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Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333436. [PMID: 38744462 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Inherited peripheral neuropathies (IPNs) encompass a clinically and genetically heterogeneous group of disorders causing length-dependent degeneration of peripheral autonomic, motor and/or sensory nerves. Despite gold-standard diagnostic testing for pathogenic variants in over 100 known associated genes, many patients with IPN remain genetically unsolved. Providing patients with a diagnosis is critical for reducing their 'diagnostic odyssey', improving clinical care, and for informed genetic counselling. The last decade of massively parallel sequencing technologies has seen a rapid increase in the number of newly described IPN-associated gene variants contributing to IPN pathogenesis. However, the scarcity of additional families and functional data supporting variants in potential novel genes is prolonging patient diagnostic uncertainty and contributing to the missing heritability of IPNs. We review the last decade of IPN disease gene discovery to highlight novel genes, structural variation and short tandem repeat expansions contributing to IPN pathogenesis. From the lessons learnt, we provide our vision for IPN research as we anticipate the future, providing examples of emerging technologies, resources and tools that we propose that will expedite the genetic diagnosis of unsolved IPN families.
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Affiliation(s)
- Jevin M Parmar
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Preventive Genetics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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Timothy KW, Bauer R, Larkin KA, Walsh EP, Abrams DJ, Corcia CG, Valsamakis A, Pitt GS, Dick IE, Golden A. A Natural History Study of Timothy Syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307583. [PMID: 38826393 PMCID: PMC11142284 DOI: 10.1101/2024.05.20.24307583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Timothy syndrome (OMIM #601005) is a rare disease caused by variants in the gene CACNA1C . Timothy syndrome patients were first identified as having a cardiac presentation of Long QT and syndactyly of the fingers and/or toes, and an identical variant in CACNA1C , Gly406Arg. However, since this original identification, more individuals harboring diverse variants in CACNA1C have been identified and have presented with various cardiac and extra-cardiac symptoms. Furthermore, it has remained underexplored whether individuals harboring canonical Gly406Arg variants in mutually exclusive exon 8A (Timothy syndrome 1) or exon 8 (Timothy syndrome 2) have additional symptoms. Here, we describe the first Natural History Study for Timothy syndrome, providing a thorough resource describing the current understanding of disease manifestation in Timothy syndrome patients. Parents of Timothy syndrome children were queried regarding a wide-ranging set of symptoms and features via a survey. Importantly, we find that in addition to cardiac concerns, Timothy syndrome patients commonly share extra-cardiac features including neurodevelopmental impairments, hypoglycemia, and respiratory problems. Our work expands the current understanding of the disorder to better inform the care of Timothy syndrome patients.
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Cipriano L, Piscopo R, Aiello C, Novelli A, Iolascon A, Piscopo C. Expanding the Phenotype of the CACNA1C-Associated Neurological Disorders in Children: Systematic Literature Review and Description of a Novel Mutation. CHILDREN (BASEL, SWITZERLAND) 2024; 11:541. [PMID: 38790536 PMCID: PMC11119747 DOI: 10.3390/children11050541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024]
Abstract
Background: CACNA1C gene encodes the alpha 1 subunit of the CaV1.2 L-type Ca2+ channel. Pathogenic variants in this gene have been associated with cardiac rhythm disorders such as long QT syndrome, Brugada syndrome and Timothy syndrome. Recent evidence has suggested the possible association between CACNA1C mutations and neurologically-isolated (in absence of cardiac involvement) phenotypes in children, giving birth to a wider spectrum of CACNA1C-related clinical presentations. However, to date, little is known about the variety of both neurological and non-neurological signs/symptoms in the neurologically-predominant phenotypes. Methods and Results: We conducted a systematic review of neurologically-predominant presentations without cardiac conduction defects, associated with CACNA1C mutations. We also reported a novel de novo missense pathogenic variant in the CACNA1C gene of a children patient presenting with constructional, dressing and oro-buccal apraxia associated with behavioral abnormalities, mild intellectual disability, dental anomalies, gingival hyperplasia and mild musculoskeletal defects, without cardiac conduction defects. Conclusions: The present study highlights the importance of considering the investigation of the CACNA1C gene in children's neurological isolated syndromes, and expands the phenotype of the CACNA1C related conditions. In addition, the present study highlights that, even in absence of cardiac conduction defects, nuanced clinical manifestations of the Timothy syndrome (e.g., dental and gingival defects) could be found. These findings suggest the high variable expressivity of the CACNA1C gene and remark that the absence of cardiac involvement should not mislead the diagnosis of a CACNA1C related disorder.
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Affiliation(s)
- Lorenzo Cipriano
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (L.C.); (A.I.)
| | - Raffaele Piscopo
- Department of Neuroscience, Reproductive and Odontostomatological Sciences, University Federico II, 80131 Naples, Italy;
| | - Chiara Aiello
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy; (C.A.); (A.N.)
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, 00146 Rome, Italy; (C.A.); (A.N.)
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy; (L.C.); (A.I.)
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. “Antonio Cardarelli”, 80131 Naples, Italy
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4
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker PB, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. Sci Rep 2024; 14:6362. [PMID: 38493204 PMCID: PMC10944514 DOI: 10.1038/s41598-024-56684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter- and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of antigens. In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface antigens that could be targeted by antibodies and chimeric antigen receptor-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas) and 9166 normal tissue samples (from the Genotype-Tissue Expression project), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN, which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative antigens. Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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Affiliation(s)
- Takahide Nejo
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lin Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Senthilnath Lakshmanachetty
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Marco Gallus
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Darwin W Kwok
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lee H Chen
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Diego A Carrera
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Michael Y Zhang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Gabriella C Maldonado
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akane Yamamichi
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Payal B Watchmaker
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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Cao J, Wei Z, Nie Y, Chen HZ. Therapeutic potential of alternative splicing in cardiovascular diseases. EBioMedicine 2024; 101:104995. [PMID: 38350330 PMCID: PMC10874720 DOI: 10.1016/j.ebiom.2024.104995] [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: 09/24/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
RNA splicing is an important RNA processing step required by multiexon protein-coding mRNAs and some noncoding RNAs. Precise RNA splicing is required for maintaining gene and cell function; however, mis-spliced RNA transcripts can lead to loss- or gain-of-function effects in human diseases. Mis-spliced RNAs induced by gene mutations or the dysregulation of splicing regulators may result in frameshifts, nonsense-mediated decay (NMD), or inclusion/exclusion of exons. Genetic animal models have characterised multiple splicing factors required for cardiac development or function. Moreover, sarcomeric and ion channel genes, which are closely associated with cardiovascular function and disease, are hotspots for AS. Here, we summarise splicing factors and their targets that are associated with cardiovascular diseases, introduce some therapies potentially related to pathological AS targets, and raise outstanding questions and future directions in this field.
