Objective and Background:
Our aim was to characterize the association of 2 functional sing... more Objective and Background:
Our aim was to characterize the association of 2 functional single nucleotide polymorphisms (rs6311 and rs6314) in the serotonin 2A receptor gene (HTR2A) with severity of depression symptoms in children with autism spectrum disorder. These polymorphisms have been shown to be associated with depression symptom severity and response to selective serotonin reuptake inhibitor drugs in adults with diagnosed depressive disorder.
Methods:
Parents of 104 children with autism spectrum disorder rated their children’s depressive symptoms using a validated scale based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. We compared severity of depression symptoms across the rs6311 and rs6314 genotypes, measured from the children’s genomic DNA.
Results:
Children homozygous for the G allele of rs6311 had significantly more severe depression symptoms than those with G/A or A/A genotypes (P=0.025). The effect size (partial eta-squared) was small (ηp2=0.047) but was somewhat larger when we controlled for severity of generalized anxiety disorder symptoms (P=0.006, ηp2=0.072). When we restricted our analyses to white participants, our results were essentially the same as for the entire sample (P=0.004, ηp2=0.086). There was no significant association between rs6314 (C/C versus T carriers) and severity of depression.
Conclusions:
Our findings suggest that the HTR2A functional rs6311 polymorphism, which other studies have associated with differential HTR2A mRNA expression, may modulate the severity of depression symptoms in children with autism spectrum disorder. These tentative, hypothesis-generating findings need replication with larger, independent samples.
Background
Prefrontal behavior and activity in humans are heritable. Studies in animals demons... more Background
Prefrontal behavior and activity in humans are heritable. Studies in animals demonstrate an interaction between dopamine D2 receptors and nicotinic acetylcholine receptors on prefrontal behavior but evidence in humans is weak. Therefore, we hypothesize that genetic variation regulating dopamine D2 and nicotinic acetylcholine receptor signaling impact prefrontal cortex activity and related cognition. To test this hypothesis in humans, we explored the interaction between functional genetic variants in the D2 receptor gene (DRD2, rs1076560) and in the nicotinic receptor α5 gene (CHRNA5, rs16969968) on both dorsolateral prefrontal cortex mediated behavior and physiology during working memory and on prefrontal gray matter volume.
Methods
A large sample of healthy subjects was compared for genotypic differences for DRD2 rs1076560 (G>T) and CHNRA5 rs16969968 (G>A) on prefrontal phenotypes, including cognitive performance at the N-Back task, prefrontal physiology with BOLD fMRI during performance of the 2-Back working memory task, and prefrontal morphometry with structural MRI.
Results
We found that DRD2 rs1076560 and CHNRA5 rs16969968 interact to modulate cognitive function, prefrontal physiology during working memory, and prefrontal gray matter volume. More specifically, CHRNA5-AA/DRD2-GT subjects had greater behavioral performance, more efficient prefrontal cortex activity at 2Back working memory task, and greater prefrontal gray matter volume than the other genotype groups.
Conclusions
The present data extend previous studies in animals and enhance our understanding of dopamine and acetylcholine signaling in the human prefrontal cortex, demonstrating interactions elicited by working memory that are modulated by genetic variants in DRD2 and CHRNA5.
I read with great interest this article correlating neuroanatomical changes in casual cannabis u... more I read with great interest this article correlating neuroanatomical changes in casual cannabis users versus non-users. However, the authors repeatedly and explicitly state a causative relationship between the cannabis use and the anatomic changes throughout the article, only to state in the second-to-last paragraph that no causative relationship can be concluded due to the cross-sectional design of this study. Even more, the press release from the Society for Neuroscience [1] and the narrative in news stories resulting from this manuscript [2,3] do not explicitly state this very obvious caveat. While the correlative relationship reported here is statistically strong, a longitudinal study design is necessary to make the causative claims throughout the first 29 paragraphs and abstract of this manuscript. Again, this very critical distinction in study design is not noted until the end of the manuscript. A plausible alternative interpretation of this data is that the neuroanatomical abnormalities predate the drug use and make the individuals more likely to use cannabis. By reversing the causative relationship here, we would suppose that greater anatomical changes would cause increased consumption. With that said, there is abundant evidence showing an empirical link between tetrahydrocannabinol administration and neuroanatomical changes in rodents. However, the repeated claims of a causative relationship in this manuscript and related press articles are not warranted based solely on the results reported here.
References
[1]. Society for Neuroscience Press Release. "BRAIN CHANGES ARE ASSOCIATED WITH CASUAL MARIJUANA USE IN YOUNG ADULTS". Accessed April 16th, 2014 at http://www.sfn.org/Press-Room/News-Release- Archives/2014/Brain-Changes-Are-Associated-with-Casual-Marijuana-Use-in- Young-Adults
The serotonin 2A receptor gene (HTR2A) harbors two functional single nucleotide polymorphisms (SN... more The serotonin 2A receptor gene (HTR2A) harbors two functional single nucleotide polymorphisms (SNPs) that are frequent in populations of African and European descent; rs6311, which affects mRNA expression, and rs6314, which changes the amino acid sequence of the encoded protein and affects the signaling properties of the receptor. Multiple clinical associations support a role for these SNPs in cognitive and neuropsychiatric phenotypes, although studies in autism spectrum disorder (ASD) remain equivocal. Here, we tested transmission disequilibrium of rs6311 and rs6314 in a cohort of 158 ASD trios (simplex and multiplex), observing significant under-transmission of the minor “A” allele of rs6311 to offspring with ASD (permuted P = 0.0004). Consistent with our previous findings in the dorsolateral prefrontal cortex of unaffected individuals, rs6311/A decreases expression of HTR2A mRNA with an extended 5′ untranslated region (UTR) in the frontopolar cortex in brain samples from 54 ASD patients and controls. Interpreting the clinical results in the context of our mRNA expression analysis, we speculate that any risk associated with rs6311 is conferred by greater expression of the long 5′UTR mRNA isoform. The current study corroborates earlier associations between rs6311 and ASD in a family study, supporting the hypothesis that rs6311 plays a modulatory role in ASD risk.
Background
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-ac... more Background
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals.
Results
We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals.
Conclusions
These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
The integration of research on neuroimaging and pharmacogenetics holds promise for improving trea... more The integration of research on neuroimaging and pharmacogenetics holds promise for improving treatment for neuropsychiatric conditions. Neuroimaging may provide a more sensitive early measure of treatment response in genetically defined patient groups, and could facilitate development of novel therapies based on an improved understanding of pathogenic mechanisms underlying pharmacogenetic associations. This review summarizes progress in efforts to incorporate neuroimaging into genetics and treatment research on major psychiatric disorders such as schizophrenia, major depressive disorder, bipolar disorder, attention-deficit/hyperactivity disorder, and addiction. Methodological challenges include: performing genetic analyses in small study populations used in imaging studies; inclusion of patients with psychiatric comorbidities; and the extensive variability across studies in neuroimaging protocols, neurobehavioral task probes, and analytic strategies. Moreover, few studies use pharmacogenetic designs that permit testing of genotype x drug effects. As a result of these limitations, few findings have been fully replicated. Future studies that pre-screen participants for genetic variants selected a priori based on drug metabolism and targets have the greatest potential to advance the science and practice of psychiatric treatment.
""Background
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic ta... more ""Background
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic target for serotonin in the human brain and a therapeutic drug target. Despite hundreds of genetic associations investigating HTR2A polymorphisms in neuropsychiatric disorders and therapies, the role of genetic HTR2A variability in health and disease remains uncertain.
Methods
To discover and characterize regulatory HTR2A variants, we sequenced whole transcriptomes from 10 human brain regions with massively parallel RNA sequencing and measured allelic expression of multiple HTR2A messenger (m)RNA transcript variants. Following discovery of functional variants, we further characterized their impact on genetic expression in vitro.
Results
Three polymorphisms modulate the use of novel alternative exons and untranslated regions (UTRs), changing expression of RNA and protein. The frequent promoter variant rs6311, widely implicated in human neuropsychiatric disorders, decreases usage of an upstream transcription start site encoding a longer 5′UTR with greater translation efficiency. rs76665058, located in an extended 3′UTR and unique to individuals of African descent, modulates allelic HTR2A mRNA expression. The third single nucleotide polymorphism, unannotated and present in only a single subject, directs alternative splicing of exon 2. Targeted analysis of HTR2A in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study reveals associations between functional variants and depression severity or citalopram response.
Conclusions
Regulatory polymorphisms modulate HTR2A mRNA expression in an isoform-specific manner, directing the usage of novel untranslated regions and alternative exons. These results provide a foundation for delineating the role of HTR2A and serotonin signaling in central nervous system disorders.""
