Combinations of SNP genotypes from the Wellcome Trust Case Control Study of bipolar patients.

OBJECTIVES: Combinations of genetic variants are the basis for polygenic disorders. We examined combinations of SNP genotypes taken from the 446 729 SNPs in The Wellcome Trust Case Control Study of bipolar patients. METHODS: Parallel computing by graphics processing units, cloud computing, and data mining tools were used to scan The Wellcome Trust data set for combinations. RESULTS: Two clusters of combinations were significantly associated with bipolar disorder. One cluster contained 68 combinations, each of which included five SNP genotypes. Of the 1998 patients, 305 had combinations from this cluster in their genome, but none of the 1500 controls had any of these combinations in their genome. The other cluster contained six combinations, each of which included five SNP genotypes. Of the 1998 patients, 515 had combinations from the cluster in their genome, but none of the 1500 controls had any of these combinations in their genome. CONCLUSION: Clusters of combinations of genetic variants can be considered general risk factors for polygenic disorders, whereas accumulation of combinations from the clusters in the genome of a patient can be considered a personal risk factor.

Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes.

Meta-analyses of large-scale association studies typically proceed solely within one data type and do not exploit the potential complementarities in other sources of molecular evidence. Here, we present an approach to combine heterogeneous data from genome-wide association (GWA) studies, protein-protein interaction screens, disease similarity, linkage studies, and gene expression experiments into a multi-layered evidence network which is used to prioritize the entire protein-coding part of the genome identifying a shortlist of candidate genes. We report specifically results on bipolar disorder, a genetically complex disease where GWA studies have only been moderately successful. We validate one such candidate experimentally, YWHAH, by genotyping five variations in 640 patients and 1,377 controls. We found a significant allelic association for the rs1049583 polymorphism in YWHAH (adjusted P = 5.6e-3) with an odds ratio of 1.28 [1.12-1.48], which replicates a previous case-control study. In addition, we demonstrate our approach's general applicability by use of type 2 diabetes data sets. The method presented augments moderately powered GWA data, and represents a validated, flexible, and publicly available framework for identifying risk genes in highly polygenic diseases. The method is made available as a web service at www.cbs.dtu.dk/services/metaranker.

Association analysis of ANK3 gene variants in nordic bipolar disorder and schizophrenia case-control samples.

Genetic variants in ankyrin 3 (ANK3) have recently been shown to be associated with bipolar disorder (BD). We genotyped three ANK3 SNPs previously found to be associated with BD (rs10994336, rs1938526, and rs9804190) in a Scandinavian BD case-control sample (N = 854/2,614). Due to evidence of genetic overlap between BD and schizophrenia (SZ), we also genotyped these three SNPs in a Scandinavian SZ case-control sample (N = 1,073/2,919). Combining our Scandinavian samples with an Icelandic sample (N = 435 BD cases, 651 SZ cases, and 11,491 healthy controls), we found rs10994336 and rs9804190 to be nominally significantly associated with BD in this combined Nordic BD sample (N = 1,289/14,105). Nominal P was 0.015/0.018 (fixed/random effect) for rs10994336 (Bonferroni corrected P = 0.044/0.053) and 0.023 for rs9804190 (Bonferroni corrected P = 0.069). None of the SNPs were significantly associated with SZ in the combined Nordic SZ case-control sample (N = 1,724/14,410). These results further support that ANK3 is a susceptibility gene specific to BD and that more than one risk locus is involved.

Risperidone treatment increases CB1 receptor binding in rat brain.

BACKGROUND/AIMS: Body weight gain is a common side effect of treatment with antipsychotics, but the mechanisms underlying this weight gain are unknown. Several factors may be involved in antipsychotic-induced body weight gain including the cannabinoid receptor 1 (CB(1)), the serotonin receptor 2C, the ghrelin receptor, neuropeptide Y, adiponectin and proopiomelanocortin. We investigated whether the expression of these factors was affected in rats chronically treated with the antipsychotic risperidone. METHODS: Male Sprague-Dawley rats were treated with risperidone (1.0 mg/kg/day) or vehicle (20% hydroxypropyl beta-cyclodextrin) for 28 days. Expression of the aforementioned factors were examined together with plasma prolactin and ghrelin levels. RESULTS: No difference in body weight gained during treatment was observed between risperidone and vehicle treated rats, but plasma risperidone levels positively correlated with visceral fat mass. Risperidone treatment increased CB(1) receptor binding in the arcuate nucleus (40%), hippocampus (25-30%) and amygdala (35%) without concurrent alterations in the CB(1) receptor mRNA. Risperidone treatment increased adiponectin mRNA. CONCLUSION: The present study showed that risperidone treatment altered CB(1) receptor binding in the rat brain. Risperidone-induced adiposity and metabolic dysfunction in the clinic may be explained by increased CB(1) receptor density in brain regions involved in appetite and regulation of metabolic function.

