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Whole transcriptome analysis of osteosarcoma

Kõks, S., Reimann, E., Maasalu, K., Kõks, G., Xuan, D.H., Prans, E. and Märtson, A. (2016) Whole transcriptome analysis of osteosarcoma. The FASEB Journal, 30 (1 Supp).

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Osteosarcoma (OS) has highly unstable genome and therefore its analysis is still challenging and our knowledge about the OS is limited. In the present study we analysed whole transcriptome (RNA-seq) in eighteen tumour-normal paired samples collected in the Hue University Hospital, Vietnam. We extracted total RNA from the bone tissue and performed paired-end RNA sequencing with SOLID 5500W system. Raw reads were mapped against human genome version hg19 using Lifecsope software. Mapping identified 21632 genes to be transcribed in our samples. After pairwise comparison between tumour and normal tissue we found 4092 (19%) genes were up-regulated and 2683 (12%) genes were down-regulated in tumour with the FDR adjusted p-value below 0.1. The most significantly down-regulated genes were BTNL9, DNASE1L3, CAMP, LEPR. They had logFC 1.4....1.5. The most up-regulated genes were COL11A1, COL2A1, COL10A1, TGFBI, TREM2. They had logFC 1.5...1.3 with. The differentially expressed genes with the lowest adjusted p-values were BTNL9, MMP14, ABCA10, ACACB and COL11A1. BTNL9 is butyrophilin-like 9 gene and its function is very poorly known. One recent study found significant association between germline missense variants in the BTNL2 gene and prostate cancer. BTNL genes are important in inflammation and immunity. Up-regulation of MMP14 and different collagen genes indicates the reorganisation of extracellular matrix. Indeed, when reapplied reactome tool to analyse for enrichment of molecular pathways, we found significant enrichment of “collagen degradation”, degradation of extracellular matrix” and “extracellular matrix organisation” pathways. In conclusion, we were able to describe the transcriptome of the OS and its functional significance.

Item Type: Journal Article
Publisher: FASEB
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