Most protein coding genes generate multiple RNA transcripts through alternative splicing, variabl... more Most protein coding genes generate multiple RNA transcripts through alternative splicing, variable 3' and 5'UTRs, and RNA editing. While drug design typically targets the main transcript, alternative transcripts can have profound physiological effects, encoding proteins with distinct functions or regulatory properties. Formation of these alternative transcripts is tissue-selective and context-dependent, creating opportunities for more effective and targeted therapies with reduced adverse effects. Moreover, genetic variation can tilt the balance of alternative versus constitutive transcripts or generate aberrant transcripts that contribute to disease risk. Additionally, environmental factors and drugs modulate RNA splicing, affording new opportunities for the treatment of splicing disorders. For example, therapies targeting specific mRNA transcripts with splice-site directed oligonucleotides that correct aberrant splicing are already in clinical trials for genetic disorders such as Duchenne muscular dystrophy. High-throughput sequencing technologies facilitate discovery of novel RNA transcripts and protein isoforms, with applications ranging from neuromuscular disorders to cancer. Consideration of a gene’s transcript diversity should become an integral part of drug design, development, and therapy.
The dopamine receptor D2 (encoded by DRD2) is implicated in susceptibility to mental disorders an... more The dopamine receptor D2 (encoded by DRD2) is implicated in susceptibility to mental disorders and cocaine abuse, but mechanisms responsible for this relationship remain uncertain. DRD2 mRNA exists in two main splice isoforms with distinct functions: D2 long (D2L) and D2 short (D2S, lacking exon 6), expressed mainly postsynaptically and presynaptically, respectively. Two intronic single-nucleotide polymorphisms (SNPs rs2283265 (intron 5) and rs1076560 (intron 6)) in high linkage disequilibrium (LD) with each other have been reported to alter D2S/D2L splicing and several behavioral traits in human subjects, such as memory processing. To assess the role of DRD2 variants in cocaine abuse, we measured levels of D2S and D2L mRNA in human brain autopsy tissues (prefrontal cortex and putamen) obtained from cocaine abusers and controls, and genotyped a panel of DRD2 SNPs (119 abusers and 95 controls). Robust effects of rs2283265 and rs1076560 on reducing formation of D2S relative to D2L were confirmed. The minor alleles of rs2283265/rs1076560 were considerably more frequent in Caucasians (18%) compared with African Americans (7%). Also, in Caucasians, rs2283265/rs1076560 minor alleles were significantly overrepresented in cocaine abusers compared with controls (rs2283265: 25 to 9%, respectively; p=0.001; OR=3.4 (1.7-7.1)). Several SNPs previously implicated in diverse clinical association studies are in high LD with rs2283265/rs1076560 and could have served as surrogate markers. Our results confirm the role of rs2283265/rs1076560 in D2 alternative splicing and support a strong role in susceptibility to cocaine abuse.
The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms ar... more The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms are promising biomarkers that have proven difficult to uncover. They come in two flavors: those that affect transcription (regulatory single-nucleotide polymorphisms (rSNPs)) and those that affect RNA functions such as splicing, turnover, and translation (termed structural RNA SNPs (srSNPs)). This review focuses on the role of srSNPs in drug metabolism, transport, and response. An understanding of the nature and diversity of srSNPs and rSNPs enables clinical scientists to evaluate genetic biomarkers.
Interactions between presynaptic and postsynaptic cellular adhesion molecules (CAMs) drive synaps... more Interactions between presynaptic and postsynaptic cellular adhesion molecules (CAMs) drive synapse maturation during development. These trans-synaptic interactions are regulated by alternative splicing of CAM RNAs, which ultimately determines neurotransmitter phenotype. The diverse assortment of RNAs produced by alternative splicing generates countless protein isoforms necessary for guiding specialized cell-to-cell connectivity. Failure to generate the appropriate synaptic adhesion proteins is associated with disrupted glutamatergic and gamma-aminobutyric acid signaling, resulting in loss of activity-dependent neuronal plasticity, and risk for developmental disorders, including autism. While the majority of genetic mutations currently linked to autism are rare variants that change the protein-coding sequence of synaptic candidate genes, regulatory polymorphisms affecting constitutive and alternative splicing have emerged as risk factors in numerous other diseases, accounting for an estimated 40–60% of general disease risk. Here, we review the relationship between aberrant RNA splicing of synapse-related genes and autism spectrum disorders.
CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotin... more CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotine addiction and lung cancer. Previous studies demonstrate significant associations between promoter polymorphisms and CHRNA5 mRNA expression, but the responsible sequence variants remain uncertain. To search for cis-regulatory variants, we measured allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanned the CHRNA5 locus for regulatory variants. A cluster of six frequent single-nucleotide polymorphisms (rs1979905, rs1979906, rs1979907, rs880395, rs905740, and rs7164030), in complete linkage disequilibrium (LD), fully account for a >2.5-fold allelic expression difference and a fourfold increase in overall CHRNA5 mRNA expression. This proposed enhancer region resides more than 13 kilobases upstream of the CHRNA5 transcription start site. The same upstream variants failed to affect CHRNA5 mRNA expression in peripheral blood lymphocytes, indicating tissue-specific gene regulation. Other promoter polymorphisms were also correlated with overall CHRNA5 mRNA expression in the brain, but were inconsistent with allelic mRNA expression ratios, a robust and proximate measure of cis-regulatory variants. The enhancer region and the nonsynonymous polymorphism rs16969968 generate three main haplotypes that alter the risk of developing nicotine dependence. Ethnic differences in LD across the CHRNA5 locus require consideration of upstream enhancer variants when testing clinical associations.
Several studies suggest that prenatal stress is a possible risk factor in the development of auti... more Several studies suggest that prenatal stress is a possible risk factor in the development of autism spectrum disorders. However, many children exposed to stress prenatally are born healthy and develop typically, suggesting that other factors must contribute to autism. Genes that contribute to stress reactivity may, therefore, exacerbate prenatal stress-mediated behavioral changes in the adult offspring. One candidate gene linked to increased stress reactivity encodes the serotonin transporter. Specifically, an insertion/deletion (long/short allele) polymorphism upstream of the serotonin transporter gene correlates with differential expression and function of the serotonin transporter and a heightened response to stressors. Heterozygous serotonin transporter knockout mice show reductions in serotonin transporter expression similar to the human short polymorphism. In this study, the role of prenatal stress and maternal serotonin transporter genotype were assessed in mice to determine whether their combined effect produces reductions in social behavior in the adult offspring. Pregnant serotonin transporter heterozygous knockout and wild-type dams were placed in either a control condition or subjected to chronic variable stress. The adult offspring were subsequently assessed for social interaction and anxiety using a three-chamber social approach task, ultrasonic vocalization detection, elevated-plus maze and an open field task. Results indicated that prenatal stress and reduced serotonin transporter expression of the dam may have the combined effect of producing changes in social interaction and social interest in the offspring consistent with those observed in autism spectrum disorder. This data indicates a possible combined effect of maternal serotonin transporter genotype and prenatal stress contributing to the production of autistic-like behaviors in offspring.
Semantic and episodic memory networks function as highly interconnected systems, both relying on ... more Semantic and episodic memory networks function as highly interconnected systems, both relying on the hippocampal/medial temporal lobe complex (HC/MTL). Episodic memory encoding triggers the retrieval of semantic information, serving to incorporate contextual relationships between the newly acquired memory and existing semantic representations. While emotional material augments episodic memory encoding at the time of stimulus presentation, interactions between emotion and semantic memory that contribute to subsequent episodic recall are not well understood. Using a modified oddball task, we examined the modulatory effects of negative emotion on semantic interactions with episodic memory by measuring the free-recall of serially presented neutral or negative words varying in semantic relatedness. We found increased free-recall for words related to and preceding emotionally negative oddballs, suggesting that negative emotion can indirectly facilitate episodic free-recall by enhancing semantic contributions during encoding. Our findings demonstrate the ability of emotion and semantic memory to interact to mutually enhance free-recall.
"OBJECTIVES:
Our purpose is to investigate cognitive performance and extrapyramidal function ear... more "OBJECTIVES:
Our purpose is to investigate cognitive performance and extrapyramidal function early after ecstasy use.
BACKGROUND:
Ecstasy, containing 3,4 methylenedioxymethamphetamine, has shown evidence of causing cognitive deficits and parkinsonian signs. Previous research has examined cognitive performance after a period of prolonged abstinence, but research assessing the early effects of ecstasy after recent use is limited despite temporal neurochemical differences demonstrated in nonhuman models.
METHODS:
This study compared task performance between 13 ecstasy users (10 to 15 h postdrug use) and a control group on a battery of neuropsychologic assessments while matching for education level, sleep deprivation, and premorbid IQ. The groups were also compared on measures relating to parkinsonian signs.
RESULTS:
The ecstasy subjects showed impairments on measures of executive function as evaluated by Raven's Standard Progressive Matrices (SPM) and the Wisconsin Card Sorting Task (WCST). Short-delay free recall memory was also impaired in ecstasy subjects on the California Verbal Learning Test (CVLT-II). No extrapyramidal motor impairments were detected.
CONCLUSIONS:
These deficits resemble deficits previously reported in chronic ecstasy use but also seem to reveal transient impairments in executive function. Future research is needed to better understand the neurologic and neuropsychologic implications of ecstasy use across time and extent of use."