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Affiliation(s)
- Jun Cao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, 100124, PR China; University of Texas Medical Branch at Galveston, TX, 77555, USA
| | - Ziyu Wei
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100037, China.
| | - Hou-Zao Chen
- Department of Biochemistry & Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences, Beijing, China.
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6
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Jones EF, Howton TC, Flanary VL, Clark AD, Lasseigne BN. Long-read RNA sequencing identifies region- and sex-specific C57BL/6J mouse brain mRNA isoform expression and usage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575219. [PMID: 38260631 PMCID: PMC10802568 DOI: 10.1101/2024.01.11.575219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alternative splicing (AS) contributes to the biological heterogeneity between species, sexes, tissues, and cell types. Many diseases are either caused by alterations in AS or by alterations to AS. Therefore, measuring AS accurately and efficiently is critical for assessing molecular phenotypes, including those associated with disease. Long-read sequencing enables more accurate quantification of differentially spliced isoform expression than short-read sequencing approaches, and third-generation platforms facilitate high-throughput experiments. To assess differences in AS across the cerebellum, cortex, hippocampus, and striatum by sex, we generated and analyzed Oxford Nanopore Technologies (ONT) long-read RNA sequencing (lrRNA-Seq) C57BL/6J mouse brain cDNA libraries. From >85 million reads that passed quality control metrics, we calculated differential gene expression (DGE), differential transcript expression (DTE), and differential transcript usage (DTU) across brain regions and by sex. We found significant DGE, DTE, and DTU across brain regions and that the cerebellum had the most differences compared to the other three regions. Additionally, we found region-specific differential splicing between sexes, with the most sex differences in DTU in the cortex and no DTU in the hippocampus. We also report on two distinct patterns of sex DTU we observed, sex-divergent and sex-specific, that could potentially help explain sex differences in the prevalence and prognosis of various neurological and psychiatric disorders in future studies. Finally, we built a Shiny web application for researchers to explore the data further. Our study provides a resource for the community; it underscores the importance of AS in biological heterogeneity and the utility of long-read sequencing to better understand AS in the brain.
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Affiliation(s)
- Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Timothy C. Howton
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Amanda D. Clark
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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7
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Liu A, Fernandes BS, Citu C, Zhao Z. Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: an integrative study of single-nucleus transcriptomes and genetic association. Alzheimers Res Ther 2024; 16:3. [PMID: 38167548 PMCID: PMC10762817 DOI: 10.1186/s13195-023-01372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Recently, single-nucleus RNA-seq (snRNA-seq) analyses have revealed important cellular and functional features of Alzheimer's disease (AD), a prevalent neurodegenerative disease. However, our knowledge regarding intercellular communication mediated by dysregulated ligand-receptor (LR) interactions remains very limited in AD brains. METHODS We systematically assessed the intercellular communication networks by using a discovery snRNA-seq dataset comprising 69,499 nuclei from 48 human postmortem prefrontal cortex (PFC) samples. We replicated the findings using an independent snRNA-seq dataset of 56,440 nuclei from 18 PFC samples. By integrating genetic signals from AD genome-wide association studies (GWAS) summary statistics and whole genome sequencing (WGS) data, we prioritized AD-associated Gene Ontology (GO) terms containing dysregulated LR interactions. We further explored drug repurposing for the prioritized LR pairs using the Therapeutic Targets Database. RESULTS We identified 190 dysregulated LR interactions across six major cell types in AD PFC, of which 107 pairs were replicated. Among the replicated LR signals, we found globally downregulated communications in the astrocytes-to-neurons signaling axis, characterized, for instance, by the downregulation of APOE-related and Calmodulin (CALM)-related LR interactions and their potential regulatory connections to target genes. Pathway analyses revealed 44 GO terms significantly linked to AD, highlighting Biological Processes such as 'amyloid precursor protein processing' and 'ion transmembrane transport,' among others. We prioritized several drug repurposing candidates, such as cromoglicate, targeting the identified dysregulated LR pairs. CONCLUSIONS Our integrative analysis identified key dysregulated LR interactions in a cell type-specific manner and the associated GO terms in AD, offering novel insights into potential therapeutic targets involved in disrupted cell-cell communication in AD.
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Affiliation(s)
- Andi Liu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 600, Houston, TX, 77030, USA
| | - Brisa S Fernandes
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 600, Houston, TX, 77030, USA
| | - Citu Citu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 600, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 600, Houston, TX, 77030, USA.
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.
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8
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Fernando MB, Fan Y, Zhang Y, Kammourh S, Murphy AN, Ghorbani S, Onatzevitch R, Pero A, Padilla C, Flaherty EK, Prytkova IK, Cao L, Williams S, Fang G, Slesinger PA, Brennand KJ. Precise Therapeutic Targeting of Distinct NRXN1+/- Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564543. [PMID: 37961635 PMCID: PMC10634884 DOI: 10.1101/2023.10.28.564543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
As genetic studies continue to identify risk loci that are significantly associated with risk for neuropsychiatric disease, a critical unanswered question is the extent to which diverse mutations--sometimes impacting the same gene-- will require tailored therapeutic strategies. Here we consider this in the context of rare neuropsychiatric disorder-associated copy number variants (2p16.3) resulting in heterozygous deletions in NRXN1, a pre-synaptic cell adhesion protein that serves as a critical synaptic organizer in the brain. Complex patterns of NRXN1 alternative splicing are fundamental to establishing diverse neurocircuitry, vary between the cell types of the brain, and are differentially impacted by unique (non-recurrent) deletions. We contrast the cell-type-specific impact of patient-specific mutations in NRXN1 using human induced pluripotent stem cells, finding that perturbations in NRXN1 splicing result in divergent cell-type-specific synaptic outcomes. Via distinct loss-of-function (LOF) and gain-of-function (GOF) mechanisms, NRXN1+/- deletions cause decreased synaptic activity in glutamatergic neurons, yet increased synaptic activity in GABAergic neurons. Stratification of patients by LOF and GOF mechanisms will facilitate individualized restoration of NRXN1 isoform repertoires; towards this, antisense oligonucleotides knockdown mutant isoform expression and alters synaptic transcriptional signatures, while treatment with β-estradiol rescues synaptic function in glutamatergic neurons. Given the increasing number of mutations predicted to engender both LOF and GOF mechanisms in brain disease, our findings add nuance to future considerations of precision medicine.
