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Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis

Background: Breast cancer (BC) is a major leading cause of woman deaths worldwide. Increasing evidence has revealed that stemness features are related to the prognosis and progression of tumors. Nevertheless, the roles of stemness-index-related long noncoding RNAs (lncRNAs) in BC remain unclear. Met...

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Autores principales: Qian, Da, Qian, Cheng, Ye, Buyun, Xu, Ming, Wu, Danping, Li, Jialu, Li, Dong, Yu, Bin, Tao, Yijing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8902307/
https://www.ncbi.nlm.nih.gov/pubmed/35273635
http://dx.doi.org/10.3389/fgene.2022.760514
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author Qian, Da
Qian, Cheng
Ye, Buyun
Xu, Ming
Wu, Danping
Li, Jialu
Li, Dong
Yu, Bin
Tao, Yijing
author_facet Qian, Da
Qian, Cheng
Ye, Buyun
Xu, Ming
Wu, Danping
Li, Jialu
Li, Dong
Yu, Bin
Tao, Yijing
author_sort Qian, Da
collection PubMed
description Background: Breast cancer (BC) is a major leading cause of woman deaths worldwide. Increasing evidence has revealed that stemness features are related to the prognosis and progression of tumors. Nevertheless, the roles of stemness-index-related long noncoding RNAs (lncRNAs) in BC remain unclear. Methods: Differentially expressed stemness-index-related lncRNAs between BC and normal samples in The Cancer Genome Atlas database were screened based on weighted gene co-expression network analysis and differential analysis. Univariate Cox and least absolute shrinkage and selection operator regression analyses were performed to identify prognostic lncRNAs and construct a stemness-index-related lncRNA signature. Time-dependent receiver operating characteristic curves were plotted to evaluate the predictive capability of the stemness-index-related lncRNA signature. Moreover, correlation analysis and functional enrichment analyses were conducted to investigate the stemness-index-related lncRNA signature-related biological function. Finally, a quantitative real-time polymerase chain reaction was used to detect the expression levels of lncRNAs. Results: A total of 73 differentially expressed stemness-index-related lncRNAs were identified. Next, FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were used to construct a stemness-index-related lncRNA signature, and receiver operating characteristic curves indicated that stemness-index-related lncRNA signature could predict the prognosis of BC well. Moreover, functional enrichment analysis suggested that differentially expressed genes between the high-risk group and low-risk group were mainly involved in immune-related biological processes and pathways. Furthermore, functional enrichment analysis of lncRNA-related protein-coding genes revealed that FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were associated with neuroactive ligand–receptor interaction, AMPK signaling pathway, PPAR signaling pathway, and cGMP-PKG signaling pathway. Finally, quantitative real-time polymerase chain reaction revealed that FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the potential diagnostic biomarkers of BC. Conclusion: The stemness-index-related lncRNA signature based on FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 could be used as an independent predictor for the survival of BC, and FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the diagnostic markers of BC.
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spelling pubmed-89023072022-03-09 Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis Qian, Da Qian, Cheng Ye, Buyun Xu, Ming Wu, Danping Li, Jialu Li, Dong Yu, Bin Tao, Yijing Front Genet Genetics Background: Breast cancer (BC) is a major leading cause of woman deaths worldwide. Increasing evidence has revealed that stemness features are related to the prognosis and progression of tumors. Nevertheless, the roles of stemness-index-related long noncoding RNAs (lncRNAs) in BC remain unclear. Methods: Differentially expressed stemness-index-related lncRNAs between BC and normal samples in The Cancer Genome Atlas database were screened based on weighted gene co-expression network analysis and differential analysis. Univariate Cox and least absolute shrinkage and selection operator regression analyses were performed to identify prognostic lncRNAs and construct a stemness-index-related lncRNA signature. Time-dependent receiver operating characteristic curves were plotted to evaluate the predictive capability of the stemness-index-related lncRNA signature. Moreover, correlation analysis and functional enrichment analyses were conducted to investigate the stemness-index-related lncRNA signature-related biological function. Finally, a quantitative real-time polymerase chain reaction was used to detect the expression levels of lncRNAs. Results: A total of 73 differentially expressed stemness-index-related lncRNAs were identified. Next, FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were used to construct a stemness-index-related lncRNA signature, and receiver operating characteristic curves indicated that stemness-index-related lncRNA signature could predict the prognosis of BC well. Moreover, functional enrichment analysis suggested that differentially expressed genes between the high-risk group and low-risk group were mainly involved in immune-related biological processes and pathways. Furthermore, functional enrichment analysis of lncRNA-related protein-coding genes revealed that FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 were associated with neuroactive ligand–receptor interaction, AMPK signaling pathway, PPAR signaling pathway, and cGMP-PKG signaling pathway. Finally, quantitative real-time polymerase chain reaction revealed that FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the potential diagnostic biomarkers of BC. Conclusion: The stemness-index-related lncRNA signature based on FAM83H-AS1, HID1-AS1, HOXB-AS1, RP11-1070N10.3, RP11-1100L3.8, and RP11-696F12.1 could be used as an independent predictor for the survival of BC, and FAM83H-AS1, HID1-AS1, RP11-1100L3.8, and RP11-696F12.1 might be used as the diagnostic markers of BC. Frontiers Media S.A. 2022-02-22 /pmc/articles/PMC8902307/ /pubmed/35273635 http://dx.doi.org/10.3389/fgene.2022.760514 Text en Copyright © 2022 Qian, Qian, Ye, Xu, Wu, Li, Li, Yu and Tao. 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 Genetics
Qian, Da
Qian, Cheng
Ye, Buyun
Xu, Ming
Wu, Danping
Li, Jialu
Li, Dong
Yu, Bin
Tao, Yijing
Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title_full Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title_fullStr Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title_full_unstemmed Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title_short Development and Validation of a Novel Stemness-Index-Related Long Noncoding RNA Signature for Breast Cancer Based on Weighted Gene Co-Expression Network Analysis
title_sort development and validation of a novel stemness-index-related long noncoding rna signature for breast cancer based on weighted gene co-expression network analysis
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8902307/
https://www.ncbi.nlm.nih.gov/pubmed/35273635
http://dx.doi.org/10.3389/fgene.2022.760514
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