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Ho XD, Nguyen HG, Trinh LH, Reimann E, Prans E, Kõks G, Maasalu K, Le VQ, Nguyen VH, Le NTN, Phung P, Märtson A, Lattekivi F, Kõks S. Analysis of the Expression of Repetitive DNA Elements in Osteosarcoma. Front Genet 2017; 8:193. [PMID: 29250102 PMCID: PMC5714928 DOI: 10.3389/fgene.2017.00193] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/15/2017] [Indexed: 02/05/2023] Open
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.
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Affiliation(s)
- Xuan D Ho
- Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue, Vietnam.,Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Hoang G Nguyen
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Le H Trinh
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Ene Reimann
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Gea Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu, Estonia
| | - Van Q Le
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Van H Nguyen
- Department of Oncology, Hanoi Medical University, Hanoi, Vietnam
| | - Nghi T N Le
- Department of Orthopedics, College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Phuong Phung
- Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Aare Märtson
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu, Estonia
| | - Freddy Lattekivi
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
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Ho XD, Phung P, Q Le V, H Nguyen V, Reimann E, Prans E, Kõks G, Maasalu K, Le NT, H Trinh L, G Nguyen H, Märtson A, Kõks S. Whole transcriptome analysis identifies differentially regulated networks between osteosarcoma and normal bone samples. Exp Biol Med (Maywood) 2017; 242:1802-1811. [PMID: 29050494 DOI: 10.1177/1535370217736512] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We performed whole transcriptome analysis of osteosarcoma bone samples. Initially, we sequenced total RNA from 36 fresh-frozen samples (18 tumoral bone samples and 18 non-tumoral paired samples) matching in pairs for each osteosarcoma patient. We also performed independent gene expression analysis of formalin-fixed paraffin-embedded samples to verify the RNAseq results. Formalin-fixed paraffin-embedded samples allowed us to analyze the effect of chemotherapy. Data were analyzed with DESeq2, edgeR and Reactome packages of R. We found 5365 genes expressed differentially between the normal bone and osteosarcoma tissues with an FDR below 0.05, of which 3399 genes were upregulated and 1966 were downregulated. Among those genes, BTNL9, MMP14, ABCA10, ACACB, COL11A1, and PKM2 were expressed differentially with the highest significance between tumor and normal bone. Functional annotation with the reactome identified significant changes in the pathways related to the extracellular matrix degradation and collagen biosynthesis. It was suggested that chemotherapy may induce the modification of ECM with important collagen biosynthesis. Taken together, our results indicate that changes in the degradation of extracellular matrix seem to be an important mechanism of osteosarcoma and efficient chemotherapy induces the genes related to bone formation. Impact statement Osteosarcoma is a rare disease but it is of interest to many scientists all over the world because the current standard treatment still has poor results. We sequenced total RNA from 36 fresh-frozen paired samples (18 tumoral bone samples and 18 non-tumoral paired samples) from osteosarcoma patients. We found that differences in the gene expressions between the normal and affected bones reflected the changes in the regulation of the degradation of collagen and extracellular matrix. We believe that these findings contribute to the understanding of OS and suggest ideas for further studies.
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Affiliation(s)
- Xuan Dung Ho
- 1 Department of Oncology, 155407 College of Medicine and Pharmacy , Hue University, Hue 53000, Vietnam.,2 Department of Pathophysiology, 37546 University of Tartu , Tartu 50411, Estonia
| | - Phuong Phung
- 1 Department of Oncology, 155407 College of Medicine and Pharmacy , Hue University, Hue 53000, Vietnam
| | - Van Q Le
- 3 Department of Oncology, Hanoi Medical University, Hanoi 15000, Vietnam
| | - Van H Nguyen
- 3 Department of Oncology, Hanoi Medical University, Hanoi 15000, Vietnam
| | - Ene Reimann
- 2 Department of Pathophysiology, 37546 University of Tartu , Tartu 50411, Estonia.,4 Department of Reproductive Biology, 85334 Estonian University of Life Sciences , Tartu 51014, Estonia
| | - Ele Prans
- 2 Department of Pathophysiology, 37546 University of Tartu , Tartu 50411, Estonia
| | - Gea Kõks
- 2 Department of Pathophysiology, 37546 University of Tartu , Tartu 50411, Estonia
