Table_4_Genetic Regulation of Liver Metabolites and Transcripts Linking to Biochemical-Clinical Parameters.XLSX

Given the central metabolic role of the liver, hepatic metabolites and transcripts reflect the organismal physiological state. Biochemical-clinical plasma biomarkers, hepatic metabolites, transcripts, and single nucleotide polymorphism (SNP) genotypes of some 300 pigs were integrated by weighted correlation networks and genome-wide association analyses. Network-based approaches of transcriptomic and metabolomics data revealed linked of transcripts and metabolites of the pentose phosphate pathway (PPP). This finding was evidenced by using a NADP/NADPH assay and HDAC4 and G6PD transcript quantification with the latter coding for first limiting enzyme of this pathway and by RNAi knockdown experiments of HDAC4. Other transcripts including ARG2 and SLC22A7 showed link to amino acids and biomarkers. The amino acid metabolites were linked with transcripts of immune or acute phase response signaling, whereas the carbohydrate metabolites were highly enrich in cholesterol biosynthesis transcripts. Genome-wide association analyses revealed 180 metabolic quantitative trait loci (mQTL) (p < 10-4). Trans-4-hydroxy-L-proline (p = 6 × 10-9), being strongly correlated with plasma creatinine (CREA), showed strongest association with SNPs on chromosome 6 that had pleiotropic effects on PRODH2 expression as revealed by multivariate analysis. Consideration of shared marker association with biomarkers, metabolites, and transcripts revealed 144 SNPs associated with 44 metabolites and 69 transcripts that are correlated with each other, representing 176 mQTL and expression quantitative trait loci (eQTL). This is the first work to report genetic variants associated with liver metabolite and transcript levels as well as blood biochemical-clinical parameters in a healthy porcine model. The identified associations provide links between variation at the genome, transcriptome, and metabolome level molecules with clinically relevant phenotypes. This approach has the potential to detect novel biomarkers displaying individual variation and promoting predictive biology in medicine and animal breeding.

鉴于肝脏在机体代谢中的核心作用，肝脏代谢物与转录本可反映生物体的生理状态。本研究通过加权共表达网络分析与全基因组关联分析，整合了约300头猪的血浆临床生化生物标志物、肝脏代谢物、转录本以及单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因型数据。基于转录组与代谢组数据的网络分析方法，揭示了磷酸戊糖途径（pentose phosphate pathway, PPP）中转录本与代谢物之间的关联。该研究结论通过两项实验得到验证：其一为采用NADP/NADPH检测法以及HDAC4与G6PD转录本定量实验（其中G6PD编码该途径的首个限速酶）；其二为开展HDAC4的RNA干扰敲低实验。其余转录本（包括ARG2与SLC22A7）则与氨基酸及生物标志物存在关联。氨基酸代谢物与免疫或急性期应答信号通路相关的转录本存在关联，而碳水化合物代谢物则显著富集于胆固醇生物合成相关的转录本中。全基因组关联分析共鉴定出180个代谢数量性状位点（metabolic quantitative trait loci, mQTL）（p < 10^-4）。反式-4-羟基-L-脯氨酸（p = 6 × 10^-9）与血浆肌酐（creatinine, CREA）显著相关，其与6号染色体上的SNP位点关联性最强；多变量分析显示，这些SNP位点对PRODH2的表达具有多效性影响。通过分析生物标志物、代谢物与转录本共有的标记关联，本研究共鉴定出144个SNP位点，这些位点分别与44种代谢物及69个相互关联的转录本相关，对应176个mQTL与表达数量性状位点（expression quantitative trait loci, eQTL）。本研究是首个在健康猪模型中报道与肝脏代谢物、转录本水平以及血液生化临床参数相关的遗传变异的研究。本研究鉴定出的关联关系，搭建了基因组、转录组与代谢组层面的分子变异与临床相关表型之间的桥梁。该方法有望筛选出存在个体差异的新型生物标志物，推动医学与动物育种领域的预测生物学发展。