Quantitative Trait Locus Mapping for Acute Functional Tolerance to Ethanol in the L × S Recombinant Inbred Panel

Identification of novel genetic loci and candidate genes for progressive ethanol consumption in diversity outbred mice

Mouse behavioral genetic mapping studies can identify genomic intervals modulating complex traits under well-controlled environmental conditions and have been used to study ethanol behaviors to aid in understanding genetic risk and the neurobiology of alcohol use disorder (AUD). However, historically such studies have produced large confidence intervals, thus complicating identification of potential causal candidate genes. Diversity Outbred (DO) mice offer the ability to perform high-resolution quantitative trait loci (QTL) mapping on a very genetically diverse background, thus facilitating identification of candidate genes. Here, we studied a population of 636 male DO mice with four weeks of intermittent ethanol access via a three-bottle choice procedure, producing a progressive ethanol consumption phenotype. QTL analysis identified 3 significant (Chrs 3, 4, and 12) and 13 suggestive loci for ethanol-drinking behaviors with narrow confidence intervals (1-4 Mbp for significant QTLs). Results suggested that genetic influences on initial versus progressive ethanol consumption were localized to different genomic intervals. A defined set of positional candidate genes were prioritized using haplotype analysis, identified coding polymorphisms, prefrontal cortex transcriptomics data, human GWAS data and prior rodent gene set data for ethanol or other misused substances. These candidates included Car8, the lone gene with a significant cis-eQTL within a Chr 4 QTL for week four ethanol consumption. These results represent the highest-resolution genetic mapping of ethanol consumption behaviors in mice to date, providing identification of novel loci and candidate genes for study in relation to the neurobiology of AUD.

Translational relevance of forward genetic screens in animal models for the study of psychiatric disease

Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.

GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data

A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.

Fyn-dependent gene networks in acute ethanol sensitivity

Studies in humans and animal models document that acute behavioral responses to ethanol are predisposing factor for the risk of long-term drinking behavior. Prior microarray data from our laboratory document strain- and brain region-specific variation in gene expression profile responses to acute ethanol that may be underlying regulators of ethanol behavioral phenotypes. The non-receptor tyrosine kinase Fyn has previously been mechanistically implicated in the sedative-hypnotic response to acute ethanol. To further understand how Fyn may modulate ethanol behaviors, we used whole-genome expression profiling. We characterized basal and acute ethanol-evoked (3 g/kg) gene expression patterns in nucleus accumbens (NAC), prefrontal cortex (PFC), and ventral midbrain (VMB) of control and Fyn knockout mice. Bioinformatics analysis identified a set of Fyn-related gene networks differently regulated by acute ethanol across the three brain regions. In particular, our analysis suggested a coordinate basal decrease in myelin-associated gene expression within NAC and PFC as an underlying factor in sensitivity of Fyn null animals to ethanol sedation. An in silico analysis across the BXD recombinant inbred (RI) strains of mice identified a significant correlation between Fyn expression and a previously published ethanol loss-of-righting-reflex (LORR) phenotype. By combining PFC gene expression correlates to Fyn and LORR across multiple genomic datasets, we identified robust Fyn-centric gene networks related to LORR. Our results thus suggest that multiple system-wide changes exist within specific brain regions of Fyn knockout mice, and that distinct Fyn-dependent expression networks within PFC may be important determinates of the LORR due to acute ethanol. These results add to the interpretation of acute ethanol behavioral sensitivity in Fyn kinase null animals, and identify Fyn-centric gene networks influencing variance in ethanol LORR. Such networks may also inform future design of pharmacotherapies for the treatment and prevention of alcohol use disorders.

Ethanol tolerance and withdrawal severity in high drinking in the dark selectively bred mice

BACKGROUND

Mouse lines are being selectively bred in replicate for high blood ethanol concentrations (BECs) achieved after limited access of ethanol (EtOH) drinking early in the circadian dark phase. High Drinking in the Dark-1 (HDID-1) mice are in selected generation S21, and the replicate HDID-2 line in generation S14. Tolerance and withdrawal symptoms are 2 of the 7 diagnostic criteria for alcohol dependence. Withdrawal severity has been found in mouse studies to be negatively genetically correlated with EtOH preference drinking.

METHODS

To determine other traits genetically correlated with high DID, we compared naïve animals from both lines with the unselected, segregating progenitor stock, HS/Npt. Differences between HDID-1 and HS would imply commonality of genetic influences on DID and these traits.