Stress-induced activation of the locus ceruleus-norepinephrine (LC-NE) system produces significan... more Stress-induced activation of the locus ceruleus-norepinephrine (LC-NE) system produces significant cognitive and behavioral effects, including enhanced arousal and attention. Improvements in discrimination task performance and memory have been attributed to this stress response. In contrast, for other cognitive functions that require cognitive flexibility, increased activity of the LC-NE system may produce deleterious effects. The aim of the present study was to determine the effect of pharmacological modulation of the LC-NE system on stress-induced impairments in cognitive flexibility performance in healthy individuals. Cognitive performance, plus psychological and physiological parameters for 16 adults without any history of anxiety disorders, was assessed during four test sessions: stress and no-stress, with each condition tested after administration of propranolol and placebo. The Trier Social Stress Test, a public-speaking and mental arithmetic stressor, was presented to participants for the stress sessions, whereas a similar, but nonstressful, control task (reading, counting) was utilized for the no-stress sessions. Tests of cognitive flexibility included lexical-semantic and associative problem-solving tasks (anagrams, Compound Remote Associates Test). Visuo-spatial memory and motor processing speed tests served as control tasks. Results indicate that (1) stress impaired performance on cognitive flexibility tasks, but not control tasks; (2) compared to placebo, cognitive flexibility improved during stress with propranolol. Therefore, psychological stress, such as public speaking, negatively impacts performance on tasks requiring cognitive flexibility in normal individuals, and this effect is reversed by beta-adrenergic antagonism. This may provide support for the hypothesis that stress-related impairments in cognitive flexibility are related to the noradrenergic system.
Introduction: Genetic variants within nicotinic receptors have been shown to modulate an individu... more Introduction: Genetic variants within nicotinic receptors have been shown to modulate an individual’s risk for nicotine dependence. Among the most reproducible risk factor is a non-synonymous polymorphism (rs16969968) within the alpha5 nicotinic receptor subunit gene, CHRNA5. Genetic factors also contribute to CHRNA5 mRNA expression and risk for substance abuse, but the specific variants responsible for changes in mRNA expression are unclear. Methodology: To determine the presence of cis-acting functional genetic variants contributing to CHRNA5 mRNA expression, we measured allelic expression of CHRNA5 within post-mortem human prefrontal cortex brain tissue. Using allelic expression as a phenotype, we scanned the CHRNA5 gene locus for polymorphisms responsible for imbalanced allelic expression. Polymorphisms determined to be responsible for allelic expression were genotyped in our full brain cohort and total CHRNA5 expression was compared across genotype using quantitative PCR. We then tested these expression-related variants for clinical association with nicotine dependence. Results: We uncovered a functional genetic locus 13.5kb upstream of CHRNA5 acting as an enhancer of CHRNA5 mRNA expression. Minor allele carriers for enhancer variants displayed >2- fold differences in allelic expression, while individuals homozygous for the enhancer minor alleles expressed >4-fold more cortical CHRNA5 mRNA. Haplotype structure analysis predicts that the enhancer SNPs rarely occur on the same allele as the previously implicated non-synonymous variant. Taking into account this relationship, enhancer region SNPs confer significant risk only when you control for the presence of the non-synonymous variant in a joint SNP analysis. Conclusions: Polymorphisms within a transcriptional enhancer located 13.5kb upstream of CHRNA5 modulate CHRNA5 mRNA transcription. These enhancer variants confer risk for nicotine dependence in a context-dependent manner. Understanding the biological functions of these clinically relevant genetic variants revealed a SNP-SNP interaction increasing risk for nicotine dependence that is otherwise obscured by haplotype structure when using traditional clinical association methods. These findings aid in the construction of complex biological or genetic models of nicotine dependence that mimic human factors. The relevance of the enhancer CHRNA5 polymorphism in other brain regions and peripheral tissues (e.g., the lung) needs further study. Moreover, identification of functional CHRNA5 variants facilitates the analysis of gene-gene interactions with respect to nicotine and other drug addictions.
Background: Clinical genetic association studies and gene sequencing frequently implicate cellula... more Background: Clinical genetic association studies and gene sequencing frequently implicate cellular adhesion molecules, such as neurexins and neuroligins, as autism risk genes. These genes can regulate the maturation of glutamatergic and GABAergic synapses based on the expression of alternatively spliced mRNA transcripts. Often, the consequence of diseas eassociated variants in cellular adhesion molecules is marked changes in synapse structure and/or function, especially relating to glutamatergic or GABAergic signaling. Objectives: The goal of this study is to uncover cis-acting variants responsible for directing mRNA expression by measuring allelic expression of genes related to synapse structure and signaling in human frontopolar cortex tissue from autistic patients and typically-developed controls. Methods: mRNA and genomic DNA was isolated from 56 postmortem frontopolar cortex tissues provided by the Autism Tissue Program. Allele-specific expression was measured via quantitative SNaPshot for synapse-related genes CNTNAP2, CNTN4, DLG4, EPB41L1, NRCAM, and PCDH9; glutamatergic and GABAergic genes GABRB3, GAD1, GRIA2, GRM5, SLC1A1, SLC1A2, SLC25A12, and SLC6A1, and alternative splicing genes HNRNPA3, NCBP2, NOVA1, RBFOX1, and SF4. Results: Significant and robust allelic expression differences were observed for CNTNAP2, DLG4, EPB41L1, NRCAM, GAD1, GRIA2, SLC1A1, RBFOX1, HNRNPA3, NOVA1, and SF4, suggesting the presence of cis-acting functional variants responsible for modulated mRNA expression in these genes. For most genes, including DLG4, EPB41L1, NRCAM, GAD1, GRIA2, and RBFOX1, significant allelic differences were only observed in a small number of autistic patients, suggesting the variants responsible for directing differential mRNA expression of these genes are rare. In contrast, significant allelic expression differences for SLC1A1 and CNTNAP2 were observed for multiple samples from both the ASD and control cohorts, suggesting the presence of common cis-acting functional variants driving expression of these genes. Conclusions: Differential mRNA expression of numerous genes pertinent to synapse structure and function are driven by cis-acting genetic factors. For some genes, the responsible genetic factors appear to be rare and we observed their presence only in brain samples from autistic patients. This scenario fits the hypothesis that highly-penetrant rare mutations could be responsible for producing autistic phenotypes. In contrast, the presence of common functional variants in CNTNAP2 and SLC1A1 in both autism and control cohorts argue for the role of disorder-modifying genetic variants in these genes, with the ability to affect either language (CNTNAP2) or restrictive and repetitive behaviors (SLC1A1). Further studies are necessary to evaluate the clinical relevance of expression-related functional variants in autism.
Objective and Background:
Our aim was to characterize the association of 2 functional sing... more Objective and Background:
Our aim was to characterize the association of 2 functional single nucleotide polymorphisms (rs6311 and rs6314) in the serotonin 2A receptor gene (HTR2A) with severity of depression symptoms in children with autism spectrum disorder. These polymorphisms have been shown to be associated with depression symptom severity and response to selective serotonin reuptake inhibitor drugs in adults with diagnosed depressive disorder.
Methods:
Parents of 104 children with autism spectrum disorder rated their children’s depressive symptoms using a validated scale based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. We compared severity of depression symptoms across the rs6311 and rs6314 genotypes, measured from the children’s genomic DNA.
Results:
Children homozygous for the G allele of rs6311 had significantly more severe depression symptoms than those with G/A or A/A genotypes (P=0.025). The effect size (partial eta-squared) was small (ηp2=0.047) but was somewhat larger when we controlled for severity of generalized anxiety disorder symptoms (P=0.006, ηp2=0.072). When we restricted our analyses to white participants, our results were essentially the same as for the entire sample (P=0.004, ηp2=0.086). There was no significant association between rs6314 (C/C versus T carriers) and severity of depression.
Conclusions:
Our findings suggest that the HTR2A functional rs6311 polymorphism, which other studies have associated with differential HTR2A mRNA expression, may modulate the severity of depression symptoms in children with autism spectrum disorder. These tentative, hypothesis-generating findings need replication with larger, independent samples.
Background
Prefrontal behavior and activity in humans are heritable. Studies in animals demons... more Background
Prefrontal behavior and activity in humans are heritable. Studies in animals demonstrate an interaction between dopamine D2 receptors and nicotinic acetylcholine receptors on prefrontal behavior but evidence in humans is weak. Therefore, we hypothesize that genetic variation regulating dopamine D2 and nicotinic acetylcholine receptor signaling impact prefrontal cortex activity and related cognition. To test this hypothesis in humans, we explored the interaction between functional genetic variants in the D2 receptor gene (DRD2, rs1076560) and in the nicotinic receptor α5 gene (CHRNA5, rs16969968) on both dorsolateral prefrontal cortex mediated behavior and physiology during working memory and on prefrontal gray matter volume.
Methods
A large sample of healthy subjects was compared for genotypic differences for DRD2 rs1076560 (G>T) and CHNRA5 rs16969968 (G>A) on prefrontal phenotypes, including cognitive performance at the N-Back task, prefrontal physiology with BOLD fMRI during performance of the 2-Back working memory task, and prefrontal morphometry with structural MRI.
