Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders

Abstract

Genome-wide association studies (GWAS) of complex traits, such as alcohol use disorders (AUD), usually identify variants in non-coding regions and cannot by themselves distinguish whether the associated variants are functional or in linkage disequilibrium with the functional variants. Transcriptome studies can identify genes whose expression differs between alcoholics and controls. To test which variants associated with AUD may cause expression differences, we integrated data from deep RNA-seq and GWAS of four postmortem brain regions from 30 subjects with AUD and 30 controls to analyze allele-specific expression (ASE). We identified 88 genes with differential ASE in subjects with AUD compared to controls. Next, to test one potential mechanism contributing to the differential ASE, we analyzed single nucleotide polymorphisms (SNPs) in the 3′ untranslated regions (3′UTR) of these genes. Of the 88 genes with differential ASE, 61 genes contained 437 SNPs in the 3′UTR with at least one heterozygote among the subjects studied. Using a modified PASSPORT-seq (parallel assessment of polymorphisms in miRNA target-sites by sequencing) assay, we identified 25 SNPs that affected RNA levels in a consistent manner in two neuroblastoma cell lines, SH-SY5Y and SK-N-BE(2). Many of these SNPs are in binding sites of miRNAs and RNA-binding proteins, indicating that these SNPs are likely causal variants of AUD-associated differential ASE. In sum, we demonstrate that a combination of computational and experimental approaches provides a powerful strategy to uncover functionally relevant variants associated with the risk for AUD.

Meso-limbic Gene Expression Findings from Mouse Cocaine Self-Administration Recapitulate Human Cocaine Use Disorder

“…In light of the current study, we suggest various directions for future 432 research. Relatively large post-mortem human brain samples are publically 433 available for alcohol 39 and opiates 40 and could be integrated with a multitude of 434 traits from model systems. Animal models of compulsive drug use (e.g., escalated 435 use, aversion resistant users etc.)…”

Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome

“…With no evidence that this risk haplotype harbors an eQTL for glomerular NPHS1, we hypothesized that the NPHS1 transcript derived from the risk haplotype would be differentially expressed compared to that from the reference haplotype (allele-specific expression [ASE]), as ASE has been reported to be associated with susceptibility to diseases, including inflammatory bowel disease, autism spectrum disorder, and alcohol use disorders. [23][24][25] We used phasing and allele specific expression from RNA-seq (phASER) to quantify haplotype abundance, then quantified the "magnitude of ASE" as the degree of deviation from the expected 1:1 ratio of expression from each chromosome j0.5 -(haplotype A/ total count)j. In patients with the risk haplotype, haplotype A harbors all 5 NPHS1 risk variants; in patients without the risk haplotype, haplotype A was randomly selected from one of their 2 haplotypes.…”

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.)

“…The former considers the minor allele frequency (MAF) and the degree of missing data and heterozygosity, etc., whereas the latter mostly considers missing levels, population stratification, and independency among individuals [ 82 ]. The entire set of heterozygous SNPs are typically used in human GWAS analysis [ 83 ]. In peanuts, a high level of heterozygosity may not be expected as peanut is a self-pollinating crop revealed to have a low outcrossing rate ranging from 1.9% to 8% [ 84 ].…”