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Mušálková D, Přistoupilová A, Jedličková I, Hartmannová H, Trešlová H, Nosková L, Hodaňová K, Bittmanová P, Stránecký V, Jiřička V, Langmajerová M, Woodbury‐Smith M, Zarrei M, Trost B, Scherer SW, Bleyer AJ, Vevera J, Kmoch S. Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12882. [PMID: 38359179 PMCID: PMC10869132 DOI: 10.1111/gbb.12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
The genetic correlates of extreme impulsive violence are poorly understood, and there have been few studies that have characterized a large group of affected individuals both clinically and genetically. We performed whole exome sequencing (WES) in 290 males with the life-course-persistent, extremely impulsively violent form of antisocial personality disorder (APD) and analyzed the spectrum of rare protein-truncating variants (rPTVs). Comparisons were made with 314 male controls and publicly available genotype data. Functional annotation tools were used for biological interpretation. Participants were significantly more likely to harbor rPTVs in genes that are intolerant to loss-of-function variants (odds ratio [OR] 2.06; p < 0.001), specifically expressed in brain (OR 2.80; p = 0.036) and enriched for those involved in neurotransmitter transport and synaptic processes. In 60 individuals (20%), we identified rPTVs that we classified as clinically relevant based on their clinical associations, biological function and gene expression patterns. Of these, 37 individuals harbored rPTVs in 23 genes that are associated with a monogenic neurological disorder, and 23 individuals harbored rPTVs in 20 genes reportedly intolerant to loss-of-function variants. The analysis presents evidence in support of a model where presence of either one or several private, functionally relevant mutations contribute significantly to individual risk of life-course-persistent APD and reveals multiple individuals who could be affected by clinically unrecognized neuropsychiatric Mendelian disease. Thus, Mendelian diseases and increased rPTV burden may represent important factors for the development of extremely impulsive violent life-course-persistent forms of APD irrespective of their clinical presentation.
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Affiliation(s)
- Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Petra Bittmanová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Václav Jiřička
- Department of PsychologyPrison Service of the Czech RepublicPragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Michaela Langmajerová
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Marc Woodbury‐Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Faculty of Medical Sciences, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Molecular Genetics and McLaughlin CentreUniversity of TorontoTorontoOntarioCanada
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Section on Nephrology, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Jan Vevera
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
- Department of PsychiatryUniversity Hospital PilsenPilsenCzech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
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Scott MR, McClung CA. Bipolar Disorder. Curr Opin Neurobiol 2023; 83:102801. [PMID: 38223491 PMCID: PMC10786345 DOI: 10.1016/j.conb.2023.102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This review focuses on recent advances made towards understanding the neurobiology of bipolar disorder (BD), a chronic neuropsychiatric illness characterized by altered mood and energy states. The past few years have seen the completion of the largest genetic studies by far, which have emphasized the polygenic nature of BD as well as it's connection to other psychiatric illnesses. Furthermore, the use of inducible pluripotent stem cells has rapidly expanded. These studies support previous work that implicates dysregulation of neurodevelopment, mitochondria, and calcium homeostasis, while also allowing for investigation into the underlying mechanisms of individual responsivity to lithium. Sleep and circadian rhythms have also been heavily implicated in BD, from disruptions in activity patterns to molecular abnormalities.
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Affiliation(s)
- Madeline R Scott
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Gislason H. SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands. BMC Genomics 2023; 24:707. [PMID: 37996805 PMCID: PMC10666429 DOI: 10.1186/s12864-023-09763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals. RESULTS We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years [Formula: see text] with a maximum consanguineous population in year [Formula: see text] and similarly consanguineous between years [Formula: see text]. The ancestry analysis shows the population descends from founders of [Formula: see text] European and [Formula: see text] Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants. CONCLUSIONS The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.
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Affiliation(s)
- Hannes Gislason
- Faculty of Science and Technology, University of the Faroe Islands, Tórshavn, Faroe Islands.
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Hara T, Owada Y, Takata A. Genetics of bipolar disorder: insights into its complex architecture and biology from common and rare variants. J Hum Genet 2023; 68:183-191. [PMID: 35614313 DOI: 10.1038/s10038-022-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a common mental disorder characterized by recurrent mood episodes, which causes major socioeconomic burdens globally. Though its disease pathogenesis is largely unknown, the high heritability of BD indicates strong contributions from genetic factors. In this review, we summarize the recent achievements in the genetics of BD, particularly those from genome-wide association study (GWAS) of common variants and next-generation sequencing analysis of rare variants. These include the identification of dozens of robust disease-associated loci, deepening of our understanding of the biology of BD, objective description of correlations with other psychiatric disorders and behavioral traits, formulation of methods for predicting disease risk and drug response, and the discovery of a single gene associated with bipolar disorder and schizophrenia spectrum with a large effect size. On the other hand, the findings to date have not yet made a clear contribution to the improvement of clinical psychiatry of BD. We overview the remaining challenges as well as possible paths to resolve them, referring to studies of other major neuropsychiatric disorders.
