Kondrogenezde Gen İfade Kalıpları ve Fenotipik İlişkiler: İskelet Displazisi Nozolojisine Dair Yaklaşımlar

Yıl 2024, Cilt: 46 Sayı: 4, 570 - 584, 16.07.2024

Beren Karaosmanoğlu , M. Samil Ozisin , Gozde Imren , Ekim Zihni Taşkıran

https://doi.org/10.20515/otd.1493433

Öz

Kondrogenez olarak bilinen mezenkimal kök hücrelerin (MKH) kondrositlere farklılaşması, kıkırdak oluşumu ve iskelet gelişiminde temel rol oynayan karmaşık bir süreçtir. Bu çalışma, RNA-seq verilerini kullanarak kondrojenezin çeşitli aşamalarındaki (erken, orta ve geç) transkripsiyonel dinamikleri ve fenotipik korelasyonları aydınlatmaktadır. Çalışmada, Transkripsiyon faktörlerinin (TF'ler) ve RNA-bağlayıcı proteinlerin (RBP'ler) diferansiyel ekspresyonuna odaklandık. En yüksek ifade dönemlerinde kritik genleri belirledik ve bu zamansal kalıpları görselleştirmek için ısı haritaları oluşturduk. Ayrıca, DisGeNET veri tabanını kullanarak iskelet displazisi nozoloji genlerinin kapsamlı bir analizini yaptık, en yüksek ekspresyon dönemlerini ve fenotipik etkilerini belirledik. Bulgularımız, erken evre (D1) gen ifadesinin kraniyofasiyal gelişim ve uzuv oluşumu anomalileri ile bağlantılı olduğunu, öncelikle ECM organizasyonu ve sinyal iletiminden sorumlu genleri içerdiğini ortaya koymaktadır. Orta evre (D7) genleri, kondrosit proliferasyonu ve matris birikimindeki rolleri vurgulayarak kıkırdak matris bileşimi ve iskelet büyümesi ile ilişkilidir. Geç evre (D21) genleri kemik mineral yoğunluğu, kıkırdak bütünlüğü ve eklem oluşumunda rol oynayarak kıkırdak dokusunun olgunlaşmasını ve işlevselliğini sağlar. Bu çalışma, kondrogenez sırasında gen ekspresyon düzenleyicilerinin ve fenotipik korelasyonlarının ayrıntılı bir analizini sunarak, kıkırdak gelişimi ve iskelet displazilerini yönlendiren moleküler mekanizmalar hakkında fikir vermektedir. Bu zamansal gen ifadesi modellerinin anlaşılması, kondrojenez hakkındaki bilgilerimizi artırmakta ve kıkırdakla ilgili hastalıklar için hedefe yönelik tedavilerin geliştirilmesine yardımcı olmaktadır. Bu bulgular, farklılaşma süreci boyunca gen ifadesinin dinamik düzenlemesini yakalamada zaman noktası analizlerinin öneminin altını çizmektedir.

Anahtar Kelimeler

kondrogenez, iskelet displazisi, transkriptomik

Gene Expression Patterns and Phenotypic Associations in Chondrogenesis: Insights into Skeletal Dysplasia Nosology

Öz

The differentiation of mesenchymal stem cells (MSCs) into chondrocytes, known as chondrogenesis, is a complex process that plays a fundamental role in cartilage formation and skeletal development. This study elucidates the transcriptional dynamics and phenotypic correlations at various stages of chondrogenesis (early, mid, and late) using RNA-seq data. We focused on the differential expression of transcription factors (TFs) and RNA-binding proteins (RBPs). We identified critical genes during their highest expression periods and generated heatmaps to visualize these temporal patterns. Additionally, we conducted a comprehensive analysis of skeletal dysplasia nosology genes, determining their highest expression periods and phenotypic implications using the DisGeNET database. Our findings reveal that early-stage (D1) gene expression is linked to craniofacial development and limb formation anomalies, primarily involving genes responsible for extracellular matrix (ECM) organization and signal transduction. Mid-stage (D7) genes are associated with cartilage matrix composition and skeletal growth, highlighting roles in chondrocyte proliferation and matrix deposition. Late-stage (D21) genes are implicated in bone mineral density, cartilage integrity, and joint formation, ensuring the maturation and functionality of cartilage tissue. This study provides a detailed analysis of gene expression regulators and their phenotypic correlations during chondrogenesis, offering insights into the molecular mechanisms driving cartilage development and skeletal dysplasias. Understanding these temporal gene expression patterns enhances our knowledge of chondrogenesis and aids in developing targeted therapies for cartilage-related diseases. These findings underscore the significance of time-point analyses in capturing the dynamic regulation of gene expression throughout the differentiation process.

