scholarly journals Integrating brain methylome with GWAS for psychiatric risk gene discovery

2018 ◽  
Author(s):  
Shizhong Han ◽  
Ying Lin ◽  
Minghui Wang ◽  
Fernando S. Goes ◽  
Kai Tan ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Prefrontal Cortex ◽  
Human Brain ◽  
Association Study ◽  
Psychiatric Disorders ◽  
Gene Discovery ◽  
Cpg Sites ◽  
Risk Gene ◽  
Risk Variants ◽  
Trait Associations

AbstractDNA methylation (DNAm) is heritable and plays a role in brain development and function through transcriptional regulation. Aberrant DNAm in human brain has been linked to psychiatric disorders, potentially as mediators of common genetic risk variants. In this study, we hypothesize that common risk variants for psychiatric disorders may act through affecting DNAm level in human brain. We first aimed to investigate the heritability pattern of DNAm levels in the human prefrontal cortex. Secondly, through imputation-driven methylome-wide association study (MWAS), we aimed to identify CpG sites whose methylation levels are genetically associated and that show methylation-trait associations in the prefrontal cortex of patients with schizophrenia or bipolar disorder. Our heritability analysis showed that, of ~370,000 CpG sites measured with the Illumina HumanMethylation450 microarray, 17% were heritable (p < 0.05), with a mean heritability of 0.22. Heritable CpG sites were enriched in intergenic regions, CpG shore, and regulatory regions in prefrontal cortex. Our MWAS approach identified known and potentially novel risk genes harboring CpG sites of methylation-trait associations for schizophrenia or bipolar disorder, which were not detectable using three alternative strategies (blood-based methylome reference, transcriptome-wide association study, and two gene-based association tests). Gene set enrichment analysis for genes with methylation-trait association evidence revealed pathways clearly related to neuronal functions, but also highlighted additional biological mechanisms that may underlie psychiatric disorders, such as microRNA-related regulation. In conclusion, our results showed the power of integrating brain methylation data with GWAS for psychiatric risk gene discovery, with potential applications in brain-related disorders or traits.

scholarly journals Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk association

2019 ◽  
Author(s):  
Alexi Nott ◽  
Inge R. Holtman ◽  
Nicole G. Coufal ◽  
Johannes C.M. Schlachetzki ◽  
Miao Yu ◽  
...  
Keyword(s):  
Human Brain ◽  
Psychiatric Disorders ◽  
Complex Traits ◽  
Disease Risk ◽  
Cell Types ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Cell Type ◽  
Risk Variants ◽  
Cell Type Specific

AbstractUnique cell type-specific patterns of activated enhancers can be leveraged to interpret non-coding genetic variation associated with complex traits and diseases such as neurological and psychiatric disorders. Here, we have defined active promoters and enhancers for major cell types of the human brain. Whereas psychiatric disorders were primarily associated with regulatory regions in neurons, idiopathic Alzheimer’s disease (AD) variants were largely confined to microglia enhancers. Interactome maps connecting GWAS variants in cell type-specific enhancers to gene promoters revealed an extended microglia gene network in AD. Deletion of a microglia-specific enhancer harboring AD-risk variants ablated BIN1 expression in microglia but not in neurons or astrocytes. These findings revise and expand the genes likely to be influenced by non-coding variants in AD and suggest the probable brain cell types in which they function.One Sentence SummaryIdentification of cell type-specific regulatory elements in the human brain enables interpretation of non-coding GWAS risk variants.

scholarly journals Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders

2018 ◽  
Author(s):  
Claudio Toma ◽  
Kerrie D. Pierce ◽  
Alex D. Shaw ◽  
Anna Heath ◽  
Philip B. Mitchell ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Intellectual Disability ◽  
Candidate Gene ◽  
Psychiatric Disorders ◽  
Rare Variants ◽  
Focal Epilepsy ◽  
Psychiatric Diseases ◽  
Risk Gene ◽  
Functional Snps ◽  
Sequence Variations

