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Published on: October 16, 2013
Bioinformatics Analysis and Experimental Verification Identify Downregulation of COL27A1 in Poor Segmental Congenital
Zongshan Hu1, Yanjie Xu1, Jie Li1
1Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China.
Insights
This study identified COL27A1 as a key biomarker for poor segmental congenital scoliosis (PSCS) progression. Downregulation of COL27A1 in PSCS patients suggests it as a potential therapeutic target for this spinal deformity.
Area of Science:
- Genetics and Bioinformatics
- Developmental Biology
- Orthopedics
Background:
- Congenital scoliosis (CS) is a birth defect with poor segmental congenital scoliosis (PSCS) as a subtype.
- Delayed intervention for PSCS can lead to severe disability and paralysis.
Purpose of the Study:
- To identify core biomarkers for PSCS progression using bioinformatics and experimental verification.
- To elucidate the pathogenic mechanism of PSCS and identify potential therapeutic targets.
Main Methods:
- Utilized GEO database (GSE11854) for somite formation gene expression data.
- Employed R packages (edgeR, clusterProfiler, DESeq2) for differential gene expression (DEG) analysis, GO/KEGG/DO annotation, and LASSO regression.
- Performed RNA sequencing on peripheral blood samples from healthy donors and PSCS patients.
- Validated COL27A1 expression using RT-PCR assay.
Main Results:
- Identified 443 DEGs related to somite formation, enriched in TGF-β signaling pathway and spinal deformity.
- LASSO regression identified 9 DEGs as signature markers for somite formation.
- Discovered 162 DEGs in PSCS patients, associated with cardiac myofibril assembly and muscle structure.
- COL27A1 was the sole intersecting gene between somite formation predictors and PSCS DEGs, found to be significantly downregulated in PSCS patients.
Conclusions:
- Novel differentially expressed genes (DEGs) related to PSCS pathogenesis were identified.
- COL27A1 is a potential therapeutic target for PSCS.
- Findings may aid in developing therapeutic strategies for PSCS.
Background:
Congenital scoliosis (CS) represents the congenital defect disease, and poor segmental congenital scoliosis (PSCS) represents one of its types. Delayed intervention can result in disability and paralysis. In this study, we would identify the core biomarkers for PSCS progression through bioinformatics analysis combined with experimental verification.
Methods:
This work obtained the GSE11854 expression dataset associated with somite formation in the GEO database, which covers data of 13 samples. Thereafter, we utilized the edgeR of the R package to obtain DEGs in this dataset. Then, GO annotation, KEGG analyses, and DO annotation of DEGs were performed by "clusterProfiler" of the R package. This study performed LASSO regression for screening the optimal predicting factors for somite formation. Through RNA sequencing based on peripheral blood samples from healthy donors and PSCS cases, we obtained the RNA expression patterns and screen out DEGs using the R package DESeq2. The present work analyzed COL27A1 expression in PSCS patients by the RT-PCR assay.
Results:
A total of 443 genes from the GSE11854 dataset were identified as DEGs, which were involved in BP associated with DNA replication, CC associated with chromosomal region, and MF associated with ATPase activity. These DEGs were primarily enriched in the TGF-β signaling pathway and spinal deformity. Further, LASSO regression suggested that 9 DEGs acted as the signature markers for somite formation. We discovered altogether 162 DEGs in PSCS patients, which were involved in BP associated with cardiac myofibril assembly and MF associated with structural constituent of muscle. However, these 162 DEGs were not significantly correlated with any pathways. Finally, COL27A1 was identified as the only intersected gene between the best predictors for somite formation and PSCS-related DEGs, which was significantly downregulated in PSCS patients.
Conclusion:
This work sheds novel lights on DEGs related to the PSCS pathogenic mechanism, and COL27A1 is the possible therapeutic target for PSCS. Findings in this work may contribute to developing therapeutic strategies for PSCS.
