Computational and functional strategies to decipher lncRNAs in human atherosclerosis

破译人类动脉粥样硬化中 lncRNA 的计算和功能策略

• 批准号: 10557797
• 负责人: Mingyao Li
• 金额: $ 66.03万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-02-01 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10557797
• 关键词: Address; Algorithms; Alleles; Arterial Fatty Streak; Atherosclerosis; Biological Models; Blood Vessels; Cardiovascular Diseases; Carotid Artery Plaques; Carotid Atherosclerotic Disease; Cells; Clinical; Complex; Computing Methodologies; Coronary heart disease; Coupled; Data; Data Set; Disease; Endarterectomy; Etiology; Event; Gene Chips; Genetic; Genetic Transcription; Genomics; Histologic; Human; Knowledge; Laboratories; Lesion; Messenger RNA; Methods; Modeling; Mus; Myocardial Infarction; Patients; Precision therapeutics; Protein Isoforms; Role; Sample Size; Sampling; Signal Transduction; Specificity; System; Tissues; Transcript; Untranslated RNA; Up-Regulation; Variant; biobank; cardiovascular disorder risk; case control; clinical translation; cost; differential expression; follow-up; functional genomics; genetic association; genome wide association study; genomic data; human model; in vivo; in vivo Model; induced pluripotent stem cell; innovation; novel; single-cell RNA sequencing; therapeutic target; transcriptome sequencing; translational therapeutics

This proposal addresses knowledge gaps in cell-specific function and disease causation of long non-coding RNAs (lncRNAs) in human atherosclerosis. Despite prominent examples of functional lncRNAs in cardiovascular diseases (CVD), their lack of conservation and cell-specificity have limited our understanding of their role in CVD. These challenges are particularly problematic in human atherosclerosis which is characterized by complex multi- cellular lesions. Further, recent single cell (sc)RNAseq data including our preliminary studies suggest that, relative to mRNAs, lncRNA expression in primary human cells may be restricted to key cell subpopulations. An overarching hypothesis is that many human lncRNAs modulate atherosclerosis and CVD risk via their discrete expression and function in specific lesion cell subpopulations. Thus, more precise knowledge of lncRNA cell-specific relationship to human atherosclerosis is required to drive mechanism-based clinical translation. Here we address key questions for lncRNAs in human atherosclerosis and CVD risk. First, which lncRNAs are expressed in human lesions and associate with clinical CVD? Second, for lncRNAs expressed in human lesions, in which specific lesion cell subpopulation are they functional? In Aim 1, we will address the first issue by analyzing differential expression of lncRNAs through deep RNAseq of a large nested case-control (n=260 with “symptomatic/unstable” and n=260 with “asymptomatic/stable” plaques) study of carotid atherosclerosis from the Munich Vascular Biobank (MVB). We will also determine whether lncRNAs demonstrate differential allele specific expression (ASE) between symptomatic/unstable vs. asymptomatic/stable plaques and if cis-eQTL variants for lncRNAs with differential ASE are associated with coronary heart disease (CHD) in large public genetic datasets. Prioritized lncRNAs will undergo cell-specific functional genomic follow-up in human vascular cells including our human induced pluripotent stem cell (hIPSC) vascular models. In Aim 2, we propose to use a novel deconvolution algorithm and integration of large-scale bulk RNAseq data from Aim 1 with selective single cell (sc)RNAseq of fresh lesions (n=60) to identify subpopulations and their lncRNAs that associate with symptomatic/unstable plaques and have causal genetic relationships to CHD. ScRNAseq of the fresh carotid lesions will be used to cluster cells and identify lesion subpopulations. Result from this analysis will permit computational deconvolution of the cell subpopulation composition of all MVB bulk RNAseq lesions (n=520) and assignment of subpopulation-specific lncRNA expression and relationship to symptomatic/unstable plaques. Subpopulation-specific lncRNA cis-eQTLs also will be identified and used to determine their causal relationship to CHD in genetic datasets. These findings, coupled to subpopulation-specific functional studies, will define subpopulation-specific lncRNA functions in human atherosclerosis. Our proposal leverages unique genomic data, innovative computational methods and functional genomics, and interdisciplinary expertise to direct in vivo translation and precision therapeutic targeting of cell-specific vascular lncRNA functions in atherosclerotic CVD.