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Affiliation(s)
- Tomonori Hara
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.,Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Yuji Owada
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8575, Japan
| | - Atsushi Takata
- Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan.
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Li X, Ma S, Yan W, Wu Y, Kong H, Zhang M, Luo X, Xia J. dbBIP: a comprehensive bipolar disorder database for genetic research. Database (Oxford) 2022; 2022:6627538. [PMID: 35779245 PMCID: PMC9250320 DOI: 10.1093/database/baac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/28/2022] [Accepted: 06/11/2022] [Indexed: 11/17/2022]
Abstract
Bipolar disorder (BIP) is one of the most common hereditary psychiatric disorders worldwide. Elucidating the genetic basis of BIP will play a pivotal role in mechanistic delineation. Genome-wide association studies (GWAS) have successfully reported multiple susceptibility loci conferring BIP risk, thus providing insight into the effects of its underlying pathobiology. However, difficulties remain in the extrication of important and biologically relevant data from genetic discoveries related to psychiatric disorders such as BIP. There is an urgent need for an integrated and comprehensive online database with unified access to genetic and multi-omics data for in-depth data mining. Here, we developed the dbBIP, a database for BIP genetic research based on published data. The dbBIP consists of several modules, i.e.: (i) single nucleotide polymorphism (SNP) module, containing large-scale GWAS genetic summary statistics and functional annotation information relevant to risk variants; (ii) gene module, containing BIP-related candidate risk genes from various sources and (iii) analysis module, providing a simple and user-friendly interface to analyze one’s own data. We also conducted extensive analyses, including functional SNP annotation, integration (including summary-data-based Mendelian randomization and transcriptome-wide association studies), co-expression, gene expression, tissue expression, protein–protein interaction and brain expression quantitative trait loci analyses, thus shedding light on the genetic causes of BIP. Finally, we developed a graphical browser with powerful search tools to facilitate data navigation and access. The dbBIP provides a comprehensive resource for BIP genetic research as well as an integrated analysis platform for researchers and can be accessed online at http://dbbip.xialab.info. Database URL: http://dbbip.xialab.info
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Affiliation(s)
- Xiaoyan Li
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Shunshuai Ma
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Wenhui Yan
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Yong Wu
- Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology , 93 Youyi Road, Qiaokou District, Wuhan, Hubei 430030, China
| | - Hui Kong
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Mingshan Zhang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
| | - Xiongjian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , 32 Jiaochang East Road, Wuhua District, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences , 19 Qingsong Road, Panlong District, Kunming, Yunnan 650204, China
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University , 111 Jiulong Road, Shushan District, Hefei, Anhui 230601, China
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Abstract
BACKGROUND To date, besides genome-wide association studies, a variety of other genetic analyses (e.g. polygenic risk scores, whole-exome sequencing and whole-genome sequencing) have been conducted, and a large amount of data has been gathered for investigating the involvement of common, rare and very rare types of DNA sequence variants in bipolar disorder. Also, non-invasive neuroimaging methods can be used to quantify changes in brain structure and function in patients with bipolar disorder. AIMS To provide a comprehensive assessment of genetic findings associated with bipolar disorder, based on the evaluation of different genomic approaches and neuroimaging studies. METHOD We conducted a PubMed search of all relevant literatures from the beginning to the present, by querying related search strings. RESULTS ANK3, CACNA1C, SYNE1, ODZ4 and TRANK1 are five genes that have been replicated as key gene candidates in bipolar disorder pathophysiology, through the investigated studies. The percentage of phenotypic variance explained by the identified variants is small (approximately 4.7%). Bipolar disorder polygenic risk scores are associated with other psychiatric phenotypes. The ENIGMA-BD studies show a replicable pattern of lower cortical thickness, altered white matter integrity and smaller subcortical volumes in bipolar disorder. CONCLUSIONS The low amount of explained phenotypic variance highlights the need for further large-scale investigations, especially among non-European populations, to achieve a more complete understanding of the genetic architecture of bipolar disorder and the missing heritability. Combining neuroimaging data with genetic data in large-scale studies might help researchers acquire a better knowledge of the engaged brain regions in bipolar disorder.