Results
We found that DRD2 rs1076560 and CHNRA5 rs16969968 interact to modulate cognitive function, prefrontal physiology during working memory, and prefrontal gray matter volume. More specifically, CHRNA5-AA/DRD2-GT subjects had greater behavioral performance, more efficient prefrontal cortex activity at 2Back working memory task, and greater prefrontal gray matter volume than the other genotype groups.
Conclusions
The present data extend previous studies in animals and enhance our understanding of dopamine and acetylcholine signaling in the human prefrontal cortex, demonstrating interactions elicited by working memory that are modulated by genetic variants in DRD2 and CHRNA5.
I read with great interest this article correlating neuroanatomical changes in casual cannabis u... more I read with great interest this article correlating neuroanatomical changes in casual cannabis users versus non-users. However, the authors repeatedly and explicitly state a causative relationship between the cannabis use and the anatomic changes throughout the article, only to state in the second-to-last paragraph that no causative relationship can be concluded due to the cross-sectional design of this study. Even more, the press release from the Society for Neuroscience [1] and the narrative in news stories resulting from this manuscript [2,3] do not explicitly state this very obvious caveat. While the correlative relationship reported here is statistically strong, a longitudinal study design is necessary to make the causative claims throughout the first 29 paragraphs and abstract of this manuscript. Again, this very critical distinction in study design is not noted until the end of the manuscript. A plausible alternative interpretation of this data is that the neuroanatomical abnormalities predate the drug use and make the individuals more likely to use cannabis. By reversing the causative relationship here, we would suppose that greater anatomical changes would cause increased consumption. With that said, there is abundant evidence showing an empirical link between tetrahydrocannabinol administration and neuroanatomical changes in rodents. However, the repeated claims of a causative relationship in this manuscript and related press articles are not warranted based solely on the results reported here.
References
[1]. Society for Neuroscience Press Release. "BRAIN CHANGES ARE ASSOCIATED WITH CASUAL MARIJUANA USE IN YOUNG ADULTS". Accessed April 16th, 2014 at http://www.sfn.org/Press-Room/News-Release- Archives/2014/Brain-Changes-Are-Associated-with-Casual-Marijuana-Use-in- Young-Adults
The serotonin 2A receptor gene (HTR2A) harbors two functional single nucleotide polymorphisms (SN... more The serotonin 2A receptor gene (HTR2A) harbors two functional single nucleotide polymorphisms (SNPs) that are frequent in populations of African and European descent; rs6311, which affects mRNA expression, and rs6314, which changes the amino acid sequence of the encoded protein and affects the signaling properties of the receptor. Multiple clinical associations support a role for these SNPs in cognitive and neuropsychiatric phenotypes, although studies in autism spectrum disorder (ASD) remain equivocal. Here, we tested transmission disequilibrium of rs6311 and rs6314 in a cohort of 158 ASD trios (simplex and multiplex), observing significant under-transmission of the minor “A” allele of rs6311 to offspring with ASD (permuted P = 0.0004). Consistent with our previous findings in the dorsolateral prefrontal cortex of unaffected individuals, rs6311/A decreases expression of HTR2A mRNA with an extended 5′ untranslated region (UTR) in the frontopolar cortex in brain samples from 54 ASD patients and controls. Interpreting the clinical results in the context of our mRNA expression analysis, we speculate that any risk associated with rs6311 is conferred by greater expression of the long 5′UTR mRNA isoform. The current study corroborates earlier associations between rs6311 and ASD in a family study, supporting the hypothesis that rs6311 plays a modulatory role in ASD risk.
Background
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-ac... more Background
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals.
Results
We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals.
Conclusions
These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
The integration of research on neuroimaging and pharmacogenetics holds promise for improving trea... more The integration of research on neuroimaging and pharmacogenetics holds promise for improving treatment for neuropsychiatric conditions. Neuroimaging may provide a more sensitive early measure of treatment response in genetically defined patient groups, and could facilitate development of novel therapies based on an improved understanding of pathogenic mechanisms underlying pharmacogenetic associations. This review summarizes progress in efforts to incorporate neuroimaging into genetics and treatment research on major psychiatric disorders such as schizophrenia, major depressive disorder, bipolar disorder, attention-deficit/hyperactivity disorder, and addiction. Methodological challenges include: performing genetic analyses in small study populations used in imaging studies; inclusion of patients with psychiatric comorbidities; and the extensive variability across studies in neuroimaging protocols, neurobehavioral task probes, and analytic strategies. Moreover, few studies use pharmacogenetic designs that permit testing of genotype x drug effects. As a result of these limitations, few findings have been fully replicated. Future studies that pre-screen participants for genetic variants selected a priori based on drug metabolism and targets have the greatest potential to advance the science and practice of psychiatric treatment.
""Background
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic ta... more ""Background
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic target for serotonin in the human brain and a therapeutic drug target. Despite hundreds of genetic associations investigating HTR2A polymorphisms in neuropsychiatric disorders and therapies, the role of genetic HTR2A variability in health and disease remains uncertain.
Methods
To discover and characterize regulatory HTR2A variants, we sequenced whole transcriptomes from 10 human brain regions with massively parallel RNA sequencing and measured allelic expression of multiple HTR2A messenger (m)RNA transcript variants. Following discovery of functional variants, we further characterized their impact on genetic expression in vitro.
Results
Three polymorphisms modulate the use of novel alternative exons and untranslated regions (UTRs), changing expression of RNA and protein. The frequent promoter variant rs6311, widely implicated in human neuropsychiatric disorders, decreases usage of an upstream transcription start site encoding a longer 5′UTR with greater translation efficiency. rs76665058, located in an extended 3′UTR and unique to individuals of African descent, modulates allelic HTR2A mRNA expression. The third single nucleotide polymorphism, unannotated and present in only a single subject, directs alternative splicing of exon 2. Targeted analysis of HTR2A in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study reveals associations between functional variants and depression severity or citalopram response.
Conclusions
Regulatory polymorphisms modulate HTR2A mRNA expression in an isoform-specific manner, directing the usage of novel untranslated regions and alternative exons. These results provide a foundation for delineating the role of HTR2A and serotonin signaling in central nervous system disorders.""
Most protein coding genes generate multiple RNA transcripts through alternative splicing, variabl... more Most protein coding genes generate multiple RNA transcripts through alternative splicing, variable 3' and 5'UTRs, and RNA editing. While drug design typically targets the main transcript, alternative transcripts can have profound physiological effects, encoding proteins with distinct functions or regulatory properties. Formation of these alternative transcripts is tissue-selective and context-dependent, creating opportunities for more effective and targeted therapies with reduced adverse effects. Moreover, genetic variation can tilt the balance of alternative versus constitutive transcripts or generate aberrant transcripts that contribute to disease risk. Additionally, environmental factors and drugs modulate RNA splicing, affording new opportunities for the treatment of splicing disorders. For example, therapies targeting specific mRNA transcripts with splice-site directed oligonucleotides that correct aberrant splicing are already in clinical trials for genetic disorders such as Duchenne muscular dystrophy. High-throughput sequencing technologies facilitate discovery of novel RNA transcripts and protein isoforms, with applications ranging from neuromuscular disorders to cancer. Consideration of a gene’s transcript diversity should become an integral part of drug design, development, and therapy.
The dopamine receptor D2 (encoded by DRD2) is implicated in susceptibility to mental disorders an... more The dopamine receptor D2 (encoded by DRD2) is implicated in susceptibility to mental disorders and cocaine abuse, but mechanisms responsible for this relationship remain uncertain. DRD2 mRNA exists in two main splice isoforms with distinct functions: D2 long (D2L) and D2 short (D2S, lacking exon 6), expressed mainly postsynaptically and presynaptically, respectively. Two intronic single-nucleotide polymorphisms (SNPs rs2283265 (intron 5) and rs1076560 (intron 6)) in high linkage disequilibrium (LD) with each other have been reported to alter D2S/D2L splicing and several behavioral traits in human subjects, such as memory processing. To assess the role of DRD2 variants in cocaine abuse, we measured levels of D2S and D2L mRNA in human brain autopsy tissues (prefrontal cortex and putamen) obtained from cocaine abusers and controls, and genotyped a panel of DRD2 SNPs (119 abusers and 95 controls). Robust effects of rs2283265 and rs1076560 on reducing formation of D2S relative to D2L were confirmed. The minor alleles of rs2283265/rs1076560 were considerably more frequent in Caucasians (18%) compared with African Americans (7%). Also, in Caucasians, rs2283265/rs1076560 minor alleles were significantly overrepresented in cocaine abusers compared with controls (rs2283265: 25 to 9%, respectively; p=0.001; OR=3.4 (1.7-7.1)). Several SNPs previously implicated in diverse clinical association studies are in high LD with rs2283265/rs1076560 and could have served as surrogate markers. Our results confirm the role of rs2283265/rs1076560 in D2 alternative splicing and support a strong role in susceptibility to cocaine abuse.
The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms ar... more The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms are promising biomarkers that have proven difficult to uncover. They come in two flavors: those that affect transcription (regulatory single-nucleotide polymorphisms (rSNPs)) and those that affect RNA functions such as splicing, turnover, and translation (termed structural RNA SNPs (srSNPs)). This review focuses on the role of srSNPs in drug metabolism, transport, and response. An understanding of the nature and diversity of srSNPs and rSNPs enables clinical scientists to evaluate genetic biomarkers.