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Affiliation(s)
- Michael B. Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
| | - Yu Fan
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yanchun Zhang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sarah Kammourh
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aleta N. Murphy
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sadaf Ghorbani
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
- Haukeland University Hospital, Bergen, Norway
| | - Ryan Onatzevitch
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adriana Pero
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Christopher Padilla
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Erin K. Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Iya K. Prytkova
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lei Cao
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Sarah Williams
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gang Fang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Paul A. Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Black Family Stem Cell Institute, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06520
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9
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Baker MR, Lee AS, Rajadhyaksha AM. L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. Channels (Austin) 2023; 17:2176984. [PMID: 36803254 PMCID: PMC9980663 DOI: 10.1080/19336950.2023.2176984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/01/2023] [Indexed: 02/21/2023] Open
Abstract
Recent human genetic studies have linked a variety of genetic variants in the CACNA1C and CACNA1D genes to neuropsychiatric and neurodevelopmental disorders. This is not surprising given the work from multiple laboratories using cell and animal models that have established that Cav1.2 and Cav1.3 L-type calcium channels (LTCCs), encoded by CACNA1C and CACNA1D, respectively, play a key role in various neuronal processes that are essential for normal brain development, connectivity, and experience-dependent plasticity. Of the multiple genetic aberrations reported, genome-wide association studies (GWASs) have identified multiple single nucleotide polymorphisms (SNPs) in CACNA1C and CACNA1D that are present within introns, in accordance with the growing body of literature establishing that large numbers of SNPs associated with complex diseases, including neuropsychiatric disorders, are present within non-coding regions. How these intronic SNPs affect gene expression has remained a question. Here, we review recent studies that are beginning to shed light on how neuropsychiatric-linked non-coding genetic variants can impact gene expression via regulation at the genomic and chromatin levels. We additionally review recent studies that are uncovering how altered calcium signaling through LTCCs impact some of the neuronal developmental processes, such as neurogenesis, neuron migration, and neuron differentiation. Together, the described changes in genomic regulation and disruptions in neurodevelopment provide possible mechanisms by which genetic variants of LTCC genes contribute to neuropsychiatric and neurodevelopmental disorders.
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Affiliation(s)
- Madelyn R. Baker
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, USA
| | - Andrew S. Lee
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Anjali M. Rajadhyaksha
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine, New York, USA
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10
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker P, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564156. [PMID: 37961484 PMCID: PMC10634890 DOI: 10.1101/2023.10.26.564156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter-and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of neoantigens. Results In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface neoantigens that could be targeted by antibodies and chimeric antigen receptor (CAR)-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas [TCGA]) and 9,166 normal tissue samples (from the Genotype-Tissue Expression project [GTEx]), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN , which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative neoantigens. Conclusions Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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11
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Dahimene S, Page KM, Nieto-Rostro M, Pratt WS, Dolphin AC. The Interplay Between Splicing of Two Exon Combinations Differentially Affects Membrane Targeting and Function of Human Ca V2.2. FUNCTION 2023; 5:zqad060. [PMID: 38020068 PMCID: PMC10666670 DOI: 10.1093/function/zqad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
N-type calcium channels (CaV2.2) are predominantly localized in presynaptic terminals, and are particularly important for pain transmission in the spinal cord. Furthermore, they have multiple isoforms, conferred by alternatively spliced or cassette exons, which are differentially expressed. Here, we have examined alternatively spliced exon47 variants that encode a long or short C-terminus in human CaV2.2. In the Ensembl database, all short exon47-containing transcripts were associated with the absence of exon18a, therefore, we also examined the effect of inclusion or absence of exon18a, combinatorially with the exon47 splice variants. We found that long exon47, only in the additional presence of exon18a, results in CaV2.2 currents that have a 3.6-fold greater maximum conductance than the other three combinations. In contrast, cell-surface expression of CaV2.2 in both tsA-201 cells and hippocampal neurons is increased ∼4-fold by long exon47, relative to short exon47, in either the presence or the absence of exon18a. This surprising discrepancy between trafficking and function indicates that cell-surface expression is enhanced by long exon47, independently of exon18a. However, in the presence of long exon47, exon18a mediates an additional permissive effect on CaV2.2 gating. We also investigated the single-nucleotide polymorphism in exon47 that has been linked to schizophrenia and Parkinson's disease, which we found is only non-synonymous in the short exon47 C-terminal isoform, resulting in two minor alleles. This study highlights the importance of investigating the combinatorial effects of exon inclusion, rather than each in isolation, in order to increase our understanding of calcium channel function.
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Affiliation(s)
- Shehrazade Dahimene
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Karen M Page
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Manuela Nieto-Rostro
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Wendy S Pratt
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
| | - Annette C Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, UK
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12
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Boboc IKS, Cojocaru A, Nedelea G, Catalin B, Bogdan M, Calina D. Chronic Administration of Ion Channel Blockers Impact Microglia Morphology and Function in a Murine Model of Alzheimer's Disease. Int J Mol Sci 2023; 24:14474. [PMID: 37833922 PMCID: PMC10572937 DOI: 10.3390/ijms241914474] [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: 08/11/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
As the population ages, a high prevalence of multimorbidity will affect the way physicians need to think about drug interactions. With microglia's important involvement in the pathology and progression of Alzheimer's disease (AD), understanding whether systemically administered drugs intended for other affections could impact microglia function, already impacted by the presence of beta-amyloid, is important. The aim of this study was to evaluate morphological changes of microglia, using in vivo 2-photon laser scanning microscopy, in a murine model of AD under systemic administration of sodium or calcium ion channel blockers in order to establish potential effects that these drugs might have on microglia under neuro-inflammatory conditions. A total of 30 mice (age 14-16 weeks, weight 20-25 g) were used, with 25 APP randomly divided into three groups. The remaining animals were CX3CR1GFP/GFP male mice (n = 5) used as WT controls. After baseline behavior testing, all animals received daily intraperitoneal injections for 30 days according to the assigned group [WT (n = 5), Control (n = 5), Carbamazepine (n = 10), and Verapamil (n = 10)]. The results showed that the Verapamil treatment improved short-term memory and enhanced exploratory behavior in APP mice. The Carbamazepine treatment also improved short-term memory but did not elicit significant changes in anxiety-related behavior. Both Verapamil and Carbamazepine reduced the surveillance speed of microglia processes and changed microglia morphology in the cortex compared to the Control group. Due to their complex molecular machinery, microglia are potentially affected by drugs that do not target them specifically, and, as such, investigating these interactions could prove beneficial in our management of neurodegenerative pathologies.
