Annotating genetic variants to target genes using H-MAGMA.

An outstanding goal in modern genomics is to systematically predict the functional outcome of noncoding variation associated with complex traits. To address this, we developed Hi-C-coupled multi-marker analysis of genomic annotation (H-MAGMA), which builds on traditional MAGMA-a gene-based analysis tool that assigns variants to their target genes-by incorporating 3D chromatin configuration in assigning variants to their putative target genes. Applying this approach, we identified key biological pathways implicated in a wide range of brain disorders and showed its utility in complementing other functional genomic resources such as expression quantitative trait loci-based variant annotation. Here, we provide a detailed protocol for generating the H-MAGMA variant-gene annotation file by using chromatin interaction data from the adult human brain. In addition, we provide an example of how H-MAGMA is run by using genome-wide association study summary statistics of Parkinson's disease. Lastly, we generated variant-gene annotation files for 28 tissues and cell types, with the hope of contributing a resource for researchers studying a broad set of complex genetic disorders. H-MAGMA can be performed in <2 h for any cell type in which Hi-C data are available.

Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits.

Cigarette smoking and alcohol use are among the most prevalent substances used worldwide and account for a substantial proportion of preventable morbidity and mortality, underscoring the public health significance of understanding their etiology. Genome-wide association studies (GWAS) have successfully identified genetic variants associated with cigarette smoking and alcohol use traits. However, the vast majority of risk variants reside in non-coding regions of the genome, and their target genes and neurobiological mechanisms are unknown. Chromosomal conformation mappings can address this knowledge gap by charting the interaction profiles of risk-associated regulatory variants with target genes. To investigate the functional impact of common variants associated with cigarette smoking and alcohol use traits, we applied Hi-C coupled MAGMA (H-MAGMA) built upon cortical and newly generated midbrain dopaminergic neuronal Hi-C datasets to GWAS summary statistics of nicotine dependence, cigarettes per day, problematic alcohol use, and drinks per week. The identified risk genes mapped to key pathways associated with cigarette smoking and alcohol use traits, including drug metabolic processes and neuronal apoptosis. Risk genes were highly expressed in cortical glutamatergic, midbrain dopaminergic, GABAergic, and serotonergic neurons, suggesting them as relevant cell types in understanding the mechanisms by which genetic risk factors influence cigarette smoking and alcohol use. Lastly, we identified pleiotropic genes between cigarette smoking and alcohol use traits under the assumption that they may reveal substance-agnostic, shared neurobiological mechanisms of addiction. The number of pleiotropic genes was ~26-fold higher in dopaminergic neurons than in cortical neurons, emphasizing the critical role of ascending dopaminergic pathways in mediating general addiction phenotypes. Collectively, brain region- and neuronal subtype-specific 3D genome architecture helps refine neurobiological hypotheses for smoking, alcohol, and general addiction phenotypes by linking genetic risk factors to their target genes.

Content appealing to youth and spend characteristics of electronic cigarette video advertisements.

BACKGROUND: The US electronic cigarette (ECIG) market and use behavior continues to rise, warranting investigation of ECIG advertisement (ad) content within media channels frequented by youth including internet and television (TV). In order to inform potential policy regulations, this content analysis sought to assess the prevalence of youth-appealing content and spend characteristics among ECIG video ads. METHODS: Between 2015 and 2016, 46 ECIG video ads were identified using an ad-tracking firm and were coded using the Content Appealing to Youth (CAY) index. Bivariate analyses and analysis of variance were used to compare CAY indices between online and TV ads and by ECIG brands. Ad-specific spend and source information, including website/TV program targeted were examined descriptively. RESULTS: Common youth-appealing features included use of animation (56.5%) and content related to positive sensations (52.2%), promoting mood (34.8%), individuality/freedom (23.9%) and addiction (19.6%). Features not associated with youth appeal also were prevalent. Few differences were observed by media source or ECIG brand. TV ads accounted for the largest spend, and Vuse was the top spending brand. Websites/TV programs were diverse. CONCLUSIONS: Findings support regulatory efforts to restrict the use of youth-appealing content within ECIG ads as well as the reduction of media sources available for ECIG marketing.

Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits.

Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.

A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles.

Most risk variants for brain disorders identified by genome-wide association studies reside in the noncoding genome, which makes deciphering biological mechanisms difficult. A commonly used tool, multimarker analysis of genomic annotation (MAGMA), addresses this issue by aggregating single nucleotide polymorphism associations to nearest genes. Here we developed a platform, Hi-C-coupled MAGMA (H-MAGMA), that advances MAGMA by incorporating chromatin interaction profiles from human brain tissue across two developmental epochs and two brain cell types. By analyzing gene regulatory relationships in the disease-relevant tissue, H-MAGMA identified neurobiologically relevant target genes. We applied H-MAGMA to five psychiatric disorders and four neurodegenerative disorders to interrogate biological pathways, developmental windows and cell types implicated for each disorder. Psychiatric-disorder risk genes tended to be expressed during mid-gestation and in excitatory neurons, whereas neurodegenerative-disorder risk genes showed increasing expression over time and more diverse cell-type specificities. H-MAGMA adds to existing analytic frameworks to help identify the neurobiological principles of brain disorders.

Adolescent intermittent ethanol impairs behavioral flexibility in a rat foraging task in adulthood.

Alcohol exposure is linked to behavioral flexibility deficits in humans, but it is unclear when the critical exposure occurred or if alcohol exposure alone is sufficient to produce behavior deficits. Increasing evidence shows that binge levels of alcohol during adolescence are particularly harmful to the brain, producing physiological and behavioral effects that can persist into adulthood. The present study determined whether adolescent intermittent ethanol (AIE) in rats impaired action selection in a discriminative stimulus task using a foraging response. Rats were exposed to ethanol during adolescence (5 g/kg/day, IG, 2-days-on/2-days-off, postnatal day 25-54). In adulthood, they learned to dig for food reward buried in one of two media, cued with one of two odors. AIE and control rats both learned to discriminate between olfactory cues, but AIE rats were impaired when reversing that learned association (first intra-dimensional reversal). However, AIE rats were faster to reinstate the original odor discrimination rule (second reversal), suggesting perseverative behavior. Next, the reward location was cued by digging media rather than odor. Both groups learned this extra-dimensional shift; however, control rats were slower to reach criterion. These findings are consistent with studies of people with substance abuse disorder, who learn new stimulus-response associations similarly to, or better than, control subjects, but perseverate when attempting to replace a well-learned association. These data suggest that adolescent binge-alcohol exposure contributes to behavioral flexibility deficits observed in adulthood.