Interactions between presynaptic and postsynaptic cellular adhesion molecules (CAMs) drive synaps... more Interactions between presynaptic and postsynaptic cellular adhesion molecules (CAMs) drive synapse maturation during development. These trans-synaptic interactions are regulated by alternative splicing of CAM RNAs, which ultimately determines neurotransmitter phenotype. The diverse assortment of RNAs produced by alternative splicing generates countless protein isoforms necessary for guiding specialized cell-to-cell connectivity. Failure to generate the appropriate synaptic adhesion proteins is associated with disrupted glutamatergic and gamma-aminobutyric acid signaling, resulting in loss of activity-dependent neuronal plasticity, and risk for developmental disorders, including autism. While the majority of genetic mutations currently linked to autism are rare variants that change the protein-coding sequence of synaptic candidate genes, regulatory polymorphisms affecting constitutive and alternative splicing have emerged as risk factors in numerous other diseases, accounting for an estimated 40–60% of general disease risk. Here, we review the relationship between aberrant RNA splicing of synapse-related genes and autism spectrum disorders.
CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotin... more CHRNA5, encoding the nicotinic α5 subunit, is implicated in multiple disorders, including nicotine addiction and lung cancer. Previous studies demonstrate significant associations between promoter polymorphisms and CHRNA5 mRNA expression, but the responsible sequence variants remain uncertain. To search for cis-regulatory variants, we measured allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanned the CHRNA5 locus for regulatory variants. A cluster of six frequent single-nucleotide polymorphisms (rs1979905, rs1979906, rs1979907, rs880395, rs905740, and rs7164030), in complete linkage disequilibrium (LD), fully account for a >2.5-fold allelic expression difference and a fourfold increase in overall CHRNA5 mRNA expression. This proposed enhancer region resides more than 13 kilobases upstream of the CHRNA5 transcription start site. The same upstream variants failed to affect CHRNA5 mRNA expression in peripheral blood lymphocytes, indicating tissue-specific gene regulation. Other promoter polymorphisms were also correlated with overall CHRNA5 mRNA expression in the brain, but were inconsistent with allelic mRNA expression ratios, a robust and proximate measure of cis-regulatory variants. The enhancer region and the nonsynonymous polymorphism rs16969968 generate three main haplotypes that alter the risk of developing nicotine dependence. Ethnic differences in LD across the CHRNA5 locus require consideration of upstream enhancer variants when testing clinical associations.
Several studies suggest that prenatal stress is a possible risk factor in the development of auti... more Several studies suggest that prenatal stress is a possible risk factor in the development of autism spectrum disorders. However, many children exposed to stress prenatally are born healthy and develop typically, suggesting that other factors must contribute to autism. Genes that contribute to stress reactivity may, therefore, exacerbate prenatal stress-mediated behavioral changes in the adult offspring. One candidate gene linked to increased stress reactivity encodes the serotonin transporter. Specifically, an insertion/deletion (long/short allele) polymorphism upstream of the serotonin transporter gene correlates with differential expression and function of the serotonin transporter and a heightened response to stressors. Heterozygous serotonin transporter knockout mice show reductions in serotonin transporter expression similar to the human short polymorphism. In this study, the role of prenatal stress and maternal serotonin transporter genotype were assessed in mice to determine whether their combined effect produces reductions in social behavior in the adult offspring. Pregnant serotonin transporter heterozygous knockout and wild-type dams were placed in either a control condition or subjected to chronic variable stress. The adult offspring were subsequently assessed for social interaction and anxiety using a three-chamber social approach task, ultrasonic vocalization detection, elevated-plus maze and an open field task. Results indicated that prenatal stress and reduced serotonin transporter expression of the dam may have the combined effect of producing changes in social interaction and social interest in the offspring consistent with those observed in autism spectrum disorder. This data indicates a possible combined effect of maternal serotonin transporter genotype and prenatal stress contributing to the production of autistic-like behaviors in offspring.
Semantic and episodic memory networks function as highly interconnected systems, both relying on ... more Semantic and episodic memory networks function as highly interconnected systems, both relying on the hippocampal/medial temporal lobe complex (HC/MTL). Episodic memory encoding triggers the retrieval of semantic information, serving to incorporate contextual relationships between the newly acquired memory and existing semantic representations. While emotional material augments episodic memory encoding at the time of stimulus presentation, interactions between emotion and semantic memory that contribute to subsequent episodic recall are not well understood. Using a modified oddball task, we examined the modulatory effects of negative emotion on semantic interactions with episodic memory by measuring the free-recall of serially presented neutral or negative words varying in semantic relatedness. We found increased free-recall for words related to and preceding emotionally negative oddballs, suggesting that negative emotion can indirectly facilitate episodic free-recall by enhancing semantic contributions during encoding. Our findings demonstrate the ability of emotion and semantic memory to interact to mutually enhance free-recall.
"OBJECTIVES:
Our purpose is to investigate cognitive performance and extrapyramidal function ear... more "OBJECTIVES:
Our purpose is to investigate cognitive performance and extrapyramidal function early after ecstasy use.
BACKGROUND:
Ecstasy, containing 3,4 methylenedioxymethamphetamine, has shown evidence of causing cognitive deficits and parkinsonian signs. Previous research has examined cognitive performance after a period of prolonged abstinence, but research assessing the early effects of ecstasy after recent use is limited despite temporal neurochemical differences demonstrated in nonhuman models.
METHODS:
This study compared task performance between 13 ecstasy users (10 to 15 h postdrug use) and a control group on a battery of neuropsychologic assessments while matching for education level, sleep deprivation, and premorbid IQ. The groups were also compared on measures relating to parkinsonian signs.
RESULTS:
The ecstasy subjects showed impairments on measures of executive function as evaluated by Raven's Standard Progressive Matrices (SPM) and the Wisconsin Card Sorting Task (WCST). Short-delay free recall memory was also impaired in ecstasy subjects on the California Verbal Learning Test (CVLT-II). No extrapyramidal motor impairments were detected.
CONCLUSIONS:
These deficits resemble deficits previously reported in chronic ecstasy use but also seem to reveal transient impairments in executive function. Future research is needed to better understand the neurologic and neuropsychologic implications of ecstasy use across time and extent of use."
Stress-induced activation of the locus ceruleus-norepinephrine (LC-NE) system produces significan... more Stress-induced activation of the locus ceruleus-norepinephrine (LC-NE) system produces significant cognitive and behavioral effects, including enhanced arousal and attention. Improvements in discrimination task performance and memory have been attributed to this stress response. In contrast, for other cognitive functions that require cognitive flexibility, increased activity of the LC-NE system may produce deleterious effects. The aim of the present study was to determine the effect of pharmacological modulation of the LC-NE system on stress-induced impairments in cognitive flexibility performance in healthy individuals. Cognitive performance, plus psychological and physiological parameters for 16 adults without any history of anxiety disorders, was assessed during four test sessions: stress and no-stress, with each condition tested after administration of propranolol and placebo. The Trier Social Stress Test, a public-speaking and mental arithmetic stressor, was presented to participants for the stress sessions, whereas a similar, but nonstressful, control task (reading, counting) was utilized for the no-stress sessions. Tests of cognitive flexibility included lexical-semantic and associative problem-solving tasks (anagrams, Compound Remote Associates Test). Visuo-spatial memory and motor processing speed tests served as control tasks. Results indicate that (1) stress impaired performance on cognitive flexibility tasks, but not control tasks; (2) compared to placebo, cognitive flexibility improved during stress with propranolol. Therefore, psychological stress, such as public speaking, negatively impacts performance on tasks requiring cognitive flexibility in normal individuals, and this effect is reversed by beta-adrenergic antagonism. This may provide support for the hypothesis that stress-related impairments in cognitive flexibility are related to the noradrenergic system.
Introduction: Genetic variants within nicotinic receptors have been shown to modulate an individu... more Introduction: Genetic variants within nicotinic receptors have been shown to modulate an individual’s risk for nicotine dependence. Among the most reproducible risk factor is a non-synonymous polymorphism (rs16969968) within the alpha5 nicotinic receptor subunit gene, CHRNA5. Genetic factors also contribute to CHRNA5 mRNA expression and risk for substance abuse, but the specific variants responsible for changes in mRNA expression are unclear. Methodology: To determine the presence of cis-acting functional genetic variants contributing to CHRNA5 mRNA expression, we measured allelic expression of CHRNA5 within post-mortem human prefrontal cortex brain tissue. Using allelic expression as a phenotype, we scanned the CHRNA5 gene locus for polymorphisms responsible for imbalanced allelic expression. Polymorphisms determined to be responsible for allelic expression were genotyped in our full brain cohort and total CHRNA5 expression was compared across genotype using quantitative PCR. We then tested these expression-related variants for clinical association with nicotine dependence. Results: We uncovered a functional genetic locus 13.5kb upstream of CHRNA5 acting as an enhancer of CHRNA5 mRNA expression. Minor allele carriers for enhancer variants displayed >2- fold differences in allelic expression, while individuals homozygous for the enhancer minor alleles expressed >4-fold more cortical CHRNA5 mRNA. Haplotype structure analysis predicts that the enhancer SNPs rarely occur on the same allele as the previously implicated non-synonymous variant. Taking into account this relationship, enhancer region SNPs confer significant risk only when you control for the presence of the non-synonymous variant in a joint SNP analysis. Conclusions: Polymorphisms within a transcriptional enhancer located 13.5kb upstream of CHRNA5 modulate CHRNA5 mRNA transcription. These enhancer variants confer risk for nicotine dependence in a context-dependent manner. Understanding the biological functions of these clinically relevant genetic variants revealed a SNP-SNP interaction increasing risk for nicotine dependence that is otherwise obscured by haplotype structure when using traditional clinical association methods. These findings aid in the construction of complex biological or genetic models of nicotine dependence that mimic human factors. The relevance of the enhancer CHRNA5 polymorphism in other brain regions and peripheral tissues (e.g., the lung) needs further study. Moreover, identification of functional CHRNA5 variants facilitates the analysis of gene-gene interactions with respect to nicotine and other drug addictions.
