Genomic and Transcriptomic Characterization of Pre-operative Chemotherapy Response in Patients with Osteosarcoma

Abstract

Abstract Osteosarcoma is a heterogeneous disease with regard to its chemotherapy response and clinical outcomes. This study aims to investigate the genomic and transcriptomic characteristics related to pre-operative chemotherapy response. Samples from 25 osteosarcoma patients were collected to perform both whole exome and transcriptome sequencing. Osteosarcoma had the relatively high level of chromosomal copy number variant (CNV) burden. Chemotherapy responders showed the higher chromosomal CNV burden than non-responders (p = 0.0775). The percentage of COSMIC signature 3, associated with homologous recombination repair deficiency, was higher in responders (56%) than in non-responders (45%). Transcriptomic analysis suggested that 11 genes were significantly up-regulated in responders and 18 genes were up-regulated in non-responders. Both GSEA and KEGG enrichment analysis indicted that four pathways related to cardiomyopathy were up-regulated in responders, while neuroactive ligand−receptor interaction was up-regulated in non-responders. Finally, a random forest-based classifier was developed to classify chemotherapy response using 23 differentially expressed genes, with the area under the curve of 0.843 (95% CI, 0.654-1.000). Osteosarcoma had the heterogeneous mutational profile with frequent occurrence of CNVs. Transcriptomic analysis identified several signaling pathways associated with chemotherapy responsiveness to osteosarcoma. Transcriptomic characteristics classifier provides a potential research direction for predicting the chemotherapy response.