Association study of PDE4B gene variants in Scandinavian schizophrenia and bipolar disorder multicenter case-control samples.

The phosphodiesterase 4B (PDE4B), which is involved in cognitive function in animal models, is a candidate susceptibility gene for schizophrenia (SZ) and bipolar disorder (BP). Variations in PDE4B have previously been associated with SZ, with a suggested gender-specific effect. We have genotyped and analyzed 40 and 72 tagging single nucleotide polymorphisms (tagSNPs) in SZ and BP multicenter samples, respectively, from the Scandinavian Collaboration on Psychiatric Etiology (SCOPE), involving 837 SZ cases and 1,473 controls plus 594 BP cases and 1,421 partly overlapping controls. Six and 16 tagSNPs were nominally associated (0.0005 < or = P < or = 0.05) with SZ and BP, respectively, in the combined samples or in gender-specific subgroups. None of these findings remained significant after correction for multiple testing. However, a number of tagSNPs found to be nominally associated with SZ and BP were located in a high LD region spanning the splice site of PDE4B3, an isoform with altered brain expression in BP patients. Four tagSNPs were associated with SZ in women, but none in men, in agreement with the previously reported gender-specific effect. Proxies of two nominally associated SNPs in the SZ sample were also associated with BP, but the genotypic effect (i.e., homozygosity for the minor allele), pointed in opposite directions. Finally, four SNPs were found to be associated with Positive And Negative Syndrome Scale (PANSS) positive symptom scores in a subgroup of SZ patients (n = 153) or SZ female patients (n = 70). Further studies are needed to evaluate the implicated PDE4B region of interest, for potential involvement in SZ and BP susceptibility.

Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a scandinavian case-control sample.

A recent genome-wide association study (GWAS) found significant association between the PALB2 SNP rs420259 and bipolar disorder (BD). The intracellular functions of the expressed proteins from the breast cancer risk genes PALB2 and BRCA2 are closely related. Therefore, we investigated the relation between genetic variants in PALB2 and BRCA2 and BD. Due to increasing evidence of genetic overlap between BD and schizophrenia (SCZ), we also investigated association with SCZ. In a Scandinavian case-control sample (n = 686/2,538) we found the BRCA2 SNP rs9567552 to be significantly associated with BD (Nominal P = 0.00043). Additionally, we replicated the association between PALB2 SNP rs420259 and BD (Nominal P = 0.025). We then combined our sample with another Nordic case-control sample (n = 435/11,491) from Iceland, and added results from the Wellcome Trust Case Control Consortium (WTCCC) (n = 1,868/2,938) and the STEP-UCL/ED-DUB-STEP2 study (n = 2,558/3,274) in a meta-analysis which revealed a P-value of 1.2 × 10(-5) for association between PALB2 SNP rs420259 and BD (n = 5,547/20,241). Neither the PALB2 SNP rs420259 nor the BRCA2 SNP rs9567552 were nominally significantly associated with the SCZ phenotype in our Scandinavian sample (n = 781/2,839). Our findings support PALB2 and BRCA2 as risk genes specifically for BD, and suggest that altered DNA repair related to neurogenesis may be involved in BD pathophysiology. © 2010 Wiley-Liss, Inc.

The serotonin transporter and 5HT2A receptor in rat brain after localized lesions.

OBJECTIVES: Post-stroke depression and depression after traumatic brain lesion are most often seen when the lesion includes frontal areas. The development of depression may include the serotonergic system because selective serotonin reuptake inhibitors (SSRIs) can be used to treat the depression. The purpose of the present study was to examine whether serotonin transporter density or 5HT2A serotonin receptor density is changed in specific brain areas following anterior or posterior lesions in the two hemispheres. METHODS: Localized heat-induced brain lesions were induced in rats, and the densities of the serotonin transporter and 5HT2A receptor were measured by quantitative autoradiography in eight and 15 different brain areas, respectively. RESULTS: A decrease in serotonin transporter density was detected in some frontal rat brain areas, and an increase in serotonin transporter density was detected in the right median raphe nucleus. No change was detected for 5HT2A receptor density.

Combinations of Genetic Variants Occurring Exclusively in Patients.