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Affiliation(s)
- Mojtaba Oraki Kohshour
- Institute of Psychiatric Phenomics and Genomics, University Hospital LMU Munich, Germany; and Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Iran
| | - Sergi Papiol
- Institute of Psychiatric Phenomics and Genomics, University Hospital LMU Munich, Germany; and Department of Psychiatry and Psychotherapy, University Hospital LMU Munich, Germany
| | - Christopher R K Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, USA
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, University Hospital LMU Munich, Germany; and Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, USA
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Sheikh TI, Harripaul R, Vasli N, Ghadami M, Santangelo SL, Ayub M, Sasanfar R, Vincent JB. Heterozygous De Novo Truncating Mutation of Nucleolin in an ASD Individual Disrupts Its Nucleolar Localization. Genes (Basel) 2021; 13:51. [PMID: 35052391 PMCID: PMC8774667 DOI: 10.3390/genes13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Nucleolin (NCL/C23; OMIM: 164035) is a major nucleolar protein that plays a critical role in multiple processes, including ribosome assembly and maturation, chromatin decondensation, and pre-rRNA transcription. Due to its diverse functions, nucleolin has frequently been implicated in pathological processes, including cancer and viral infection. We recently identified a de novo frameshifting indel mutation of NCL, p.Gly664Glufs*70, through whole-exome sequencing of autism spectrum disorder trios. Through the transfection of constructs encoding either a wild-type human nucleolin or a mutant nucleolin with the same C-terminal sequence predicted for the autism proband, and by using co-localization with the nucleophosmin (NPM; B23) protein, we have shown that the nucleolin mutation leads to mislocalization of the NCL protein from the nucleolus to the nucleoplasm. Moreover, a construct with a nonsense mutation at the same residue, p.Gly664*, shows a very similar effect on the location of the NCL protein, thus confirming the presence of a predicted nucleolar location signal in this region of the NCL protein. Real-time fluorescence recovery experiments show significant changes in the kinetics and mobility of mutant NCL protein in the nucleoplasm of HEK293Tcells. Several other studies also report de novoNCL mutations in ASD or neurodevelopmental disorders. The altered mislocalization and dynamics of mutant NCL (p.G664Glufs*70/p.G664*) may have relevance to the etiopathlogy of NCL-related ASD and other neurodevelopmental phenotypes.
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Affiliation(s)
- Taimoor I. Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
| | - Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nasim Vasli
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
| | - Majid Ghadami
- Department of Educational Sciences, Farhangian University, Tehran 19989-63341, Iran;
| | - Susan L. Santangelo
- Center for Psychiatric Research, Maine Medical Center Research Institute, Portland, ME 04101, USA;
- Department of Psychiatry, Tufts University School of Medicine, Boston, MA 02110, USA
- Department of Psychiatry, Maine Medical Center, Portland, ME 04102, USA
| | - Muhammad Ayub
- Department of Psychiatry, Queen’s University, Kingston, ON K7L 7X3, Canada;
- Department of Academic Psychiatry, University College London, London WC1E 6BT, UK
| | - Roksana Sasanfar
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA;
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada; (T.I.S.); (R.H.)
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
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Raghu P, Basak B, Krishnan H. Emerging perspectives on multidomain phosphatidylinositol transfer proteins. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158984. [PMID: 34098114 PMCID: PMC7611342 DOI: 10.1016/j.bbalip.2021.158984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/09/2022]
Abstract
The phosphatidylinositol transfer protein domain (PITPd) is an evolutionarily conserved protein that is able to transfer phosphatidylinositol between membranes in vitro and in vivo. However some animal genomes also include genes that encode proteins where the PITPd is found in cis with a number of additional domains and recent large scale genome sequencing efforts indicate that this type of multidomain architecture is widespread in the animal kingdom. In Drosophila photoreceptors, the multidomain phosphatidylinositol transfer protein RDGB is required to regulate phosphoinositide turnover during G-protein activated phospholipase C signalling. Recent studies in flies and mammalian cell culture models have begun to elucidate functions for the non-PITPd of RDGB and its vertebrate orthologs. We review emerging evidence on the genomics, functional and cell biological perspectives of these multi-domain PITPd containing proteins.
