Identification of Cell Subpopulations and Interactive Signaling Pathways From a Single-Cell RNA Sequencing Dataset in Osteosarcoma: A Comprehensive Bioinformatics Analysis

Abstract

Osteosarcoma is a type of highly aggressive bone tumor arising from primitive cells of mesenchymal origin in adults and is associated with a high rate of tumor relapse. However, there is an urgent need to clarify the molecular mechanisms underlying osteosarcoma development. The present study performed integrated bioinformatics analysis in a single-cell RNA sequencing dataset and explored the potential interactive signaling pathways associated with osteosarcoma development. Single-cell transcriptomic analysis of osteosarcoma tissues was performed by using the Seurat R package, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes was performed by using the clusterProfiler R package, and the cell–cell interaction analysis was performed by using the CellPhoneDB package. Our results showed that 11 clustered cell types were identified across 11 osteosarcoma tissues, with cell types including “osteoblastic”, “myeloid”, “osteoblastic_proli”, “osteoclast”, and “tumor-infiltrating lymphocytes (TILs)” as the main types. The DEGs between different cell types from primary, metastatic, and recurrent osteosarcomas were mainly enriched in the GO terms including “negative regulation of hydrolase activity”, “regulation of peptidase activity”, “regulation of binding”, “negative regulation of proteolysis”, and “negative regulation of peptidase activity” and in the KEGG pathways including “transcriptional misregulation in cancer”, “cellular senescence”, “apoptosis”, “FoxO signaling pathway”, “cell cycle”, “NF-kappa B signaling pathway”, “p53 signaling pathway”, “pentose phosphate pathway”, and “protein export”. For the cell–cell communication network analysis, the different interaction profiles between cell types were detected among primary, metastatic, and recurrent osteosarcomas. Further exploration of the KEGG pathway revealed that these ligand/receptor interactions may be associated with the NF-κB signaling pathway and its interacted mediators. In conclusion, the present study for the first time explored the scRNA-seq dataset in osteosarcoma, and our results revealed the 11 clustered cell types and demonstrated the novel cell–cell interactions among different cell types in primary, metastatic, and recurrent osteosarcomas. The NF-κB signaling pathway may play a key role in regulating the TME of osteosarcoma. The present study may provide new insights into understanding the molecular mechanisms of osteosarcoma pathophysiology.