Human Genetic Association Studies Research Articles

Acute behavioral effects of nicotine in male and female HINT1 knockout mice

Human genetic association and brain expression studies, and mouse behavioral and molecular studies implicate a role for the histidine triad nucleotide-binding protein 1 (HINT1) in schizophrenia, bipolar disorder, depression and anxiety. The high comorbidity between smoking and psychiatric disorders, schizophrenia in particular, is well established. Associations with schizophrenia and HINT1 are also sex specific, with effects more predominant in males; however, it is unknown if sex differences associated with the gene extend to other phenotypes. Thus, in this study, using a battery of behavioral tests, we elucidated the role of HINT1 in acute nicotine-mediated behaviors using male and female HINT1 wild-type (+/+) and knockout (-/-) mice. The results show that male HINT1 -/- mice were less sensitive to acute nicotine-induced antinociception in the tail-flick, but not hot-plate test. At low nicotine doses, male and female HINT1 -/- mice were less sensitive to nicotine-induced hypomotility, although the effect was more pronounced in females. Baseline differences in locomotor activity observed in male HINT1 +/+ and -/- mice were absent in females. Nicotine did not produce an anxiolytic effect in male HINT1 -/- mice, but rather an anxiogenic response. Diazepam also failed to induce an anxiolytic response in these mice, suggesting a general anxiety phenotype not specific to nicotine. Differences in anxiety-like behavior were not observed in female mice. These results further support a role for HINT1 in nicotine-mediated behaviors and suggest that alterations in the gene may have differential effects on phenotype in males and females.

Mouse genetic and phenotypic resources for human genetics

The use of model organisms to provide information on gene function has proved to be a powerful approach to our understanding of both human disease and fundamental mammalian biology. Large-scale community projects using mice, based on forward and reverse genetics, and now the pan-genomic phenotyping efforts of the International Mouse Phenotyping Consortium, are generating resources on an unprecedented scale, which will be extremely valuable to human genetics and medicine. We discuss the nature and availability of data, mice and embryonic stem cells from these large-scale programmes, the use of these resources to help prioritize and validate candidate genes in human genetic association studies, and how they can improve our understanding of the underlying pathobiology of human disease.

Genetic Variation, Protein Composition and Potential Influences on Tendon Properties in Humans

Sequence variations in genes that code for proteins involved in homeostatic processes within tendons may influence tendon mechanical properties. Since variants of the four genes COL5A1, TNC, MMP3 and GDF5 have been implicated in the aetiopathogenesis of tendinopathies, which is ultimately characterised by abnormal structural and regulatory processes, sequence variations in these four genes may also influence how the tendon functions mechanically, even in the absence of tendinopathy. For example, two reports of association between variation in the COL5A1 gene and measures of flexibility complement reported associations between genotype and incidence of tendinopathy. Non-genetic factors such as age, body mass and physical activity status influence risk of tendon injury and physical performance potential independently from genomics, and also in gene-environment interactions. However, these non-genetic factors are often not considered in genetic association studies, probably due to their retrospective nature. Further research examining COL5A1, TNC, MMP3 and GDF5, as well as other genes that may influence the maintenance of tendon homeostasis such as COL1A1 which regulates the production of collagen type 1, the most abundant structural component of tendon is encouraged. Establishing the genetic basis of tendon properties in asymptomatic populations may advance understanding of some aspects relevant to physical performance and of the aetiology of tendinopathies. To improve understanding, accurate and reproducible assessments of tendon properties are required. However, no valid and reliable assessments of tendon properties, such as those involving in vivo ultrasound imaging techniques, have yet been applied to genetic association studies in humans.

Pharmacogenetics of smoking cessation: role of nicotine target and metabolism genes.

