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Front Genet. 2017 Nov 30;8:193. doi: 10.3389/fgene.2017.00193. eCollection 2017.

Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma.

Author information

1
Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue, Vietnam.
2
Department of Pathophysiology, University of Tartu, Tartu, Estonia.
3
Department of Oncology, Hanoi Medical University, Hanoi, Vietnam.
4
Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia.
5
Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.
6
Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu, Estonia.
7
Department of Orthopedics, College of Medicine and Pharmacy, Hue University, Hue, Vietnam.

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.

KEYWORDS:

human endogenous retrovirus; osteosarcoma; repetitive elements; satellite; sequence; transposable elements

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