Cargando…

Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq

OBJECTIVE: Osteosarcoma (OS) is a malignant bone tumor with high morbidity in young adults and adolescents. This study aimed to discover potential early diagnosis biomarkers in OS. RESULTS: In total, 111 differentially expressed genes (DEGs) were identified in primary OS compared with normal control...

Descripción completa

Detalles Bibliográficos
Autores principales: Yang, Yihao, Zhang, Ya, Qu, Xin, Xia, Junfeng, Li, Dongqi, Li, Xiaojuan, Wang, Yu, He, Zewei, Li, Su, Zhou, Yonghong, Xie, Lin, Yang, Zuozhang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals LLC 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349981/
https://www.ncbi.nlm.nih.gov/pubmed/27888627
http://dx.doi.org/10.18632/oncotarget.13554
_version_ 1782514575874195456
author Yang, Yihao
Zhang, Ya
Qu, Xin
Xia, Junfeng
Li, Dongqi
Li, Xiaojuan
Wang, Yu
He, Zewei
Li, Su
Zhou, Yonghong
Xie, Lin
Yang, Zuozhang
author_facet Yang, Yihao
Zhang, Ya
Qu, Xin
Xia, Junfeng
Li, Dongqi
Li, Xiaojuan
Wang, Yu
He, Zewei
Li, Su
Zhou, Yonghong
Xie, Lin
Yang, Zuozhang
author_sort Yang, Yihao
collection PubMed
description OBJECTIVE: Osteosarcoma (OS) is a malignant bone tumor with high morbidity in young adults and adolescents. This study aimed to discover potential early diagnosis biomarkers in OS. RESULTS: In total, 111 differentially expressed genes (DEGs) were identified in primary OS compared with normal controls and 235 DEGs were identified in metastatic OS compared with primary OS. AURKB and PPP2R2B were the significantly up-regulated and down-regulated hub proteins, respectively, in the PPI protein-protein network (PPI) network of primary OS. ISG15 and BTRC were the significantly up-regulated and down-regulated hub proteins, respectively, in the network of metastatic OS. The DEGs in metastatic OS compared with primary OS were significantly enriched in the arachidonic acid metabolism, malaria, and chemokine signaling pathways. Finally, we employed quantitative real-time polymerase chain reaction (qRT-PCR) to validate the expression levels of candidate DEGs and the results indicated that our bioinformatics approach was acceptable. MATERIALS AND METHODS: The mRNA expression profiling of 20 subjects was obtained through high-throughput RNA-sequencing. DEGs were identified between primary OS and normal Control, and between primary OS and metastatic OS, respectively. Functional annotation and PPI networks were used to obtain insights into the functions of DEGs. qRT-PCR was performed to detect the expression levels of dysregulated genes in OS. CONCLUSIONS: Our work might provide groundwork for the further exploration of tumorigenesis and metastasis mechanisms of OS.
format Online
Article
Text
id pubmed-5349981
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher Impact Journals LLC
record_format MEDLINE/PubMed
spelling pubmed-53499812017-04-06 Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq Yang, Yihao Zhang, Ya Qu, Xin Xia, Junfeng Li, Dongqi Li, Xiaojuan Wang, Yu He, Zewei Li, Su Zhou, Yonghong Xie, Lin Yang, Zuozhang Oncotarget Research Paper OBJECTIVE: Osteosarcoma (OS) is a malignant bone tumor with high morbidity in young adults and adolescents. This study aimed to discover potential early diagnosis biomarkers in OS. RESULTS: In total, 111 differentially expressed genes (DEGs) were identified in primary OS compared with normal controls and 235 DEGs were identified in metastatic OS compared with primary OS. AURKB and PPP2R2B were the significantly up-regulated and down-regulated hub proteins, respectively, in the PPI protein-protein network (PPI) network of primary OS. ISG15 and BTRC were the significantly up-regulated and down-regulated hub proteins, respectively, in the network of metastatic OS. The DEGs in metastatic OS compared with primary OS were significantly enriched in the arachidonic acid metabolism, malaria, and chemokine signaling pathways. Finally, we employed quantitative real-time polymerase chain reaction (qRT-PCR) to validate the expression levels of candidate DEGs and the results indicated that our bioinformatics approach was acceptable. MATERIALS AND METHODS: The mRNA expression profiling of 20 subjects was obtained through high-throughput RNA-sequencing. DEGs were identified between primary OS and normal Control, and between primary OS and metastatic OS, respectively. Functional annotation and PPI networks were used to obtain insights into the functions of DEGs. qRT-PCR was performed to detect the expression levels of dysregulated genes in OS. CONCLUSIONS: Our work might provide groundwork for the further exploration of tumorigenesis and metastasis mechanisms of OS. Impact Journals LLC 2016-11-24 /pmc/articles/PMC5349981/ /pubmed/27888627 http://dx.doi.org/10.18632/oncotarget.13554 Text en Copyright: © 2016 Yang et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Paper
Yang, Yihao
Zhang, Ya
Qu, Xin
Xia, Junfeng
Li, Dongqi
Li, Xiaojuan
Wang, Yu
He, Zewei
Li, Su
Zhou, Yonghong
Xie, Lin
Yang, Zuozhang
Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title_full Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title_fullStr Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title_full_unstemmed Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title_short Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
title_sort identification of differentially expressed genes in the development of osteosarcoma using rna-seq
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349981/
https://www.ncbi.nlm.nih.gov/pubmed/27888627
http://dx.doi.org/10.18632/oncotarget.13554
work_keys_str_mv AT yangyihao identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT zhangya identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT quxin identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT xiajunfeng identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT lidongqi identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT lixiaojuan identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT wangyu identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT hezewei identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT lisu identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT zhouyonghong identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT xielin identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq
AT yangzuozhang identificationofdifferentiallyexpressedgenesinthedevelopmentofosteosarcomausingrnaseq