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Affiliation(s)
- Padinjat Raghu
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India.
| | - Bishal Basak
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India
| | - Harini Krishnan
- National Centre for Biological Sciences, TIFR-GKVK Campus, Bellary Road, Bengaluru 560065, India
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Jia X, Goes FS, Locke AE, Palmer D, Wang W, Cohen-Woods S, Genovese G, Jackson AU, Jiang C, Kvale M, Mullins N, Nguyen H, Pirooznia M, Rivera M, Ruderfer DM, Shen L, Thai K, Zawistowski M, Zhuang Y, Abecasis G, Akil H, Bergen S, Burmeister M, Chapman S, DelaBastide M, Juréus A, Kang HM, Kwok PY, Li JZ, Levy SE, Monson ET, Moran J, Sobell J, Watson S, Willour V, Zöllner S, Adolfsson R, Blackwood D, Boehnke M, Breen G, Corvin A, Craddock N, DiFlorio A, Hultman CM, Landen M, Lewis C, McCarroll SA, Richard McCombie W, McGuffin P, McIntosh A, McQuillin A, Morris D, Myers RM, O'Donovan M, Ophoff R, Boks M, Kahn R, Ouwehand W, Owen M, Pato C, Pato M, Posthuma D, Potash JB, Reif A, Sklar P, Smoller J, Sullivan PF, Vincent J, Walters J, Neale B, Purcell S, Risch N, Schaefer C, Stahl EA, Zandi PP, Scott LJ. Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Mol Psychiatry 2021; 26:5239-5250. [PMID: 33483695 PMCID: PMC8295400 DOI: 10.1038/s41380-020-01006-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Bipolar disorder (BD) is a serious mental illness with substantial common variant heritability. However, the role of rare coding variation in BD is not well established. We examined the protein-coding (exonic) sequences of 3,987 unrelated individuals with BD and 5,322 controls of predominantly European ancestry across four cohorts from the Bipolar Sequencing Consortium (BSC). We assessed the burden of rare, protein-altering, single nucleotide variants classified as pathogenic or likely pathogenic (P-LP) both exome-wide and within several groups of genes with phenotypic or biologic plausibility in BD. While we observed an increased burden of rare coding P-LP variants within 165 genes identified as BD GWAS regions in 3,987 BD cases (meta-analysis OR = 1.9, 95% CI = 1.3-2.8, one-sided p = 6.0 × 10-4), this enrichment did not replicate in an additional 9,929 BD cases and 14,018 controls (OR = 0.9, one-side p = 0.70). Although BD shares common variant heritability with schizophrenia, in the BSC sample we did not observe a significant enrichment of P-LP variants in SCZ GWAS genes, in two classes of neuronal synaptic genes (RBFOX2 and FMRP) associated with SCZ or in loss-of-function intolerant genes. In this study, the largest analysis of exonic variation in BD, individuals with BD do not carry a replicable enrichment of rare P-LP variants across the exome or in any of several groups of genes with biologic plausibility. Moreover, despite a strong shared susceptibility between BD and SCZ through common genetic variation, we do not observe an association between BD risk and rare P-LP coding variants in genes known to modulate risk for SCZ.
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Affiliation(s)
- Xiaoming Jia
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Adam E Locke
- Division of Genomics & Bioinformatics, Department of Medicine and McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Duncan Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Weiqing Wang
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Cohen-Woods
- Discipline of Psychology and Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, SA, Australia
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Niamh Mullins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hoang Nguyen
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Core, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - Margarita Rivera
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain
| | - Douglas M Ruderfer
- Departments of Medicine, Psychiatry, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ling Shen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Khanh Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yongwen Zhuang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gonçalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Huda Akil
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sinéad Chapman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Melissa DelaBastide
- Division of Research, Cold Spring Harbor Laboratory, Cold Spring, Harbor, NY, 11797, USA
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jun Z Li
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Eric T Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Jennifer Moran
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Janet Sobell
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
| | - Stanley Watson
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Virginia Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rolf Adolfsson
- Departments of Clinical Sciences and Psychiatry, Umea University, Umea, Sweden
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gerome Breen
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Aiden Corvin
- Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nick Craddock
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Arianna DiFlorio
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Landen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Cathryn Lewis
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - W Richard McCombie
- Division of Research, Cold Spring Harbor Laboratory, Cold Spring, Harbor, NY, 11797, USA
| | - Peter McGuffin
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Andrew McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | | | - Derek Morris
- Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Discipline of Biochemistry, Neuroimaging and Cognitive Genomics (NICOG) Centre, National University of Ireland Galway, Galway, Ireland
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Michael O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Roel Ophoff
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Marco Boks
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Rene Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Willem Ouwehand
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Michael Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Carlos Pato
