1
|
Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA. Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582195. [PMID: 38464225 PMCID: PMC10925118 DOI: 10.1101/2024.02.26.582195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of common variants associated with alcohol consumption. In contrast, rare variants have only begun to be studied for their role in alcohol consumption. No studies have examined whether common and rare variants implicate the same genes and molecular networks. To address this knowledge gap, we used publicly available alcohol consumption GWAS summary statistics (GSCAN, N=666,978) and whole exome sequencing data (Genebass, N=393,099) to identify a set of common and rare variants for alcohol consumption. Gene-based analysis of each dataset have implicated 294 (common variants) and 35 (rare variants) genes, including ethanol metabolizing genes ADH1B and ADH1C, which were identified by both analyses, and ANKRD12, GIGYF1, KIF21B, and STK31, which were identified only by rare variant analysis, but have been associated with related psychiatric traits. We then used a network colocalization procedure to propagate the common and rare gene sets onto a shared molecular network, revealing significant overlap. The shared network identified gene families that function in alcohol metabolism, including ADH, ALDH, CYP, and UGT. 74 of the genes in the network were previously implicated in comorbid psychiatric or substance use disorders, but had not previously been identified for alcohol-related behaviors, including EXOC2, EPM2A, CACNB3, and CACNG4. Differential gene expression analysis showed enrichment in the liver and several brain regions supporting the role of network genes in alcohol consumption. Thus, genes implicated by common and rare variants identify shared functions relevant to alcohol consumption, which also underlie psychiatric traits and substance use disorders that are comorbid with alcohol use.
Collapse
Affiliation(s)
- Brittany S Leger
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
2
|
Kato H, Kimura H, Kushima I, Takahashi N, Aleksic B, Ozaki N. The genetic architecture of schizophrenia: review of large-scale genetic studies. J Hum Genet 2023; 68:175-182. [PMID: 35821406 DOI: 10.1038/s10038-022-01059-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Schizophrenia is a complex and often chronic psychiatric disorder with high heritability. Diagnosis of schizophrenia is still made clinically based on psychiatric symptoms; no diagnostic tests or biomarkers are available. Pathophysiology-based diagnostic scheme and treatments are also not available. Elucidation of the pathogenesis is needed for development of pathology-based diagnostics and treatments. In the past few decades, genetic research has made substantial advances in our understanding of the genetic architecture of schizophrenia. Rare copy number variations (CNVs) and rare single-nucleotide variants (SNVs) detected by whole-genome CNV analysis and whole-genome/-exome sequencing analysis have provided the great advances. Common single-nucleotide polymorphisms (SNPs) detected by large-scale genome-wide association studies have also provided important information. Large-scale genetic studies have been revealed that both rare and common genetic variants play crucial roles in this disorder. In this review, we focused on CNVs, SNVs, and SNPs, and discuss the latest research findings on the pathogenesis of schizophrenia based on these genetic variants. Rare variants with large effect sizes can provide mechanistic hypotheses. CRISPR-based genetics approaches and induced pluripotent stem cell technology can facilitate the functional analysis of these variants detected in patients with schizophrenia. Recent advances in long-read sequence technology are expected to detect variants that cannot be detected by short-read sequence technology. Various studies that bring together data from common variant and transcriptomic datasets provide biological insight. These new approaches will provide additional insight into the pathophysiology of schizophrenia and facilitate the development of pathology-based therapeutics.
Collapse
Affiliation(s)
- Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Nagahide Takahashi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| |
Collapse
|
3
|
Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes. Transl Psychiatry 2022; 12:265. [PMID: 35811316 PMCID: PMC9271461 DOI: 10.1038/s41398-022-02033-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 01/16/2023] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable, complex disorder in which rare variants contribute significantly to disease risk. Although many genes have been associated with ASD, there have been few genetic studies of ASD in the Japanese population. In whole exomes from a Japanese ASD sample of 309 cases and 299 controls, rare variants were associated with ASD within specific neurodevelopmental gene sets, including highly constrained genes, fragile X mental retardation protein target genes, and genes involved in synaptic function, with the strongest enrichment in trans-synaptic signaling (p = 4.4 × 10-4, Q-value = 0.06). In particular, we strengthen the evidence regarding the role of ABCA13, a synaptic function-related gene, in Japanese ASD. The overall results of this case-control exome study showed that rare variants related to synaptic function are associated with ASD susceptibility in the Japanese population.
