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Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer
Based on the importance of basement membrane (BM) in cancer invasion and metastasis, we constructed a BM-associated lncRNA risk model to group bladder cancer (BCa) patients. Transcriptional and clinical data of BCa patients were downloaded from The Cancer Genome Atlas (TCGA), and the expressed genes...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590283/ https://www.ncbi.nlm.nih.gov/pubmed/36300088 http://dx.doi.org/10.3389/fonc.2022.994703 |
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author | Feng, Lixiang Yang, Jun Zhang, Wei Wang, Xiong Li, Lili Peng, Min Luo, Pengcheng |
author_facet | Feng, Lixiang Yang, Jun Zhang, Wei Wang, Xiong Li, Lili Peng, Min Luo, Pengcheng |
author_sort | Feng, Lixiang |
collection | PubMed |
description | Based on the importance of basement membrane (BM) in cancer invasion and metastasis, we constructed a BM-associated lncRNA risk model to group bladder cancer (BCa) patients. Transcriptional and clinical data of BCa patients were downloaded from The Cancer Genome Atlas (TCGA), and the expressed genes of BM-related proteins were obtained from the BM-BASE database. We download the GSE133624 chip data from the GEO database as an external validation dataset. We screened for statistically different BM genes between tumors and adjacent normal tissues. Co-expression analysis of lncRNAs and differentially expressed BM genes was performed to identify BM-related lncRNAs. Then, differentially expressed BM-related lncRNAs (DEBMlncRNAs) between tumor and normal tissues were identified. Univariate/multivariate Cox regression analysis was performed to select lncRNAs for risk assessment. LASSO analysis was performed to build a prognostic model. We constructed a model containing 8 DEBMlncRNAs (AC004034.1, AL662797.1, NR2F1-AS1, SETBP1-DT, AC011503.2, AC093010.2, LINC00649 and LINC02321). The prognostic risk model accurately predicted the prognosis of BCa patients and revealed that tumor aggressiveness and distant metastasis were associated with higher risk scores. In this model, we constructed a nomogram to assist clinical decision-making based on clinicopathological characteristics such as age, T, and N. The model also showed good predictive power for the tumor microenvironment and mutational burden. We validated the expression of eight lncRNAs using the dataset GSE133624 and two human bladder cancer cell lines (5637, BIU-87) and examined the expression and cellular localization of LINC00649 and AC011503.2 using a human bladder cancer tissue chip. We found that knockdown of LINC00649 expression in 5637 cells promoted the proliferation of 5637 cells.Our eight DEBMlncRNA risk models provide new insights into predicting prognosis, tumor invasion, and metastasis in BCa patients. |
format | Online Article Text |
id | pubmed-9590283 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95902832022-10-25 Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer Feng, Lixiang Yang, Jun Zhang, Wei Wang, Xiong Li, Lili Peng, Min Luo, Pengcheng Front Oncol Oncology Based on the importance of basement membrane (BM) in cancer invasion and metastasis, we constructed a BM-associated lncRNA risk model to group bladder cancer (BCa) patients. Transcriptional and clinical data of BCa patients were downloaded from The Cancer Genome Atlas (TCGA), and the expressed genes of BM-related proteins were obtained from the BM-BASE database. We download the GSE133624 chip data from the GEO database as an external validation dataset. We screened for statistically different BM genes between tumors and adjacent normal tissues. Co-expression analysis of lncRNAs and differentially expressed BM genes was performed to identify BM-related lncRNAs. Then, differentially expressed BM-related lncRNAs (DEBMlncRNAs) between tumor and normal tissues were identified. Univariate/multivariate Cox regression analysis was performed to select lncRNAs for risk assessment. LASSO analysis was performed to build a prognostic model. We constructed a model containing 8 DEBMlncRNAs (AC004034.1, AL662797.1, NR2F1-AS1, SETBP1-DT, AC011503.2, AC093010.2, LINC00649 and LINC02321). The prognostic risk model accurately predicted the prognosis of BCa patients and revealed that tumor aggressiveness and distant metastasis were associated with higher risk scores. In this model, we constructed a nomogram to assist clinical decision-making based on clinicopathological characteristics such as age, T, and N. The model also showed good predictive power for the tumor microenvironment and mutational burden. We validated the expression of eight lncRNAs using the dataset GSE133624 and two human bladder cancer cell lines (5637, BIU-87) and examined the expression and cellular localization of LINC00649 and AC011503.2 using a human bladder cancer tissue chip. We found that knockdown of LINC00649 expression in 5637 cells promoted the proliferation of 5637 cells.Our eight DEBMlncRNA risk models provide new insights into predicting prognosis, tumor invasion, and metastasis in BCa patients. Frontiers Media S.A. 2022-10-10 /pmc/articles/PMC9590283/ /pubmed/36300088 http://dx.doi.org/10.3389/fonc.2022.994703 Text en Copyright © 2022 Feng, Yang, Zhang, Wang, Li, Peng and Luo https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Oncology Feng, Lixiang Yang, Jun Zhang, Wei Wang, Xiong Li, Lili Peng, Min Luo, Pengcheng Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title | Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title_full | Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title_fullStr | Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title_full_unstemmed | Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title_short | Prognostic significance and identification of basement membrane-associated lncRNA in bladder cancer |
title_sort | prognostic significance and identification of basement membrane-associated lncrna in bladder cancer |
topic | Oncology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590283/ https://www.ncbi.nlm.nih.gov/pubmed/36300088 http://dx.doi.org/10.3389/fonc.2022.994703 |
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