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
- SUNY Downstate Medical Center, Brooklyn, NY, 11203, USA
| | - Michele Pato
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Psychiatry, SUNY Downstate Medical Center, Brooklyn, NY, 11203, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Pamela Sklar
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jordan Smoller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - John Vincent
- Molecular Neuropsychiatry and Development Laboratory, Campbell Family Mental Health Research Institute, Center for Addiction & Mental Health, Toronto, ON, Canada
- Department of Psychiatry and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - James Walters
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Benjamin Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shaun Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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10
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Integration analysis of methylation quantitative trait loci and GWAS identify three schizophrenia risk variants. Neuropsychopharmacology 2020; 45:1179-1187. [PMID: 31910432 PMCID: PMC7235211 DOI: 10.1038/s41386-020-0605-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/31/2019] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with schizophrenia (SCZ). However, prioritizing risk variants and regulatory elements for follow-up functional studies remains a major challenge. Therefore, we performed an integrated analysis to identify variants who affect methylation levels of nearby genes and contribute to the risk of SCZ, and to explore the potential role of these variants in SCZ pathogenesis. First, we used the Summary data-based Mendelian Randomization (SMR) method to integrate GWAS and methylation quantitative trait loci data. Then, the SNP-methylation combinations as associated with SCZ were replicated across multiple samples. Totally, we identified and replicated 14 and one SNP-methylation combinations in blood and brain tissues, respectively, that significantly associated with SCZ. Furthermore, our expression quantitative trait loci analysis, differential methylation analysis, neuroimaging genetics, and cognitive genetics analysis consistently supported the potential roles of these 15 SNPs in the pathogenesis of SCZ. Finally, using the convergent functional genomics method, we prioritized three risk SNPs, including rs3765971 (RERE, PSMR = 3.87 × 10-8), rs55742290 (ARL6IP4, PSMR = 1.50 × 10-7), and rs7293091 (CENPM, PSMR = 5.09 × 10-7), may represent promising risk variants in SCZ. These convergent lines of evidence suggest that three risk variants may be involved in the pathogenesis of SCZ. Further investigation of the roles of these variants in the pathogenesis of SCZ is warranted.
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11
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The black sheep of the family- whole-exome sequencing in family of lithium response discordant bipolar monozygotic twins. Eur Neuropsychopharmacol 2020; 34:19-27. [PMID: 32305265 DOI: 10.1016/j.euroneuro.2020.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/06/2020] [Indexed: 01/20/2023]
Abstract
Twin studies are among the most promising strategies for studying heritable disorders, including bipolar disorder (BD). The aim of the present study was to identify distinguishing genes between monozygotic (MZ) twins with different BD phenotype and compare them to their non-affected siblings. Whole-exome sequencing (WES) can identify rare and structural variants that could detect the polygenetic burden of complex disorders. WES was performed on a family composed of two MZ twins with BD, their unaffected brother and unaffected parents. The twins have a discordant response to lithium and distinct course of illness. Following WES, six genes of particular interest emerged: Neurofibromin type 1 (NF1), Biorientation of chromosomes in cell division 1 (BOD1), Golgi-associated gamma adaptin ear-containing ARF binding protein 3 (GGA3), Disrupted in schizophrenia 1 (DISC1), Neuromedin U receptor 2 (NMUR2), and Huntingtin interacting protein 1-related (HIP1R). Interestingly, many of these influence glutamatergic pathways and thus the findings may have therapeutical implications. These results may provide important insights to unveil genetic underpinnings of BD and the response to lithium.
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12
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Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome. Transl Psychiatry 2020; 10:124. [PMID: 32345981 PMCID: PMC7188882 DOI: 10.1038/s41398-020-0783-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies on bipolar disorders (BD) have revealed an additive polygenic contribution of common single-nucleotide polymorphisms (SNPs). However, these SNPs explain only 25% of the overall genetic variance and suggest a role of rare variants in BD vulnerability. Here, we combined high-throughput genotyping data and whole-exome sequencing in cohorts of individuals with BD as well as in multiplex families with a high density of affected individuals in order to determine the contribution of both common and rare variants to BD genetic vulnerability. Using polygenic risk scores (PRS), we showed a strong contribution of common polymorphisms previously associated with BD and schizophrenia (SZ) and noticed that those specifically associated with SZ contributed more in familial forms of BD than in non-familial ones. The analysis of rare damaging variants shared by affected individuals in multiplex families with BD revealed a single interaction network enriched in neuronal and developmental biological pathways, as well as in the regulation of gene expression. We identified four genes with a higher mutation rate in individuals with BD than in the general population and showed that mutations in two of them were associated with specific clinical manifestations. In addition, we showed a significant negative correlation between PRS and the number of rare damaging variants specifically in unaffected individuals of multiplex families. Altogether, our results suggest that common and rare genetic variants both contribute to the familial aggregation of BD and this genetic architecture may explain the heterogeneity of clinical manifestations in multiplex families.