Anahtar Kelimeler

transcriptomics, skeletal dysplasias, chondrogenesis

Kaynakça

• 1. Richter W. Mesenchymal stem cells and cartilage in situ regeneration. J Intern Med. 2009;266:390-405.
• 2. Goldring MB, Tsuchimochi K, Ijiri K. The control of chondrogenesis. J Cell Biochem. 2006;97:33-44.
• 3. Liu CF, Samsa WE, Zhou G, Lefebvre V. Transcriptional control of chondrocyte specification and differentiation. Semin Cell Dev Biol. 2017;62:34-49.
• 4. Gao Y, Liu S, Huang J, Guo W, Chen J, Zhang L, et al. The ECM-cell interaction of cartilage extracellular matrix on chondrocytes. Biomed Res Int. 2014;2014:648459.
• 5. Zhou G, Zheng Q, Engin F, Munivez E, Chen Y, Sebald E, et al. Dominance of SOX9 function over RUNX2 during skeletogenesis. Proc Natl Acad Sci U S A. 2006;103(50):19004-9.
• 6. Akiyama H, Chaboissier MC, Martin JF, Schedl A, de Crombrugghe B. The transcription factor Sox9 has essential roles in successive steps of the chondrocyte differentiation pathway and is required for expression of Sox5 and Sox6. Genes Dev. 2002;16(21):2813-28.
• 7. Ionescu A, Kozhemyakina E, Nicolae C, Kaestner KH, Olsen BR, Lassar AB. FoxA family members are crucial regulators of the hypertrophic chondrocyte differentiation program. Dev Cell. 2012;22(5):927-39.
• 8. Maes C, Araldi E, Haigh K, Khatri R, Van Looveren R, Giaccia AJ, et al. VEGF-independent cell-autonomous functions of HIF-1α regulating oxygen consumption in fetal cartilage are critical for chondrocyte survival. J Bone Miner Res. 2012;27(3):596-609.
• 9. Krakow D. Skeletal dysplasias. Clin Perinatol. 2015;42(2):301-19, viii.
• 10. Unger S, Ferreira CR, Mortier GR, Ali H, Bertola DR, Calder A, et al. Nosology of genetic skeletal disorders: 2023 revision. Am J Med Genet A. 2023;191(5):1164-209.
• 11. Marzin P, Cormier-Daire V. New perspectives on the treatment of skeletal dysplasia. Ther Adv Endocrinol Metab. 2020;11:2042018820904016.
• 12. Oseni AO, Butler PE, Seifalian AM. Gene Expression Profile during Chondrogenesis in Human Bone Marrow Derived Mesenchymal Stem Cells using a cDNA Microarray. J Tissue Eng Regen Med. 2011;5(7):496-503.
• 13. Diekman BO, Estes BT, Guilak F. The effects of five factors relevant to in vitro chondrogenesis of human mesenchymal stem cells using factorial design and high throughput mRNA-Profiling. PLoS One. 2014;9(5).
• 14. Craft AM, Rockel JS, Nartiss Y, Kandel RA, Alman BA, Keller GM. Gene expression profile in human induced pluripotent stem cells chondrogenic differentiation in vitro, part A. Biotechnol Bioeng. 2017;114(8):1835-47.
• 15. Craft AM, Rockel JS, Nartiss Y, Kandel RA, Alman BA, Keller GM. Gene expression profile in human induced pluripotent stem cells chondrogenic differentiation in vitro, part B. Biotechnol Bioeng. 2017;114(8):1848-62.
• 16. Peng H, Li X, Shou D, Xu S, Zhang W. Gene expression profiling identification of gene expression in human MSC chondrogenic differentiation. BMC Genomics. 2018;19(1):160.
• 17. Huynh NPT, Zhang B, Guilak F. High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis. FASEB J. 2019;33(1):358-72.
• 18. Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA‐seq data. BMC Bioinformatics. 2018;19:1-24.
• 19. Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, et al. Gene set knowledge discovery with enrichr. Curr Protoc. 2021;1.
• 20. Piñero J, Ramírez-Anguita JM, Saüch-Pitarch J, Ronzano F, Centeno E, Sanz F, et al. The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res. 2020;48(D1).
• 21. Green JD, Tollemar V, Dougherty M, Yan Z, Yin L, Ye J, et al. Multifaceted signaling regulators of chondrogenesis: Implications in cartilage regeneration and tissue engineering. Genes Dis. 2015;2(4):307-27.
• 22. O'Conor CJ, Case N, Guilak F. Mechanical regulation of chondrogenesis. Stem Cell Res Ther. 2013;4(4):61.
• 23. Alcaide-Ruggiero L, Cugat R, Domínguez JM. Proteoglycans in Articular Cartilage and Their Contribution to Chondral Injury and Repair Mechanisms. Int J Mol Sci. 2023;24(13):10824.
• 24. Theocharis AD, Skandalis SS, Gialeli C, Karamanos NK. Extracellular matrix structure. Adv Drug Deliv Rev. 2016;97:4-27.
• 25. Baralle FE, Giudice J. Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol. 2017;18(7):437-51.
• 26. Gong M, Liang T, Zhang H, Chen S, Hu Y, Zhou J, et al. Gene expression profiling: identification of gene expression in human MSC chondrogenic differentiation. Am J Transl Res. 2018;10(11):3555-66.
• 27. Hallett SA, Ono W, Ono N. The hypertrophic chondrocyte: To be or not to be. Histol Histopathol. 2021;36(10):1021-36.
• 28. Muzi-Falconi M, Brown GW, Kelly TJ. Controlling initiation during the cell cycle. DNA replication. Curr Biol. 1996;6(3):229-33.
• 29. Jing Y, Wang Z, Li H, Ma C, Feng J. Chondrogenesis defines future skeletal patterns via cell transdifferentiation from chondrocytes to bone cells. Curr Osteoporos Rep. 2020 Jun;18(3):199-209.