RESULTS

Female HDID-1 and HDID-2 mice tended to develop less tolerance than HS to EtOH hypothermia after their third daily injection. A trend toward greater tolerance was seen in the HDID males. HDID-1, HDID-2, and control HS lines did not differ in the severity of acute or chronic withdrawal from EtOH as indexed by the handling-induced convulsion (HIC). Both HDID-1 and HDID-2 mice tended to have greater HIC scores than HS regardless of drug treatment.

CONCLUSIONS

These results show that tolerance to EtOH's hypothermic effects may share some common genetic control with reaching high BECs after DID, a finding consistent with other data regarding genetic contributions to EtOH responses. Withdrawal severity was not negatively genetically correlated with DID, unlike its correlation with preference drinking, underscoring the genetic differences between preference drinking and DID. HDID lines showed greater basal HIC scores than HS, suggestive of greater central nervous system excitability.

Quantitative trait loci for sensitivity to ethanol intoxication in a C57BL/6J×129S1/SvImJ inbred mouse cross

Individual variation in sensitivity to acute ethanol (EtOH) challenge is associated with alcohol drinking and is a predictor of alcohol abuse. Previous studies have shown that the C57BL/6J (B6) and 129S1/SvImJ (S1) inbred mouse strains differ in responses on certain measures of acute EtOH intoxication. To gain insight into genetic factors contributing to these differences, we performed quantitative trait locus (QTL) analysis of measures of EtOH-induced ataxia (accelerating rotarod), hypothermia, and loss of righting reflex (LORR) duration in a B6 × S1 F2 population. We confirmed that S1 showed greater EtOH-induced hypothermia (specifically at a high dose) and longer LORR compared to B6. QTL analysis revealed several additive and interacting loci for various phenotypes, as well as examples of genotype interactions with sex. QTLs for different EtOH phenotypes were largely non-overlapping, suggesting separable genetic influences on these behaviors. The most compelling main-effect QTLs were for hypothermia on chromosome 16 and for LORR on chromosomes 4 and 6. Several QTLs overlapped with loci repeatedly linked to EtOH drinking in previous mouse studies. The architecture of the traits we examined was complex but clearly amenable to dissection in future studies. Using integrative genomics strategies, plausible functional and positional candidates may be found. Uncovering candidate genes associated with variation in these phenotypes in this population could ultimately shed light on genetic factors underlying sensitivity to EtOH intoxication and risk for alcoholism in humans.

Molecular targets of alcohol action: Translational research for pharmacotherapy development and screening

Alcohol abuse and dependence are multifaceted disorders with neurobiological, psychological, and environmental components. Research on other complex neuropsychiatric diseases suggests that genetically influenced intermediate characteristics affect the risk for heavy alcohol consumption and its consequences. Diverse therapeutic interventions can be developed through identification of reliable biomarkers for this disorder and new pharmacological targets for its treatment. Advances in the fields of genomics and proteomics offer a number of possible targets for the development of new therapeutic approaches. This brain-focused review highlights studies identifying neurobiological systems associated with these targets and possible pharmacotherapies, summarizing evidence from clinically relevant animal and human studies, as well as sketching improvements and challenges facing the fields of proteomics and genomics. Concluding thoughts on using results from these profiling technologies for medication development are also presented.

Alcohol research: past, present, and future

Created forty years ago, the National Institute on Alcohol Abuse and Alcoholism (NIAAA) has played a major role in the great strides made in the understanding, treatment, prevention, and public acceptance of alcohol-use disorders. Throughout most of U.S. history "habitual drunkenness" was viewed as a problem of moral degeneracy or character flaw inherent in the individual. However, the wealth of scientific evidence amassed throughout NIAAA's history has established alcoholism as a medical condition, that is, as a disease for which affected individuals should feel no shame or be treated with disdain. We look at the developments in alcohol epidemiology, typology, etiology, prevention, and treatment research over the past 40 years. We also discuss how NIAAA addresses alcohol disorders from a life-course framework, affecting all stages of the lifespan, from fetus through child, adolescent, and young adult, to midlife/senior adult, with each stage involving different risks, consequences, prevention efforts, and treatment strategies.