Background: Clinical genetic association studies and gene sequencing frequently implicate cellula... more Background: Clinical genetic association studies and gene sequencing frequently implicate cellular adhesion molecules, such as neurexins and neuroligins, as autism risk genes. These genes can regulate the maturation of glutamatergic and GABAergic synapses based on the expression of alternatively spliced mRNA transcripts. Often, the consequence of diseas eassociated variants in cellular adhesion molecules is marked changes in synapse structure and/or function, especially relating to glutamatergic or GABAergic signaling. Objectives: The goal of this study is to uncover cis-acting variants responsible for directing mRNA expression by measuring allelic expression of genes related to synapse structure and signaling in human frontopolar cortex tissue from autistic patients and typically-developed controls. Methods: mRNA and genomic DNA was isolated from 56 postmortem frontopolar cortex tissues provided by the Autism Tissue Program. Allele-specific expression was measured via quantitative SNaPshot for synapse-related genes CNTNAP2, CNTN4, DLG4, EPB41L1, NRCAM, and PCDH9; glutamatergic and GABAergic genes GABRB3, GAD1, GRIA2, GRM5, SLC1A1, SLC1A2, SLC25A12, and SLC6A1, and alternative splicing genes HNRNPA3, NCBP2, NOVA1, RBFOX1, and SF4. Results: Significant and robust allelic expression differences were observed for CNTNAP2, DLG4, EPB41L1, NRCAM, GAD1, GRIA2, SLC1A1, RBFOX1, HNRNPA3, NOVA1, and SF4, suggesting the presence of cis-acting functional variants responsible for modulated mRNA expression in these genes. For most genes, including DLG4, EPB41L1, NRCAM, GAD1, GRIA2, and RBFOX1, significant allelic differences were only observed in a small number of autistic patients, suggesting the variants responsible for directing differential mRNA expression of these genes are rare. In contrast, significant allelic expression differences for SLC1A1 and CNTNAP2 were observed for multiple samples from both the ASD and control cohorts, suggesting the presence of common cis-acting functional variants driving expression of these genes. Conclusions: Differential mRNA expression of numerous genes pertinent to synapse structure and function are driven by cis-acting genetic factors. For some genes, the responsible genetic factors appear to be rare and we observed their presence only in brain samples from autistic patients. This scenario fits the hypothesis that highly-penetrant rare mutations could be responsible for producing autistic phenotypes. In contrast, the presence of common functional variants in CNTNAP2 and SLC1A1 in both autism and control cohorts argue for the role of disorder-modifying genetic variants in these genes, with the ability to affect either language (CNTNAP2) or restrictive and repetitive behaviors (SLC1A1). Further studies are necessary to evaluate the clinical relevance of expression-related functional variants in autism.
Rapid technological advances have evolved our understanding of human disorders with a complex gen... more Rapid technological advances have evolved our understanding of human disorders with a complex genetic architecture. The identification of candidate genes from association studies allows researchers to investigate how allelic variation impacts expression and function of transcripts. The pathogenesis of several mental illnesses likely involves epistatic interactions between susceptibility genes, each of small effect. Furthermore, interactions may occur across stages of neurodevelopment resulting in diverse clinical manifestations. New tools have increased the potential of psychiatric genetics and given insight into possible causal factors and therapeutic outcomes. This session will highlight intriguing examples of genetic and neuropathologic studies demonstrating the advantages of these approaches. Dr. Thomas Hyde will discuss interactions between a schizophrenia-associated risk allele in GAD1 and the expression of GABA signaling-related transcripts. Carlo Colantuoni will present work on integrated transcriptional patterns in the neocortex with genetic polymorphism data that has gained insight into gene-gene interactions that range from the molecular partnership of individual gene products to the massively complex interplay of genome-wide interaction networks across the lifetime. Ryan Smith will show evidence for allelic mRNA expression differences in genes relating to synaptic signaling that also contribute risk for autism spectrum disorders. Erin Newburn will conclude with work on the DLG4 gene exploring expression of multiple transcripts and allelic associations with diagnosis of schizophrenia and clinical phenotypes. The goal of this session is to demonstrate the variety of approaches that may be used to unravel how multiple genes of small effect act together to produce profound changes in brain structure and function, leading to illnesses such as schizophrenia and autism.
The CHRNA5/A3/B4 gene cluster region on human chromosome 15 has been associated with smoking-rela... more The CHRNA5/A3/B4 gene cluster region on human chromosome 15 has been associated with smoking-related behaviors and/or smoking-related diseases in multiple studies, including age of initiation, “pleasurable buzz” during early experimentation with smoking, cigarettes per day, age-dependent nicotine dependence, nicotine dependence, and lung cancer. In addition, it has been associated with alcohol dependence, level of response to alcohol, and cocaine dependence. Furthermore, a dense coverage of single nucleotide polymorphisms (SNPs) in all CHRN genes has identified multiple distinct loci (independent signals) in the CHRNA5/A3/B4 cluster. Functional work has provided evidence that the risk allele at rs16969968 which changes an amino acid in CHRNA5 leads to decreased response to a nicotine agonist, but it remains unclear what functional SNP(s) might underlie the other genetic signals, and how these different loci may interact within this cluster and/or across other CHRN genes. Progress toward understanding the molecular complexity of the CHRNA5/A3/B4 region and its contribution toward specific drug-related “endophenotypes” will be presented through four ongoing projects. First, Dr. Richard Grucza will provide human genetic data supporting the hypothesis that the RISK allele of rs16969968 for nicotine dependence is a PROTECTIVE allele for cocaine dependence. Dr. Marissa Ehringer will present human genetic data illustrating a possible role of these genes in general disinhibitory behaviors, and in vitro molecular genetic studies of specific SNPs. Ryan Smith has conducted experiments demonstrating allelespecific mRNA expression of the CHRNA5, providing insight into underlying mechanisms which may regulate gene expression. Finally, Dr. Jerry Stitzel will share exciting new findings from mouse genetic studies which support human genetic evidence for gene-gene interaction between CHRNA5 and CHRNA4. Together, these studies highlight the complexity of nicotinic receptor gene regulation and its role in mediating drug-related behaviors. Continued efforts should lead to the development of improved prevention, diagnostic, and treatment approaches for these diseases.
Background: Multiple studies have reported that prenatal stress is a possible risk factor for th... more Background: Multiple studies have reported that prenatal stress is a possible risk factor for the development of autism spectrum disorder (ASD). In rodents, adult rats exposed to prenatal stress display a significant reduction in sociability, a diagnostic hallmark for ASD in humans. Genes that contribute to stress reactivity may, therefore, exacerbate prenatal stress-mediated behavioral changes in the adult offspring. Humans with the short allele of an insertion/deletion polymorphism of the SLC6A4 gene, which reduces the expression and function of the serotonin transporter (SERT), display increased stress reactivity. Some studies also link this gene locus and specific polymorphism to ASD. Heterozygous SERT knockout mice (SERT +/-) show reductions in SERT function and expression similar to the human short polymorphism.
Objectives: We wished to examine the role of SERT function and prenatal stress in mice, in order to determine whether they interact to produce reductions in social behavior in the adult offspring.
Methods: We subjected pregnant SERT +/- dams to chronic variable stress and subsequently tested the adult offspring for sociability using a 3-chamber social approach task (Nadler et al., 2004).
Results: Offspring male SERT +/- mice exposed to prenatal stress displayed reduced social novelty-seeking behavior, as they spent significantly less time socially interacting with a novel versus familiar mouse. Wild-type and unstressed SERT +/- male mice displayed typical social novelty-seeking behavior.
Conclusions: Our findings indicate that prenatal stress may interact with reduced SERT function to produce changes in sociability consistent with those observed in ASD. Given previous research implicating the SERT gene locus and prenatal stress as possible risk factors for ASD, our findings provide evidence for a possible interaction between these environmental and genetic factors that contribute to the production of autistic-like behavior in mice.
