Leal-Gutierrez, J. D. | bioRxiv Science

bioRxiv2024

Genome-Wide Association Study in Outbred Heterogeneous Stock Rats Identifies Multiple Loci for the Incentive Salience of Reward Cues.

Addiction vulnerability is associated with the tendency to attribute incentive salience to reward predictive cues; both addiction and the attribution of incentive salience are influenced by environmental and genetic factors. To characterize the genetic contributions to incentive salience attribution, we performed a genome-wide association study (GWAS) in a cohort of 1,645 genetically diverse heterogeneous stock (HS) rats. We tested HS rats in a Pavlovian conditioned approach task, in which we characterized the individual responses to food-associated stimuli ("cues"). Rats exhibited either cue-directed "sign-tracking" behavior or food-cup directed "goal-tracking" behavior. We then used the conditioned reinforcement procedure to determine whether rats would perform a novel operant response for unrewarded presentations of the cue. We found that these measures were moderately heritable (SNP heritability, h2 = .189-.215). GWAS identified 14 quantitative trait loci (QTLs) for 11 of the 12 traits we examined. Interval sizes of these QTLs varied widely. 7 traits shared a QTL on chromosome 1 that contained a few genes (e.g. Tenm4, Mir708) that have been associated with substance use disorders and other mental health traits in humans. Other candidate genes (e.g. Wnt11, Pak1) in this region had coding variants and expression-QTLs in mesocorticolimbic regions of the brain. We also conducted a Phenome-Wide Association Study (PheWAS) on other behavioral measures in HS rats and found that regions containing QTLs on chromosome 1 were also associated with nicotine self-administration in a separate cohort of HS rats. These results provide a starting point for the molecular genetic dissection of incentive salience and provide further support for a relationship between attribution of incentive salience and drug abuse-related traits.

neuroscience↗

bioRxiv2023

Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR, ATF3, GATA3, HNF1B, POU2F2, and TFCP2 transcription factors as potential candidates to explain incomplete penetrance

1Human unilateral renal agenesis is a congenital urinary tract malformation. Affected individuals have only one kidney, which is often an asymptomatic developmental defect. A total of 5,585 male and female HS rats were assessed for unilateral renal agenesis and genotyped for 3513,321 markers. The R package SAIGEgds was used for the association analysis. The adjusted p-value threshold for the association analysis determined by permutation was equal to 5.6 (-log10). Two additional datasets were used as validation tests. Population two included 1,577 rats genotyped for 7,425,889 markers and a case-control imbalance equal to 1:174; population three included 1,407 rats, genotyped for 254,932 markers and case-control ratio equal to 1:38. The python package GxTheta was used to perform a polygenic epistasis analysis for the analyzed HS rat population. A founder haplotype mosaic determination was performed using the R package QTL2. Associated regions were selected for further analysis, including long-read PacBio sequencing for founder individuals and a founder haplotype prediction test. A similarity analysis at a genomic level and for loci encoding transcription factors predicted to interact with selected sequences inside the associated loci were accomplished. A total of 1,181 polymorphisms were associated with URA. All associated polymorphisms were located on chromosome 14 between 32.9 and 36.6 Mb. The most significant polymorphism was chr14:36,411,266, a G/T transversion. The same associated region was identified in population three. Polygenic epistasis was determined as not predominant for the presentation of URA. Based on the haplotype mosaic probability estimation, cases display a higher probability of inheriting the ACI allele. The long-read sequencing analysis showed the presence of an Erv insertion inside the intron one of the KIT gene located inside the associated region. The Erv insertion comprises one Erv sequence and two Ltr sequences located downstream and upstream of the former. No Erv insertion was identified for the founder strain BN. For ACI and HSRA, only one Ltr sequence was identified. One hundred and seven genes encoding TFs that recognize binding sites on the Erv insertion were analyzed for sequence similarity against the reference HSRA. The TF similarity score analysis for the interaction genotype and phenotype showed significance after FDR correction for 20 TFs, including AHR, HNF1B, JUNB, RARG, and RXRA. A mechanism identifying URA as a threshold phenotype is suggested in HS rats. It implies the existence of a minimum threshold for the final number of nephrons and kidney associated structures required for stalling the apoptotic process of the metanephric rudiments. Animals exhibiting a quantitative cumulative defect would express URA, being this malformation identified as a phenotype with decreased penetrance in the assessed population of HS rats. All these processes are described as mediated by KIT and TFs able to interact with sequences of the Erv insertion.

genetics↗