Identifying quantitative trait loci (QTLs) and genes (QTGs) for alcohol-related phenotypes in mice

Alcoholism is a complex clinical disorder with genetic and environmental contributions. Although no animal model duplicates alcoholism, models for specific factors, such as the withdrawal syndrome, are useful to identify potential genetic determinants of liability in humans. Murine models have been invaluable to identify quantitative trait loci (QTLs) that influence a variety of alcohol responses. However, the QTL regions are typically large, at least initially, and contain numerous genes, making identification of the causal quantitative trait gene(s) (QTGs) challenging. Here, we present QTG identification strategies currently used in the field of alcohol genetics and discuss relevance to alcoholic human populations.

Review. Neurogenetic studies of alcohol addiction

Neurogenetic studies of alcohol dependence have relied substantially on genetic animal models, particularly rodents. Studies of inbred strains, selectively bred lines and mutants bearing genes whose function has been targeted for over or under expression are reviewed. Studies focused on gene expression changes are the most recent contributors to this literature, and some genetic effects may work through epigenetic mechanisms. In a few instances, interesting parallels have been revealed between genetic risk in humans and studies in non-human animal models. Future approaches are likely to be increasingly complex.

No effect of prenatal alcohol exposure on activity in three inbred strains of mice

AIMS

Prenatal exposure to alcohol can have adverse effects on the developing fetus. Two of the hallmarks of children exposed to alcohol prenatally are attention deficits and hyperactivity. While hyperactivity has been observed in rats following prenatal ethanol exposure, few studies have examined these effects in mice. The present study investigated the effects of prenatal ethanol exposure on activity in mice from three inbred strains: C57BL/6 (B6), Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS).

METHODS

On Days 7 through 18 of gestation, mice were intragastrically intubated twice daily with either 3.0 g/kg ethanol (E) or an isocaloric amount of maltose-dextrin (MD); non-intubated control (NIC) litters were also generated. Offspring activity was monitored at 30, 60, 90 and 150 days of age.

RESULTS

While results showed no effects of prenatal ethanol exposure on any measures of activity, we did observe differences in baseline activity among the strains. ISS mice were more active than B6 and ILS for all activity measures except stereotypy; B6 mice had higher measures of stereotypy than ILS and ISS. Younger mice were more active than older mice. The only sex effects were on measures of stereotypy, where males had higher scores.

CONCLUSIONS

Mice are an excellent organism to study genetic influences on many phenotypes. However, our study and others have shown few effects of prenatal ethanol exposure on behavior in mice. It appears as if the prenatal period in mice, corresponding to organogenesis, is not a sensitive period for producing behavioral deficits following ethanol exposure. It is likely that the first 2 weeks postnatally, corresponding to the brain growth spurt, are more sensitive for producing behavioral effects.

Genomic insights into acute alcohol tolerance

Alcohol "sensitivity" has been proposed as a predictive factor for development of alcohol dependence (Schuckit et al., 2005). Most measures of alcohol sensitivity in humans and animals include a component that can be ascribed to acute functional tolerance (AFT). AFT is a form of tolerance that develops within a single period of alcohol exposure and has a genetic component. We used microarray technology as well as quantitative trait locus analysis of phenotypic and gene expression data across 30 BXD recombinant inbred strains of mice, 20 inbred strains of mice, and two replicate lines of mice selectively bred for differences in AFT, to identify differentially expressed candidate genes that contribute to predisposition to AFT. Eight candidate genes were identified by our statistical and filtering methods. The location of brain expression of these genes was mapped using the Allen Brain Atlas (http://www.brain-map.org), and the transcript location and molecular pathway analysis indicated that brain structures and biochemical pathways implicated in long-term potentiation and memory might also participate in the generation of acute functional alcohol tolerance.

Ethanol sensitivity and tolerance in long-term memory mutants of Drosophila melanogaster

BACKGROUND

It has become increasingly clear that molecular and neural mechanisms underlying learning and memory and drug addiction are largely shared. To confirm and extend these findings, we analyzed ethanol-responsive behaviors of a collection of Drosophila long-term memory mutants.

METHODS

For each mutant, sensitivity to the acute uncoordinating effects of ethanol was quantified using the inebriometer. Additionally, 2 distinct forms of ethanol tolerance were measured: rapid tolerance, which develops in response to a single brief exposure to a high concentration of ethanol vapor; and chronic tolerance, which develops following a sustained low-level exposure.

RESULTS

Several mutants were identified with altered sensitivity, rapid or chronic tolerance, while a number of mutants exhibited multiple defects.