ABSTRACTThe contactin-associated protein-like 2 (CNTNAP2) gene is a member of the neurexin superfamily. CNTNAP2 was implicated in the cortical dysplasia-focal epilepsy (CDFE) syndrome, a recessive disease characterized by intellectual disability, epilepsy, language impairments and autistic features. Associated SNPs and heterozygous deletions in CNTNAP2 have also frequently been reported in autism, schizophrenia and other psychiatric or neurological disorders. We aim here to gain conclusive evidence for the role of CNTNAP2 in susceptibility to psychiatric disorders by the comprehensive analysis of large genomic datasets. In this study we used: i) summary statistics from the Psychiatric Genomics Consortium (PGC) GWAS; ii) examined all reported CNTNAP2 structural variants in patients and controls; iii) performed cross-disorder analysis of functional or previously associated SNPs; iv) and conducted burden tests for pathogenic rare variants using sequencing data (4,483 ASD and 6,135 schizophrenia cases, and 13,042 controls).In a CNV mircroarray study, we previously identified a 131kb deletion in CNTNAP2 intron 1, removing a FOXP2 transcription factor binding site in an extended BD family. Here we perform a quantitative-PCR validation showing imperfect segregation with disease (5 bipolar disorder relatives). The distribution of CNVs across CNTNAP2 in psychiatric cases from previous reports was no different from controls of the database of genomic variants. Gene-based association testing did not implicate common variants in autism, schizophrenia or other psychiatric phenotypes. The association of proposed functional SNPs rs7794745 and rs2710102, reported to influence brain connectivity, was not replicated; nor did functional SNPs yield significant results in meta-analysis across psychiatric disorders. Disrupting CNTNAP2 rare variant burden was not higher in autism or schizophrenia compared to controls. This large comprehensive candidate gene study indicates that CNTNAP2 may not be a robust risk gene for psychiatric phenotypes.AUTHOR SUMMARYGenetic mutations that disrupt both copies of the CNTNAP2 gene lead to severe disease, characterized by profound intellectual disability, epilepsy, language difficulties and autistic traits. Researchers hypothesized that this gene may also be involved in autism given some overlapping clinical features with this disease. Indeed, several large DNA deletions affecting one of the two copies of CNTNAP2 were found in some patients with autism, and later also in patients with schizophrenia, bipolar disorder, ADHD and epilepsy, suggesting that this gene was involved in several psychiatric or neurologic diseases. Other studies considered genetic sequence variations that are common in the general population, and suggested that two such sequence variations in CNTNAP2 predispose to psychiatric diseases by influencing the functionality and connectivity of the brain. In the current study, we report the deletion of one copy of CNTNAP2 in a patient with bipolar disorder from an extended family where five relatives were affected with this condition. To better understand the involvement of CNTNAP2 in risk of mental illness, we performed several genetic analyses using a series of large publically available or in-house datasets, comprising many thousands of patients and controls. Despite the previous consideration of CNTNAP2 as a strong candidate gene for autism or schizophrenia, we show that neither common, deletion nor ultra-rare variants in CNTNAP2 are likely to play a major role in risk of psychiatric diseases.

scholarly journals Genome-wide association study identifies SESTD1 as a novel risk gene for lithium-responsive bipolar disorder

2015 ◽  
Vol 21 (9) ◽  
pp. 1290-1297 ◽  
Author(s):  
J Song ◽  
◽  
S E Bergen ◽  
A Di Florio ◽  
R Karlsson ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Risk Gene ◽  
Genome Wide

scholarly journals Erratum: Genome-wide association study identifies SESTD1 as a novel risk gene for lithium-responsive bipolar disorder

2017 ◽  
Vol 22 (8) ◽  
pp. 1223-1223 ◽  
Author(s):  
J Song ◽  
◽  
S E Bergen ◽  
A Di Florio ◽  
R Karlsson ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Risk Gene ◽  
Genome Wide

The Orbitofrontal Cortex

2019 ◽  
Author(s):  
Edmund T. Rolls
Keyword(s):  
Bipolar Disorder ◽  
Human Brain ◽  
Obsessive Compulsive Disorder ◽  
Orbitofrontal Cortex ◽  
Multidisciplinary Approach ◽  
Animal Behaviour ◽  
Obsessive Compulsive ◽  
Undergraduate Level ◽  
Compulsive Disorder

The book will be valuable for those in the fields of neuroscience, neurology, psychology, psychiatry, biology, animal behaviour, economics, and philosophy, from the undergraduate level upwards. The book is unique in providing a coherent multidisciplinary approach to understanding the functions of one of the most interesting regions of the human brain, in both health and in disease, including depression, bipolar disorder, autism, and obsessive-compulsive disorder. There is no competing book published in the last 10 years.

scholarly journals Identification and functional characterization of the extremely long allele of the serotonin transporter-linked polymorphic region

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tempei Ikegame ◽  
Yosuke Hidaka ◽  
Yutaka Nakachi ◽  
Yui Murata ◽  
Risa Watanabe ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Psychiatric Disorders ◽  
Serotonin Transporter ◽  
Tandem Repeats ◽  
Large Population ◽  
Functional Characterization ◽  
Luciferase Assay ◽  
Elderly Subjects ◽  
Polymorphic Region ◽  
Rare Alleles

