Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq

Abstract

ObjectiveOsteosarcoma (OS) is a malignant bone tumor with high morbidity in young adults and adolescents. This study aimed to discover potential early diagnosis biomarkers in OS.ResultsIn total, 111 differentially expressed genes (DEGs) were identified in primary OS compared with normal controls and 235 DEGs were identified in metastatic OS compared with primary OS. AURKB and PPP2R2B were the significantly up-regulated and down-regulated hub proteins, respectively, in the PPI protein-protein network (PPI) network of primary OS. ISG15 and BTRC were the significantly up-regulated and down-regulated hub proteins, respectively, in the network of metastatic OS. The DEGs in metastatic OS compared with primary OS were significantly enriched in the arachidonic acid metabolism, malaria, and chemokine signaling pathways. Finally, we employed quantitative real-time polymerase chain reaction (qRT-PCR) to validate the expression levels of candidate DEGs and the results indicated that our bioinformatics approach was acceptable.Materials and MethodsThe mRNA expression profiling of 20 subjects was obtained through high-throughput RNA-sequencing. DEGs were identified between primary OS and normal Control, and between primary OS and metastatic OS, respectively. Functional annotation and PPI networks were used to obtain insights into the functions of DEGs. qRT-PCR was performed to detect the expression levels of dysregulated genes in OS.ConclusionsOur work might provide groundwork for the further exploration of tumorigenesis and metastasis mechanisms of OS.

Yeast and other lower eukaryotic organisms for studies of Vps13 proteins in health and disease

“…Furthermore, there are reports of putative associations of hVPS13A , hVPS13C and hVPD13D variations with schizophrenia . Finally, alterations in the expression level and/or mutations in all human VPS13 genes have been observed in specific cancers …”

“…14,15 Finally, alterations in the expression level and/or mutations in all human VPS13 genes have been observed in specific cancers. [16][17][18][19][20][21]…”

VPS13A, a closely associated mitochondrial protein, is required for efficient lysosomal degradation

“…Mutations in VPS13B lead to Cohen syndrome (Kolehmainen et al, 2003); mutations in VPS13C have been identified as a cause of an autosomal-recessive, early-onset and severe form of Parkinson's disease (Lesage et al, 2016; Schormair et al, 2018); and, most recently, mutations in VPS13D have been linked to other movement disorders (Gauthier et al, 2018; Seong et al, 2018). In addition, genomic data have identified VPS13A-D variants in other neurological disorders (Fromer et al, 2014; McCarthy et al, 2014; Meda et al, 2012), in various types of cancer (An et al, 2012; Furukawa et al, 2011; Morisaki et al, 2014; Park et al, 2016b; Yang et al, 2016b) and in diabetes (Grarup et al, 2011; Saxena et al, 2010; Strawbridge et al, 2011; Windholz et al, 2011).…”

Identification of Biomarkers for Osteosarcoma Based on Integration Strategy

“…Cellular or tissuespecific expression of lncRNAs is associated with a variety of biological behaviors of tumors. Recently, many studies have found potential targets related to OS through next-generation sequencing and provided a theoretical basis for further studies on the occurrence and development of OS [14][15][16].…”