Genetic diversity is a major factor driving phenotypic differences between individuals. The w... more Genetic diversity is a major factor driving phenotypic differences between individuals. The wide spectrum of heritable traits ranges from mild personality differences to extreme instances of Mendelian genetic disorders. Consequently, researchers have expended significant resources attempting to find genetic variants that contribute to phenotypic diversity, especially those relating to human disease. Past efforts have been most successful at uncovering highly penetrant mutations that occur in the protein coding regions of genes. Promoter and intronic variants can also have drastic effects on phenotype, with recent estimates suggesting that variants acting at the RNA level contribute to greater than 60% of all genetic disease. Most of these genetic variants affect RNA processing, especially transcript splicing.
Here, I present a series of studies exploring relationships between genetic variants that significantly affect RNA expression and three neurological phenotypes. First, I uncovered a transcription enhancer region contributing to nicotinic α5 receptor subunit mRNA expression and subsequently tested its relationship to nicotine addiction. Next, I revealed a significant correlation between splicing of serotonin 2A receptor mRNA transcripts and a genetic variant implicated in clinical responsiveness to atypical antipsychotics and antidepressants. Finally, in a survey of autism-related risk genes, I uncovered evidence for genetic variations affecting mRNA expression in multiple genes, including cellular adhesion molecules, alternative splicing molecules, and integral components of glutamatergic and gamma-aminobutyric acid signaling. The broad range of neurological phenotypes affected by non-protein coding variants investigated here suggests a pervasive role for RNA processing in human disease. The accumulation of these RNA processing variants throughout human evolution is discussed in the context of human disease.
Uploads
Papers by Ryan Smith
Our aim was to characterize the association of 2 functional single nucleotide polymorphisms (rs6311 and rs6314) in the serotonin 2A receptor gene (HTR2A) with severity of depression symptoms in children with autism spectrum disorder. These polymorphisms have been shown to be associated with depression symptom severity and response to selective serotonin reuptake inhibitor drugs in adults with diagnosed depressive disorder.
Methods:
Parents of 104 children with autism spectrum disorder rated their children’s depressive symptoms using a validated scale based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. We compared severity of depression symptoms across the rs6311 and rs6314 genotypes, measured from the children’s genomic DNA.
Results:
Children homozygous for the G allele of rs6311 had significantly more severe depression symptoms than those with G/A or A/A genotypes (P=0.025). The effect size (partial eta-squared) was small (ηp2=0.047) but was somewhat larger when we controlled for severity of generalized anxiety disorder symptoms (P=0.006, ηp2=0.072). When we restricted our analyses to white participants, our results were essentially the same as for the entire sample (P=0.004, ηp2=0.086). There was no significant association between rs6314 (C/C versus T carriers) and severity of depression.
Conclusions:
Our findings suggest that the HTR2A functional rs6311 polymorphism, which other studies have associated with differential HTR2A mRNA expression, may modulate the severity of depression symptoms in children with autism spectrum disorder. These tentative, hypothesis-generating findings need replication with larger, independent samples.
Prefrontal behavior and activity in humans are heritable. Studies in animals demonstrate an interaction between dopamine D2 receptors and nicotinic acetylcholine receptors on prefrontal behavior but evidence in humans is weak. Therefore, we hypothesize that genetic variation regulating dopamine D2 and nicotinic acetylcholine receptor signaling impact prefrontal cortex activity and related cognition. To test this hypothesis in humans, we explored the interaction between functional genetic variants in the D2 receptor gene (DRD2, rs1076560) and in the nicotinic receptor α5 gene (CHRNA5, rs16969968) on both dorsolateral prefrontal cortex mediated behavior and physiology during working memory and on prefrontal gray matter volume.
Methods
A large sample of healthy subjects was compared for genotypic differences for DRD2 rs1076560 (G>T) and CHNRA5 rs16969968 (G>A) on prefrontal phenotypes, including cognitive performance at the N-Back task, prefrontal physiology with BOLD fMRI during performance of the 2-Back working memory task, and prefrontal morphometry with structural MRI.
Results
We found that DRD2 rs1076560 and CHNRA5 rs16969968 interact to modulate cognitive function, prefrontal physiology during working memory, and prefrontal gray matter volume. More specifically, CHRNA5-AA/DRD2-GT subjects had greater behavioral performance, more efficient prefrontal cortex activity at 2Back working memory task, and greater prefrontal gray matter volume than the other genotype groups.
Conclusions
The present data extend previous studies in animals and enhance our understanding of dopamine and acetylcholine signaling in the human prefrontal cortex, demonstrating interactions elicited by working memory that are modulated by genetic variants in DRD2 and CHRNA5.
References
[1]. Society for Neuroscience Press Release. "BRAIN CHANGES ARE ASSOCIATED WITH CASUAL MARIJUANA USE IN YOUNG ADULTS". Accessed April 16th, 2014 at http://www.sfn.org/Press-Room/News-Release- Archives/2014/Brain-Changes-Are-Associated-with-Casual-Marijuana-Use-in- Young-Adults
[2]. Ritter, M. "Study finds signs of brain changes in pot smokers". Associated Press. Access April 16th, 2014 at http://hosted.ap.org/dynamic/stories/U/US_MED_MARIJUANA_BRAIN?SITE=AP&SECTION=HOME&TEMPLATE=DEFAULT&CTIME=2014 -04-15-18-07-53
[3]. Dobuzinskis, A. "Casual pot use causes brain abnormalities in the young: study". Reuters. Accessed April 16th, 2014 at http://www.reuters.com/article/2014/04/16/us-usa-marijuana-study- idUSBREA3F04F20140416"
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals.
Results
We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals.
Conclusions
These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic target for serotonin in the human brain and a therapeutic drug target. Despite hundreds of genetic associations investigating HTR2A polymorphisms in neuropsychiatric disorders and therapies, the role of genetic HTR2A variability in health and disease remains uncertain.
Methods
To discover and characterize regulatory HTR2A variants, we sequenced whole transcriptomes from 10 human brain regions with massively parallel RNA sequencing and measured allelic expression of multiple HTR2A messenger (m)RNA transcript variants. Following discovery of functional variants, we further characterized their impact on genetic expression in vitro.
Results
Three polymorphisms modulate the use of novel alternative exons and untranslated regions (UTRs), changing expression of RNA and protein. The frequent promoter variant rs6311, widely implicated in human neuropsychiatric disorders, decreases usage of an upstream transcription start site encoding a longer 5′UTR with greater translation efficiency. rs76665058, located in an extended 3′UTR and unique to individuals of African descent, modulates allelic HTR2A mRNA expression. The third single nucleotide polymorphism, unannotated and present in only a single subject, directs alternative splicing of exon 2. Targeted analysis of HTR2A in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study reveals associations between functional variants and depression severity or citalopram response.
Conclusions
Regulatory polymorphisms modulate HTR2A mRNA expression in an isoform-specific manner, directing the usage of novel untranslated regions and alternative exons. These results provide a foundation for delineating the role of HTR2A and serotonin signaling in central nervous system disorders.""
Our purpose is to investigate cognitive performance and extrapyramidal function early after ecstasy use.
BACKGROUND:
Ecstasy, containing 3,4 methylenedioxymethamphetamine, has shown evidence of causing cognitive deficits and parkinsonian signs. Previous research has examined cognitive performance after a period of prolonged abstinence, but research assessing the early effects of ecstasy after recent use is limited despite temporal neurochemical differences demonstrated in nonhuman models.
METHODS:
This study compared task performance between 13 ecstasy users (10 to 15 h postdrug use) and a control group on a battery of neuropsychologic assessments while matching for education level, sleep deprivation, and premorbid IQ. The groups were also compared on measures relating to parkinsonian signs.
RESULTS:
The ecstasy subjects showed impairments on measures of executive function as evaluated by Raven's Standard Progressive Matrices (SPM) and the Wisconsin Card Sorting Task (WCST). Short-delay free recall memory was also impaired in ecstasy subjects on the California Verbal Learning Test (CVLT-II). No extrapyramidal motor impairments were detected.
CONCLUSIONS:
These deficits resemble deficits previously reported in chronic ecstasy use but also seem to reveal transient impairments in executive function. Future research is needed to better understand the neurologic and neuropsychologic implications of ecstasy use across time and extent of use."
Talks by Ryan Smith
Conference Presentations by Ryan Smith
Our aim was to characterize the association of 2 functional single nucleotide polymorphisms (rs6311 and rs6314) in the serotonin 2A receptor gene (HTR2A) with severity of depression symptoms in children with autism spectrum disorder. These polymorphisms have been shown to be associated with depression symptom severity and response to selective serotonin reuptake inhibitor drugs in adults with diagnosed depressive disorder.
Methods:
Parents of 104 children with autism spectrum disorder rated their children’s depressive symptoms using a validated scale based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, 4th edition. We compared severity of depression symptoms across the rs6311 and rs6314 genotypes, measured from the children’s genomic DNA.
Results:
Children homozygous for the G allele of rs6311 had significantly more severe depression symptoms than those with G/A or A/A genotypes (P=0.025). The effect size (partial eta-squared) was small (ηp2=0.047) but was somewhat larger when we controlled for severity of generalized anxiety disorder symptoms (P=0.006, ηp2=0.072). When we restricted our analyses to white participants, our results were essentially the same as for the entire sample (P=0.004, ηp2=0.086). There was no significant association between rs6314 (C/C versus T carriers) and severity of depression.