Many smokers attempt to quit smoking but few are successful in the long term. The heritability of nicotine addiction and smoking relapse have been documented, and research is focused on identifying specific genetic influences on the ability to quit smoking and response to specific medications. Research in genetically modified cell lines and mice has identified nicotine acetylcholine receptor subtypes that mediate the pharmacological and behavioral effects of nicotine sensitivity and withdrawal. Human genetic association studies have identified single nucleotide polymorphisms (SNPs) in genes encoding nicotine acetylcholine receptor subunits and nicotine metabolizing enzymes that influence smoking cessation phenotypes. There is initial promising evidence for a role in smoking cessation for SNPs in the β2 and α5/α3/β4 nAChR subunit genes; however, effects are small and not consistently replicated. There are reproducible and clinically significant associations of genotypic and phenotypic measures of CYP2A6 enzyme activity and nicotine metabolic rate with smoking cessation as well as response to nicotine replacement therapies and bupropion. Prospective clinical trials to identify associations of genetic variants and gene-gene interactions on smoking cessation are needed to generate the evidence base for both medication development and targeted therapy approaches based on genotype.

Use of Functional Genomics to Identify Candidate Genes Underlying Human Genetic Association Studies of Vascular Diseases

Recent genome-wide association studies have identified hundreds of genetic loci as being associated with vascular diseases or traits and their risk factors. Many of the loci uncovered represent novel discoveries with no obvious candidate genes and molecular mechanisms, testifying to the complexity of vascular diseases. To understand the functional consequences of genetic variations and help pinpoint the underlying genes and mechanisms of common complex diseases, functional genomics that integrate genetic variations and intermediate molecular traits such as gene expression has been extensively studied in the past few years. This review summarizes the key concepts of functional genomics, the current state of the field, and its application in vascular diseases.

Genetics and outcomes after traumatic brain injury (TBI): What do we know about pediatric TBI?

Human genetic association studies in individuals with traumatic brain injury (TBI) have increased rapidly over the past few years. Recently, several review articles evaluated the association of genetics with outcomes after TBI. However, almost all of the articles discussed in these reviews focused on adult TBI. The primary objective of this review is to gain a better understanding of which genes and/or genetic polymorphisms have been evaluated in pediatric TBI. Our initial search identified 113 articles. After review of these articles only 5 genetic association studies specific to pediatric TBI were identified. All five of these studies evaluated the apolipoprotein (APOE) gene. The study design and methods of these identified papers will be discussed. An additional search was then performed to evaluate genes beyond APOE that have been evaluated in adult TBI; findings from these studies are highlighted. Larger genetic studies will need to be performed in the future to better elucidate the association of APOE and other genes with outcomes after TBI in children. There is great potential to utilized genetic information to inform prognosis and management after TBI in children; however, we have much work ahead of us to reach the goal of individualized management.

Abstract 17451: Dense Genotyping of Candidate Gene Loci Identifies Variants Associated with Oxidized Ldl Serum Levels

Background: Oxidized low-density lipoprotein (oxLDL) as a marker of oxidative stress has been proposed to play an important role in the development of atherosclerosis. OxLDL consists of a number of heterogeneously modified particles, including apoB, phospholipids, LDL-cholesterol, and unsaturated fatty acids. Serum levels of oxLDL are known to be heritable, but the degree of heritability has not been established yet. Methods: We used a high-density genotyping array containing single-nucleotide polymorphisms (SNPs) from oxLDL candidate genes selected on known biology of oxLDL metabolism, mouse genetic studies, and human genetic association studies. SNP selection was based on tagging SNPs and included low-frequency nonsynonymous SNPs. 1,332 men and women from a randomly drawn subsample of the baseline examination of the MONICA/KORA Augsburg Cohort Study, conducted between 1984 and 1995, with measurements of oxLDL (Mercodia assay) and genotyping by the 50K IBC Chip comprised the study population. Linear regression analysis with adjustment for age, sex and survey was applied to assess the associations between gene variants and oxLDL levels. Statistical significance was defined as 5.0e-6 accounting for multiple testing. Results: Eight SNPs showed a statistically significant association with ox-LDL and were located at chromosome 2 in the APOB gene with rs676210 having the strongest association (p value = 4.13e-12). All eight SNPs had minor allele frequencies above 20% showing a substantial gene variation. Conclusions: In summary, we identified variants in the APOB gene that are associated with levels of oxLDL in the general population. These findings may not only enhance our understanding of oxidative pathways and lipid metabolism and function, but may also pave the way for novel research avenues.