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13
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Mosheva M, Serretti A, Stukalin Y, Fabbri C, Hagin M, Horev S, Mantovani V, Bin S, Mattiaccio A, Nivoli A, Vieta E, Popovic D. Association between CANCA1C gene rs1034936 polymorphism and alcohol dependence in bipolar disorder. J Affect Disord 2020; 261:181-186. [PMID: 31634677 DOI: 10.1016/j.jad.2019.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/10/2019] [Accepted: 10/09/2019] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Bipolar disorder (BD) is a highly heritable and disabling mental illness, commonly associated with substance abuse, being alcohol abuse the most frequent. Comorbid BD and substance abuse disorders are often associated with high levels of health service utilization and destabilization of the course of illness resulting in poor treatment outcomes. Although recent genome-wide association studies have detected a number of risk genes for BD, the data is still sparse and inconclusive for those genes that may contribute to the increased risk of comorbid alcohol abuse (AA) in BD. The primary aim of the present study was to investigate the effects of 46 single-nucleotide polymorphisms (SNPs) within eight genes on different phenotypes of BD patients, such as comorbid alcohol abuse. We further assessed clinical variables associated with AA. METHODS One-hundred fifty-eight BD I and II patients were enrolled in a naturalistic cohort study. Genomic DNA of 92 patients was extracted from whole blood using standard procedures and 46 tag SNPs in eight genes of interest (ANK, CACNA1C, CACNB2, FKBP5, GRM7, ITIH3, SYNE1 and TCF4) were genotyped. RESULTS Seventy-one patients out of 158 (45%) satisfied diagnostic criteria for comorbid AA. Among 46 SNPs analyzed, the only SNP associated with comorbid AA was rs1034936 polymorphism in the CANCA1C gene. This polymorphism was also associated with lifetime cocaine abuse, manic switch and current atypical antipsychotics. CONCLUSIONS Our findings suggest a role of rs1034936 CACNA1C gene variant in BD-AA group. Despite their preliminary nature, the present results may provide new insight on mechanisms underlying AA in BD.
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Affiliation(s)
- Mariela Mosheva
- Bipolar Disorders Programme, Psychiatry B, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Yelena Stukalin
- School of Behavioral Sciences, Tel Aviv-Yaffo Academic College, Tel-Aviv, Israel
| | - Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Michal Hagin
- Bipolar Disorders Programme, Psychiatry B, Sheba Medical Center, Tel Hashomer, Israel
| | - Sagi Horev
- Bipolar Disorders Programme, Psychiatry B, Sheba Medical Center, Tel Hashomer, Israel; Semmelewis University, Budapest, Hungary
| | - Vilma Mantovani
- Centre for Applied Biomedical Research - CRBA, University of Bologna, St. Orsola Hospital, Bologna, Italy
| | - Sofia Bin
- Centre for Applied Biomedical Research - CRBA, University of Bologna, St. Orsola Hospital, Bologna, Italy
| | - Alessandro Mattiaccio
- Centre for Applied Biomedical Research - CRBA, University of Bologna, St. Orsola Hospital, Bologna, Italy
| | - Alessandra Nivoli
- Clinica Psichiatrica, Dipartimento di Medicina Clinica e Sperimentale, University of Sassari, Italy
| | - Eduard Vieta
- Barcelona Bipolar Disorders Program, Hospital Clinic, IDIBAPS, CIBERSAM, University of Barcelona, Spain
| | - Dina Popovic
- Bipolar Disorders Programme, Psychiatry B, Sheba Medical Center, Tel Hashomer, Israel.
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14
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Han MR, Han KM, Kim A, Kang W, Kang Y, Kang J, Won E, Tae WS, Cho Y, Ham BJ. Whole-exome sequencing identifies variants associated with structural MRI markers in patients with bipolar disorders. J Affect Disord 2019; 249:159-168. [PMID: 30772743 DOI: 10.1016/j.jad.2019.02.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/29/2019] [Accepted: 02/10/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Bipolar disorder (BD) is one of the most heritable psychiatric disorders. A growing number of whole-exome sequencing (WES) studies for BD has been performed, however, no research has examined the association between single nucleotide variants (SNVs) from WES and structural magnetic resonance imaging (MRI) data. METHODS We sequenced whole-exomes in 53 patients with BD and 82 healthy control participants at an initial discovery stage and investigated the impacts of SNVs in risk genes from WES analysis on the cortical gray-matter thickness and integrity of white matter tracts and in the following stage. Cortical thickness and white matter integrity were investigated using the FreeSurfer and TRACULA (Tracts Constrained by UnderLying Anatomy). RESULTS We identified 122 BD-related genes including KMT2C, AHNAK, CDH23, DCHS1, FRAS1, MACF1 and RYR3 and observed 27 recurrent copy number alteration regions including gain on 8p23.1 and loss on 15q11.1 - q11.2. Among them, single nucleotide polymorphism (SNP) rs4639425 in KMT2C gene, which regulates histone H3 lysine 4 (H3K4) methylation involved in chromatin remodeling, was associated with widespread alterations of white matter integrity including the cingulum, uncinate fasciculus, cortico-spinal tract, and superior longitudinal fasciculus. LIMITATION The small sample size of patients with BD in the genome data may cause our study to be underpowered when searching for putative rare mutations. CONCLUSION This study first combined a WES approach and neuroimaging findings in psychiatric disorders. We postulate the rs4639425 may be associated with BD-related microstructural changes of white matter tracts.