In studies of polygenic disorders, scanning the genetic variants can be used to identify variant combinations. Combinations that are exclusively found in patients can be separated from those combinations occurring in control persons. Statistical analyses can be performed to determine whether the combinations that occur exclusively among patients are significantly associated with the investigated disorder. This research strategy has been applied in materials from various polygenic disorders, identifying clusters of patient-specific genetic variant combinations that are significant associated with the investigated disorders. Combinations from these clusters are found in the genomes of up to 55% of investigated patients, and are not present in the genomes of any control persons.

Combinations of genetic variants associated with bipolar disorder.

The main objective of the study was to find genetic variants that in combination are significantly associated with bipolar disorder. In previous studies of bipolar disorder, combinations of three and four single nucleotide polymorphisms (SNP) genotypes taken from 803 SNPs were analyzed, and five clusters of combinations were found to be significantly associated with bipolar disorder. In the present study, combinations of ten SNP genotypes taken from the same 803 SNPs were analyzed, and one cluster of combinations was found to be significantly associated with bipolar disorder. Combinations from the new cluster and from the five previous clusters were identified in the genomes of 266 or 44% of the 607 patients in the study whereas none of the 1355 control participants had any of these combinations in their genome.The SNP genotypes in the smaller combinations were the normal homozygote, heterozygote or variant homozygote. In the combinations containing 10 SNP genotypes almost all the genotypes were the normal homozygote. Such a finding may indicate that accumulation in the genome of combinations containing few SNP genotypes may be a risk factor for bipolar disorder when those combinations contain relatively many rare SNP genotypes, whereas combinations need to contain many SNP genotypes to be a risk factor when most of the SNP genotypes are the normal homozygote.

Association of the 5-HT2A receptor gene polymorphism 102T/C with ischemic stroke.

Serotonin (5-HT) has been implicated in a number of cardiovascular disorders due to its ability to induce vascular contraction and platelet aggregation through activation of the 5-HT2 receptor family. In this study, we investigated the association of stroke in a Scandinavian population with two common polymorphisms in the 5-HT2A receptor gene. The two polymorphisms under investigation, namely the 102T/C and the -1438A/G variations of the 5-HT2A receptor gene, were examined in a case control association study involving 99 stroke patients and a comparable number of controls. Among patients, the prevalence of the homozygous 102T/T genotype was significantly higher than in controls (28.3% vs 13.5%; p < 0.01). The allelic frequency of 102T carriers was also significantly higher in stroke patients than in controls (p = 0.002, OR = 1.88, 95% CI, 1.27-2.80). The association between the 102T allele and stroke was significant in both males and females. There was no association between stroke and the -1438A/G polymorphism. Taken together, this study indicates that the 102T/C polymorphism in the 5-HT2A receptor gene could be an independent risk factor for developing stroke.

Combinations of genetic data in a study of oral cancer.

In the single locus strategy a number of genetic variants are analyzed, in order to find variants that are distributed significantly different between controls and patients. A supplementary strategy is to analyze combinations of genetic variants. A combination that is the genetic basis for a polygenic disorder will not occur in in control persons genetically unrelated to patients, so the strategy is to analyze combinations of genetic variants present exclusively in patients. In a previous study of oral cancer and leukoplakia 325 SNPs were analyzed. This study has been supplemented with an analysis of combinations of two SNP genotypes from among the 325 SNPs. Two clusters of combinations containing 95 patient specific combinations were significantly associated with oral cancer or leukoplakia. Of 373 patients with oral cancer 205 patients had a number of these 95 combinations in their genome, whereas none of 535 control persons had any of these combinations in their genome.

Combinations of Genetic Data Present in Bipolar Patients, but Absent in Control Persons.

The main objective of the study was to find combinations of genetic variants significantly associated with bipolar disorder. In a previous study of bipolar disorder, combinations of three single nucleotide polymorphism (SNP) genotypes taken from 803 SNPs were analyzed, and four clusters of combinations were found to be significantly associated with bipolar disorder. In the present study, combinations of four SNP genotypes taken from the same 803 SNPs were analyzed, and one cluster of combinations was found to be significantly associated with bipolar disorder. Combinations from the new cluster and from the four previous clusters were identified in the genomes of 209 of the 607 patients in the study whereas none of the 1355 control participants had any of these combinations in their genome.

Selective serotonin reuptake inhibitors and the risk of stroke: a population-based case-control study.