Abstract 17304: Dense Genotyping of Candidate Gene Loci Identifies Variants Associated with Soluble E-Selectin Levels

Background: Elevated soluble (s) E-selectin levels have been associated with various cardiovascular diseases. Recently, genetic variants in the ABO blood group have been related to E-selectin levels in a small cohort of patients with type 1 diabetes. We evaluated whether this association is reproducible in a population-based sample. Methods: We used a high-density genotyping array containing single-nucleotide polymorphisms (SNPs) from E-selectin candidate genes (50K IBC Chip) selected on known biology of E-selectin metabolism, mouse genetic studies, and human genetic association studies. SNP selection was based on tagging SNPs and included low-frequency nonsynonymous SNPs. 1,508 men and women from a randomly drawn subsample of the baseline examination of the MONICA/KORA Augsburg Cohort Study, conducted between 1984 and 1995, with measurements of sE-selectin and genotyping by the 50K IBC Chip comprised the study population. Linear regression analysis with adjustment for age, sex and survey was applied to assess associations between gene variants and sE-selectin levels. The significance level was defined as 5.0e-6 accounting for multiple testing. Results: Twelve SNPs, all from the ABO blood group candidate gene (ABO) were significantly associated with levels of E-selectin. The strongest association was observed for rs651007 with a change of E-selectin level per one copy of the minor allele of -18.59 ng/ml (p=5.79*10-56). All twelve SNPs had minor allele frequencies above 20% showing a substantial gene variation. Conclusions: Our findings indicate that the genetic variants at the ABO locus affect sE-selectin levels. These findings may not only enhance our understanding of adhesion molecule biology, but may also provide a focus for several novel research avenues.

Pain, analgesia and genetics

In the clinical setting, there is marked intersubject variability in the intensity of pain reported by patients with apparently similar pain states, as well as widely differing analgesic dosing requirements between individuals to produce satisfactory pain relief with tolerable side-effects. Genetic and environmental factors as well as their interaction are implicated, and these are discussed in this review. Pioneering work undertaken in mice more than a decade ago, showed a strong genetic contribution to levels of nociception/hypersensitivity as well as levels of antinociception produced by commonly available analgesic agents. To date more than 300 candidate 'pain' genes have been identified as potentially contributing to heritable differences in pain sensitivity and analgesic responsiveness in animals and humans, with this information available in a publicly accessible database http://www.jbldesign.com/jmogil/enter.html. Since then, many genetic association studies have been conducted in humans to investigate the possibility that single nucleotide polymorphisms (SNPs) in an individual gene may explain drug inefficacy or excessive toxicity experienced by a small subset of the whole population who have the rare allele for a particular SNP. Despite the fact that SNPs in more than 20 genes that affect pain sensitivity or contribute to interindividual variability in responses to analgesic medications have been identified in the human genome, much of the data is conflicting. Apart from deficiencies in the design and conduct of human genetic association studies, recent research from other fields has implicated epigenetic mechanisms that facilitate dynamic gene-environment communication, as a possible explanation.

