Background The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon Hypertensive (LH) and Lyon Normotensive (LN) rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, an F2 intercross between LH and LN was comprehensively studied. Methods and Results Multi-dimensional data were obtained including genotypes of 1536 SNPs, 23 physiological traits and more than 150 billion nucleotides of RNA-seq reads from the livers of F2 intercross offspring and parental rats. Phenotypic and expression QTL were mapped. Application of systems biology methods identified 17 candidate MetS genes. Several putative causal cis-eQTL were identified corresponding with pQTL loci. We found an eQTL hotspot on rat chromosome 17 that is causally associated with multiple MetS-related traits, and found RGD1562963, a gene regulated in cis by this eQTL hotspot, as the most likely eQTL driver gene directly affected by genetic variation between LH and LN rats. Conclusions Our study sheds light on the intricate pathogenesis of MetS and demonstrates that systems biology with high-throughput sequencing is a powerful method to study the etiology of complex genetic diseases.

Hypertension is a major risk factor for cardiovascular disease, Type 2 diabetes, and end organ failure, and is often found concomitant with disorders characteristic of the Metabolic Syndrome (MetS), including obesity, dyslipidemia, and insulin resistance. While the associated features often occur together, the pathway(s) or mechanism(s) linking hypertension in MetS are not well understood. Previous work determined that genetic variation on rat chromosome 17 (RNO17) contributes to several MetS-defining traits (including hypertension, obesity, and dyslipidemia) in the Lyon Hypertensive (LH) rat, a genetically determined MetS model. We hypothesized that at least some of the traits on RNO17 are controlled by a single gene with pleiotropic effects. To address this hypothesis, consomic and congenic strains were developed, whereby a defined fragment of RNO17 from the LH rat was substituted with the control Lyon Normotensive (LN) rat, and MetS phenotypes were measured in the resultant progeny. Compared to LH rats, LH-17LN consomic rats have significantly reduced body weight, blood pressure, and lipid profiles. A congenic strain (LH-17LNc), with a substituted fragment at the distal end of RNO17 (17q12.3; 74–97 Mb; rn4 assembly), showed differences from the LH rat in blood pressure and serum total cholesterol and triglycerides. Interestingly, there was no difference in body weight between the LH-17LNc and the parental LH rat. These data indicate that blood pressure and serum lipids are regulated by a gene(s) in the distal congenic interval, and could be due to pleiotropy. The data also indicate that body weight is not determined by the same gene(s) at this locus. Interestingly, only two small haplotypes spanning a total of approximately 0.5 Mb differ between the LH and LN genomes in the congenic interval. Genes in these haplotypes are strong candidate genes for causing dyslipidemia in the LH rat. Overall, MetS, even in a simplified genetic model such as the LH-17LN rat, is likely due to both independent and pleiotropic gene effects.

The metabolic syndrome (MetS) - hypertension, obesity, dyslipidemia, and insulin resistance - is a major risk factor for cardiovascular disease and stroke. Our overall goal is to identify novel genes and pathways causing MetS. Our previous work determined that rat chromosome 17 (RNO17) contributes to several MetS-defining traits (including high blood pressure, obesity, and dyslipidemia) in the Lyon Hypertensive (LH) rat, a genetically determined MetS rat model. We hypothesized that at least some of the traits on RNO17 are controlled by a single gene with pleiotropic effects. To address this hypothesis, we generated congenic strains where a defined fragment of RNO17 from the LH rat was substituted by that of the control Lyon Normotensive (LN) rat, and measured MetS phenotypes. One congenic (LH-17 LN a), with the proximal 30 Mb of RNO17 from the LH genome substituted with that of the LN genome, did not show significant differences from the LH parental strain. However, another congenic strain (LH-17 LN c), with a substituted fragment at the distal end of RNO17 (84-97 Mb), showed significant differences from the LH rat in serum total cholesterol (3.15 ± 0.15 vs. 4.29 ± 0.17 mMol; p<0.01) and triglycerides (0.47 ± 0.06 vs. 1.27± 0.13 mMol; p<0.001), and a trend for reduced blood pressure (SBP 150.8 ± 3.4 vs. 157.1 ± 1.7 mmHg; p=0.1). Interestingly, there was no difference in body weight between the LH-17 LN c and the parental LH rat (440 + 7.2 vs. 435 + 9.1 g). These data indicate that serum cholesterol and triglycerides, and possibly blood pressure are regulated by a gene(s) in the distal congenic interval, and could be due to pleiotropy. The data also indicate body weight is not determined by the same gene(s). Interestingly, only two small haplotypes spanning a total of 1 Mb differ between the LH and LN genomes in the congenic interval. Genes in these haplotypes are being studied as candidate genes for causing dyslipidemia in the LH rat. Overall MetS, even in a simplified genetic model such as the LH-17 LN rat, is likely due to both independent and pleiotropic gene effects.

The Lyon Hypertensive (LH) rat is an inbred model of Metabolic Syndrome, exhibiting spontaneous hypertension, high body weight, high plasma lipids, altered insulin:glucose ratio. The Lyon Normotensive (LN) control strain, selectively bred for normal blood pressure from the same Sprague Dawley (SD) colony, is genetically quite similar to the LH, but displays no features of MetS. Genetic mapping in an LHxLN cross determined that all of the MetS phenotypes mapped to rat chromosome (RNO 17). In order to identify the gene(s) causing MetS on RNO17 we generated a consomic strain (LH-17 LN ) where the LH RNO17 was replaced with that of the LN strain. Substitution of the single chromosome was sufficient to significantly lower blood pressure lower systolic blood pressure (145 + 2 vs. 161 + 2 mmHg; p<0.05), body weight (408 + 6 vs 453 + 5 g; p<0.05), and plasma cholesterol (2.5 ± 0.1 vs 2.9 ± 0.08; p<0.05) compared to the LH parental strain. To identify putative causal genes for MetS, we fine-mapped RNO17 in silico utilizing the genome sequence of the LH and LN rat strains. The genomes of the LH and LN strains are highly similar, differing by <0.02% at the sequence level (in comparison, humans typically differ by about 1%). Moreover, we have shown that the variants cluster into <500 divergent haplotype blocks with an average length of 880 kb, which are presumed to contain the genetic variation causing the phenotypic variation between the LH and LN strains. On RNO17 there are just 14 divergent haplotypes, containing 11 genes with coding sequence differences in the LH. The combined in vivo and in silico approaches allowed for the identification of candidate causal variants for the phenotypes on RNO17 and will be studied further to determine their role(s) in MetS.