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Affiliation(s)
- Mi-Ryung Han
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Man Han
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Aram Kim
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Wooyoung Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Youbin Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - June Kang
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Republic of Korea
| | - Eunsoo Won
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woo-Suk Tae
- Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea; Brain Convergence Research Center, Korea University Anam Hospital, Seoul, Republic of Korea.
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15
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Nitric oxide signalling and antidepressant action revisited. Cell Tissue Res 2019; 377:45-58. [PMID: 30649612 DOI: 10.1007/s00441-018-02987-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
Abstract
Studies about the pathogenesis of mood disorders have consistently shown that multiple factors, including genetic and environmental, play a crucial role on their development and neurobiology. Multiple pathological theories have been proposed, of which several ultimately affects or is a consequence of dysfunction in brain neuroplasticity and homeostatic mechanisms. However, current clinical available pharmacological intervention, which is predominantly monoamine-based, suffers from a partial and lacking response even after weeks of continuous treatment. These issues raise the need for better understanding of aetiologies and brain abnormalities in depression, as well as developing novel treatment strategies. Nitric oxide (NO) is a gaseous unconventional neurotransmitter, which regulates and governs several important physiological functions in the central nervous system, including processes, which can be associated with the development of mood disorders. This review will present general aspects of the NO system in depression, highlighting potential targets that may be utilized and further explored as novel therapeutic targets in the future pharmacotherapy of depression. In particular, the review will link the importance of neuroplasticity mechanisms governed by NO to a possible molecular basis for the antidepressant effects.
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16
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Sheerin CM, Vladimirov V, Williamson V, Bountress K, K Danielson C, Ruggiero K, Amstadter AB. A preliminary investigation of rare variants associated with genetic risk for PTSD in a natural disaster-exposed adolescent sample. Eur J Psychotraumatol 2019; 10:1688935. [PMID: 31839899 PMCID: PMC6896412 DOI: 10.1080/20008198.2019.1688935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Posttraumatic stress disorder (PTSD) involves a complex interaction of biological, psychological, and social factors. Numerous studies have demonstrated genetic variation associated with the development of PTSD, primarily in adults. However, the contribution of low frequency and rare genetic variants to PTSD is unknown to date. Moreover, there is limited work on genetic risk for PTSD in child and adolescent populations. Objective: This preliminary study aimed to identify the low frequency and rare genetic variation that contributes to PTSD using an exome array. Method: This post-disaster, adolescent sample (n = 707, 51% females, M age = 14.54) was assessed for PTSD diagnosis and symptom count following tornado exposure. Results: Gene-based models, covarying for ancestry principal components, age, sex, tornado severity, and previous trauma identified variants in four genes associated with diagnosis and 276 genes associated with symptom count (at p adj < .001). Functional class analyses suggested an association with variants in the nonsense class (nonsynonymous variant that results in truncation of, and usually non-functional, protein) with both outcomes. An exploratory gene network pathway analysis showed a great number of significant genes involved in brain and immune function, illustrating the usefulness of downstream examination of gene-based findings that may point to relevant biological processes. Conclusions: While further investigation in larger samples is warranted, findings align with extant PTSD literature that has identified variants associated with biological conditions such as immune function.