Commentary: Research Highlights (Neuronal Nicotinic Acetylcholine Receptors: Emerging Therapeutic Targets for Alcoholism)

Alcoholism and alcohol use disorders (AUDs) impact millions of people and represent a significant global public health problem. According to the World Health Organization, alcoholism related deaths are estimated to account 3.2% of all deaths worldwide. Fetal alcohol syndrome, an important form of mental disability, caused by alcohol abuse and addiction by pregnant women, is on the rise. Previous research suggests that alcoholism is a progressive relapsing disorder of the brain and needs effective treatment to remain abstinent. Due to modest efficacy with currently approved medications, there is a need for new therapeutic strategies for the management of alcoholism. Evidence indicates that neuronal nicotinic acetylcholine receptors (nAChRs) are critical targets for the development of improved pharmacotherapies for alcoholism. However, it is not clear which subtypes of the neuronal nAChR are involved in alcoholism. Recent human genetic association studies have implicated the gene cluster CHRNA3-CHRNA5-CHRNB4 encoding the α3, α5, and β4 subunits of the nAChR in susceptibility to develop nicotine and alcohol dependence, indicating a potential role of these nAChR subunits. To examine the role of the α3 and β4 subunits of the nAChR in alcoholism, Chatterjee and colleagues have developed and characterized high-affinity partial agonists at α3β4 nAChRs, CP-601932, and PF-4575180 in preclinical models of alcoholism. The results suggest that both CP-601932 and PF- 4575180 selectively reduce alcohol but not sucrose self-administration, following long-term exposure. The authors also demonstrated that the functional potencies of CP-601932 and PF-4575180 at α3β4 nAChRs correlate with these compounds' unbound brain concentrations. These data indicate that the effects on alcohol self-administration are mediated by α3β4 nAChRs. Overall, the study suggests that α3β4 nAChRs could be critical therapeutic targets for the treatment of alcoholism and AUDs. In addition, the clinically safe novel partial nAChR agonist CP-601932 has the potential to reduce smoking in alcoholics with co-morbid nicotine dependence. This is due to similar affinity of the novel compound for α4β2 nAChRs that are involved in nicotine addiction. Future clinical studies in subjects with alcoholism and AUDs could further advance its development and use in humans.

AMD-associated complement factor H variant Y402H protects from streptococcal infections—Evidence from bacterial in vitro survival and human genetic association studies

AMD-associated complement factor H variant Y402H protects from streptococcal infections—Evidence from bacterial in vitro survival and human genetic association studies

Physical Confirmation and Mapping of Overlapping Rat Mammary Carcinoma Susceptibility QTLs, Mcs2 and Mcs6

Only a portion of the estimated heritability of breast cancer susceptibility has been explained by individual loci. Comparative genetic approaches that first use an experimental organism to map susceptibility QTLs are unbiased methods to identify human orthologs to target in human population-based genetic association studies. Here, overlapping rat mammary carcinoma susceptibility (Mcs) predicted QTLs, Mcs6 and Mcs2, were physically confirmed and mapped to identify the human orthologous region. To physically confirm Mcs6 and Mcs2, congenic lines were established using the Wistar-Furth (WF) rat strain, which is susceptible to developing mammary carcinomas, as the recipient (genetic background) and either Wistar-Kyoto (WKy, Mcs6) or Copenhagen (COP, Mcs2), which are resistant, as donor strains. By comparing Mcs phenotypes of WF.WKy congenic lines with distinct segments of WKy chromosome 7 we physically confirmed and mapped Mcs6 to ∼33 Mb between markers D7Rat171 and gUwm64-3. The predicted Mcs2 QTL was also physically confirmed using segments of COP chromosome 7 introgressed into a susceptible WF background. The Mcs6 and Mcs2 overlapping genomic regions contain multiple annotated genes, but none have a clear or well established link to breast cancer susceptibility. Igf1 and Socs2 are two of multiple potential candidate genes in Mcs6. The human genomic region orthologous to rat Mcs6 is on chromosome 12 from base positions 71,270,266 to 105,502,699. This region has not shown a genome-wide significant association to breast cancer risk in pun studies of breast cancer susceptibility.