| | - Katre Maasalu
- 5 Department of Traumatology and Orthopedics, 37546 University of Tartu , Tartu 50411, Estonia.,6 Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu 50406, Estonia
| | - Nghi Tn Le
- 7 Department of Orthopedics, 155407 College of Medicine and Pharmacy , Hue University, Hue 53000, Vietnam
| | - Le H Trinh
- 3 Department of Oncology, Hanoi Medical University, Hanoi 15000, Vietnam
| | - Hoang G Nguyen
- 3 Department of Oncology, Hanoi Medical University, Hanoi 15000, Vietnam
| | - Aare Märtson
- 5 Department of Traumatology and Orthopedics, 37546 University of Tartu , Tartu 50411, Estonia.,6 Clinic of Traumatology and Orthopaedics of Tartu University Hospital, Tartu 50406, Estonia
| | - Sulev Kõks
- 2 Department of Pathophysiology, 37546 University of Tartu , Tartu 50411, Estonia.,4 Department of Reproductive Biology, 85334 Estonian University of Life Sciences , Tartu 51014, Estonia
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Ho XD, Phung P, LE VQ, Nguyen VH, Reimann E, Prans E, Kõks G, Maasalu K, Märtson A, Le NTN, Trinh LH, Nguyen HG, Kõks S. Whole transcriptome analysis to reveal differentially expressed genes between paired osteosarcoma and normal bone samples. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e22508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Xuan Dung Ho
- College of Medicine and Pharmacy, Hue University, Hue, Viet Nam
| | - Phuong Phung
- Oncology Department, College of Medicine and Pharmacy, Hue University, Hue, Viet Nam
| | | | | | - Ene Reimann
- Department of pathophysiology, University of Tartu, Tartu, Estonia
| | - Ele Prans
- Department of pathophysiology, University of Tartu, Tartu, Estonia
| | - Gea Kõks
- Department of pathophysiology, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Department of Traumatology and Orthopedics, University of Tartu, Estonia, Tartu, Estonia
| | - Aare Märtson
- Department of Traumatology and Orthopedics, University of Tartu, Estonia, Tartu, Estonia
| | - nghi Thanh Nhan Le
- Department of Orthopedics, College of Medicine and Pharmacy, Hue University, Hue, Viet Nam
| | - Le Huy Trinh
- department of oncology, Hanoi medical university, Hanoi, Viet Nam
| | | | - Sulev Kõks
- Department of pathophysiology, University of Tartu, Tartu, Estonia
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O'Rourke S, Tatsuno G, Yu B, Phung P, Mesa K, To B, Limoli K, Wrin T. Mutations in the V1 domain of Thai CRF01-AE viruses that confer sensitivity/resistance to broadly neutralizing antibodies. Retrovirology 2012. [PMCID: PMC3441766 DOI: 10.1186/1742-4690-9-s2-p106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- S O'Rourke
- Monogram Biosciences, San Francisco, CA, USA
| | - G Tatsuno
- Monogram Biosciences, San Francisco, CA, USA
| | - B Yu
- Monogram Biosciences, San Francisco, CA, USA
| | - P Phung
- Monogram Biosciences, San Francisco, CA, USA
| | - K Mesa
- Monogram Biosciences, San Francisco, CA, USA
| | - B To
- Monogram Biosciences, San Francisco, CA, USA
| | - K Limoli
- Monogram Biosciences, San Francisco, CA, USA
| | - T Wrin
- Monogram Biosciences, San Francisco, CA, USA
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Evans MC, Paquet A, Phung P, Parikh A, Petropoulos C, Wrin T, Haddad M. Novel computational methods for predicting epitopes of potent and broadly neutralizing HIV-1 antibodies. Retrovirology 2012. [PMCID: PMC3442070 DOI: 10.1186/1742-4690-9-s2-p353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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O'Rourke SM, Sutthent R, Limoli KL, Phung P, Tatsuno GP, To B, Mesa KA, Frigon N, Higgins KW, Wrin T, Berman PW. Mapping epitopes on CRF01_AE viruses recognized by broadly neutralizing antibodies in sera from elite neutralizers from North America and Thailand. Retrovirology 2012. [PMCID: PMC3442094 DOI: 10.1186/1742-4690-9-s2-p90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Phogat SK, Walker L, Wagner D, Chan-Hui P, Simek M, Phung P, Wrin T, Mitcham J, Investigator P, Kaminsky S, Zamb T, Moyle M, Koff W, Burton D. S021-06 OA. Potent and broad neutralizing antibodies from HIV-1 non-clade B infected donor reveal a new HIV-1 vaccine target. Retrovirology 2009. [PMCID: PMC2767577 DOI: 10.1186/1742-4690-6-s3-o6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Binley J, Wrin T, Pantophlet R, Phung P, Crooks ET, Lapedes A, Taylor N, Cavacini L, Steigler G, Kunert R, Katinger H, Petropoulos C, Richman D, Morris L, Sutthent R, Burton DR. P04-03. Cross-clade neutralization analysis of plasmas from clade B, C and CRF01_AE HIV-infected donors. Retrovirology 2009. [PMCID: PMC2767815 DOI: 10.1186/1742-4690-6-s3-p31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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