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Affiliation(s)
- Ianis Kevyn Stefan Boboc
- Department of Pharmacology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Experimental Research Centre for Normal and Pathological Aging, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- U.M.F. Doctoral School Craiova, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Alexandru Cojocaru
- Experimental Research Centre for Normal and Pathological Aging, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Physiology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Gabriel Nedelea
- Experimental Research Centre for Normal and Pathological Aging, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Bogdan Catalin
- Experimental Research Centre for Normal and Pathological Aging, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
- Department of Physiology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Maria Bogdan
- Department of Pharmacology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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13
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Liu A, Fernandes BS, Citu C, Zhao Z. Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: An integrative study of single-nucleus transcriptomes and genetic association. RESEARCH SQUARE 2023:rs.3.rs-3335643. [PMID: 37790454 PMCID: PMC10543294 DOI: 10.21203/rs.3.rs-3335643/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Recently, single-nucleus RNA-seq (snRNA-seq) analyses have revealed important cellular and functional features of Alzheimer's disease (AD), a prevalent neurodegenerative disease. However, our knowledge regarding intercellular communication mediated by dysregulated ligand-receptor (LR) interactions remains very limited in AD brains. Methods We systematically assessed the intercellular communication networks by using a discovery snRNA-seq dataset comprising 69,499 nuclei from 48 human postmortem prefrontal cortex (PFC) samples. We replicated the findings using an independent snRNA-seq dataset of 56,440 nuclei from 18 PFC samples. By integrating genetic signals from AD genome-wide association studies (GWAS) summary statistics and whole genome sequencing (WGS) data, we prioritized AD-associated Gene Ontology (GO) terms containing dysregulated LR interactions. We further explored drug repurposing for the prioritized LR pairs using the Therapeutic Targets Database. Results We identified 316 dysregulated LR interactions across six major cell types in AD PFC, of which 210 pairs were replicated. Among the replicated LR signals, we found globally downregulated communications in astrocytes-to-neurons signaling axis, characterized, for instance, by the downregulation of APOE-related and Calmodulin (CALM)-related LR interactions and their potential regulatory connections to target genes. Pathway analyses revealed 60 GO terms significantly linked to AD, highlighting Biological Processes such as 'amyloid precursor protein processing' and 'ion transmembrane transport', among others. We prioritized several drug repurposing candidates, such as cromoglicate, targeting the identified dysregulated LR pairs. Conclusions Our integrative analysis identified key dysregulated LR interactions in a cell type-specific manner and the associated GO terms in AD, offering novel insights into potential therapeutic targets involved in disrupted cell-cell communication in AD.
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Affiliation(s)
- Andi Liu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston
| | - Brisa S Fernandes
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Citu Citu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston
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14
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Hughes AEO, Montgomery MC, Liu C, Weimer ET. Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing. Front Immunol 2023; 14:1199618. [PMID: 37662944 PMCID: PMC10471969 DOI: 10.3389/fimmu.2023.1199618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/05/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction While tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes. Methods cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within individual reads. Results Splice variants were rare among class I HLA genes (median exon retention rate 99%-100%), except for several HLA-C alleles with exon 5 spliced out of up to 15% of reads. Splice variants were also rare among class II HLA genes (median exon retention rate 98%-100%), except for HLA-DQB1. Consistent with previous work, exon 5 of HLA-DQB1 was spliced out in alleles with a mutated splice acceptor site at rs28688207. Surprisingly, a 28% loss of exon 5 was also observed in HLA-DQB1 alleles with an intact splice acceptor site at rs28688207. Discussion We describe a simple bioinformatic workflow to quantify allele-specific expression of HLA transcript isoforms. Further studies are warranted to characterize the repertoire of HLA transcripts expressed in different cell types and tissues across diverse populations.
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Affiliation(s)
- Andrew E. O. Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Maureen C. Montgomery
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
| | - Chang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Eric T. Weimer
- Molecular Immunology Laboratory, McLendon Clinical Laboratories, University of North Carolina Hospitals, Chapel Hill, NC, United States
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States
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15
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Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat Commun 2023; 14:4760. [PMID: 37553321 PMCID: PMC10409798 DOI: 10.1038/s41467-023-40083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
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Affiliation(s)
- Feng Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yang Xu
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Noah Smith
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber Notaro
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samantha Gaerlan
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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16
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Abstract
OBJECTIVE Due to the phenotypic heterogeneity and etiological complexity of bipolar disorder (BD), many patients do not respond well to the current medications, and developing novel effective treatment is necessary. Whether any BD genome-wide association study (GWAS) risk genes were targets of existing drugs or novel drugs that can be repurposed in the clinical treatment of BD is a hot topic in the GWAS era of BD. METHODS A list of 425 protein-coding BD risk genes was distilled through the BD GWAS, and 4479 protein-coding druggable targets were retrieved from the druggable genome. The overlapped genes/targets were subjected to further analyses in DrugBank, Pharos, and DGIdb datasets in terms of their FDA status, mechanism of action and primary indication, to identify their potential for repurposing. RESULTS We identified 58 BD GWAS risk genes grouped as the druggable targets, and several genes were given higher priority. These BD risk genes were targets of antipsychotics, antidepressants, antiepileptics, calcium channel antagonists, as well as anxiolytics and analgesics, either existing clinically-approved drugs for BD or the drugs than can be repurposed for treatment of BD in the future. Those genes were also likely relevant to BD pathophysiology, as many of them encode ion channel, ion transporter or neurotransmitter receptor, or the mice manipulating those genes are likely to mimic the phenotypes manifest in BD patients. CONCLUSIONS This study identifies several targets that may facilitate the discovery of novel treatments in BD, and implies the value of conducting GWAS into clinical translation.
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Affiliation(s)
- Hao-Xiang Qi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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17
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Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
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Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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18
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Liu H, Liu H, Wang L, Song L, Jiang G, Lu Q, Yang T, Peng H, Cai R, Zhao X, Zhao T, Wu H. Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform. Nat Commun 2023; 14:3085. [PMID: 37248244 DOI: 10.1038/s41467-023-38621-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
Isoforms of a gene may contribute to diverse biological functions. In the cochlea, the repertoire of alternative isoforms remains unexplored. We integrated single-cell short-read and long-read RNA sequencing techniques and identified 236,012 transcripts, 126,612 of which were unannotated in the GENCODE database. Then we analyzed and verified the unannotated transcripts using RNA-seq, RT-PCR, Sanger sequencing, and MS-based proteomics approaches. To illustrate the importance of identifying spliced isoforms, we investigated otoferlin, a key protein involved in synaptic transmission in inner hair cells (IHCs). Upon deletion of the canonical otoferlin isoform, the identified short isoform is able to support normal hearing thresholds but with reduced sustained exocytosis of IHCs, and further revealed otoferlin functions in endocytic membrane retrieval that was not well-addressed previously. Furthermore, we found that otoferlin isoforms are associated with IHC functions and auditory phenotypes. This work expands our mechanistic understanding of auditory functions at the level of isoform resolution.
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Affiliation(s)
- Huihui Liu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hongchao Liu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Longhao Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Lei Song
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Guixian Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Qing Lu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hu Peng
- Department of Otolaryngology-Head and Neck Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
| | - Ruijie Cai
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Xingle Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Ting Zhao
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, 200011, China.
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Walker LC, de la Hoya M, Wiggins GA, Lindy A, Vincent LM, Parsons M, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.24.23286431. [PMID: 36865205 PMCID: PMC9980257 DOI: 10.1101/2023.02.24.23286431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
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Abstract
The CACNA1C gene encodes the pore-forming subunit of the CaV1.2 L-type Ca2+ channel, a critical component of membrane physiology in multiple tissues, including the heart, brain, and immune system. As such, mutations altering the function of these channels have the potential to impact a wide array of cellular functions. The first mutations identified within CACNA1C were shown to cause a severe, multisystem disorder known as Timothy syndrome (TS), which is characterized by neurodevelopmental deficits, long-QT syndrome, life-threatening cardiac arrhythmias, craniofacial abnormalities, and immune deficits. Since this initial description, the number and variety of disease-associated mutations identified in CACNA1C have grown tremendously, expanding the range of phenotypes observed in affected patients. CACNA1C channelopathies are now known to encompass multisystem phenotypes as described in TS, as well as more selective phenotypes where patients may exhibit predominantly cardiac or neurological symptoms. Here, we review the impact of genetic mutations on CaV1.2 function and the resultant physiological consequences.