Conclusions:
Our findings suggest that the HTR2A functional rs6311 polymorphism, which other studies have associated with differential HTR2A mRNA expression, may modulate the severity of depression symptoms in children with autism spectrum disorder. These tentative, hypothesis-generating findings need replication with larger, independent samples.
Prefrontal behavior and activity in humans are heritable. Studies in animals demonstrate an interaction between dopamine D2 receptors and nicotinic acetylcholine receptors on prefrontal behavior but evidence in humans is weak. Therefore, we hypothesize that genetic variation regulating dopamine D2 and nicotinic acetylcholine receptor signaling impact prefrontal cortex activity and related cognition. To test this hypothesis in humans, we explored the interaction between functional genetic variants in the D2 receptor gene (DRD2, rs1076560) and in the nicotinic receptor α5 gene (CHRNA5, rs16969968) on both dorsolateral prefrontal cortex mediated behavior and physiology during working memory and on prefrontal gray matter volume.
Methods
A large sample of healthy subjects was compared for genotypic differences for DRD2 rs1076560 (G>T) and CHNRA5 rs16969968 (G>A) on prefrontal phenotypes, including cognitive performance at the N-Back task, prefrontal physiology with BOLD fMRI during performance of the 2-Back working memory task, and prefrontal morphometry with structural MRI.
Results
We found that DRD2 rs1076560 and CHNRA5 rs16969968 interact to modulate cognitive function, prefrontal physiology during working memory, and prefrontal gray matter volume. More specifically, CHRNA5-AA/DRD2-GT subjects had greater behavioral performance, more efficient prefrontal cortex activity at 2Back working memory task, and greater prefrontal gray matter volume than the other genotype groups.
Conclusions
The present data extend previous studies in animals and enhance our understanding of dopamine and acetylcholine signaling in the human prefrontal cortex, demonstrating interactions elicited by working memory that are modulated by genetic variants in DRD2 and CHRNA5.
References
[1]. Society for Neuroscience Press Release. "BRAIN CHANGES ARE ASSOCIATED WITH CASUAL MARIJUANA USE IN YOUNG ADULTS". Accessed April 16th, 2014 at http://www.sfn.org/Press-Room/News-Release- Archives/2014/Brain-Changes-Are-Associated-with-Casual-Marijuana-Use-in- Young-Adults
[2]. Ritter, M. "Study finds signs of brain changes in pot smokers". Associated Press. Access April 16th, 2014 at http://hosted.ap.org/dynamic/stories/U/US_MED_MARIJUANA_BRAIN?SITE=AP&SECTION=HOME&TEMPLATE=DEFAULT&CTIME=2014 -04-15-18-07-53
[3]. Dobuzinskis, A. "Casual pot use causes brain abnormalities in the young: study". Reuters. Accessed April 16th, 2014 at http://www.reuters.com/article/2014/04/16/us-usa-marijuana-study- idUSBREA3F04F20140416"
Measuring allelic RNA expression ratios is a powerful approach for detecting cis-acting regulatory variants, RNA editing, loss of heterozygosity in cancer, copy number variation, and allele-specific epigenetic gene silencing. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying allelic expression imbalance (AEI), but numerous factors bias allelic RNA ratio measurements. Here, we compare RNA-Seq allelic ratios measured in nine different human brain regions with a highly sensitive and accurate SNaPshot measure of allelic RNA ratios, identifying factors affecting reliable allelic ratio measurement. Accounting for these factors, we subsequently surveyed the variability of RNA editing across brain regions and across individuals.
Results
We find that RNA-Seq allelic ratios from standard alignment methods correlate poorly with SNaPshot, but applying alternative alignment strategies and correcting for observed biases significantly improves correlations. Deploying these methods on a transcriptome-wide basis in nine brain regions from a single individual, we identified genes with AEI across all regions (SLC1A3, NHP2L1) and many others with region-specific AEI. In dorsolateral prefrontal cortex (DLPFC) tissues from 14 individuals, we found evidence for frequent regulatory variants affecting RNA expression in tens to hundreds of genes, depending on stringency for assigning AEI. Further, we find that the extent and variability of RNA editing is similar across brain regions and across individuals.
Conclusions
These results identify critical factors affecting allelic ratios measured by RNA-Seq and provide a foundation for using this technology to screen allelic RNA expression on a transcriptome-wide basis. Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain. With respect to RNA editing, the similarities within and between individuals leads us to conclude that this post-transcriptional process is under heavy regulatory influence to maintain an optimal degree of editing for normal biological function.
The 5-hydroxytryptamine 2A receptor, encoded by HTR2A, is a major postsynaptic target for serotonin in the human brain and a therapeutic drug target. Despite hundreds of genetic associations investigating HTR2A polymorphisms in neuropsychiatric disorders and therapies, the role of genetic HTR2A variability in health and disease remains uncertain.
Methods
To discover and characterize regulatory HTR2A variants, we sequenced whole transcriptomes from 10 human brain regions with massively parallel RNA sequencing and measured allelic expression of multiple HTR2A messenger (m)RNA transcript variants. Following discovery of functional variants, we further characterized their impact on genetic expression in vitro.
Results
Three polymorphisms modulate the use of novel alternative exons and untranslated regions (UTRs), changing expression of RNA and protein. The frequent promoter variant rs6311, widely implicated in human neuropsychiatric disorders, decreases usage of an upstream transcription start site encoding a longer 5′UTR with greater translation efficiency. rs76665058, located in an extended 3′UTR and unique to individuals of African descent, modulates allelic HTR2A mRNA expression. The third single nucleotide polymorphism, unannotated and present in only a single subject, directs alternative splicing of exon 2. Targeted analysis of HTR2A in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study reveals associations between functional variants and depression severity or citalopram response.
Conclusions
Regulatory polymorphisms modulate HTR2A mRNA expression in an isoform-specific manner, directing the usage of novel untranslated regions and alternative exons. These results provide a foundation for delineating the role of HTR2A and serotonin signaling in central nervous system disorders.""
Our purpose is to investigate cognitive performance and extrapyramidal function early after ecstasy use.
BACKGROUND:
Ecstasy, containing 3,4 methylenedioxymethamphetamine, has shown evidence of causing cognitive deficits and parkinsonian signs. Previous research has examined cognitive performance after a period of prolonged abstinence, but research assessing the early effects of ecstasy after recent use is limited despite temporal neurochemical differences demonstrated in nonhuman models.
METHODS:
This study compared task performance between 13 ecstasy users (10 to 15 h postdrug use) and a control group on a battery of neuropsychologic assessments while matching for education level, sleep deprivation, and premorbid IQ. The groups were also compared on measures relating to parkinsonian signs.
RESULTS:
The ecstasy subjects showed impairments on measures of executive function as evaluated by Raven's Standard Progressive Matrices (SPM) and the Wisconsin Card Sorting Task (WCST). Short-delay free recall memory was also impaired in ecstasy subjects on the California Verbal Learning Test (CVLT-II). No extrapyramidal motor impairments were detected.
CONCLUSIONS:
These deficits resemble deficits previously reported in chronic ecstasy use but also seem to reveal transient impairments in executive function. Future research is needed to better understand the neurologic and neuropsychologic implications of ecstasy use across time and extent of use."
Objectives: We wished to examine the role of SERT function and prenatal stress in mice, in order to determine whether they interact to produce reductions in social behavior in the adult offspring.
Methods: We subjected pregnant SERT +/- dams to chronic variable stress and subsequently tested the adult offspring for sociability using a 3-chamber social approach task (Nadler et al., 2004).
Results: Offspring male SERT +/- mice exposed to prenatal stress displayed reduced social novelty-seeking behavior, as they spent significantly less time socially interacting with a novel versus familiar mouse. Wild-type and unstressed SERT +/- male mice displayed typical social novelty-seeking behavior.
Conclusions: Our findings indicate that prenatal stress may interact with reduced SERT function to produce changes in sociability consistent with those observed in ASD. Given previous research implicating the SERT gene locus and prenatal stress as possible risk factors for ASD, our findings provide evidence for a possible interaction between these environmental and genetic factors that contribute to the production of autistic-like behavior in mice.
Here, I present a series of studies exploring relationships between genetic variants that significantly affect RNA expression and three neurological phenotypes. First, I uncovered a transcription enhancer region contributing to nicotinic α5 receptor subunit mRNA expression and subsequently tested its relationship to nicotine addiction. Next, I revealed a significant correlation between splicing of serotonin 2A receptor mRNA transcripts and a genetic variant implicated in clinical responsiveness to atypical antipsychotics and antidepressants. Finally, in a survey of autism-related risk genes, I uncovered evidence for genetic variations affecting mRNA expression in multiple genes, including cellular adhesion molecules, alternative splicing molecules, and integral components of glutamatergic and gamma-aminobutyric acid signaling. The broad range of neurological phenotypes affected by non-protein coding variants investigated here suggests a pervasive role for RNA processing in human disease. The accumulation of these RNA processing variants throughout human evolution is discussed in the context of human disease.