Integrative analysis of metabolites is essential to obtain a comprehensive view of dysregulated biological pathways leading to a disease. Despite the great potential of metabolites their system level analysis has been limited. Global measurements of the metabolites by liquid chromatography-mass spectrometry (MS) detects metabolites features changing in a disease. However, identification of each feature is a bottleneck in metabolomics, in which a fraction of them are identified via tandem MS. Consequently, the scarcity of these data add additional barriers to decipher their biological meaning, especially in relation to other 'omic data such as proteomics. To address these challenges, a novel network-based approach called PIUMet is described. PIUMet infers dysregulated pathways and components from the differential metabolite features between control and disease systems without the need for the prior identification. The application of PIUMet is demonstrated by integrative analysis of untargeted lipid profiling data of a cell line model of Huntington's disease. The results show that PIUMet inferred dysregulation of sphingolipid metabolism in the disease cells. Additionally, PIUMet identified disease-modifying metabolite in the pathway that remained undetected experimentally. Furthermore, the lipidomic data of these cell lines was integrated with global phospho-proteomic ones. Integrative analysis of these data using PIUMet was shown to systematically lead to identifying dysregulated proteins in the disease cells that cannot be distinguished with individual analysis of each dataset.
代谢物的综合分析对于全面了解导致疾病的失调
生物通路至关重要。尽管代谢物具有巨大的潜力,但其系统级分析一直受到限制。通过
液相色谱-质谱法(MS)对代谢物进行全面测量,可以检测出疾病中代谢物的变化特征。然而,每个特征的鉴定是代谢组学的一个瓶颈,其中只有一小部分是通过串联质谱鉴定的。因此,这些数据的稀缺性为解读其
生物学意义增加了额外的障碍,特别是与蛋白质组学等其他 "omic "数据相比。为了应对这些挑战,本文介绍了一种名为
PIUMet 的基于网络的新方法。
PIUMet 可从对照组和疾病组之间不同的代谢物特征中推断出失调的通路和成分,而无需事先进行识别。通过综合分析亨廷顿氏病
细胞系模型的非靶向脂质分析数据,展示了
PIUMet 的应用。结果表明,
PIUMet 可以推断疾病细胞中的鞘脂代谢失调。此外,
PIUMet 还在通路中发现了实验未检测到的可改变疾病的代谢物。此外,这些
细胞系的脂质组数据还与全局
磷蛋白组数据进行了整合。结果表明,使用
PIUMet 对这些数据进行整合分析,可以系统地识别出疾病细胞中的失调蛋白质,而这些蛋白质是无法通过对每个数据集的单独分析来区分的。