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Affiliation(s)
- Kevin G Herold
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - John W Hussey
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ivy E Dick
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA.
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21
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Hamim I, Sekine KT, Komatsu K. How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape? PLANT MOLECULAR BIOLOGY 2022; 110:469-484. [PMID: 35962900 DOI: 10.1007/s11103-022-01305-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Long-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as well as contributing to emerging areas of interest in plant-pathogen interactions, disease management techniques, and the introduction of new plant varieties or cultivars. Long-read sequencing (LRS) technologies are progressively being implemented to study plants and pathogens of agricultural importance, which have substantial economic effects. The variability and complexity of the genome and transcriptome affect plant growth, development and pathogen responses. Overcoming the limitations of second-generation sequencing, LRS technology has significantly increased the length of a single contiguous read from a few hundred to millions of base pairs. Because of the longer read lengths, new analysis methods and tools have been developed for plant and pathogen genomics and transcriptomics. LRS technologies enable faster, more efficient, and high-throughput ultralong reads, allowing direct sequencing of genomes that would be impossible or difficult to investigate using short-read sequencing approaches. These benefits include genome assembly in repetitive areas, creating more comprehensive and exact genome determinations, assembling full-length transcripts, and detecting DNA and RNA alterations. Furthermore, these technologies allow for the identification of transcriptome diversity, significant structural variation analysis, and direct epigenetic mark detection in plant and pathogen genomic regions. LRS in plant pathology is found efficient for identifying and characterization of effectors in plants as well as known and unknown plant pathogens. In this review, we investigate how these technologies are transforming the landscape of determination and characterization of plant and pathogen genomes and transcriptomes efficiently and accurately. Moreover, we highlight potential areas of interest offered by LRS technologies for future study into plant-pathogen interactions, disease control strategies, and the development of new plant varieties or cultivars.
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Affiliation(s)
- Islam Hamim
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
- International Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ken-Taro Sekine
- Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.
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22
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Borbás J, Vámos M, Hategan L, Hanák L, Farkas N, Szakács Z, Csupor D, Tél B, Kupó P, Csányi B, Nagy V, Komócsi A, Habon T, Hegyi P, Sepp R. Geno- and phenotypic characteristics and clinical outcomes of CACNA1C gene mutation associated Timothy syndrome, “cardiac only” Timothy syndrome and isolated long QT syndrome 8: A systematic review. Front Cardiovasc Med 2022; 9:1021009. [DOI: 10.3389/fcvm.2022.1021009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/02/2022] [Indexed: 11/30/2022] Open
Abstract
BackgroundMutations in the CACNA1C gene–encoding for the major Ca2+ channel of the heart–may exhibit a variety of clinical manifestations. These include typical or atypical Timothy syndromes (TS) which are associated with multiple organ manifestations, and cardiac involvement in form of malignant arrhythmias, QTc prolongation, or AV block. “Cardiac only” Timothy syndrome (COTS) shows no extracardiac manifestation, whereas some CACNA1C gene mutations are associated with QTc prolongation alone (isolated long QT syndrome 8, LQT8).MethodsA systematic search of the literature reporting cases of CACNA1C gene mutation associated syndromes, including TS, COTS and isolated LQT8 via major databases published from 2004 through 2019 was performed. Detailed patient-level phenotypic and genotypic characteristics, as well as long-term outcome measures were collected and compared between pre-specified patient groups, defined both on phenotype and genotype.ResultsA total of 59 TS, 6 COTS, and 20 isolated LQT8 index cases were identified. Apart of syndactyly or baldness, there were no major differences regarding clinical manifestations or outcome measures between TS subtypes, either defining TS subtypes on the genotype or based on the phenotype. Both subtypes were characterized by an extreme degree of QTc prolongation (median ≥600 ms) which were reflected in high major adverse cardiac event rate. On the other hand, there were marked differences between TS, COTS, and isolated LQT8. Timothy syndrome was characterized by a much earlier disease onset, much more pronounced QTc prolongation and much higher mortality rate than COTS or isolated LQT8. Similar differences were observed comparing CACNA1C exon 8/8A vs. non-exon 8/8A mutation carriers. TS showed a high degree of genetic homogeneity, as the p.Gly406Arg mutation either in exon 8 or exon 8A alone was responsible for 70% of the cases.ConclusionsClinical phenotypes associated with mutations in the CACNA1C gene show important clinical differences. Timothy syndrome is associated with the most severe clinical phenotype and with the highest risk of morbidity and mortality. However, distinguishing TS subtypes, in any form, are not supported by our data.Systematic review registration[https://www.crd.york.ac.uk/prospero/], identifier [CRD42020184737].
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Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022; 31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant splicing underlies many human diseases, including cancer, cardiovascular diseases and neurological disorders. Genome-wide mapping of splicing quantitative trait loci (sQTLs) has shown that genetic regulation of alternative splicing is widespread. However, identification of the corresponding isoform or protein products associated with disease-associated sQTLs is challenging with short-read RNA-seq, which cannot precisely characterize full-length transcript isoforms. Furthermore, contemporary sQTL interpretation often relies on reference transcript annotations, which are incomplete. Solutions to these issues may be found through integration of newly emerging long-read sequencing technologies. Long-read sequencing offers the capability to sequence full-length mRNA transcripts and, in some cases, to link sQTLs to transcript isoforms containing disease-relevant protein alterations. Here, we provide an overview of sQTL mapping approaches, the use of long-read sequencing to characterize sQTL effects on isoforms, the linkage of RNA isoforms to protein-level functions and comment on future directions in the field. Based on recent progress, long-read RNA sequencing promises to be part of the human disease genetics toolkit to discover and treat protein isoforms causing rare and complex diseases.
