Abstract
Osteosarcoma (OS) is a rare malignant bone tumor. It affects mostly young persons and has poor outcome with the present treatment. No improvement was observed since the introduction of chemotherapy. The better understanding of osteosarcoma development could indicate better management strategy. Repetitive DNA elements were found to play a role in cancer mechanism especially in epithelial tumors but not yet analyzed in osteosarcoma. We conducted the study to analyse the expression profile of repetitive elements (RE) in osteosarcoma.Methods: Fresh bone paired (tumor and normal bone) samples were obtained from excised parts of tumors of 18 patients with osteosarcoma. We performed sequencing of RNA extracted from 36 samples (18 tumor tissues and 18 normal bone for controls), mapped raw reads to the human genome and identified the REs. EdgeR package was used to analyse the difference in expression of REs between osteosarcoma and normal bone.Results: 82 REs were found differentially expressed (FDR < 0.05) between osteosarcoma and normal bone. Out of all significantly changed REs, 35 were upregulated and 47 were downregulated. HERVs (THE1C-int, LTR5, MER57F and MER87B) and satellite elements (HSATII, ALR-alpha) were the most significantly differential expressed elements between osteosarcoma and normal tissues. These results suggest significant impact of REs in the osteosarcoma. The role of REs should be further studied to understand the mechanism they have in the genesis of osteosarcoma.
Highlights
Osteosarcoma is a rare cancer which affects 0.2–0.35/100 000 across countries with a slightly higher frequency in male than female (Mirabello et al, 2009a; Valery et al, 2015)
Affected sites were at femur 55.56%, tibia (33.33%) and humerus (11.11%)
We found 82 repetitive elements which were expressed differentially with significance false discovery rate (FDR)
Summary
Osteosarcoma is a rare cancer which affects 0.2–0.35/100 000 across countries with a slightly higher frequency in male than female (Mirabello et al, 2009a; Valery et al, 2015). It is the most common malignant bone tumor (Mirabello et al, 2009b). There is a lower second peak in elderly (Mirabello et al, 2009a; Hung et al, 2014). Introduction of effective chemotherapy during 1960s−1980s increased the cure rate from
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