دورية أكاديمية
أعرض في EDS

Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection.

التفاصيل البيبلوغرافية
العنوان: Prior metabolite extraction fully preserves RNAseq quality and enables integrative multi-'omics analysis of the liver metabolic response to viral infection.
المؤلفون: Madaj ZB; Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA.; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA., Dahabieh MS; Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA., Kamalumpundi V; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Muhire B; Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA., Pettinga J; Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA.; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA., Siwicki RA; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Genomics Core, Van Andel Institute, Grand Rapids, MI, USA., Ellis AE; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Isaguirre C; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA., Escobar Galvis ML; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA., DeCamp L; Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA., Jones RG; Department of Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA., Givan SA; Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI, USA.; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA., Adams M; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Genomics Core, Van Andel Institute, Grand Rapids, MI, USA., Sheldon RD; Core Technologies and Services, Van Andel Institute, Grand Rapids, MI, USA.; Mass Spectrometry Core, Van Andel Institute, Grand Rapids, MI, USA.
المصدر: RNA biology [RNA Biol] 2023 Jan; Vol. 20 (1), pp. 186-197.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Taylor & Francis Country of Publication: United States NLM ID: 101235328 Publication Model: Print Cited Medium: Internet ISSN: 1555-8584 (Electronic) Linking ISSN: 15476286 NLM ISO Abbreviation: RNA Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: 2015- : Philadelphia, PA : Taylor & Francis
Original Publication: Georgetown, TX : Landes Bioscience,
مواضيع طبية MeSH: Metabolomics* , Virus Diseases*, Animals ; Mice ; Sequence Analysis, RNA ; Liver ; RNA
مستخلص: 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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معلومات مُعتمدة: R01 AI165722 United States AI NIAID NIH HHS
فهرسة مساهمة: Keywords: RNA; Transcriptomics; integrated omics; mass spectrometry; metabolomics; systems biology
المشرفين على المادة: 63231-63-0 (RNA)
تواريخ الأحداث: Date Created: 20230425 Date Completed: 20230426 Latest Revision: 20240526
رمز التحديث: 20240526
مُعرف محوري في PubMed: PMC10132226
DOI: 10.1080/15476286.2023.2204586
PMID: 37095747
قاعدة البيانات: MEDLINE
الوصف
تدمد:1555-8584
DOI:10.1080/15476286.2023.2204586