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Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of General Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
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Harrison PJ, Husain SM, Lee H, Los Angeles AD, Colbourne L, Mould A, Hall NAL, Haerty W, Tunbridge EM. CACNA1C (Ca V1.2) and other L-type calcium channels in the pathophysiology and treatment of psychiatric disorders: Advances from functional genomics and pharmacoepidemiology. Neuropharmacology 2022; 220:109262. [PMID: 36154842 DOI: 10.1016/j.neuropharm.2022.109262] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/09/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022]
Abstract
A role for voltage-gated calcium channels (VGCCs) in psychiatric disorders has long been postulated as part of a broader involvement of intracellular calcium signalling. However, the data were inconclusive and hard to interpret. We review three areas of research that have markedly advanced the field. First, there is now robust genomic evidence that common variants in VGCC subunit genes, notably CACNA1C which encodes the L-type calcium channel (LTCC) CaV1.2 subunit, are trans-diagnostically associated with psychiatric disorders including schizophrenia and bipolar disorder. Rare variants in these genes also contribute to the risk. Second, pharmacoepidemiological evidence supports the possibility that calcium channel blockers, which target LTCCs, might have beneficial effects on the onset or course of these disorders. This is especially true for calcium channel blockers that are brain penetrant. Third, long-range sequencing is revealing the repertoire of full-length LTCC transcript isoforms. Many novel and abundant CACNA1C isoforms have been identified in human and mouse brain, including some which are enriched compared to heart or aorta, and predicted to encode channels with differing functional and pharmacological properties. These isoforms may contribute to the molecular mechanisms of genetic association to psychiatric disorders. They may also enable development of therapeutic agents that can preferentially target brain LTCC isoforms and be of potential value for psychiatric indications.
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Affiliation(s)
- Paul J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK; Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK.
| | - Syed M Husain
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Hami Lee
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK
| | | | - Lucy Colbourne
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK; Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Arne Mould
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK; Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Nicola A L Hall
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK; Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK
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Arjun McKinney A, Petrova R, Panagiotakos G. Calcium and activity-dependent signaling in the developing cerebral cortex. Development 2022; 149:276624. [PMID: 36102617 PMCID: PMC9578689 DOI: 10.1242/dev.198853] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Calcium influx can be stimulated by various intra- and extracellular signals to set coordinated gene expression programs into motion. As such, the precise regulation of intracellular calcium represents a nexus between environmental cues and intrinsic genetic programs. Mounting genetic evidence points to a role for the deregulation of intracellular calcium signaling in neuropsychiatric disorders of developmental origin. These findings have prompted renewed enthusiasm for understanding the roles of calcium during normal and dysfunctional prenatal development. In this Review, we describe the fundamental mechanisms through which calcium is spatiotemporally regulated and directs early neurodevelopmental events. We also discuss unanswered questions about intracellular calcium regulation during the emergence of neurodevelopmental disease, and provide evidence that disruption of cell-specific calcium homeostasis and/or redeployment of developmental calcium signaling mechanisms may contribute to adult neurological disorders. We propose that understanding the normal developmental events that build the nervous system will rely on gaining insights into cell type-specific calcium signaling mechanisms. Such an understanding will enable therapeutic strategies targeting calcium-dependent mechanisms to mitigate disease.
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Affiliation(s)
- Arpana Arjun McKinney
- University of California 1 Graduate Program in Developmental and Stem Cell Biology , , San Francisco, CA 94143 , USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California 2 , San Francisco, CA 94143 , USA
- University of California 3 Department of Biochemistry and Biophysics , , San Francisco, CA 94143 , USA
- Kavli Institute for Fundamental Neuroscience, University of California 4 , San Francisco, CA 94143 , USA
| | - Ralitsa Petrova
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California 2 , San Francisco, CA 94143 , USA
- University of California 3 Department of Biochemistry and Biophysics , , San Francisco, CA 94143 , USA
- Kavli Institute for Fundamental Neuroscience, University of California 4 , San Francisco, CA 94143 , USA
| | - Georgia Panagiotakos
- University of California 1 Graduate Program in Developmental and Stem Cell Biology , , San Francisco, CA 94143 , USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California 2 , San Francisco, CA 94143 , USA
- University of California 3 Department of Biochemistry and Biophysics , , San Francisco, CA 94143 , USA
- Kavli Institute for Fundamental Neuroscience, University of California 4 , San Francisco, CA 94143 , USA
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Colbourne L, Harrison PJ. Brain-penetrant calcium channel blockers are associated with a reduced incidence of neuropsychiatric disorders. Mol Psychiatry 2022; 27:3904-3912. [PMID: 35618884 PMCID: PMC9708561 DOI: 10.1038/s41380-022-01615-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 02/08/2023]
Abstract
Calcium channel blockers (CCBs) differ in their ability to penetrate into the brain. Pharmacoepidemiological studies suggest that CCBs as a class may have beneficial effects on the risks and outcomes of some psychiatric and neurological disorders. It is plausible but unknown whether this effect relates to their brain penetrance. To address this, we used the TriNetX electronic health records network to identify people prescribed a brain-penetrant CCB (BP-CCB), or those given amlodipine, a CCB with low brain penetrability. We created cohorts of patients who, prior to first CCB exposure, either had to have, or could not have had, a recorded ICD-10 diagnosis in any of the following categories: psychotic disorder; affective disorder (including bipolar disorder and major depressive disorder); anxiety disorder; substance use disorder; sleep disorder; delirium; dementia, or movement disorder. Cohort pairs were propensity score matched for age, sex, race, blood pressure, body mass index, and a range of other variables. The outcomes were the incidence of these disorders measured over a two-year exposure period. Matched cohort sizes ranged from 17,896 to 49,987. In people with no prior history of psychiatric or neurodegenerative disorder, there was a significantly lower incidence of most disorders with BP-CCBs compared to amlodipine, with risk ratios ranging from 0.64 to 0.88 and an overall risk ratio of 0.88, i.e. a risk reduction of 12%. In people who did have a prior psychiatric or neurodegenerative diagnosis, differences were much smaller, but again showed lower risks for several disorders with BP-CCBs compared to amlodipine. The differences were somewhat more marked in women and in people less than 60 years old. Results were similar when comparing BP-CCBs with verapamil and diltiazem. We also compared BP-CCBs with angiotensin receptor blockers, and found an overall risk ratio of 0.94 in favour of BP-CCBs, but with differential effects across disorders including a higher risk of psychotic disorder and dementia, but a lower risk for anxiety and sleep disorders. In some analyses, there was evidence of residual confounding even after the extensive matching, in that negative control outcomes showed a reduced incidence with BP-CCBs relative to the comparator cohort. In summary, CCBs that readily penetrate the brain are associated with a lower incidence of neuropsychiatric disorders, especially first diagnoses, compared to CCBs which do not. This may reflect their blockade of neuronal voltage-gated calcium channels. The findings encourage repurposing trials using existing BP-CCBs, and suggest that novel BP-CCBs with enhanced and more selective central actions might have greater therapeutic potential for psychiatric and neurodegenerative disorders.
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Affiliation(s)
- Lucy Colbourne
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK.
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, OX3 7JX, UK.
