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:	Mei-hua Bao, Ruo-qi Zhang, Xiao-shan Huang, Ji Zhou, Zhen Guo, Bao-feng Xu, Rui Liu
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	atherosclerosis unstable plaques RNA-seq proteome transcriptome Genetics QH426-470
Acceso en línea:	https://doaj.org/article/129d1dd045564c4884833f55dd3deeb4
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spelling	oai:doaj.org-article:129d1dd045564c4884833f55dd3deeb42021-11-04T06:28:56ZTranscriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques1664-802110.3389/fgene.2021.755507https://doaj.org/article/129d1dd045564c4884833f55dd3deeb42021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.755507/fullhttps://doaj.org/toc/1664-8021Atherosclerosis 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.Mei-hua BaoMei-hua BaoRuo-qi ZhangXiao-shan HuangJi ZhouZhen GuoBao-feng XuBao-feng XuRui LiuRui LiuFrontiers Media S.A.articleatherosclerosisunstable plaquesRNA-seqproteometranscriptomeGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	atherosclerosis unstable plaques RNA-seq proteome transcriptome Genetics QH426-470
spellingShingle	atherosclerosis unstable plaques RNA-seq proteome transcriptome Genetics QH426-470 Mei-hua Bao Mei-hua Bao Ruo-qi Zhang Xiao-shan Huang Ji Zhou Zhen Guo Bao-feng Xu Bao-feng Xu Rui Liu Rui Liu Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques
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.
format	article
author	Mei-hua Bao Mei-hua Bao Ruo-qi Zhang Xiao-shan Huang Ji Zhou Zhen Guo Bao-feng Xu Bao-feng Xu Rui Liu Rui Liu
author_facet	Mei-hua Bao Mei-hua Bao Ruo-qi Zhang Xiao-shan Huang Ji Zhou Zhen Guo Bao-feng Xu Bao-feng Xu Rui Liu Rui Liu
author_sort	Mei-hua Bao
title	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_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_sort	transcriptomic and proteomic profiling of human stable and unstable carotid atherosclerotic plaques
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/129d1dd045564c4884833f55dd3deeb4
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Transcriptomic and Proteomic Profiling of Human Stable and Unstable Carotid Atherosclerotic Plaques

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