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

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

Makale detayları

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

Yazarlar:

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

Yayıncı:

Eskişehir Osmangazi University

Ana Başlıklar:

Çocuk Genetik Hastalıkları

Dergi:

Osmangazi Tıp Dergisi Vol.46 Issue 4, pp.570-584

Belge Tipi:

Makale

Yayın Tarihi:

7/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001314146

pISSN:

1305-4953

Anahtar kelimeler:

Özet:

 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.

 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.

 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.

 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 TFler ve RNA-bağlayıcı proteinlerin RBPler 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.

Makale detayları

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

Yazarlar:

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

Yayıncı:

Eskişehir Osmangazi University

Ana Başlıklar:

Çocuk Genetik Hastalıkları

Dergi:

Osmangazi Tıp Dergisi Vol.46 Issue 4, pp.570-584

Belge Tipi:

Makale

Yayın Tarihi:

7/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001314146

pISSN:

1305-4953

transcriptomics

skeletal dysplasias

chondrogenesiskondrogenez

iskelet displazisi

transkriptomik

Sayı

Makale detayları

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

Yazarlar: Beren Karaosmanoğlu | M. Samil Ozisin | Gozde Imren | Ekim Zihni Taşkıran

Yayıncı: Eskişehir Osmangazi University

Ana Başlıklar: Çocuk Genetik Hastalıkları

Dergi: Osmangazi Tıp Dergisi Vol.46 Issue 4, pp.570-584

Belge Tipi: Makale

Yayın Tarihi: 7/2024

Belge Dili: İngilizce

Document ID (Org No.): 2001314146

pISSN: 1305-4953

transcriptomics

skeletal dysplasias

chondrogenesiskondrogenez

iskelet displazisi

transkriptomik

Sayı

Yazarlar:

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

Yayıncı:

Eskişehir Osmangazi University

Ana Başlıklar:

Çocuk Genetik Hastalıkları

Dergi:

Osmangazi Tıp Dergisi Vol.46 Issue 4, pp.570-584

Belge Tipi:

Makale

Yayın Tarihi:

7/2024

Belge Dili:

İngilizce

Document ID (Org No.):

2001314146

pISSN:

1305-4953