BACKGROUND AND PURPOSE: Selective serotonin reuptake inhibitors (SSRIs) have been associated with increased risk of bleeding complications, possibly as a result of inhibition of platelet aggregation. Little is known about the risk of intracerebral hemorrhage in users of SSRIs and whether the effect on platelet aggregation reduces the risk of ischemic stroke. We used population-based data to estimate the risk of hemorrhagic and ischemic stroke in users of SSRIs. METHODS: We performed a nested case-control study in Funen County (465 000 inhabitants), Denmark. All patients with a first-ever stroke discharge diagnosis in the period of 1994 to 1999 were identified, and a validated diagnosis of stroke was reached in 4765 cases. In all, 40 000 controls were randomly selected from the background population. Information on drug use for cases and controls was retrieved from a prescription registry with full coverage of the county. Odds ratios were adjusted for age, sex, calendar year, and use of other medication. To evaluate the effect of various potential confounders not recorded in the register data, we performed separate analyses on data from 2 large population-based surveys with more detailed information on risk factors. RESULTS: Of 659 patients with hemorrhagic stroke, 21 were current users of SSRIs. The adjusted odds ratio of hemorrhagic stroke in current SSRI users compared with never users was 1.0 [95% confidence interval (CI), 0.6 to 1.6]. Of 2717 patients with ischemic stroke, 100 were current users of SSRIs, and the adjusted odds ratio of ischemic stroke in cases compared with controls was 1.1 (95% CI, 0.9 to 1.4). The survey data indicated that additional confounder control would not have led to an increase in the relative risk estimates. CONCLUSIONS: Current exposure to SSRIs is not associated with increased risk of intracerebral hemorrhage and is probably not associated with a decreased risk of ischemic stroke.

Different roles of 5-HT2A and 5-HT2C receptors in regulation of female rat paced mating behaviour.

Serotonin (5-HT) receptor 2A (5-HT2A) and 2C (5-HT2C) agonists have been reported to facilitate female rat lordosis behaviour. This study investigated the acute effects of the 5-HT2A receptor agonist DOI ((+/-)-1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane) and the 5-HT2C receptor agonist MK-212 (2-chloro-6-(1-piperazinyl) pyrazine) on paced mating behaviour in a population of sexually receptive female rats in order to explore the role of 5-HT2A and 5-HT2C receptors in the mediation of female rat sexual motivation. DOI (0.5 and 1.0 mg/kg) increased female rat sexual motivation during the first of two consecutive copulatory series seen as a tendency towards a decrease in return latencies following ejaculation and decreased inter-intromission intervals. MK-212 generally increased approach latencies. 0.5 mg/kg MK-212 increased post-ejaculatory exit latency, while 1.0 and 2.0 mg/kg MK-212 increased both post-ejaculatory exit latencies and post-ejaculatory return latencies. The possibility that an increased level of anxiety confounded the effects of MK-212 on sexual motivation behaviour is discussed. The results may support the hypothesis that both 5-HT2A and 5-HT2C receptors are important in regulation of female sexual behaviour.

Pindolol and the acceleration of the antidepressant response.

BACKGROUND: It has been suggested that treatment with selective serotonin reuptake inhibitors (SSRIs) in combination with pindolol, a partial agonist at the 5-HT(1A) receptor, may produce a fast antidepressant response. However, inconsistent results have been obtained in clinical studies with combination of the two drugs. Some studies, most using paroxetine, show an acceleration of the antidepressant response, whereas studies with other SSRIs find no marked latency reduction. METHODS: The free SSRI concentration in patients either receiving the first dose, or in steady state treatment with the five different SSRIs citalopram, fluoxetine, fluvoxamine, paroxetine and sertraline was estimated using pharmacokinetic data for the individual drugs. RESULTS: Due to differences between the drugs regarding protein binding, distribution volume and affinity for the 5-HT transporter (5-HTT), the 5-HT uptake inhibition obtained with clinically relevant doses differs markedly among the SSRIs. CONCLUSIONS: A nearly complete blockade of the 5-HTT is obtained already after the first dose only with paroxetine, explaining why the latency reducing effect of pindolol preferentially is seen when pindolol is combined with paroxetine.

Serotonin, locomotion, exploration, and place recall in the rat.

Intracerebroventricular injection of 5,7-dihydroxytryptamine (5,7-DHT) led to a 90% reduction of the 5-hydroxytryptamine (5-HT) reuptake site. Behavioural symptoms were studied early (45 to 93 h) as well as late (11 to 14 days) in the postoperative period. Forty-five hours postoperatively, recall of a place navigation task in a water maze was clearly impaired in 5,7-DHT-treated animals. This impairment had disappeared by the fifth postoperative session. During the early test period, injection of scopolamine (0.5 mg/kg) or d-amphetamine (3.0 mg/kg) did not affect place recall of the vehicle-treated control group. In contrast, 5,7-DHT-treated animals were impaired by administration of scopolamine, but not d-amphetamine. During the late test period, the place recall of both groups was affected by scopolamine, but only the performance of the 5,7-DHT lesioned animals was sensitive to d-amphetamine. Locomotion was not severely affected at any time after 5,7-DHT treatment. The vertical hole-board test indicated that the exploratory activities of the animals were relatively unaffected by 5,7-DHT when measured 48 h postoperatively. At 14 days postsurgery, the 5,7-DHT-treated animals demonstrated an impaired habituation of the exploratory behaviour.

