Canon Stroke and Vascular Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.
Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA.
Mol Diagn Ther. 2020 Dec;24(6):723-736. doi: 10.1007/s40291-020-00494-3.
Long non-coding RNAs (lncRNAs) may serve as biomarkers for complex disease states, such as intracranial aneurysms. In this study, we investigated lncRNA expression differences in the whole blood of patients with unruptured aneurysms.
Whole blood RNA from 67 subjects (34 with aneurysm, 33 without) was used for next-generation RNA sequencing. Differential expression analysis was used to define a signature of intracranial aneurysm-associated lncRNAs. To estimate the signature's ability to classify aneurysms and to identify the most predictive lncRNAs, we implemented a nested cross-validation pipeline to train classifiers using linear discriminant analysis. Ingenuity pathway analysis was used to study potential biological roles of differentially expressed lncRNAs, and lncRNA ontology was used to investigate ontologies enriched in signature lncRNAs. Co-expression correlation analysis was performed to investigate associated differential protein-coding messenger RNA expression.
Of 4639 detected lncRNAs, 263 were significantly different (p < 0.05) between the two groups, and 84 of those had an absolute fold-change ≥ 1.5. An eight-lncRNA signature (q < 0.35, fold-change ≥ 1.5) was able to separate patients with and without aneurysms on principal component analysis, and had an estimated accuracy of 70.9% in nested cross-validation. Bioinformatics analyses showed that networks of differentially expressed lncRNAs (p < 0.05) were enriched for cell death and survival, connective tissue disorders, carbohydrate metabolism, and cardiovascular disease. Signature lncRNAs shared ontologies that reflected regulation of gene expression, signaling, ubiquitin processing, and p53 signaling. Co-expression analysis showed correlations with messenger RNAs related to inflammatory responses.
Differential expression in whole blood lncRNAs is detectable in patients harboring aneurysms, and reflects expression/signaling regulation, and ubiquitin and p53 pathways. Following validation in larger cohorts, these lncRNAs may be potential diagnostic targets for aneurysm detection by blood testing.
长链非编码 RNA（lncRNA）可能作为颅内动脉瘤等复杂疾病状态的生物标志物。本研究旨在探讨未破裂动脉瘤患者全血中 lncRNA 的表达差异。
采用下一代 RNA 测序技术检测 67 例患者（34 例动脉瘤患者，33 例非动脉瘤患者）的全血 RNA。采用差异表达分析定义颅内动脉瘤相关 lncRNA 的特征。为了评估该特征对动脉瘤分类的能力并确定最具预测性的 lncRNA，我们采用线性判别分析（LDA）实现了嵌套交叉验证管道来训练分类器。采用Ingenuity 通路分析研究差异表达 lncRNA 的潜在生物学作用，采用 lncRNA 本体论研究特征 lncRNA 中富集的本体。采用共表达相关性分析研究相关差异蛋白编码信使 RNA 表达。
在检测到的 4639 个 lncRNA 中，有 263 个在两组之间差异显著（p<0.05），其中 84 个的绝对倍数变化≥1.5。一个由 8 个 lncRNA 组成的特征（q<0.35，倍数变化≥1.5）可以通过主成分分析将有和无动脉瘤的患者分开，在嵌套交叉验证中的估计准确率为 70.9%。生物信息学分析表明，差异表达 lncRNA 的网络（p<0.05）富含细胞死亡和存活、结缔组织疾病、碳水化合物代谢和心血管疾病。特征 lncRNA 具有反映基因表达、信号转导、泛素加工和 p53 信号转导的调控的本体。共表达分析显示与炎症反应相关的信使 RNA 存在相关性。
在携带动脉瘤的患者中可以检测到全血 lncRNA 的差异表达，反映了表达/信号转导调控以及泛素和 p53 途径。在更大的队列中验证后，这些 lncRNA 可能成为通过血液检测检测动脉瘤的潜在诊断靶点。
