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Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration

Long non-coding RNAs (lncRNAs) are related to a variety of human diseases. However, little is known about the role of lncRNA in intervertebral disc degeneration (IDD). LncRNA expression profile of human IDD were downloaded from Gene Expression Omnibus (GEO) database. Potential biomarkers and therape...

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Autores principales: Zhan, Jiawen, Wang, Shangquan, Wei, Xu, Feng, Minshan, Yin, Xunlu, Yu, Jie, Han, Tao, Liu, Guangwei, Xuan, Wangwen, Wang, Xiaobo, Xie, Rui, Sun, Kai, Zhu, Liguo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8806434/
https://www.ncbi.nlm.nih.gov/pubmed/34402383
http://dx.doi.org/10.1080/21655979.2021.1950258
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author Zhan, Jiawen
Wang, Shangquan
Wei, Xu
Feng, Minshan
Yin, Xunlu
Yu, Jie
Han, Tao
Liu, Guangwei
Xuan, Wangwen
Wang, Xiaobo
Xie, Rui
Sun, Kai
Zhu, Liguo
author_facet Zhan, Jiawen
Wang, Shangquan
Wei, Xu
Feng, Minshan
Yin, Xunlu
Yu, Jie
Han, Tao
Liu, Guangwei
Xuan, Wangwen
Wang, Xiaobo
Xie, Rui
Sun, Kai
Zhu, Liguo
author_sort Zhan, Jiawen
collection PubMed
description Long non-coding RNAs (lncRNAs) are related to a variety of human diseases. However, little is known about the role of lncRNA in intervertebral disc degeneration (IDD). LncRNA expression profile of human IDD were downloaded from Gene Expression Omnibus (GEO) database. Potential biomarkers and therapeutic drugs for IDD were analyzed by weighted gene co-expression network analysis (WGCNA), R software package Limma, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 1455 differentially expressed genes and 423 differentially expressed lncRNAs. Twenty-six co-expression modules were obtained, among them, the tan, brown, and turquoise modules were most closely related to IDD. The turquoise module contained a large number of differential expressed lncRNAs and genes, these genes were mainly enriched in the MAPK signaling pathway, TGF-beta signaling pathway. Furthermore, we obtained 11,857 LmiRM-Degenerated, these lncRNAs and genes showed higher differential expression multiples and higher expression correlation. After constructing a disease-gene interaction network, 25 disease-specific genes and 9 disease-specific lncRNAs were identified. Combined with the drug-target gene interaction network, three drugs, namely, Calcium citrate, Calcium Phosphate, and Calcium phosphate dihydrate, which may have curative effects on IDD, were determined. Finally, a genetic diagnosis model and lncRNA diagnosis model with 100% diagnostic performance in both the training data set and the validation data set were established based on these genes and lncRNA. This study provided new diagnostic features for IDD and could help design personalized treatment of IDD.
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spelling pubmed-88064342022-02-02 Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration Zhan, Jiawen Wang, Shangquan Wei, Xu Feng, Minshan Yin, Xunlu Yu, Jie Han, Tao Liu, Guangwei Xuan, Wangwen Wang, Xiaobo Xie, Rui Sun, Kai Zhu, Liguo Bioengineered Research Paper Long non-coding RNAs (lncRNAs) are related to a variety of human diseases. However, little is known about the role of lncRNA in intervertebral disc degeneration (IDD). LncRNA expression profile of human IDD were downloaded from Gene Expression Omnibus (GEO) database. Potential biomarkers and therapeutic drugs for IDD were analyzed by weighted gene co-expression network analysis (WGCNA), R software package Limma, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 1455 differentially expressed genes and 423 differentially expressed lncRNAs. Twenty-six co-expression modules were obtained, among them, the tan, brown, and turquoise modules were most closely related to IDD. The turquoise module contained a large number of differential expressed lncRNAs and genes, these genes were mainly enriched in the MAPK signaling pathway, TGF-beta signaling pathway. Furthermore, we obtained 11,857 LmiRM-Degenerated, these lncRNAs and genes showed higher differential expression multiples and higher expression correlation. After constructing a disease-gene interaction network, 25 disease-specific genes and 9 disease-specific lncRNAs were identified. Combined with the drug-target gene interaction network, three drugs, namely, Calcium citrate, Calcium Phosphate, and Calcium phosphate dihydrate, which may have curative effects on IDD, were determined. Finally, a genetic diagnosis model and lncRNA diagnosis model with 100% diagnostic performance in both the training data set and the validation data set were established based on these genes and lncRNA. This study provided new diagnostic features for IDD and could help design personalized treatment of IDD. Taylor & Francis 2021-08-17 /pmc/articles/PMC8806434/ /pubmed/34402383 http://dx.doi.org/10.1080/21655979.2021.1950258 Text en © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Paper
Zhan, Jiawen
Wang, Shangquan
Wei, Xu
Feng, Minshan
Yin, Xunlu
Yu, Jie
Han, Tao
Liu, Guangwei
Xuan, Wangwen
Wang, Xiaobo
Xie, Rui
Sun, Kai
Zhu, Liguo
Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title_full Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title_fullStr Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title_full_unstemmed Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title_short Systematic analysis of Long non-coding RNAs reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
title_sort systematic analysis of long non-coding rnas reveals diagnostic biomarkers and potential therapeutic drugs for intervertebral disc degeneration
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8806434/
https://www.ncbi.nlm.nih.gov/pubmed/34402383
http://dx.doi.org/10.1080/21655979.2021.1950258
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