. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research, 47, W212-W224.
  17. Kostadinova, M., Raykovska, M., Simeonov, R., Lolov, S. and Mourdjeva, M., 2025. Recent advances in bone tissue engineering: enhancing the potential of mesenchymal stem cells for regenerative therapies. Current Issues in Molecular Biology, 47(4), 287.
  18. Kuçi, S., Kuçi, Z., Schäfer, R., Spohn, G., Winter, S., Schwab, M., Salzmann-Manrique, E., Klingebiel, T. and Bader, P., 2019. Molecular signature of human bone marrow-derived mesenchymal stromal cell subsets. Scientific Reports, 9(1), 1774.
  19. Li, C. Y., Wu, X. Y., Tong, J. B., Yang, X. X., Zhao, J. L., Zheng, Q. F., Zhao, G. B. and Ma, Z. J., 2015. Comparative analysis of human mesenchymal stem cells from bone marrow and adipose tissue under xeno-free conditions for cell therapy. Stem Cell Research & Therapy, 6(1), 55.
  20. Markov, V., Kusumi, K., Tadesse, M. G., William, D. A., Hall, D. M., Lounev, V., Carlton, A., Leonard, J., Cohen, R. I., Rappaport, E. F., Saitta, B., 2007. Identification of cord blood-derived mesenchymal stem/stromal cell populations with distinct growth kinetics, differentiation potentials, and gene expression profiles. Stem Cells and Development, 16(1), 53-73.
  21. Nagamura-Inoue, T. and He, H., 2014. Umbilical cord-derived mesenchymal stem cells: Their advantages and potential clinical utility. World Journal of Stem Cells, 6(2), 195-202.
  22. Nekanti, U., Mohanty, L., Venugopal, P., Balasubramanian, S., Totey, S. and Ta, M., 2010. Optimization and scale-up of Wharton's jelly-derived mesenchymal stem cells for clinical applications. Stem Cell Research, 5(3), 244-254.
  23. Pittenger, M. F., Discher, D. E., Péault, B. M., Phinney, D. G., Hare, J. M. and Caplan, A. I., 2019. Mesenchymal stem cell perspective: cell biology to clinical progress. NPJ Regenerative Medicine, 4(1), 22.
  24. Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W. & Smyth, G. K., 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47.
  25. Rojewski, M. T., Weber, B. M. and Schrezenmeier, H., 2008. Phenotypic characterization of mesenchymal stem cells from various tissues. Transfusion Medicine and Hemotherapy, 35(3), 168-184.
  26. Shakya, M., Lo, C. C. and Chain, P. S. G., 2019. Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics, 10, 904.
  27. Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Jensen, L. J. and von Mering, C., 2021. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research, 49, D605-D612.
  28. Wang, Q., Li, J., Wang, S., Deng, Q., Wang, K., Dai, X., An, Y., Dong, G., Ke, W., Chen, F. and Liu, L., 2021. Single-cell transcriptome profiling reveals molecular heterogeneity in human umbilical cord tissue and culture-expanded mesenchymal stem cells. FEBS Journal, 288(18), 5311-5330.
  29. Wang, Y., Chen, X., Cao, W. and Shi, Y., 2014. Plasticity of mesenchymal stem cells in immunomodulation: pathological and therapeutic implications. Nature Immunology, 15(11), 1009-1016.
  30. Wilson, A., Murphy, M. J., Oskarsson, T., Kaloulis, K., Bettess, M. D., Oser, G. M., Pasche, A. C., Knabenhans, C., Macdonald, H. R. and Trumpp, A., 2008. c-Myc controls the balance between hematopoietic stem cell self-renewal and differentiation. Genes & Development, 22, 2118-2123.
  31. Xu, X., Wang, Y., Tan, X., Hu, Y., Zhang, X., Zhang, M., Wang, Y., Wu, J. and Hou, Y., 2024. Intravenous application of human umbilical cord mesenchymal stem cells alleviate neuropathic pain by suppressing microglia activation in rats. Heliyon, 10(13), e33340.
  32. Yuan, Y. L., Huang, Q., Li, S., Zhang, X. and Wang, W. L., 2025. The role of heat shock proteins in tumorigenesis and their potential as targets for anti-tumor therapy. Stem Cell Research & Therapy, 178379.
  33. Zhang, C., Han, X., Liu, J., Chen, L., Lei, Y., Chen, K., Si, J., Wang, T., Zhou, H., Zhao, X. and Zhang, X., 2022. Single-cell transcriptomic analysis reveals the cellular heterogeneity of mesenchymal stem cells. Genomics, Proteomics & Bioinformatics, 20(1), 70-86.