CONCLUSIONS

The corresponding genes in these mutants represent areas of potential overlap between learning and memory and behavioral responses to alcohol. These genes also define components shared between different ethanol behavioral responses.

Overview of mouse assays of ethanol intoxication

There are many behavioral assays to assess sensitivity to ethanol intoxication in mice. Most are simple to implement, and are sensitive to a particular dose range of ethanol. Most reflect genetic influences, and each test appears to reflect the contribution of a relatively distinct collection of genes. This genetic heterogeneity implies that no single test can claim to capture the construct "ethanol intoxication" completely. Depending on the test, and when measurements are made, acute functional tolerance to even a single dose of ethanol must be considered as a contributing factor. Whether or not a test is conducted in naïve mice or as part of a test battery can influence sensitivity, and do so in a strain-dependent manner. This unit reviews existing tests and recommends several.

Are designer guppies inbred? Microsatellite variation in five strains of ornamental guppies, Poecilia reticulata, used for behavioral research

Inbred lines are an important tool of genetic studies of all traits, including behavior. Independently derived strains of ornamental "designer" guppies are readily available and predicted to be inbred; however, little is known about actual levels of inbreeding in any of these strains or whether these lines differ in genetic traits that have not been under strong directional artificial selection. We genotyped five designer strains of guppies known to vary in their responses to predator cues and a wild reference population to determine whether designer strains show evidence of inbreeding and whether the strains differed from each other at five microsatellite loci. The designer strains exhibited lower allelic diversity and observed heterozygosity than the wild population. Observed heterozygosity departed significantly from expected heterozygosity for most markers in all five strains of designer guppies. Inbreeding coefficient (f) comparisons between the wild reference population and the designer strains show considerable inbreeding in the designer strains. F(is) values for the designer strains also provide evidence of inbreeding. Finally, F(st) values indicate that the designer strains differ significantly from each other and the wild population. We therefore concluded that designer guppies are inbred compared to wild populations and differ among strains, making them useful tools for genetic studies of behavioral or life history traits.

Genetic factors influencing alcohol dependence

Plentiful data from both animal and human studies support the importance of genetic influences in substance abuse and dependence (Bierut et al., 1998; Tsuang et al., 1998; Kendler et al., 2003). This review summarizes the evidence supporting such genetic influences, places them into perspective regarding animal and human studies, discusses the importance of both genes and environment, and highlights some specific genes of interest regarding the vulnerabilities for problems associated with alcohol use disorders. A long history of repetitive heavy use of alcohol exists across generations as well as the high prevalence of alcohol-related problems in Western societies. Moreover, the information offered here addresses the importance of more general issues regarding genetics and gene expression related to alcohol abuse and dependence.

Short-term selection for acute ethanol tolerance and sensitization from an F2 population derived from the high and low alcohol-sensitive selectively bred rat lines

Previous studies have identified quantitative trait loci (QTL) in the inbred high and low alcohol-sensitive rat (IHAS1 and ILAS1) strains. The original development of the strains involved selection for ethanol sensitivity based on duration of the loss of the righting reflex (LORR) after a standard dose of ethanol. This paper confirms some of these QTL using a short-term selection procedure based on the difference between the blood ethanol level at LORR and regain of the righting response. An F(2) population of rats was developed by a reciprocal cross of IHAS1 and ILAS1 rats. Selection for five generations was carried out using delta-blood ethanol concentration (dBEC) as the selection trait, where dBEC=BECLR (BEC at loss of righting reflex)-BECRR (BEC at regain of righting reflex). The lines were labeled tolerant (TOL) or sensitive (SENS). Approximately one-third of the offspring for each generation in each line were genotyped using DNA markers that had been previously found to be linked to QTL on chromosomes 1, 2, 5, 12, and 13. By the fifth generation of selection, the lines showed a very large difference in dBEC, BECRR, and duration of LORR; BECLR showed little segregation during the selection, and latency to lose the righting reflex showed none. IHAS allele frequency increased in the SENS line for markers on chromosomes 1, 5, 12, and 13 while ILAS allele frequency increased in the TOL line. These results were in good agreement with the two previous QTL studies. On chromosome 2, the selection resulted in an accumulation of ILAS alleles in both lines. This study provides independent confirmation of the location of QTL on chromosomes 1, 5, 12, and 13 for ethanol sensitivity. It also suggests that genetic differences in duration of LORR are mediated primarily by the dBEC phenotype.