Experimental Inflammatory Bowel Disease: Insights into the Host-Microbiota Dialog

Inflammatory bowel disease appears to result from an abnormal host immune response to the intestinal microbiota. Experimental models have allowed the dissection of the complex dialog between the host and its microbiota. Through genetic manipulation of the host genome the immune compartments, cells, molecules, and genes that are critical for maintenance of intestinal homeostasis are being identified. Genetic association studies in humans have identified over 100 susceptibility loci. Although there is remarkable coherence between the experimental model and the human genetic data, a full understanding of the mechanisms involved in genetic susceptibility to IBD and of gene-gene and gene-environmental interactions will require a "next generation" of experimental models.

Dense Genotyping of Candidate Gene Loci Identifies Variants Associated With High-Density Lipoprotein Cholesterol

Plasma levels of high-density lipoprotein cholesterol (HDL-C) are known to be heritable, but only a fraction of the heritability is explained. We used a high-density genotyping array containing single-nucleotide polymorphisms (SNPs) from HDL-C candidate genes selected on known biology of HDL-C metabolism, mouse genetic studies, and human genetic association studies. SNP selection was based on tagging SNPs and included low-frequency nonsynonymous SNPs. Association analysis in a cohort containing extremes of HDL-C (case-control, n=1733) provided a discovery phase, with replication in 3 additional populations for a total meta-analysis in 7857 individuals. We replicated the majority of loci identified through genome-wide association studies and present on the array (including ABCA1, APOA1/C3/A4/A5, APOB, APOE/C1/C2, CETP, CTCF-PRMT8, FADS1/2/3, GALNT2, LCAT, LILRA3, LIPC, LIPG, LPL, LRP4, SCARB1, TRIB1, ZNF664) and provide evidence that suggests an association in several previously unreported candidate gene loci (including ABCG1, GPR109A/B/81, NFKB1, PON1/2/3/4). There was evidence for multiple, independent association signals in 5 loci, including association with low-frequency nonsynonymous variants. Genetic loci associated with HDL-C are likely to harbor multiple, independent causative variants, frequently with opposite effects on the HDL-C phenotype. Cohorts comprising subjects at the extremes of the HDL-C distribution may be efficiently used in a case-control discovery of quantitative traits.

Controlling population structure in human genetic association studies with samples of unrelated individuals

In genetic studies, associations between genotypes and phenotypes may be confounded by unrecognized population structure and/or admixture. Studies have shown that even in European populations, which are thought to be relatively homogeneous, population stratification exists and can affect the validity of association studies. A number of methods have been proposed to address this issue in recent years. Among them, the mixed-model based approach and the principal component-based approach have several advantages over other methods. However, these approaches have not been thoroughly evaluated on large human datasets. The objectives of this study are to (1) evaluate and compare the performance of the mixed-model approach and the principal component-based approach for genetic association mapping using human data consisting of unrelated individuals, and (2) understand the relationship between these two approaches. To achieve these goals, we simulate datasets based on the HapMap data under various scenarios. Our results indicate that the mixed-model approach performs well in controlling for population structure/admixture. It has similar performance as that based on principal component analysis. However, the approach combining mixed-model and principal component analysis does not perform as well as either method itself.

Statistical analysis of genetic interactions

Many common human diseases and complex traits are highly heritable and influenced by multiple genetic and environmental factors. Although genome-wide association studies (GWAS) have successfully identified many disease-associated variants, these genetic variants explain only a small proportion of the heritability of most complex diseases. Genetic interactions (gene-gene and gene-environment) substantially contribute to complex traits and diseases and could be one of the main sources of the missing heritability. This paper provides an overview of the available statistical methods and related computer software for identifying genetic interactions in animal and plant experimental crosses and human genetic association studies. The main discussion falls under the three broad issues in statistical analysis of genetic interactions: the definition, detection and interpretation of genetic interactions. Recently developed methods based on modern techniques for high-dimensional data are reviewed, including penalized likelihood approaches and hierarchical models; the relationships between these methods are also discussed. I conclude this review by highlighting some areas of future research.