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Affiliation(s)
- Christina M Sheerin
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vernell Williamson
- Molecular Diagnostics Laboratory, Virginia Commonwealth University, Richmond, VA, USA
| | - Kaitlin Bountress
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Carla K Danielson
- Departments of Nursing and Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Kenneth Ruggiero
- Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Ananda B Amstadter
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
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17
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Salvoro C, Bortoluzzi S, Coppe A, Valle G, Feltrin E, Mostacciuolo ML, Vazza G. Rare Risk Variants Identification by Identity-by-Descent Mapping and Whole-Exome Sequencing Implicates Neuronal Development Pathways in Schizophrenia and Bipolar Disorder. Mol Neurobiol 2018; 55:7366-7376. [PMID: 29411265 DOI: 10.1007/s12035-018-0922-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 01/22/2018] [Indexed: 12/31/2022]
Abstract
Schizophrenia (SCZ) and bipolar disorder (BPD) are highly heritable disorders with an estimated co-heritability of 68%. Hundreds of common alleles have been implicated, but recently a role for rare, high-penetrant variants has been also suggested in both disorders. This study investigated a familial cohort of SCZ and BPD patients from a closed population sample, where the high recurrence of the disorders and the homogenous genetic background indicate a possible enrichment in rare risk alleles. A total of 230 subjects (161 cases, 22 unaffected relatives, and 47 controls) were genetically investigated through an innovative strategy that integrates identity-by-descent (IBD) mapping and whole-exome sequencing (WES). IBD analysis allowed to track high-risk haplotypes (IBDrisk) shared exclusively by multiple patients from different families and possibly carrying the most penetrant alleles. A total of 444 non-synonymous sequence variants, of which 137 disruptive, were identified in IBDrisk haplotypes by WES. Interestingly, gene sets previously implicated in SCZ (i.e., post-synaptic density (PSD) proteins, voltage-gated calcium channels (VGCCs), and fragile X mental retardation protein (FMRP) targets) were found significantly enriched in genes carrying IBDrisk variants. Further, IBDrisk variants were preferentially affecting genes involved in the extracellular matrix (ECM) biology and axon guidance processes which appeared to be functionally connected in the pathway-derived meta-network analysis. Results thus confirm rare risk variants as key factors in SCZ and BPD pathogenesis and highlight a role for the development of neuronal connectivity in the etiology of both disorders.
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Affiliation(s)
- C Salvoro
- Department of Biology, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - A Coppe
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G Valle
- Department of Biology, University of Padova, Padova, Italy
| | - E Feltrin
- Department of Biology, University of Padova, Padova, Italy
| | | | - G Vazza
- Department of Biology, University of Padova, Padova, Italy.
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18
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Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Belonogova NM, Svishcheva GR, Wilson JF, Campbell H, Axenovich TI. Weighted functional linear regression models for gene-based association analysis. PLoS One 2018; 13:e0190486. [PMID: 29309409 PMCID: PMC5757938 DOI: 10.1371/journal.pone.0190486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 12/17/2017] [Indexed: 11/19/2022] Open
Abstract
Functional linear regression models are effectively used in gene-based association analysis of complex traits. These models combine information about individual genetic variants, taking into account their positions and reducing the influence of noise and/or observation errors. To increase the power of methods, where several differently informative components are combined, weights are introduced to give the advantage to more informative components. Allele-specific weights have been introduced to collapsing and kernel-based approaches to gene-based association analysis. Here we have for the first time introduced weights to functional linear regression models adapted for both independent and family samples. Using data simulated on the basis of GAW17 genotypes and weights defined by allele frequencies via the beta distribution, we demonstrated that type I errors correspond to declared values and that increasing the weights of causal variants allows the power of functional linear models to be increased. We applied the new method to real data on blood pressure from the ORCADES sample. Five of the six known genes with P < 0.1 in at least one analysis had lower P values with weighted models. Moreover, we found an association between diastolic blood pressure and the VMP1 gene (P = 8.18×10-6), when we used a weighted functional model. For this gene, the unweighted functional and weighted kernel-based models had P = 0.004 and 0.006, respectively. The new method has been implemented in the program package FREGAT, which is freely available at https://cran.r-project.org/web/packages/FREGAT/index.html.
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Affiliation(s)
- Nadezhda M. Belonogova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Gulnara R. Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Vavilov Institute of General Genetics, the Russian Academy of Sciences, Moscow, Russia
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Tatiana I. Axenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder. Int J Mol Sci 2017; 18:ijms18122763. [PMID: 29257106 PMCID: PMC5751362 DOI: 10.3390/ijms18122763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 11/25/2022] Open
Abstract
Bipolar disorder is a common and severe mental illness with unsolved pathophysiology. A genome-wide association study (GWAS) has been used to find a number of risk genes, but it is difficult for a GWAS to find genes indirectly associated with a disease. To find core hub genes, we introduce a network analysis after the GWAS was conducted. Six thousand four hundred fifty eight single nucleotide polymorphisms (SNPs) with p < 0.01 were sifted out from Wellcome Trust Case Control Consortium (WTCCC) dataset and mapped to 2045 genes, which are then compared with the protein–protein network. One hundred twelve genes with a degree >17 were chosen as hub genes from which five significant modules and four core hub genes (FBXL13, WDFY2, bFGF, and MTHFD1L) were found. These core hub genes have not been reported to be directly associated with BD but may function by interacting with genes directly related to BD. Our method engenders new thoughts on finding genes indirectly associated with, but important for, complex diseases.
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