Identification of Bone Morphometric Protein-Related Hub Genes and Construction of a Transcriptional Regulatory Network in Patients With Ossification of the Ligamentum Flavum.

STUDY DESIGN: Basic science laboratory study. OBJECTIVE: To identify hub genes related to bone morphogenetic proteins (BMPs) in the ossification of the ligamentum flavum (OLF) and analyze their functional characteristics. SUMMARY OF BACKGROUND DATA: The exact etiology and pathologic mechanism of OLF remain unclear. BMPs are pleiotropic osteoinductive proteins that may play a critical role in this condition. MATERIALS AND METHODS: The GSE106253 and GSE106256 data sets were downloaded from the Gene Expression Omnibus database. The messenger RNA (mRNA) and long noncoding RNA expression profiles were obtained from GSE106253. The microRNA expression profiles were obtained from GSE106256. Differentially expressed genes were identified between OLF and non-OLF groups and then intersected with BMP-related genes to obtain differentially expressed BMP-related genes. The least absolute shrinkage selection operator and support vector machine recursive feature elimination were used to screen hub genes. Furthermore, a competing endogenous RNA network was constructed to explain the expression regulation of the hub genes in OLF. Finally, the protein and mRNA expression levels of the hub genes were verified using Western blot and real-time polymerase chain reaction, respectively. RESULTS: We identified 671 Differentially expressed genes and 32 differentially expressed BMP-related genes. Hub genes ADIPOQ , SCD , SCX , RPS18 , WDR82 , and SPON1 , identified through the least absolute shrinkage selection operator and support vector machine recursive feature elimination analyses, showed high diagnostic values for OLF. Furthermore, the competing endogenous RNA network revealed the regulatory mechanisms of the hub genes. Real-time polymerase chain reaction showed that the mRNA expression of the hub genes was significantly downregulated in the OLF group compared with the non-OLF group. Western blot showed that the protein levels of ADIPOQ, SCD, WDR82 , and SPON1 were significantly downregulated, whereas those of SCX and RPS18 were significantly upregulated in the OLF group compared with the non-OLF group. CONCLUSION: This study is the first to identify BMP-related genes in OLF pathogenesis through bioinformatics analysis. ADIPOQ , SCD , SCX , RPS18 , WDR82 , and SPON1 were identified as hub genes for OLF. The identified genes may serve as potential therapeutic targets for treating patients with OLF.

Analysis of gene expression profiles in two spinal cord injury models.

OBJECTIVES: To analyze the changes of gene expression at different timepoints after spinal cord injury (SCI) with tenth segment thoracic injury. METHODS: Two SCI models, the complete paraplegia (H) and Allen's strike (D) methods were applied to induce SCI in rats, and transcriptome sequencing was performed 1, 3, 7, 14, 56, and 70 days after SCI, respectively. Principal component analysis, differentially expressed gene analysis, and hierarchical clustering analysis were applied to analyze the differentially expressed genes (DEGs). Gene Ontology GO enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, and Gene Set Enrichment Analysis revealed the pathway of gene enrichment. RESULTS: There were 1,907, 3,120, 3,728, 978, 2,319, and 3,798 DEGs in the complete paraplegia group and 2,380, 878, 1,543, 6,040, 1,945, and 3,850 DEGs in the Allen's strike method group and after SCI at 1, 3, 7, 14, 56, and 70 days, respectively. The transcriptome contours of D1, H1, D3, and H14 were clustered with C; the H56, D56, H70, and D70 transcriptome contours were similar and clustered together. H3, D7, and H7 were clustered together, and D14 was clustered separately. The transcriptome differences of the two SCI models were mainly concentrated during the first 2 weeks after SCI. The DEGs after SCI in the complete paraplegia group were more concentrated. Most of the early transcriptional regulation stabilized within 2 weeks after injury. CONCLUSIONS: There were DEGs between the two SCI models. Through the gene changes and pathway enrichment of the entire time period after SCI, the molecular mechanism of SCI repair was revealed in depth, which provided a reference for SCI treatment in the future.