AbstractSLC6A4, which encodes the serotonin transporter, has a functional polymorphism called the serotonin transporter-linked polymorphic region (5-HTTLPR). The 5-HTTLPR consists of short (S) and long (L) alleles, each of which has 14 or 16 tandem repeats. In addition, the extralong (XL) and other rare alleles have been reported in 5-HTTLPR. Although they are more frequent in Asian and African than in other populations, the extent of variations and allele frequencies (AFs) were not addressed in a large population. Here, we report the AFs of the rare alleles in a large number of Japanese subjects (N = 2894) consisting of two cohorts. The first cohort (case-control study set, CCSS) consisted of 1366 subjects, including 485 controls and 881 patients with psychosis (bipolar disorder or schizophrenia). The second cohort (the Arao cohort study set, ACSS) consisted of 1528 elderly subjects. During genotyping, we identified 11 novel 5-HTTLPR alleles, including 3 XL alleles. One novel allele had the longest subunit ever reported, consisting of 28 tandem repeats. We named this XL28-A. An in vitro luciferase assay revealed that XL28-A has no transcriptional activity. XL28-A was found in two unrelated patients with bipolar disorder in the CCSS and one healthy subject in the ACSS who did not show depressive symptoms or a decline in cognitive function. Therefore, it is unlikely that XL28-A is associated with psychiatric disorders, despite its apparent functional deficit. Our results suggest that unraveling the complex genetic variations of 5-HTTLPR will be important for further understanding its role in psychiatric disorders.

scholarly journals Involvement of the nuclear factor-κB transcriptional complex in prefrontal cortex immune activation in bipolar disorder

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kaitlyn M. Roman ◽  
Aaron K. Jenkins ◽  
David A. Lewis ◽  
David W. Volk
Keyword(s):  
Bipolar Disorder ◽  
Prefrontal Cortex ◽  
Immune Activation ◽  
Family Members ◽  
Nuclear Factor Κb ◽  
Nuclear Factor ◽  
Transcript Levels ◽  
Immune Related Genes ◽  
Transcriptional Complex ◽  
Shared Risk

AbstractBipolar disorder and schizophrenia have multiple clinical and genetic features in common, including shared risk associated with overlapping susceptibility loci in immune-related genes. Higher activity of the nuclear factor-κB (NF-κB) transcription factor complex, which regulates the transcription of multiple immune markers, has been reported to contribute to immune activation in the prefrontal cortex in schizophrenia. These findings suggest the hypothesis that elevated NF-κB activity is present in the prefrontal cortex in bipolar disorder in a manner similar to that seen in schizophrenia. Therefore, we quantified levels of NF-κB-related mRNAs in the prefrontal cortex of 35 matched pairs of bipolar disorder and unaffected comparison subjects using quantitative PCR. We found that transcript levels were higher in the prefrontal cortex of bipolar disorder subjects for several NF-κB family members, NF-κB activation receptors, and NF-κB-regulated mRNAs, and were lower for an NF-κB inhibitor. Transcript levels for NF-κB family members, NF-κB activation receptors, and NF-κB-regulated mRNAs levels were also highly correlated with each other. This pattern of elevated transcript levels for NF-κB-related markers in bipolar disorder is similar to that previously reported in schizophrenia, suggesting that cortical immune activation is a shared pathophysiological feature between the two disorders.

scholarly journals Prediction of response to drug therapy in psychiatric disorders

Open Biology ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 180031 ◽  
Author(s):  
Shani Stern ◽  
Sara Linker ◽  
Krishna C. Vadodaria ◽  
Maria C. Marchetto ◽  
Fred H. Gage
Keyword(s):  
Autism Spectrum Disorder ◽  
Bipolar Disorder ◽  
Major Depression ◽  
Personalized Medicine ◽  
Psychiatric Disorders ◽  
Association Studies ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Genome Wide Association Studies ◽  
Patient Reported

Personalized medicine has become increasingly relevant to many medical fields, promising more efficient drug therapies and earlier intervention. The development of personalized medicine is coupled with the identification of biomarkers and classification algorithms that help predict the responses of different patients to different drugs. In the last 10 years, the Food and Drug Administration (FDA) has approved several genetically pre-screened drugs labelled as pharmacogenomics in the fields of oncology, pulmonary medicine, gastroenterology, haematology, neurology, rheumatology and even psychiatry. Clinicians have long cautioned that what may appear to be similar patient-reported symptoms may actually arise from different biological causes. With growing populations being diagnosed with different psychiatric conditions, it is critical for scientists and clinicians to develop precision medication tailored to individual conditions. Genome-wide association studies have highlighted the complicated nature of psychiatric disorders such as schizophrenia, bipolar disorder, major depression and autism spectrum disorder. Following these studies, association studies are needed to look for genomic markers of responsiveness to available drugs of individual patients within the population of a specific disorder. In addition to GWAS, the advent of new technologies such as brain imaging, cell reprogramming, sequencing and gene editing has given us the opportunity to look for more biomarkers that characterize a therapeutic response to a drug and to use all these biomarkers for determining treatment options. In this review, we discuss studies that were performed to find biomarkers of responsiveness to different available drugs for four brain disorders: bipolar disorder, schizophrenia, major depression and autism spectrum disorder. We provide recommendations for using an integrated method that will use available techniques for a better prediction of the most suitable drug.

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