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Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures

OBJECTIVE: To study pyroptosis-related biomarkers that are associated with the prognosis and immune microenvironment characteristics of osteosarcoma (OS). The goal is to establish a foundation for the prognosis and treatment of OS. METHODS: We retrieved transcriptome and clinical data from The Cance...

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Autores principales: Yang, Mingyi, Zheng, Haishi, Su, Yani, Xu, Ke, Yuan, Qiling, Cai, Yongsong, Aihaiti, Yirixiati, Xu, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10661155/
https://www.ncbi.nlm.nih.gov/pubmed/38027935
http://dx.doi.org/10.1016/j.heliyon.2023.e21503
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author Yang, Mingyi
Zheng, Haishi
Su, Yani
Xu, Ke
Yuan, Qiling
Cai, Yongsong
Aihaiti, Yirixiati
Xu, Peng
author_facet Yang, Mingyi
Zheng, Haishi
Su, Yani
Xu, Ke
Yuan, Qiling
Cai, Yongsong
Aihaiti, Yirixiati
Xu, Peng
author_sort Yang, Mingyi
collection PubMed
description OBJECTIVE: To study pyroptosis-related biomarkers that are associated with the prognosis and immune microenvironment characteristics of osteosarcoma (OS). The goal is to establish a foundation for the prognosis and treatment of OS. METHODS: We retrieved transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database for 88 OS patients. Using this data, we constructed a prognostic model to identify pyroptosis-related genes (PRGs) associated with OS prognosis. To further explore the biological function of these PRGs, we performed enrichment analysis. To identify pyroptosis-related long non-coding RNAs (PRLncs) associated with the prognosis of OS, we performed co-expression analysis. Subsequently, a risk prognostic model was constructed using these PRLncs to generate a risk score, termed as PRLncs-score, thereby obtaining PRLncs associated with the prognosis of OS. The accuracy of the prognostic model was verified through survival analysis, risk curve, independent prognostic analysis, receiver operating characteristic (ROC) curve, difference analysis between high- and low-risk groups, and clinical correlation analysis. And to determine whether PRLncs-score is independent prognostic factor for OS. In addition, we further conducted external and internal validation for the risk prognosis model. Further analyses of immune cell infiltration and tumor microenvironment were performed. A pyroptosis-related competitive endogenous RNA (PRceRNA) network was constructed to obtain PRceRNAs associated with the prognosis of OS and performed gene set enrichment analysis (GSEA) on PRceRNA genes. RESULTS: We obtained five PRGs (CHMP4C, BAK1, GSDMA, CASP1, and CASP6) that predicted OS prognosis and seven PRLncs (AC090559.1, AP003119.2, CARD8-AS1, AL390728.4, SATB2-AS1, AL133215.2, and AC009495.3) and one PRceRNA (CARD8-AS1-hsa-miR-21-5p-IL1B) that predicted OS prognosis and indicated characteristics of the OS immune microenvironment. The PRLncs-score, in combination with other clinical features, was established as an independent prognostic factor for OS patients. Subsequent scrutiny of the tumor microenvironment and immune infiltration indicated that patients with low-PRLncs-scores were associated with reduced metastatic risk, improved survival rates, heightened levels of immune cells and stroma, and increased immune activity compared to those with high-PRLncs-scores. CONCLUSION: The study's findings offer insight into the prognosis of OS and its immune microenvironment, and hold promise for improving early diagnosis and immunotherapy.
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spelling pubmed-106611552023-10-31 Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures Yang, Mingyi Zheng, Haishi Su, Yani Xu, Ke Yuan, Qiling Cai, Yongsong Aihaiti, Yirixiati Xu, Peng Heliyon Research Article OBJECTIVE: To study pyroptosis-related biomarkers that are associated with the prognosis and immune microenvironment characteristics of osteosarcoma (OS). The goal is to establish a foundation for the prognosis and treatment of OS. METHODS: We retrieved transcriptome and clinical data from The Cancer Genome Atlas (TCGA) database for 88 OS patients. Using this data, we constructed a prognostic model to identify pyroptosis-related genes (PRGs) associated with OS prognosis. To further explore the biological function of these PRGs, we performed enrichment analysis. To identify pyroptosis-related long non-coding RNAs (PRLncs) associated with the prognosis of OS, we performed co-expression analysis. Subsequently, a risk prognostic model was constructed using these PRLncs to generate a risk score, termed as PRLncs-score, thereby obtaining PRLncs associated with the prognosis of OS. The accuracy of the prognostic model was verified through survival analysis, risk curve, independent prognostic analysis, receiver operating characteristic (ROC) curve, difference analysis between high- and low-risk groups, and clinical correlation analysis. And to determine whether PRLncs-score is independent prognostic factor for OS. In addition, we further conducted external and internal validation for the risk prognosis model. Further analyses of immune cell infiltration and tumor microenvironment were performed. A pyroptosis-related competitive endogenous RNA (PRceRNA) network was constructed to obtain PRceRNAs associated with the prognosis of OS and performed gene set enrichment analysis (GSEA) on PRceRNA genes. RESULTS: We obtained five PRGs (CHMP4C, BAK1, GSDMA, CASP1, and CASP6) that predicted OS prognosis and seven PRLncs (AC090559.1, AP003119.2, CARD8-AS1, AL390728.4, SATB2-AS1, AL133215.2, and AC009495.3) and one PRceRNA (CARD8-AS1-hsa-miR-21-5p-IL1B) that predicted OS prognosis and indicated characteristics of the OS immune microenvironment. The PRLncs-score, in combination with other clinical features, was established as an independent prognostic factor for OS patients. Subsequent scrutiny of the tumor microenvironment and immune infiltration indicated that patients with low-PRLncs-scores were associated with reduced metastatic risk, improved survival rates, heightened levels of immune cells and stroma, and increased immune activity compared to those with high-PRLncs-scores. CONCLUSION: The study's findings offer insight into the prognosis of OS and its immune microenvironment, and hold promise for improving early diagnosis and immunotherapy. Elsevier 2023-10-31 /pmc/articles/PMC10661155/ /pubmed/38027935 http://dx.doi.org/10.1016/j.heliyon.2023.e21503 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Yang, Mingyi
Zheng, Haishi
Su, Yani
Xu, Ke
Yuan, Qiling
Cai, Yongsong
Aihaiti, Yirixiati
Xu, Peng
Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title_full Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title_fullStr Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title_full_unstemmed Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title_short Novel pyroptosis-related lncRNAs and ceRNAs predict osteosarcoma prognosis and indicate immune microenvironment signatures
title_sort novel pyroptosis-related lncrnas and cernas predict osteosarcoma prognosis and indicate immune microenvironment signatures
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10661155/
https://www.ncbi.nlm.nih.gov/pubmed/38027935
http://dx.doi.org/10.1016/j.heliyon.2023.e21503
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