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27
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Harrison PJ, Mould A, Tunbridge EM. New drug targets in psychiatry: Neurobiological considerations in the genomics era. Neurosci Biobehav Rev 2022; 139:104763. [PMID: 35787892 DOI: 10.1016/j.neubiorev.2022.104763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/15/2022] [Accepted: 06/14/2022] [Indexed: 01/11/2023]
Abstract
After a period of withdrawal, pharmaceutical companies have begun to reinvest in neuropsychiatric disorders, due to improvements in our understanding of these disorders, stimulated in part by genomic studies. However, translating this information into disease insights and ultimately into tractable therapeutic targets is a major challenge. Here we consider how different sources of information might be integrated to guide this process. We review how an understanding of neurobiology has been used to advance therapeutic candidates identified in the pre-genomic era, using catechol-O-methyltransferase (COMT) as an exemplar. We then contrast with ZNF804A, the first genome-wide significant schizophrenia gene, and draw on some of the lessons that these and other examples provide. We highlight that, at least in the short term, the translation of potential targets for which there is orthogonal neurobiological support is likely to be more straightforward and productive than that those relying solely on genomic information. Although we focus here on information from genomic studies of schizophrenia, the points are broadly applicable across major psychiatric disorders and their symptoms.
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Affiliation(s)
- Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, UK; Oxford Health NHS Foundation Trust, Oxford, UK
| | - Arne Mould
- Department of Psychiatry, University of Oxford, Oxford, UK; Oxford Health NHS Foundation Trust, Oxford, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Oxford, UK; Oxford Health NHS Foundation Trust, Oxford, UK.
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28
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Phenotypes, mechanisms and therapeutics: insights from bipolar disorder GWAS findings. Mol Psychiatry 2022; 27:2927-2939. [PMID: 35351989 DOI: 10.1038/s41380-022-01523-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 12/25/2022]
Abstract
Genome-wide association studies (GWAS) have reported substantial genomic loci significantly associated with clinical risk of bipolar disorder (BD), and studies combining techniques of genetics, neuroscience, neuroimaging, and pharmacology are believed to help tackle clinical problems (e.g., identifying novel therapeutic targets). However, translating findings of psychiatric genetics into biological mechanisms underlying BD pathogenesis remains less successful. Biological impacts of majority of BD GWAS risk loci are obscure, and the involvement of many GWAS risk genes in this illness is yet to be investigated. It is thus necessary to review the progress of applying BD GWAS risk genes in the research and intervention of the disorder. A comprehensive literature search found that a number of such risk genes had been investigated in cellular or animal models, even before they were highlighted in BD GWAS. Intriguingly, manipulation of many BD risk genes (e.g., ANK3, CACNA1C, CACNA1B, HOMER1, KCNB1, MCHR1, NCAN, SHANK2 etc.) resulted in altered murine behaviors largely restoring BD clinical manifestations, including mania-like symptoms such as hyperactivity, anxiolytic-like behavior, as well as antidepressant-like behavior, and these abnormalities could be attenuated by mood stabilizers. In addition to recapitulating phenotypic characteristics of BD, some GWAS risk genes further provided clues for the neurobiology of this illness, such as aberrant activation and functional connectivity of brain areas in the limbic system, and modulated dendritic spine morphogenesis as well as synaptic plasticity and transmission. Therefore, BD GWAS risk genes are undoubtedly pivotal resources for modeling this illness, and might be translational therapeutic targets in the future clinical management of BD. We discuss both promising prospects and cautions in utilizing the bulk of useful resources generated by GWAS studies. Systematic integrations of findings from genetic and neuroscience studies are called for to promote our understanding and intervention of BD.
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29
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Ji Y, Wei Q, Chen R, Wang Q, Tao R, Li B. Integration of multidimensional splicing data and GWAS summary statistics for risk gene discovery. PLoS Genet 2022; 18:e1009814. [PMID: 35771864 PMCID: PMC9278751 DOI: 10.1371/journal.pgen.1009814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 07/13/2022] [Accepted: 05/26/2022] [Indexed: 12/30/2022] Open
Abstract
A common strategy for the functional interpretation of genome-wide association study (GWAS) findings has been the integrative analysis of GWAS and expression data. Using this strategy, many association methods (e.g., PrediXcan and FUSION) have been successful in identifying trait-associated genes via mediating effects on RNA expression. However, these approaches often ignore the effects of splicing, which can carry as much disease risk as expression. Compared to expression data, one challenge to detect associations using splicing data is the large multiple testing burden due to multidimensional splicing events within genes. Here, we introduce a multidimensional splicing gene (MSG) approach, which consists of two stages: 1) we use sparse canonical correlation analysis (sCCA) to construct latent canonical vectors (CVs) by identifying sparse linear combinations of genetic variants and splicing events that are maximally correlated with each other; and 2) we test for the association between the genetically regulated splicing CVs and the trait of interest using GWAS summary statistics. Simulations show that MSG has proper type I error control and substantial power gains over existing multidimensional expression analysis methods (i.e., S-MultiXcan, UTMOST, and sCCA+ACAT) under diverse scenarios. When applied to the Genotype-Tissue Expression Project data and GWAS summary statistics of 14 complex human traits, MSG identified on average 83%, 115%, and 223% more significant genes than sCCA+ACAT, S-MultiXcan, and UTMOST, respectively. We highlight MSG's applications to Alzheimer's disease, low-density lipoprotein cholesterol, and schizophrenia, and found that the majority of MSG-identified genes would have been missed from expression-based analyses. Our results demonstrate that aggregating splicing data through MSG can improve power in identifying gene-trait associations and help better understand the genetic risk of complex traits.
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Affiliation(s)
- Ying Ji
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Qiang Wei
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rui Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Quan Wang
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail: (RT); (BL)
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail: (RT); (BL)
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Baratta AM, Brandner AJ, Plasil SL, Rice RC, Farris SP. Advancements in Genomic and Behavioral Neuroscience Analysis for the Study of Normal and Pathological Brain Function. Front Mol Neurosci 2022; 15:905328. [PMID: 35813067 PMCID: PMC9259865 DOI: 10.3389/fnmol.2022.905328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Psychiatric and neurological disorders are influenced by an undetermined number of genes and molecular pathways that may differ among afflicted individuals. Functionally testing and characterizing biological systems is essential to discovering the interrelationship among candidate genes and understanding the neurobiology of behavior. Recent advancements in genetic, genomic, and behavioral approaches are revolutionizing modern neuroscience. Although these tools are often used separately for independent experiments, combining these areas of research will provide a viable avenue for multidimensional studies on the brain. Herein we will briefly review some of the available tools that have been developed for characterizing novel cellular and animal models of human disease. A major challenge will be openly sharing resources and datasets to effectively integrate seemingly disparate types of information and how these systems impact human disorders. However, as these emerging technologies continue to be developed and adopted by the scientific community, they will bring about unprecedented opportunities in our understanding of molecular neuroscience and behavior.
