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Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer
BACKGROUND: Both immune-reaction and lncRNAs play significant roles in the proliferation, invasion, and metastasis of ovarian cancer (OC). In this study, we aimed to construct an immune-related lncRNA risk model for patients with OC. METHOD: Single sample GSEA (ssGSEA) algorithm was used to analyze...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898952/ https://www.ncbi.nlm.nih.gov/pubmed/36739404 http://dx.doi.org/10.1186/s13048-023-01099-0 |
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author | Feng, Jing Yu, Yiping Yin, Wen Qian, Sumin |
author_facet | Feng, Jing Yu, Yiping Yin, Wen Qian, Sumin |
author_sort | Feng, Jing |
collection | PubMed |
description | BACKGROUND: Both immune-reaction and lncRNAs play significant roles in the proliferation, invasion, and metastasis of ovarian cancer (OC). In this study, we aimed to construct an immune-related lncRNA risk model for patients with OC. METHOD: Single sample GSEA (ssGSEA) algorithm was used to analyze the proportion of immune cells in The Cancer Genome Atlas (TCGA) and the hclust algorithm was used to conduct immune typing according to the proportion of immune cells for OC patients. The stromal and immune scores were computed utilizing the ESTIMATE algorithm. Weighted gene co-expression network analysis (WGCNA) and differentially expressed genes (DEGs) analyses were utilized to detect immune cluster-related lncRNAs. The least absolute shrinkage and selection operator (LASSO) regression was conducted for lncRNA selection. The selected lncRNAs were used to construct a prognosis-related risk model, which was then validated in Gene Expression Omnibus (GEO) database and in vitro validation. RESULTS: We identify two subtypes based on the ssGSEA analysis, high immunity cluster (immunity_H) and low immunity cluster (immunity_L). The proportion of patients in immunity_H cluster was significantly higher than that in immunity_L cluster. The ESTIMATE related scores are relative high in immunity_H group. Through WGCNA and LASSO analyses, we identified 141 immune cluster-related lncRNAs and found that these genes were mainly enriched in autophagy. A signature consisting of 7 lncRNAs, including AL391832.3, LINC00892, LINC02207, LINC02416, PSMB8.AS1, AC078788.1 and AC104971.3, were selected as the basis for classifying patients into high- and low-risk groups. Survival analysis and area under the ROC curve (AUC) of the signature pointed out that this risk model had high accuracy in predicting the prognosis of patients with OC. We also conducted the drug sensitive prediction and found that rapamycin outperformed in patient with high risk score. In vitro experiments also confirmed our prediction. CONCLUSIONS: We identified 7 immune-related prognostic lncRNAs that effectively predicted survival in OC patients. These findings may offer a valuable indicator for clinical stratification management and personalized therapeutic options for these patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13048-023-01099-0. |
format | Online Article Text |
id | pubmed-9898952 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-98989522023-02-05 Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer Feng, Jing Yu, Yiping Yin, Wen Qian, Sumin J Ovarian Res Research BACKGROUND: Both immune-reaction and lncRNAs play significant roles in the proliferation, invasion, and metastasis of ovarian cancer (OC). In this study, we aimed to construct an immune-related lncRNA risk model for patients with OC. METHOD: Single sample GSEA (ssGSEA) algorithm was used to analyze the proportion of immune cells in The Cancer Genome Atlas (TCGA) and the hclust algorithm was used to conduct immune typing according to the proportion of immune cells for OC patients. The stromal and immune scores were computed utilizing the ESTIMATE algorithm. Weighted gene co-expression network analysis (WGCNA) and differentially expressed genes (DEGs) analyses were utilized to detect immune cluster-related lncRNAs. The least absolute shrinkage and selection operator (LASSO) regression was conducted for lncRNA selection. The selected lncRNAs were used to construct a prognosis-related risk model, which was then validated in Gene Expression Omnibus (GEO) database and in vitro validation. RESULTS: We identify two subtypes based on the ssGSEA analysis, high immunity cluster (immunity_H) and low immunity cluster (immunity_L). The proportion of patients in immunity_H cluster was significantly higher than that in immunity_L cluster. The ESTIMATE related scores are relative high in immunity_H group. Through WGCNA and LASSO analyses, we identified 141 immune cluster-related lncRNAs and found that these genes were mainly enriched in autophagy. A signature consisting of 7 lncRNAs, including AL391832.3, LINC00892, LINC02207, LINC02416, PSMB8.AS1, AC078788.1 and AC104971.3, were selected as the basis for classifying patients into high- and low-risk groups. Survival analysis and area under the ROC curve (AUC) of the signature pointed out that this risk model had high accuracy in predicting the prognosis of patients with OC. We also conducted the drug sensitive prediction and found that rapamycin outperformed in patient with high risk score. In vitro experiments also confirmed our prediction. CONCLUSIONS: We identified 7 immune-related prognostic lncRNAs that effectively predicted survival in OC patients. These findings may offer a valuable indicator for clinical stratification management and personalized therapeutic options for these patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13048-023-01099-0. BioMed Central 2023-02-04 /pmc/articles/PMC9898952/ /pubmed/36739404 http://dx.doi.org/10.1186/s13048-023-01099-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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 Feng, Jing Yu, Yiping Yin, Wen Qian, Sumin Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title | Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title_full | Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title_fullStr | Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title_full_unstemmed | Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title_short | Development and verification of a 7-lncRNA prognostic model based on tumor immunity for patients with ovarian cancer |
title_sort | development and verification of a 7-lncrna prognostic model based on tumor immunity for patients with ovarian cancer |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898952/ https://www.ncbi.nlm.nih.gov/pubmed/36739404 http://dx.doi.org/10.1186/s13048-023-01099-0 |
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