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Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal carcinoma. It is particularly important to accurately judge the prognosis of patients. Since most tumor prediction models depend on the specific expression level of related genes, a better model therefore needs to be constructe...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9325030/ https://www.ncbi.nlm.nih.gov/pubmed/35891325 http://dx.doi.org/10.3390/vaccines10071161 |
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author | Wang, Gang Liu, Panhong Li, Jiangfeng Jin, Ke Zheng, Xiangyi Xie, Liping |
author_facet | Wang, Gang Liu, Panhong Li, Jiangfeng Jin, Ke Zheng, Xiangyi Xie, Liping |
author_sort | Wang, Gang |
collection | PubMed |
description | Clear cell renal cell carcinoma (ccRCC) is the most common type of renal carcinoma. It is particularly important to accurately judge the prognosis of patients. Since most tumor prediction models depend on the specific expression level of related genes, a better model therefore needs to be constructed. To provide an immune-related lncRNA (irlncRNAs) tumor prognosis model that is independent of the specific gene expression levels, we first downloaded and sorted out the data on ccRCC in the TCGA database and screened irlncRNAs using co-expression analysis and then obtained the differently expressed irlncRNA (DEirlncRNA) pairs by means of univariate analysis. In addition, we modified LASSO penalized regression. Subsequently, the ROC curve was drawn, and we compared the area under the curve, calculated the Akaike information standard value of the 5-year receiver operating characteristic curve, and determined the cut-off point to establish the best model to distinguish the high- or low-disease-risk group of ccRCC. Subsequently, we reassessed the model from the perspectives of survival, clinic-pathological characteristics, tumor-infiltrating immune cells, chemotherapeutics efficacy, and immunosuppressed biomarkers. A total of 17 DEirlncRNAs pairs (AL031710.1|AC104984.5, AC020907.4|AC127-24.4,AC091185.1|AC005104.1, AL513218.1|AC079015.1, AC104564.3|HOXB-AS3, AC003070.1|LINC01355, SEMA6A-AS1|CR936218.1, AL513327.1|AS005785.1, AC084876.1|AC009704.2, IGFL2-AS1|PRDM16-DT, AC011462.4|MMP25-AS1, AL662844.3I|TGB2-AS1, ARHGAP27P1|AC116914.2, AC093788.1|AC007098.1, MCF2L-AS1|AC093001.1, SMIM25|AC008870.2, and AC027796.4|LINC00893) were identified, all of which were included in the Cox regression model. Using the cut-off point, we can better distinguish patients according to different factors, such as survival status, invasive clinic-pathological features, tumor immune infiltration, whether they are sensitive to chemotherapy or not, and expression of immunosuppressive biomarkers. We constructed the irlncRNA model by means of pairing, which can better eliminate the dependence on the expression level of the target genes. In other words, the signature established by pairing irlncRNA regardless of expression levels showed promising clinical prediction value. |
format | Online Article Text |
id | pubmed-9325030 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-93250302022-07-27 Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma Wang, Gang Liu, Panhong Li, Jiangfeng Jin, Ke Zheng, Xiangyi Xie, Liping Vaccines (Basel) Article Clear cell renal cell carcinoma (ccRCC) is the most common type of renal carcinoma. It is particularly important to accurately judge the prognosis of patients. Since most tumor prediction models depend on the specific expression level of related genes, a better model therefore needs to be constructed. To provide an immune-related lncRNA (irlncRNAs) tumor prognosis model that is independent of the specific gene expression levels, we first downloaded and sorted out the data on ccRCC in the TCGA database and screened irlncRNAs using co-expression analysis and then obtained the differently expressed irlncRNA (DEirlncRNA) pairs by means of univariate analysis. In addition, we modified LASSO penalized regression. Subsequently, the ROC curve was drawn, and we compared the area under the curve, calculated the Akaike information standard value of the 5-year receiver operating characteristic curve, and determined the cut-off point to establish the best model to distinguish the high- or low-disease-risk group of ccRCC. Subsequently, we reassessed the model from the perspectives of survival, clinic-pathological characteristics, tumor-infiltrating immune cells, chemotherapeutics efficacy, and immunosuppressed biomarkers. A total of 17 DEirlncRNAs pairs (AL031710.1|AC104984.5, AC020907.4|AC127-24.4,AC091185.1|AC005104.1, AL513218.1|AC079015.1, AC104564.3|HOXB-AS3, AC003070.1|LINC01355, SEMA6A-AS1|CR936218.1, AL513327.1|AS005785.1, AC084876.1|AC009704.2, IGFL2-AS1|PRDM16-DT, AC011462.4|MMP25-AS1, AL662844.3I|TGB2-AS1, ARHGAP27P1|AC116914.2, AC093788.1|AC007098.1, MCF2L-AS1|AC093001.1, SMIM25|AC008870.2, and AC027796.4|LINC00893) were identified, all of which were included in the Cox regression model. Using the cut-off point, we can better distinguish patients according to different factors, such as survival status, invasive clinic-pathological features, tumor immune infiltration, whether they are sensitive to chemotherapy or not, and expression of immunosuppressive biomarkers. We constructed the irlncRNA model by means of pairing, which can better eliminate the dependence on the expression level of the target genes. In other words, the signature established by pairing irlncRNA regardless of expression levels showed promising clinical prediction value. MDPI 2022-07-21 /pmc/articles/PMC9325030/ /pubmed/35891325 http://dx.doi.org/10.3390/vaccines10071161 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Wang, Gang Liu, Panhong Li, Jiangfeng Jin, Ke Zheng, Xiangyi Xie, Liping Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title | Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title_full | Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title_fullStr | Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title_full_unstemmed | Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title_short | Novel Prognosis and Therapeutic Response Model of Immune-Related lncRNA Pairs in Clear Cell Renal Cell Carcinoma |
title_sort | novel prognosis and therapeutic response model of immune-related lncrna pairs in clear cell renal cell carcinoma |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9325030/ https://www.ncbi.nlm.nih.gov/pubmed/35891325 http://dx.doi.org/10.3390/vaccines10071161 |
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