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: 10347301
• 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 2024-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10347301
• 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; Institutes; Knowledge; Laboratories; Lesion; Messenger RNA; Methods; Modeling; Mus; Myocardial Infarction; Patients; Precision therapeutics; Protein Isoforms; Role; Sample Size; Sampling; Signal Transduction; Specificity; System; Therapeutic; Tissues; Transcript; Translations; Untranslated RNA; Up-Regulation; Variant; base; 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

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.

该提案解决了长非编码的细胞特异性功能和疾病原因方面的知识差距 人类动脉粥样硬化中的 RNA (lncRNA)。尽管功能性lncRNA在心血管领域的突出例子 疾病（CVD），其缺乏保守性和细胞特异性限制了我们对其在 CVD 中的作用的理解。 这些挑战在人类动脉粥样硬化中尤其成问题，其特点是复杂的多因素 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，原代人类细胞中的 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。从而更准确地了解 需要lncRNA细胞与人类动脉粥样硬化的特异性关系来驱动基于机制的临床 翻译。在这里，我们解决了 lncRNA 在人类动脉粥样硬化和 CVD 风险中的关键问题。首先，哪个 lncRNA 在人类病变中表达并与临床 CVD 相关？其次，对于表达的lncRNA 人类病变，它们在哪些特定病变细胞亚群中发挥功能？在目标 1 中，我们将解决第一个 通过大型嵌套病例对照的深度 RNAseq 分析 lncRNA 的差异表达来解决问题 （n=260 为“有症状/不稳定”斑块，n=260 为“无症状/稳定”斑块）颈动脉研究 来自慕尼黑血管生物库 (MVB) 的动脉粥样硬化。我们还将确定 lncRNA 是否表现出 有症状/不稳定斑块与无症状/稳定斑块之间的差异等位基因特异性表达 (ASE) 具有差异 ASE 的 lncRNA 的顺式 eQTL 变异是否与大范围冠心病 (CHD) 相关 公共遗传数据集。优先的lncRNA将在人类中进行细胞特异性功能基因组随访 血管细胞，包括我们的人类诱导多能干细胞 (hIPSC) 血管模型。在目标 2 中，我们建议 使用一种新颖的反卷积算法，并选择性地整合来自 Aim 1 的大规模批量 RNAseq 数据 新鲜病变 (n=60) 的单细胞 (sc)RNAseq 来识别与以下疾病相关的亚群及其 lncRNA 有症状/不稳定斑块，与冠心病有因果遗传关系。新鲜颈动脉的 ScRNAseq 病变将用于对细胞进行聚类并识别病变亚群。该分析的结果将允许 对所有 MVB 批量 RNAseq 病变 (n=520) 的细胞亚群组成进行计算解卷积 亚群特异性 lncRNA 表达的分配以及与症状/不稳定斑块的关系。 亚群特异性 lncRNA cis-eQTL 也将被识别并用于确定它们的因果关系 遗传数据集中的 CHD。这些发现与亚群特异性功能研究相结合，将定义 亚群特异性 lncRNA 在人类动脉粥样硬化中发挥作用。我们的提案利用了独特的基因组 数据、创新计算方法和功能基因组学以及指导体内的跨学科专业知识 动脉粥样硬化 CVD 中细胞特异性血管 lncRNA 功能的翻译和精准治疗靶向。