Determining the genetic regulation of trimethylamine N-oxide in female diversity outbred mice

Authors: JAMES, KRISTEN - University Of California, Davis; Gertz, Erik; Bennett, Brian

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/24/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: FASEB Conference: The Folic Acid, Vitamin B-12, and One-Carbon Metabolism Conference Background: Constituents of the gut microbiome metabolize choline into trimethylamine (TMA) which is absorbed by the host and oxidized to trimethylamine n-oxide (TMAO) in the liver. In human cohorts, TMAO is associated with cardiovascular disease, type 2 diabetes, kidney disease and in rodent models TMAO upregulates macrophage scavenger receptors. The genetic regulation of TMAO remains to be determined. Furthermore, Diversity Outbred (DO) mice are an advanced genetic mapping panel composed of 5 classical inbred strains (A/J, C57BL/6J, 129S1/SvImJ, NOD/LtJ, NZO/HlLtJ) and 3 wild-derived inbred strains (CAST/EiJ, PWK/PhJ, and WSB/EiJ) of mice. The DO is maintained in an outbred fashion and harbors genetic diversity similar to human levels, a wide variation in phenotypic traits and high levels of genetic resolution. These qualities make the DO an advantageous model for quantitative trait loci (QTL) analysis, a method for identifying genetic polymorphisms driving phenotypic observations. Hypothesis: Our primary hypothesis is that TMAO is a quantitative trait influenced by genetic polymorphisms. Our secondary hypothesis is that diet components such as choline and carnitine interact with genetic architecture. Assessing TMAO in a standard and high-choline diet environment will reveal the genetic architecture associated with plasma TMAO. Methods: Female DO mice (n = 190) were fed a standardized diet (AIN-76A, D10001, Research Diets, New Brunswick, NJ) for 2 weeks followed by a high-choline diet (1.2% choline chloride, TD.0904, Envigo Teklad Diets, Madison, WI) for 3 weeks. Following each diet, plasma samples were collected and pre and post plasma TMAO was measured by mass spectrometry. In order to identify genetic loci associated with circulating TMAO in standard and perturbed conditions QTL analysis was completed using the R package qtl2 (v 0.21-5) on natural log transformed data. A genome scan was conducted using a kinship matrix ("leave-one-chromosome-out" method) and batch as additive covariates. The results, given as log of the odds (LOD) scores, assessed the likelihood the genotype contributed to the phenotype and were considered significant if they surpassed the LOD threshold calculated by 1000 permutations. QTL confidence intervals were determined by calculating the upper and lower distances where the LOD score dropped by at least 1.8 from the peak SNP. Results: In standard conditions, a locus was identified on Chr 12 (99% CI, 85.2 – 88.0 Mbp) highly associated with circulating TMAO concentrations. This locus contains ~12 genes and reveals that alleles from CAST/EiJ and PWK/PhJ confer increased TMAO levels. These data replicate our previous report of the same locus associated with TMAO (Coffey et al. 2017). Interestingly, in conditions perturbed by the high-choline diet a unique locus was identified on Chr 9 (95% CI, 99.3 - 101.6 Mbp). Conclusion: The choline-related metabolite TMAO may be genetically regulated by the Chr 12 and 9 loci. The environmental conditions (such as standard versus high-choline diet) may affect the biological mechanism associated with TMAO. Further experiments such as RNA sequencing are being conducted to identify candidate genes driving the associations.