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Identification of potential crucial genes and key pathways in osteosarcoma
BACKGROUND: The aim of this study is to identify the potential pathogenic and metastasis-related differentially expressed genes (DEGs) in osteosarcoma through bioinformatic analysis of Gene Expression Omnibus (GEO) database. RESULTS: Gene expression profiles of GSE14359, GSE16088, and GSE33383, in t...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362476/ https://www.ncbi.nlm.nih.gov/pubmed/32665038 http://dx.doi.org/10.1186/s41065-020-00142-0 |
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author | Liu, Junwei Wu, Siyu Xie, Xiaoyu Wang, Ziming Lei, Qianqian |
author_facet | Liu, Junwei Wu, Siyu Xie, Xiaoyu Wang, Ziming Lei, Qianqian |
author_sort | Liu, Junwei |
collection | PubMed |
description | BACKGROUND: The aim of this study is to identify the potential pathogenic and metastasis-related differentially expressed genes (DEGs) in osteosarcoma through bioinformatic analysis of Gene Expression Omnibus (GEO) database. RESULTS: Gene expression profiles of GSE14359, GSE16088, and GSE33383, in total 112 osteosarcoma tissue samples and 7 osteoblasts, were analyzed. Seventy-four normal-primary DEGs (NPDEGs) and 764 primary-metastatic DEGs (PMDEGs) were screened. VAMP8, A2M, HLA-DRA, SPARCL1, HLA-DQA1, APOC1 and AQP1 were identified continuously upregulating during the oncogenesis and metastasis of osteosarcoma. The enriched functions and pathways of NPDEGs include procession and presentation of antigens, activation of MHC class II receptors and phagocytosis. The enriched functions and pathways of PMDEGs include mitotic nuclear division, cell adhesion molecules (CAMs) and focal adhesion. With protein-protein interaction (PPI) network analyzed by Molecular Complex Detection (MCODE) plug-in of Cytoscape software, one hub NPDEG (HLA-DRA) and 7 hub PMDEGs (CDK1, CDK20, CCNB1, MTIF2, MRPS7, VEGFA and EGF) were eventually selected, and the most significant pathways in NPDEGs module and PMDEGs module were enriched in the procession and presentation of exogenous peptide antigen via MHC class II and the nuclear division, respectively. CONCLUSIONS: By integrated bioinformatic analysis, numerous DEGs related to osteosarcoma were screened, and the hub DEGs identified in this study are possibly part of the potential biomarkers for osteosarcoma. However, further experimental studies are still necessary to elucidate the biological function and mechanism of these genes. |
format | Online Article Text |
id | pubmed-7362476 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-73624762020-07-17 Identification of potential crucial genes and key pathways in osteosarcoma Liu, Junwei Wu, Siyu Xie, Xiaoyu Wang, Ziming Lei, Qianqian Hereditas Research BACKGROUND: The aim of this study is to identify the potential pathogenic and metastasis-related differentially expressed genes (DEGs) in osteosarcoma through bioinformatic analysis of Gene Expression Omnibus (GEO) database. RESULTS: Gene expression profiles of GSE14359, GSE16088, and GSE33383, in total 112 osteosarcoma tissue samples and 7 osteoblasts, were analyzed. Seventy-four normal-primary DEGs (NPDEGs) and 764 primary-metastatic DEGs (PMDEGs) were screened. VAMP8, A2M, HLA-DRA, SPARCL1, HLA-DQA1, APOC1 and AQP1 were identified continuously upregulating during the oncogenesis and metastasis of osteosarcoma. The enriched functions and pathways of NPDEGs include procession and presentation of antigens, activation of MHC class II receptors and phagocytosis. The enriched functions and pathways of PMDEGs include mitotic nuclear division, cell adhesion molecules (CAMs) and focal adhesion. With protein-protein interaction (PPI) network analyzed by Molecular Complex Detection (MCODE) plug-in of Cytoscape software, one hub NPDEG (HLA-DRA) and 7 hub PMDEGs (CDK1, CDK20, CCNB1, MTIF2, MRPS7, VEGFA and EGF) were eventually selected, and the most significant pathways in NPDEGs module and PMDEGs module were enriched in the procession and presentation of exogenous peptide antigen via MHC class II and the nuclear division, respectively. CONCLUSIONS: By integrated bioinformatic analysis, numerous DEGs related to osteosarcoma were screened, and the hub DEGs identified in this study are possibly part of the potential biomarkers for osteosarcoma. However, further experimental studies are still necessary to elucidate the biological function and mechanism of these genes. BioMed Central 2020-07-14 /pmc/articles/PMC7362476/ /pubmed/32665038 http://dx.doi.org/10.1186/s41065-020-00142-0 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Liu, Junwei Wu, Siyu Xie, Xiaoyu Wang, Ziming Lei, Qianqian Identification of potential crucial genes and key pathways in osteosarcoma |
title | Identification of potential crucial genes and key pathways in osteosarcoma |
title_full | Identification of potential crucial genes and key pathways in osteosarcoma |
title_fullStr | Identification of potential crucial genes and key pathways in osteosarcoma |
title_full_unstemmed | Identification of potential crucial genes and key pathways in osteosarcoma |
title_short | Identification of potential crucial genes and key pathways in osteosarcoma |
title_sort | identification of potential crucial genes and key pathways in osteosarcoma |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362476/ https://www.ncbi.nlm.nih.gov/pubmed/32665038 http://dx.doi.org/10.1186/s41065-020-00142-0 |
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