AUTHOR=Ho Xuan D. , Nguyen Hoang G. , Trinh Le H. , Reimann Ene , Prans Ele , Kõks Gea , Maasalu Katre , Le Van Q. , Nguyen Van H. , Le Nghi T. N. , Phung Phuong , Märtson Aare , Lattekivi Freddy , Kõks Sulev
TITLE=Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma
JOURNAL=Frontiers in Genetics
VOLUME=8
YEAR=2017
URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2017.00193
DOI=10.3389/fgene.2017.00193
ISSN=1664-8021
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.