Collapse
|
4
|
Onitsuka T, Hirano Y, Nemoto K, Hashimoto N, Kushima I, Koshiyama D, Koeda M, Takahashi T, Noda Y, Matsumoto J, Miura K, Nakazawa T, Hikida T, Kasai K, Ozaki N, Hashimoto R. Trends in big data analyses by multicenter collaborative translational research in psychiatry. Psychiatry Clin Neurosci 2022; 76:1-14. [PMID: 34716732 PMCID: PMC9306748 DOI: 10.1111/pcn.13311] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/01/2021] [Accepted: 10/17/2021] [Indexed: 12/01/2022]
Abstract
The underlying pathologies of psychiatric disorders, which cause substantial personal and social losses, remain unknown, and their elucidation is an urgent issue. To clarify the core pathological mechanisms underlying psychiatric disorders, in addition to laboratory-based research that incorporates the latest findings, it is necessary to conduct large-sample-size research and verify reproducibility. For this purpose, it is critical to conduct multicenter collaborative research across various fields, such as psychiatry, neuroscience, molecular biology, genomics, neuroimaging, cognitive science, neurophysiology, psychology, and pharmacology. Moreover, collaborative research plays an important role in the development of young researchers. In this respect, the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) consortium and Cognitive Genetics Collaborative Research Organization (COCORO) have played important roles. In this review, we first overview the importance of multicenter collaborative research and our target psychiatric disorders. Then, we introduce research findings on the pathophysiology of psychiatric disorders from neurocognitive, neurophysiological, neuroimaging, genetic, and basic neuroscience perspectives, focusing mainly on the findings obtained by COCORO. It is our hope that multicenter collaborative research will contribute to the elucidation of the pathological basis of psychiatric disorders.
Collapse
Affiliation(s)
- Toshiaki Onitsuka
- Department of Neuroimaging Psychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoji Hirano
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Kiyotaka Nemoto
- Department of Psychiatry, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Naoki Hashimoto
- Department of Psychiatry, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Daisuke Koshiyama
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michihiko Koeda
- Department of Neuropsychiatry, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.,Department of Neuropsychiatry, Nippon Medical School, Tama Nagayama Hospital, Tokyo, Japan
| | - Tsutomu Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan.,Research Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Yoshihiro Noda
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Junya Matsumoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kenichiro Miura
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Takatoshi Hikida
- Laboratory for Advanced Brain Functions, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The International Research Center for Neurointelligence (WPI-IRCN) at The University of Tokyo Institutes for Advanced Study (UTIAS), Tokyo, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| |
Collapse
|
5
|
Jozuka R, Kimura H, Uematsu T, Fujigaki H, Yamamoto Y, Kobayashi M, Kawabata K, Koike H, Inada T, Saito K, Katsuno M, Ozaki N. Severe and long-lasting neuropsychiatric symptoms after mild respiratory symptoms caused by COVID-19: A case report. Neuropsychopharmacol Rep 2021; 42:114-119. [PMID: 34889531 PMCID: PMC8919122 DOI: 10.1002/npr2.12222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 12/25/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID‐19) is known to cause not only respiratory but also neuropsychiatric symptoms, which are assumed to be derived from a cytokine storm and its effects on the central nervous systems. Patients with COVID‐19 who develop severe respiratory symptoms are known to show severe neuropsychiatric symptoms such as cerebrovascular disease and encephalopathy. However, the detailed clinical courses of patients with neuropsychiatric symptoms caused by mild or asymptomatic COVID‐19 remain poorly understood. Here, we present a case of COVID‐19 who presented with severe and prolonged neuropsychiatric symptoms subsequent to mild respiratory symptoms. Case presentation A 55‐year‐old female with COVID‐19 accompanied by mild respiratory symptoms showed delusion, psychomotor excitement, and poor communication ability during quarantine outside the hospital. Considering her diminished respiratory symptoms, her neuropsychiatric symptoms were initially regarded as psychogenic reactions. However, as she showed progressive disturbance of consciousness accompanied by an abnormal electroencephalogram, she was diagnosed with post‐COVID‐19 encephalopathy. Although her impaired consciousness and elevated cytokine level improved after steroid pulse therapy, several neuropsychiatric symptoms, including a loss of concentration, unsteadiness while walking, and fatigue, remained. Conclusions This case suggests the importance of both recognizing that even apparently mild COVID‐19‐related respiratory symptoms can lead to severe and persistent neuropsychiatric symptoms, and elucidating the mechanisms, treatment, and long‐term course of COVID‐19‐related neuropsychiatric symptoms in the future. A 55‐year‐old female with COVID‐19 accompanied by mild respiratory symptoms was diagnosed with post‐COVID‐19 encephalopathy. Although her impaired consciousness and elevated cytokine level improved after steroid pulse therapy, several neuropsychiatric symptoms remained. This case suggests the importance of both recognizing that even apparently mild COVID‐19‐related respiratory symptoms can lead to severe and persistent neuropsychiatric symptoms.![]()
Collapse
Affiliation(s)
- Ryosuke Jozuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Uematsu
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidetsugu Fujigaki
- Department of Advanced Diagnostic System Development, Fujita Health University Graduate School of Health Science, Toyoake, Japan
| | - Yasuko Yamamoto
- Department of Advanced Diagnostic System Development, Fujita Health University Graduate School of Health Science, Toyoake, Japan
| | - Masato Kobayashi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuya Kawabata
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruki Koike
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiya Inada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kuniaki Saito
- Department of Advanced Diagnostic System Development, Fujita Health University Graduate School of Health Science, Toyoake, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|