该提案解决了细胞特异性功能的知识差距和长期非编码的疾病原因 人动脉粥样硬化中的RNA（LNCRNA）。尽管心血管中功能性LNCRNA的著名例子 疾病（CVD），他们缺乏保护和细胞特异性限制了我们对它们在CVD中的作用的理解。 这些挑战在人动脉粥样硬化中尤其有问题，其特征是复杂的多种 细胞病变。此外，最近的单细胞（SC）RNASEQ数据（包括我们的初步研究）表明，， 相对于mRNA，原代人细胞中的lncRNA表达可能仅限于关键细胞亚群。一个 总体假设是，许多人类LNCRNA通过其调节动脉粥样硬化和CVD风险 特定病变细胞亚群中的离散表达和功能。那是对的更精确的知识 LNCRNA细胞特异性与人动脉粥样硬化需要驱动基于机制的临床 翻译。在这里，我们解决了人类动脉粥样硬化和CVD风险中LNCRNA的关键问题。首先，哪个 LNCRNA在人体病变中表达并与临床CVD相关？第二，对于lncrnas表示 人体病变，在哪种特异性病变细胞亚群中起作用？在AIM 1中，我们将解决第一个 通过分析LNCRNA的差异表达通过大型嵌套的病例对照的深度RNASEQ的差异表达 （n = 260，带有“有症状/不稳定”和n = 260，带有“无症状/稳定”斑块）颈动脉研究 慕尼黑血管生物库（MVB）的动脉粥样硬化。我们还将确定LNCRNA是否证明 有症状/不稳定与无症状/稳定斑块之间的差分等位基因表达（ASE） 如果具有差异ASE的LNCRNA的顺式EQTL变体与大的冠状动脉疾病（CHD）有关 公共遗传数据集。优先的LNCRNA将在人类中接受细胞特异性的功能基因组随访 血管细胞在内，包括我们人类诱导的多能干细胞（HIPSC）血管模型。在AIM 2中，我们提出了 使用一种新型的反卷积算法和从AIM 1中的大规模批量RNASEQ数据的集成与选择性 新鲜病变（n = 60）的单细胞（SC）RNASEQ，以识别与与之相关的LNCRNA 有症状/不稳定的斑块，与CHD有因果关系。新鲜颈动脉的scrnaseq 病变将用于聚集细胞并鉴定病变亚群。该分析的结果将允许 所有MVB大量RNASEQ病变（n = 520）和 亚群特异性LNCRNA表达和与症状/不稳定斑块的关系。 还将确定亚群特异性的lncRNA顺式eqtls并用于确定其因果关系 在遗传数据集中进行CHD。这些发现与亚群特定的功能研究结合在一起，将定义 亚群特异性lncRNA在人动脉粥样硬化中起作用。我们的建议利用独特的基因组 数据，创新的计算方法和功能基因组学以及跨学科专业知识，以指导体内 动脉粥样硬化CVD中细胞特异性血管LNCRNA功能的翻译和精确治疗靶向。

项目成果

Organ-on-a-chip technology: a novel approach to investigate cardiovascular diseases.

• DOI: 10.1093/cvr/cvab088
• 发表时间: 2021-12-17
• 期刊: Cardiovascular research
• 影响因子: 10.8
• 作者: Paloschi V;Sabater-Lleal M;Middelkamp H;Vivas A;Johansson S;van der Meer A;Tenje M;Maegdefessel L
• 通讯作者: Maegdefessel L

Long Noncoding RNA MIAT Controls Advanced Atherosclerotic Lesion Formation and Plaque Destabilization.

• DOI: 10.1161/circulationaha.120.052023
• 发表时间: 2021-11-09
• 期刊: Circulation
• 影响因子: 37.8
• 作者: Fasolo F;Jin H;Winski G;Chernogubova E;Pauli J;Winter H;Li DY;Glukha N;Bauer S;Metschl S;Wu Z;Koschinsky ML;Reilly M;Pelisek J;Kempf W;Eckstein HH;Soehnlein O;Matic L;Hedin U;Bäcklund A;Bergmark C;Paloschi V;Maegdefessel L
• 通讯作者: Maegdefessel L