Associative and nonassociative learning after chronic imipramine in rats.

We investigated effects of 15 daily injections of imipramine (20 mg/kg; in one experiment also 10 and 30 mg/kg). The associative learning types (place learning and object recognition) as well as nonassociative learning (habituation of exploration in an open field and within the object recognition test) were studied. Tests were performed immediately after the final injection (early test) and 24 h after the final injection (late test). The 5-HT(1A), 5-HT(1B/D), 5-HT(2A), beta-adrenergic, D(2) receptors were assayed 24 h after the final injection and the 5-HT(2A) and beta-adrenergic receptors were also measured 60 and 96 h after the final injection. While associative types of learning were impaired in early tests, they remained unaffected in late tests and, while the nonassociative learning (habituation of exploration) remained unaffected in early tests, it was changed in late tests. Measured 24 h after the final injection, imipramine (20 and 30 mg/kg per day) down-regulated the concentration of beta-adrenergic and 5-HT(2A) receptors, while leaving all other measured receptors unaffected. However, only the down-regulation of the 5-HT(2A) receptor outlasted the initial 24-h period after the final injection. On the basis of present and previous results, we interpret the impairment of associative types of learning in early tests as a reflection of anticholinergic effects of imipramine, while the modifications of habituation of exploration in late tests are likely primarily to be mediated by imipramine-provoked regulations of serotonergic receptors.

Mania as a dysfunction of reentry: application of Edelman's and Tononi's hypothesis for consciousness in relation to a psychiatric disorder.

The concept of reentry as the most important element in a hypothesis for consciousness proposed by Edelman and Tononi is reviewed. Reentry, is a process of ongoing parallel and recursive signalling between separate neuronal groups along parallel reciprocally fibers that link these groups anatomically. Reentry alters the activity of the target areas it interconnects until a synchronous activity across these areas is created, this may be the direct biological mechanism of consciousness. The repetitive process of reentry may explain how the millisecond time scale of neural signalling is turned into the time scale of seconds characterizing our impression of the duration of a given content of consciousness. It is suggested that reentry may be faster in mania, and specifically that the repetitive recursive signalling is faster in mania, hereby allowing reentry to produce a conscious state, faster than usual. Faster reentry may on a molecular level be caused by faster propagation of nerve impulses, which may be in accordance with a number of hypotheses where mania is seen as a disorder of ionic conductance, nerve cell excitability, action potential firing, membrane abnormalities, and cortical instability. Also the antiepileptic drugs used to treat mania may point to reentry as a factor in this disorder. On a more integrated level faster reentry processes may explain several of the core symptoms of the manic state. Also the drug induced switch from depression to mania in bipolar patients may be explained by the concept of reentry.

Combinations of genetic data in a study of neuroblastoma risk genotypes.

Analysis of combinations of genetic changes that occur exclusively in patients may be a supplementary strategy to the single-locus strategy used in many genetic studies. The genotypes of 16 SNPs within susceptibility loci for neuroblastoma (NB) were analyzed in a previous study. In the present study, combinations of these genotypes have been analyzed. The theoretical number of combinations of 3 SNP genotypes taken from 16 SNPs is 15,120. Of these, 14,307 were found in 370 patients and 803 controls; 12,772 combinations were common to both patients and controls; 1,213 were found in controls only; and 322 combinations were found in patients only. Among the latter, a cluster of 24 combinations was found to be significantly associated with NB (P < 0.00001).

Genetics of complex diseases: variations on a theme.

A complex disease with an inheritable component is polygenic, meaning that several different changes in DNA are the genetic basis for the disease. Such a disease may also be genetically heterogeneous, meaning that independent changes in DNA, i.e. various genotypes, can be the genetic basis for the disease. Each of these genotypes may be characterized by specific combinations of key genetic changes. It is suggested that even if all key changes are found in genes related to the biology of a certain disease, the number of combinations may be so large that the number of different genotypes may be close to the number of patients suffering from the disease. This hypothesis is based on a study of bipolar disorder.