Biglycan regulates bone development and regeneration

Weighted Gene Co-expression Network Analysis (WGCNA) of Wnt Signaling Related to Periodontal Ligament Formation: A Bioinformatics-Based Analysis

Introduction The Wnt signaling pathway is crucial for tooth development, odontoblast differentiation, and dentin formation. It interacts with epithelial cadherin (E-cadherin) and beta-catenin in tooth development and periodontal ligament (PDL) formation. Dysregulation of Wnt signaling is linked to periodontal diseases, requiring an understanding of therapeutic interventions. Weighted gene co-expression network analysis (WGCNA) can identify co-expressed gene modules. Our study aims to identify hub genes in WGCNA analysis of Wnt signaling-based PDL formation. Methods The study used a microarray dataset GSE201313 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus to analyze the impact of DMP1 expression on XLH dental pulp cell differentiation and PDL formation. The standardized dataset was used for WGCNA analysis, which generated a co-expression network by calculating pairwise correlations between genes and constructing an adjacency matrix. The topological overlap matrix (TOM) was transformed into a hierarchical clustering tree and then cut into modules or clusters of highly interconnected genes. The module eigengene (ME) was calculated for each module, and the genes within this module were identified as hub genes. Gene ontology (GO) and KEGG pathway enrichment analysis were performed to gain insights into the biological functions of the hub genes. The integrated Differential Expression and Pathway analysis (iDEP) tool (http://bioinformatics.sdstate.edu/idep/; South Dakota State University, Brookings, USA) was used for WGCNA analysis. Results The study used the WGCNA package to analyze 1,000 differentially expressed genes, constructing a gene co-expression network and generating a hierarchical clustering tree and TOM. The analysis reveals a scale-free topology fitting index R2 and mean connectivity for various soft threshold powers, with an R2 value of 5. COL6A1, MMP3, BGN, COL1A2, and FBN2 are hub genes implicated in PDL development. Conclusion The study identified key hub genes, including COL6A1, MMP3, BGN, and FBN2, crucial for PDL formation, tissue remodeling, and cell-matrix interactions, guiding future therapeutic strategies.

Identification of the miRNA-mRNA regulatory network in a mouse model of early fracture

Fracture healing is a complex process that involves multiple molecular events, and the regulation mechanism is not fully understood. We acquired miRNA and mRNA transcriptomes of mouse fractures from the Gene Expression Omnibus database (GSE76197 and GSE192542) and integrated the miRNAs and genes that were differentially expressed in the control and fracture groups to construct regulatory networks. There were 130 differentially expressed miRNAs and 4,819 differentially expressed genes, including 72 upregulated and 58 downregulated miRNAs, along with 2,855 upregulated and 1964 downregulated genes during early fracture healing. Gene ontology analysis revealed that most of the differentially expressed genes were enriched in the extracellular matrix (ECM) structure and the ECM organization. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment suggested cell cycle, DNA replication, and mismatch repair were involved in the progression of fracture healing. Furthermore, we constructed a molecular network of miRNAs and mRNAs with inverse expression patterns to elucidate the molecular basis of miRNA-mRNA regulation in fractures. The regulatory network highlighted the potential targets, which may help to provide a mechanistic basis for therapies to improve fracture patient outcomes.

Bioinformatics Analysis and Experimental Validation of Differential Genes and Pathways in Bone Nonunions

Non-union fractures pose a significant clinical challenge, often leading to prolonged pain and disability. Understanding the molecular mechanisms underlying non-union fractures is crucial for developing effective therapeutic interventions. This study integrates bioinformatics analysis and experimental validation to unravel key genes and pathways associated with non-union fractures. We identified differentially expressed genes (DEGs) between non-union and fracture healing tissues using bioinformatics techniques. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to elucidate the biological processes and pathways involved. Common DEGs were identified, and a protein-protein interaction (PPI) network was constructed. Fibronectin-1 (FN1), Thrombospondin-1 (THBS1), and Biglycan (BGN) were pinpointed as critical target genes for non-union fracture treatment. Experimental validation involved alkaline phosphatase (ALP) and Alizarin Red staining to confirm osteogenic differentiation. Our analysis revealed significant alterations in pathways related to cell behavior, tissue regeneration, wound healing, infection, and immune responses in non-union fracture tissues. FN1, THBS1, and BGN were identified as key genes, with their upregulation indicating potential disruptions in the bone remodeling process. Experimental validation confirmed the induction of osteogenic differentiation. The study provides comprehensive insights into the molecular mechanisms of non-union fractures, emphasizing the pivotal roles of FN1, THBS1, and BGN in extracellular matrix dynamics and bone regeneration. The findings highlight potential therapeutic targets and pathways for further investigation. Future research should explore interactions between these genes, validate results using in vivo fracture models, and develop tailored treatment strategies for non-union fractures, promising significant advances in clinical management.

Mitigation of BMP-induced inflammation in craniofacial bone regeneration and improvement of bone parameters by dietary hesperidin

Based on anti-inflammatory and osteogenic properties of hesperidin (HE), we hypothesized its systemic administration could be a cost-effective method of improving BMP-induced bone regeneration. Sprague-Dawley rats were allocated into 4 groups (n = 10/group): a 5-mm critical-sized mandible defect + collagen scaffold or, scaffold + 1 µg of BMP2 with and without dietary HE at 100 mg/kg. HE was administered by oral gavage 4 weeks prior to surgeries until euthanasia at day 7 or 14 post-surgery. The healing tissue within the defect collected at day 7 was subjected to gene expression analysis. Mandibles harvested at day 14 were subjected to microcomputed tomography and histology. HE + BMP2-treated rats had a statistically significant decrease in expression of inflammatory genes compared to BMP2 alone. The high-dose BMP2 alone caused cystic-like regeneration with incomplete defect closure. HE + BMP2 showed virtually complete bone fusion. Collagen fibril birefringence pattern (red color) under polarized light indicated high organization in BMP2-induced newly formed bone (NFB) in HE-supplemented group (p < 0.05). Clear changes in osteocyte lacunae as well as a statistically significant increase in osteoclasts were found around NFB in HE-treated rats. A significant increase in trabecular volume and thickness, and trabecular and cortical density was found in femurs of HE-supplemented rats (p < 0.05). Our findings show, for the first time, that dietary HE has a remarkable modulatory role in the function of locally delivered high-dose BMP2 in bone regeneration possibly via control of inflammation, osteogenesis, changes in osteocyte and osteoclast function and collagen maturation in regenerated and native bone. In conclusion, HE had a significant skeletal bone sparing effect and the ability to provide a more effective BMP-induced craniofacial regeneration.