The Effects of Sex and Diet on Physiology and Liver Gene Expression in Diversity Outbred Mice

Abstract

Inter-individual variation in metabolic health and adiposity is driven by many factors. Diet composition and genetic background and the interactions between these two factors affect adiposity and related traits such as circulating cholesterol levels. In this study, we fed 850 Diversity Outbred mice, half females and half males, with either a standard chow diet or a high fat, high sucrose diet beginning at weaning and aged them to 26 weeks. We measured clinical chemistry and body composition at early and late time points during the study, and liver transcription at euthanasia. Males weighed more than females and mice on a high fat diet generally weighed more than those on chow. Many traits showed sex- or diet-specific changes as well as more complex sex by diet interactions. We mapped both the physiological and molecular traits and found that the genetic architecture of the physiological traits is complex, with many single locus associations potentially being driven by more than one polymorphism. For liver transcription, we find that local polymorphisms affect constitutive and sex-specific transcription, but that the response to diet is not affected by local polymorphisms. We identified two loci for circulating cholesterol levels. We performed mediation analysis by mapping the physiological traits, given liver transcript abundance and propose several genes that may be modifiers of the physiological traits. By including both physiological and molecular traits in our analyses, we have created deeper phenotypic profiles to identify additional significant contributors to complex metabolic outcomes such as polygenic obesity. We make the phenotype, liver transcript and genotype data publicly available as a resource for the research community.

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice

“…The total number of eQTLs increased to 17,278 were found when chrX eQTLs were included ( S3 and S4A Tables). Half of the autosomal eQTLs identified (6,344 out of 12,886) were not identified in earlier studies [ 46 , 48 – 50 , 69 ] and are novel, and include a large majority of the 1,524 eQTLs associated with liver-expressed lncRNA genes [ 20 ]. More autosomal eQTLs were identified in female than in male liver ( Table 1 ), similar to findings in BXD mouse liver [ 49 ], suggesting genetic regulation is more common for the female liver transcriptome.…”

“…Genetic polymorphisms can impart individual differences in drug-metabolizing enzymes [44], many of which are encoded by sex-specific genes [11,45]. Genome-wide association studies linking genetic variants and liver gene expression have identified many expression quantitative trait loci (eQTLs) for liver-expressed genes [46][47][48][49][50]. Little is known, however, about the extent to which such genetic factors impact individual variability in sex-biased gene expression.…”

Mouse Systems Genetics as a Prelude to Precision Medicine

“…Several studies proposed the use of mediation analysis to identify the causal gene (mediator) between the genetic variant (independent variable) and the trait of interest (dependent variable) ( Figure 5B) [25,78,98,99]. Mediation analysis can be used either on gene expression levels to identify the regulatory mechanisms [25,78,99] or on phenotypic traits to discover the potential causal drivers contributing to the phenotypic variances [98] ( Figure 5C upper). Contrary to mediation analysis, reverse-mediation analysis starts with the mediator (the gene with cis-QTL) and identifies its downstream targets [25] ( Figure 5C lower).…”

Cleaning Genotype Data from Diversity Outbred Mice

“…We consider data from a population of 291 Diversity Outbred (DO) mice (Gatti et al 2017), including 99 mice from generation 8 and 192 mice from generation 11. There are 150 females and 141 males.…”

“…We consider genotype data for 291 Diversity Outbred (DO) mice, including 99 mice from generation 8 and 192 mice from generation 11. These are a subset of the mice considered in Gatti et al (2017).…”