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Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques

Atherosclerosis is a chronic inflammatory disease with high prevalence and mortality. The rupture of atherosclerotic plaque is the main reason for the clinical events caused by atherosclerosis. Making clear the transcriptomic and proteomic profiles between the stabe and unstable atherosclerotic plaq...

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Autores principales: Bao, Mei-hua, Zhang, Ruo-qi, Huang, Xiao-shan, Zhou, Ji, Guo, Zhen, Xu, Bao-feng, Liu, Rui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8599967/
https://www.ncbi.nlm.nih.gov/pubmed/34804124
http://dx.doi.org/10.3389/fgene.2021.755507
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author Bao, Mei-hua
Zhang, Ruo-qi
Huang, Xiao-shan
Zhou, Ji
Guo, Zhen
Xu, Bao-feng
Liu, Rui
author_facet Bao, Mei-hua
Zhang, Ruo-qi
Huang, Xiao-shan
Zhou, Ji
Guo, Zhen
Xu, Bao-feng
Liu, Rui
author_sort Bao, Mei-hua
collection PubMed
description Atherosclerosis is a chronic inflammatory disease with high prevalence and mortality. The rupture of atherosclerotic plaque is the main reason for the clinical events caused by atherosclerosis. Making clear the transcriptomic and proteomic profiles between the stabe and unstable atherosclerotic plaques is crucial to prevent the clinical manifestations. In the present study, 5 stable and 5 unstable human carotid atherosclerotic plaques were obtained by carotid endarterectomy. The samples were used for the whole transcriptome sequencing (RNA-Seq) by the Next-Generation Sequencing using the Illumina HiSeq, and for proteome analysis by HPLC-MS/MS. The lncRNA-targeted genes and circRNA-originated genes were identified by analyzing their location and sequence. Gene Ontology and KEGG enrichment was carried out to analyze the functions of differentially expressed RNAs and proteins. The protein-protein interactions (PPI) network was constructed by the online tool STRING. The consistency of transcriptome and proteome were analyzed, and the lncRNA/circRNA-miRNA-mRNA interactions were predicted. As a result, 202 mRNAs, 488 lncRNAs, 91 circRNAs, and 293 proteins were identified to be differentially expressed between stable and unstable atherosclerotic plaques. The 488 lncRNAs might target 381 protein-coding genes by cis-acting mechanisms. Sequence analysis indicated the 91 differentially expressed circRNAs were originated from 97 protein-coding genes. These differentially expressed RNAs and proteins were mainly enriched in the terms of the cellular response to stress or stimulus, the regulation of gene transcription, the immune response, the nervous system functions, the hematologic activities, and the endocrine system. These results were consistent with the previous reported data in the dataset GSE41571. Further analysis identified CD5L, S100A12, CKB (target gene of lncRNA MSTRG.11455.17), CEMIP (target gene of lncRNA MSTRG.12845), and SH3GLB1 (originated gene of hsacirc_000411) to be critical genes in regulating the stability of atherosclerotic plaques. Our results provided a comprehensive transcriptomic and proteomic knowledge on the stability of atherosclerotic plaques.
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spelling pubmed-85999672021-11-19 Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques Bao, Mei-hua Zhang, Ruo-qi Huang, Xiao-shan Zhou, Ji Guo, Zhen Xu, Bao-feng Liu, Rui Front Genet Genetics Atherosclerosis is a chronic inflammatory disease with high prevalence and mortality. The rupture of atherosclerotic plaque is the main reason for the clinical events caused by atherosclerosis. Making clear the transcriptomic and proteomic profiles between the stabe and unstable atherosclerotic plaques is crucial to prevent the clinical manifestations. In the present study, 5 stable and 5 unstable human carotid atherosclerotic plaques were obtained by carotid endarterectomy. The samples were used for the whole transcriptome sequencing (RNA-Seq) by the Next-Generation Sequencing using the Illumina HiSeq, and for proteome analysis by HPLC-MS/MS. The lncRNA-targeted genes and circRNA-originated genes were identified by analyzing their location and sequence. Gene Ontology and KEGG enrichment was carried out to analyze the functions of differentially expressed RNAs and proteins. The protein-protein interactions (PPI) network was constructed by the online tool STRING. The consistency of transcriptome and proteome were analyzed, and the lncRNA/circRNA-miRNA-mRNA interactions were predicted. As a result, 202 mRNAs, 488 lncRNAs, 91 circRNAs, and 293 proteins were identified to be differentially expressed between stable and unstable atherosclerotic plaques. The 488 lncRNAs might target 381 protein-coding genes by cis-acting mechanisms. Sequence analysis indicated the 91 differentially expressed circRNAs were originated from 97 protein-coding genes. These differentially expressed RNAs and proteins were mainly enriched in the terms of the cellular response to stress or stimulus, the regulation of gene transcription, the immune response, the nervous system functions, the hematologic activities, and the endocrine system. These results were consistent with the previous reported data in the dataset GSE41571. Further analysis identified CD5L, S100A12, CKB (target gene of lncRNA MSTRG.11455.17), CEMIP (target gene of lncRNA MSTRG.12845), and SH3GLB1 (originated gene of hsacirc_000411) to be critical genes in regulating the stability of atherosclerotic plaques. Our results provided a comprehensive transcriptomic and proteomic knowledge on the stability of atherosclerotic plaques. Frontiers Media S.A. 2021-11-04 /pmc/articles/PMC8599967/ /pubmed/34804124 http://dx.doi.org/10.3389/fgene.2021.755507 Text en Copyright © 2021 Bao, Zhang, Huang, Zhou, Guo, Xu and Liu. 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
Bao, Mei-hua
Zhang, Ruo-qi
Huang, Xiao-shan
Zhou, Ji
Guo, Zhen
Xu, Bao-feng
Liu, Rui
Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title_full Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title_fullStr Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title_full_unstemmed Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title_short Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
title_sort transcriptomic and proteomic profiling of human stable and unstable carotid atherosclerotic plaques
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8599967/
https://www.ncbi.nlm.nih.gov/pubmed/34804124
http://dx.doi.org/10.3389/fgene.2021.755507
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