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

More than 25 loci have been linked to type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse, but identification of the underlying genes remains challenging. We describe here the positional cloning of a T1D susceptibility locus, Idd11, located on mouse chromosome 4. Sequence analysis of a series of congenic NOD mouse strains over a critical 6.9-kb interval in these mice and in 25 inbred strains identified several haplotypes, including a unique NOD haplotype, associated with varying levels of T1D susceptibility. Haplotype diversity within this interval between congenic NOD mouse strains was due to a recombination hotspot that generated four crossover breakpoints, including one with a complex conversion tract. The Idd11 haplotype and recombination hotspot are located within a predicted gene of unknown function, which exhibits decreased expression in relevant tissues of NOD mice. Notably, it was the recombination hotspot that aided our mapping of Idd11 and confirms that recombination hotspots can create genetic variation affecting a common polygenic disease. This finding has implications for human genetic association studies, which may be affected by the approximately 33,000 estimated hotspots in the genome.

Partial Agonists of the α3β4* Neuronal Nicotinic Acetylcholine Receptor Reduce Ethanol Consumption and Seeking in Rats

Alcohol use disorders (AUDs) impact millions of individuals and there remain few effective treatment strategies. Despite evidence that neuronal nicotinic acetylcholine receptors (nAChRs) have a role in AUDs, it has not been established which subtypes of the nAChR are involved. Recent human genetic association studies have implicated the gene cluster CHRNA3-CHRNA5-CHRNB4 encoding the α3, α5, and β4 subunits of the nAChR in susceptibility to develop nicotine and alcohol dependence; however, their role in ethanol-mediated behaviors is unknown due to the lack of suitable and selective research tools. To determine the role of the α3, and β4 subunits of the nAChR in ethanol self-administration, we developed and characterized high-affinity partial agonists at α3β4 nAChRs, CP-601932, and PF-4575180. Both CP-601932 and PF-4575180 selectively decrease ethanol but not sucrose consumption and operant self-administration following long-term exposure. We show that the functional potencies of CP-601932 and PF-4575180 at α3β4 nAChRs correlate with their unbound rat brain concentrations, suggesting that the effects on ethanol self-administration are mediated via interaction with α3β4 nAChRs. Also varenicline, an approved smoking cessation aid previously shown to decrease ethanol consumption and seeking in rats and mice, reduces ethanol intake at unbound brain concentrations that allow functional interactions with α3β4 nAChRs. Furthermore, the selective α4β2(*) nAChR antagonist, DHβE, did not reduce ethanol intake. Together, these data provide further support for the human genetic association studies, implicating CHRNA3 and CHRNB4 genes in ethanol-mediated behaviors. CP-601932 has been shown to be safe in humans and may represent a potential novel treatment for AUDs.

Sclerostin: A gem from the genome leads to bone-building antibodies

Sclerostin: A gem from the genome leads to bone-building antibodies

Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies

Recently, genome-wide association studies (GWAS) have linked the human LIN28B locus to height and timing of menarche [1-5]. LIN28B and its homolog LIN28 (hereafter, LIN28A) are functionally redundant RNA-binding proteins that block let-7 microRNA (miRNA) biogenesis [6-9]. lin-28 and let-7 were discovered in C. elegans as heterochronic regulators of larval and vulval development, but recently have been implicated in cancer, stem cell aging, and pluripotency [10-13]. The let-7 targets Myc, Kras, Igf2bp1 and Hmga2 are known regulators of mammalian body size and metabolism [14-18]. To explore the Lin28/let-7 pathway in vivo, we engineered transgenic mice to express Lin28a and observed increased body size, crown-rump length, and a delayed onset of puberty. While investigating metabolic and endocrine mechanisms of overgrowth, we observed increased glucose metabolism and insulin sensitivity in these transgenic mice. We report a mouse that models the human phenotypes associated with genetic variation in the Lin28/let-7 pathway.