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Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma

BACKGROUND: Osteosarcoma is a malignant bone tumor that typically occurs in adolescents or children under 20 years of age. Developing efficient clinical prognostic markers is crucial for improving the treatment of osteosarcoma patients. METHODS: Three datasets related to osteosarcoma were acquired f...

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Autores principales: Liu, Zhe, Zhong, Yun, Meng, Senling, Liao, Qinyuan, Chen, Weicai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AME Publishing Company 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848427/
https://www.ncbi.nlm.nih.gov/pubmed/35282067
http://dx.doi.org/10.21037/atm-21-6276
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author Liu, Zhe
Zhong, Yun
Meng, Senling
Liao, Qinyuan
Chen, Weicai
author_facet Liu, Zhe
Zhong, Yun
Meng, Senling
Liao, Qinyuan
Chen, Weicai
author_sort Liu, Zhe
collection PubMed
description BACKGROUND: Osteosarcoma is a malignant bone tumor that typically occurs in adolescents or children under 20 years of age. Developing efficient clinical prognostic markers is crucial for improving the treatment of osteosarcoma patients. METHODS: Three datasets related to osteosarcoma were acquired from the Gene Expression Omnibus (GEO) database. A gene signature model was established using the Limma package in the R software, univariate and multivariate survival analyses, and least absolute shrinkage and selection operator (LASSO) algorithms. The gene signature was then verified using external datasets. RESULTS: From the GEO database, 242 differentially expressed genes were identified. A total of 590 unique genes, including 380 genes from the human protein interaction network, were found to be related to biological processes such as bone development and bone cell development. Univariate Cox survival analyses revealed 43 genes that were associated with the prognosis of osteosarcoma patients. A seven-gene signature [retinitis pigmentosa 2 (RP2), polyhydroxybutyrate (PHB), myosin VI (MYO6), mutL homolog 1 (MLH1), Casein kinase 2 beta (CSNK2B), ribosomal protein L37A (RPL37A), and CCAAT/enhancer binding protein alpha (CEBPA)] was developed using LASSO regression analysis and multivariate regression analysis. This gene signature could stratify the prognostic risk of sample cases in the training set, the test set, and the external verification set (P<0.01). The area under the receiver operating characteristic curve for the 5-year survival was higher than 0.72 in both the training and verification groups. CONCLUSIONS: In this study, a seven-gene signature was developed that is highly efficient at predicting the prognosis of patients with osteosarcoma, and therefore, this signature may be a crucial guide in the treatment of these patients.
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spelling pubmed-88484272022-03-10 Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma Liu, Zhe Zhong, Yun Meng, Senling Liao, Qinyuan Chen, Weicai Ann Transl Med Original Article BACKGROUND: Osteosarcoma is a malignant bone tumor that typically occurs in adolescents or children under 20 years of age. Developing efficient clinical prognostic markers is crucial for improving the treatment of osteosarcoma patients. METHODS: Three datasets related to osteosarcoma were acquired from the Gene Expression Omnibus (GEO) database. A gene signature model was established using the Limma package in the R software, univariate and multivariate survival analyses, and least absolute shrinkage and selection operator (LASSO) algorithms. The gene signature was then verified using external datasets. RESULTS: From the GEO database, 242 differentially expressed genes were identified. A total of 590 unique genes, including 380 genes from the human protein interaction network, were found to be related to biological processes such as bone development and bone cell development. Univariate Cox survival analyses revealed 43 genes that were associated with the prognosis of osteosarcoma patients. A seven-gene signature [retinitis pigmentosa 2 (RP2), polyhydroxybutyrate (PHB), myosin VI (MYO6), mutL homolog 1 (MLH1), Casein kinase 2 beta (CSNK2B), ribosomal protein L37A (RPL37A), and CCAAT/enhancer binding protein alpha (CEBPA)] was developed using LASSO regression analysis and multivariate regression analysis. This gene signature could stratify the prognostic risk of sample cases in the training set, the test set, and the external verification set (P<0.01). The area under the receiver operating characteristic curve for the 5-year survival was higher than 0.72 in both the training and verification groups. CONCLUSIONS: In this study, a seven-gene signature was developed that is highly efficient at predicting the prognosis of patients with osteosarcoma, and therefore, this signature may be a crucial guide in the treatment of these patients. AME Publishing Company 2022-01 /pmc/articles/PMC8848427/ /pubmed/35282067 http://dx.doi.org/10.21037/atm-21-6276 Text en 2022 Annals of Translational Medicine. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Original Article
Liu, Zhe
Zhong, Yun
Meng, Senling
Liao, Qinyuan
Chen, Weicai
Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title_full Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title_fullStr Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title_full_unstemmed Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title_short Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
title_sort identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848427/
https://www.ncbi.nlm.nih.gov/pubmed/35282067
http://dx.doi.org/10.21037/atm-21-6276
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