Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection.
Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection.
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DOI：
10.1080/15476286.2023.2204586
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发表时间：
2023-01
期刊：
影响因子：
4.1
通讯作者：
Sheldon, Ryan D. D.
中科院分区：
文献类型：
--
作者：
Madaj, Zachary B.;Dahabieh, Michael S. S.;Kamalumpundi, Vijayvardhan;Muhire, Brejnev;Pettinga, J.;Siwicki, Rebecca A. A.;Ellis, Abigail E. E.;Isaguirre, Christine;Escobar Galvis, Martha L. L.;DeCamp, Lisa;Jones, Russell G. G.;Givan, Scott A. A.;Adams, Marie;Sheldon, Ryan D. D.
在这里，我们深入分析了单样本代谢物/RNA提取对多组学读出的有用性。使用注射淋巴细胞性脉络丛脑膜炎病毒（LCMV）或载体（Veh）的小鼠冷冻肝脏粉碎，我们分离了先提取（RNA）或后提取代谢产物（MetRNA）的RNA。对RNA测序（RNAseq）数据进行差异表达分析和分散，并测定差异代谢物丰度。通过主成分分析，RNA和MetRNA聚在一起，表明个体间差异是最大的方差来源。超过85%的LCMV和Veh差异表达基因在不同的提取方法中是共享的，其余15%在不同的组之间均匀随机地划分。该提取方法所特有的差异表达基因归因于0.05 FDR截点附近的随机性以及方差和平均表达的随机变化。此外，使用平均绝对差进行分析显示，不同提取方法之间转录本的分散度没有差异。总之，我们的数据表明，事先的代谢物提取保留了RNAseq数据的质量，这使我们能够自信地对单个样本的代谢组学和RNAseq数据进行综合途径富集分析。该分析显示，嘧啶代谢是lcmv影响最大的途径。对该途径中基因和代谢物的综合分析揭示了嘧啶核苷酸降解导致尿嘧啶生成的模式。支持这一观点的是，尿嘧啶是LCMV感染后血清中差异最大的代谢物之一。我们的数据表明，肝尿嘧啶输出是急性感染的一种新的表型特征，并强调了我们的综合单样本多组学方法的实用性。
Here, we provide an in-depth analysis of the usefulness of single-sample metabolite/RNA extraction for multi-‘omics readout. Using pulverized frozen livers of mice injected with lymphocytic choriomeningitis virus (LCMV) or vehicle (Veh), we isolated RNA prior (RNA) or following metabolite extraction (MetRNA). RNA sequencing (RNAseq) data were evaluated for differential expression analysis and dispersion, and differential metabolite abundance was determined. Both RNA and MetRNA clustered together by principal component analysis, indicating that inter-individual differences were the largest source of variance. Over 85% of LCMV versus Veh differentially expressed genes were shared between extraction methods, with the remaining 15% evenly and randomly divided between groups. Differentially expressed genes unique to the extraction method were attributed to randomness around the 0.05 FDR cut-off and stochastic changes in variance and mean expression. In addition, analysis using the mean absolute difference showed no difference in the dispersion of transcripts between extraction methods. Altogether, our data show that prior metabolite extraction preserves RNAseq data quality, which enables us to confidently perform integrated pathway enrichment analysis on metabolomics and RNAseq data from a single sample. This analysis revealed pyrimidine metabolism as the most LCMV-impacted pathway. Combined analysis of genes and metabolites in the pathway exposed a pattern in the degradation of pyrimidine nucleotides leading to uracil generation. In support of this, uracil was among the most differentially abundant metabolites in serum upon LCMV infection. Our data suggest that hepatic uracil export is a novel phenotypic feature of acute infection and highlight the usefulness of our integrated single-sample multi-‘omics approach.
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影响因子：
3.7
作者：
Kang J;David L;Li Y;Cang J;Chen S
通讯作者：
Chen S
影响因子：
50.3
作者：
Kaymak I;Williams KS;Cantor JR;Jones RG
通讯作者：
Jones RG
DOI：
10.1161/hcg.0000000000000032
发表时间：
2017-04
期刊：
Circulation. Cardiovascular genetics
影响因子：
--
作者：
Cheng S;Shah SH;Corwin EJ;Fiehn O;Fitzgerald RL;Gerszten RE;Illig T;Rhee EP;Srinivas PR;Wang TJ;Jain M;American Heart Association Council on Functional Genomics and Translational Biology; Council on Cardiovascular and Stroke Nursing; Council on Clinical Cardiology; and Stroke Council
通讯作者：
American Heart Association Council on Functional Genomics and Translational Biology; Council on Cardiovascular and Stroke Nursing; Council on Clinical Cardiology; and Stroke Council
影响因子：
10.5
作者：
Chamberlain, JR;Lee, Y;Engelke, DR
通讯作者：
Engelke, DR
影响因子：
30.5
作者：
Badovinac, VP;Porter, BB;Harty, JT
通讯作者：
Harty, JT