Genetic Mapping of Multiple Traits Identifies Novel Genes for Adiposity, Lipids, and Insulin Secretory Capacity in Outbred Rats

Abstract

Despite the successes of human genome-wide association studies, the causal genes underlying most metabolic traits remain unclear. We used outbred heterogeneous stock (HS) rats, coupled with expression data and mediation analysis, to identify quantitative trait loci (QTLs) and candidate gene mediators for adiposity, glucose tolerance, serum lipids, and other metabolic traits. Physiological traits were measured in 1519 male HS rats, with liver and adipose transcriptomes measured in over 410 rats. Genotypes were imputed from low coverage whole genome sequence. Linear mixed models were used to detect physiological and expression QTLs (pQTLs and eQTLs, respectively), employing both SNP- and haplotype-based models for pQTL mapping. Genes with cis-eQTLs that overlapped pQTLs were assessed as causal candidates through mediation analysis. We identified 14 SNP-based pQTLs and 19 haplotype-based pQTLs, of which 10 were in common. Using mediation, we identified the following genes as candidate mediators of pQTLs: Grk5 for a fat pad weight pQTL on Chr1, Krtcap3 for fat pad weight and serum lipids pQTLs on Chr6, Ilrun for a fat pad weight pQTL on Chr20 and Rfx6 for a whole pancreatic insulin content pQTL on Chr20. Furthermore, we verified Grk5 and Ktrcap3 using gene knock-down/out models, thereby shedding light on novel regulators of obesity.

GRK5 is required for adipocyte differentiation through ERK activation

“…The current work supports previous ndings (4,5) by showing that diet-induced obese mice versus chow-fed lean mice had increased GRK5 mRNA levels (~ 2 fold) in white, but not in brown adipose tissue (Fig. 1A-B).…”

“…Adipose tissue plays a central role in obesity resulting in adipocyte hyperplasia (increased adipocyte number) and/or adipocyte hypertrophy (increased adipocyte size), although the underlying causes of adipose tissue expansion are generally unknown. Our previous work identi ed G protein-coupled receptor (GPCR) kinase 5 (GRK5) as a candidate causal gene for visceral adiposity, where Grk5 expression positively correlated with retroperitoneal and epididymal white fat pad mass in rats (4) and Grk5 knock-down in 3T3L1 preadipocytes led to decreased total triacylglycerol (TAG) accumulation in mature adipocytes (4). In humans, GRK5 gene expression in white subcutaneous white adipose tissue is positively correlated with BMI (kg/m 2 ) in the African American Genetics of Metabolism and Expression (AAGMEx) cohort (r = 0.22, p = 0.0003), a group of 256 African Americans with in depth glucometabolic phenotyping and adipose tissue transcriptome analysis (5).…”

Changes in Environmental Stress over COVID-19 Pandemic Likely Contributed to Failure to Replicate Adiposity Phenotype Associated withKrtcap3

“…As previously described, Krtcap3 was first identified as a potential adiposity gene through GWAS analyses [10][11][12]18] and we confirmed in vivo that decreased expression of Krtcap3 led to increased adiposity [13]. We sought here to repeat the in vivo study with additional metabolic phenotyping and tissue collection in order to better understand the function of Krtcap3 in adiposity, but failed to replicate our results.…”

Bioenergetic-Related Gene Expression in the Hippocampus Predicts Internalizing vs. Externalizing Behavior in a F2Cross of Selectively-Bred Rats

“…Like previous cis -eQTL analyses, these eVariants were predominantly located within +/-400 kB of the TSS of their respective eGene ( Fig S5B ). A comparison with existing rat cis -eQTL databases (RatGTEx: 55,56 , Mitchell et al, unpublished ; and Telese et al, unpublished ), Fig S5C, indicated that most hippocampal eGenes were also significant eGenes within at least four other tissues (out of 11 tissues characterized, Fig S5D ), and confirmed that previously-identified brain cis -eQTLs showed a similar direction of effect on gene expression within the hippocampus (R=0.67-0.75, rho=0.65-0.77, Fig S7-S8 ) when there was at least a nominal ( p <0.05) relationship in our dataset, although many cis -eQTLs remained region specific. As our hippocampal cis -eQTL database represents a valuable resource for the interpretation of rat genomic results, we have shared it on RatGTEx (https://ratgtex.org/download/study-data/#HPC_F2).…”