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Affiliation(s)
- Annalisa M. Baratta
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Adam J. Brandner
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sonja L. Plasil
- Department of Pharmacology & Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Rachel C. Rice
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sean P. Farris
- Center for Neuroscience, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Sean P. Farris,
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Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity. Nat Commun 2022; 13:3507. [PMID: 35717442 PMCID: PMC9206673 DOI: 10.1038/s41467-022-31264-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/10/2022] [Indexed: 01/05/2023] Open
Abstract
Gephyrin (GPHN) regulates the clustering of postsynaptic components at inhibitory synapses and is involved in pathophysiology of neuropsychiatric disorders. Here, we uncover an extensive diversity of GPHN transcripts that are tightly controlled by splicing during mouse and human brain development. Proteomic analysis reveals at least a hundred isoforms of GPHN incorporated at inhibitory Glycine and gamma-aminobutyric acid A receptors containing synapses. They exhibit different localization and postsynaptic clustering properties, and altering the expression level of one isoform is sufficient to affect the number, size, and density of inhibitory synapses in cerebellar Purkinje cells. Furthermore, we discovered that splicing defects reported in neuropsychiatric disorders are carried by multiple alternative GPHN transcripts, demonstrating the need for a thorough analysis of the GPHN transcriptome in patients. Overall, we show that alternative splicing of GPHN is an important genetic variation to consider in neurological diseases and a determinant of the diversity of postsynaptic inhibitory synapses. The protein gephyrin is involved in organizing synapses. Here, the authors show how different transcripts of gephyrin form and regulate inhibitory synapses.
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Wang Z, Chen W, Cao Y, Dou Y, Fu Y, Zhang Y, Luo X, Kang L, Liu N, Shi YS, Li CSR, Xu Y, Guo X, Luo X. An independent, replicable, functional and significant risk variant block at intron 3 of CACNA1C for schizophrenia. Aust N Z J Psychiatry 2022; 56:385-397. [PMID: 33938268 DOI: 10.1177/00048674211009595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Genome-wide association studies have identified a significant risk gene, CACNA1C, for schizophrenia. In this study, we comprehensively investigated a large set of CACNA1C single-nucleotide polymorphisms (SNPs) to identify the replicable risk alleles for schizophrenia and explore their biological functions. METHODS One Jewish (1044 cases vs 2052 controls), one European (1350 cases vs 1378 controls) and one exploratory African American samples (98 cases vs 20 controls) were analyzed to identify replicable single-nucleotide polymorphism-schizophrenia associations. The regulatory effects of risk alleles on CACNA1C messenger RNA expression were examined. The most robust risk tagSNP (rs1006737) was meta-analyzed on 17 studies (74,122 cases vs 109,062 controls), and associated with the gray matter volumes of seven subcortical structures in 38,258 Europeans, and the surface areas and thickness of 34 cortical regions in 33,992 Europeans and 2944 non-Europeans. RESULTS Forty-seven replicable risk single-nucleotide polymorphisms, including a 20-single-nucleotide polymorphism haplotype block, were identified in our samples (1.8 × 10-4 ⩽ p ⩽ 0.049). This variant block was consistently associated with schizophrenia across four independent Psychiatric Genomics Consortium cohorts (79,645 cases vs 109,590 controls; 2.5 × 10-17 ⩽ p ⩽ 0.017). This block showed significant expression quantitative trait loci in three independent European brain cohorts (5.1 × 10-12 ⩽ p ⩽ 8.3 × 10-3) and could be tagged by the most significant risk single-nucleotide polymorphism rs1006737. The minor allele A of rs1006737 significantly increased risk for schizophrenia across the Jewish and European samples (p = 0.029 and 0.004, respectively), and this association was highly significant in the meta-analysis (p = 1.62 × 10-42). This allele also significantly altered the CACNA1C messenger RNA expression in five brain regions (5.1 × 10-12 ⩽ p ⩽ 0.05), decreased the gray matter volume of thalamus (p = 0.010), the surface area of isthmus cingulate cortex (p = 0.013) and the thickness of transverse temporal and superior temporal sulcus cortexes (0.005 ⩽ p ⩽ 0.043). CONCLUSION We identified an independent, replicable, functional, and significant risk variant block at CACNA1C for schizophrenia, which could be tagged by the most robust risk marker rs1006737, suggesting an important role of CACNA1C in the pathogenesis of schizophrenia.
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Affiliation(s)
- Zuxing Wang
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Psychosomatic Medicine of Sichuan Provincial Center for Mental Health, The Center of Psychosomatic Medicine of Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenzhong Chen
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuping Cao
- Department of Psychiatry of the Second Xiangya Hospital, Central South University; China National Clinical Research Center on Mental Disorders, China National Technology Institute on Mental Disorders, Changsha, China
| | - Yikai Dou
- Mental Health Center and Psychiatric Laboratory, The State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.,Huaxi Brain Research Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yingmei Fu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Zhang
- Department of Psychiatry, Tianjin Mental Health Center, Tianjin, China
| | - Xingqun Luo
- Department of Clinical Medicine, College of Integrated Traditional Chinese and Western Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Diseases of Tibet Autonomous Region, Xizang Minzu University School of Medicine, Xiangyang, China
| | - Na Liu
- Department of Psychiatry, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, China
| | - Yun Stone Shi
- Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Chiang-Shan R Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yifeng Xu
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyun Guo
- Department of Psychiatry, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingguang Luo
- Division of Psychiatric Genetics, Biological Psychiatry Research Center, Beijing Huilongguan Hospital, Beijing, China
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Lanzetti S, Di Biase V. Small Molecules as Modulators of Voltage-Gated Calcium Channels in Neurological Disorders: State of the Art and Perspectives. Molecules 2022; 27:1312. [PMID: 35209100 PMCID: PMC8879281 DOI: 10.3390/molecules27041312] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 01/03/2023] Open
Abstract
Voltage-gated calcium channels (VGCCs) are widely expressed in the brain, heart and vessels, smooth and skeletal muscle, as well as in endocrine cells. VGCCs mediate gene transcription, synaptic and neuronal structural plasticity, muscle contraction, the release of hormones and neurotransmitters, and membrane excitability. Therefore, it is not surprising that VGCC dysfunction results in severe pathologies, such as cardiovascular conditions, neurological and psychiatric disorders, altered glycemic levels, and abnormal smooth muscle tone. The latest research findings and clinical evidence increasingly show the critical role played by VGCCs in autism spectrum disorders, Parkinson's disease, drug addiction, pain, and epilepsy. These findings outline the importance of developing selective calcium channel inhibitors and modulators to treat such prevailing conditions of the central nervous system. Several small molecules inhibiting calcium channels are currently used in clinical practice to successfully treat pain and cardiovascular conditions. However, the limited palette of molecules available and the emerging extent of VGCC pathophysiology require the development of additional drugs targeting these channels. Here, we provide an overview of the role of calcium channels in neurological disorders and discuss possible strategies to generate novel therapeutics.
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Affiliation(s)
| | - Valentina Di Biase
- Institute of Pharmacology, Department of Medical Statistics, Informatics and Health Economics, Medical University of Innsbruck, Peter-Mayr Strasse 1, A-6020 Innsbruck, Austria;
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Disrupted Cacna1c gene expression perturbs spontaneous Ca 2+ activity causing abnormal brain development and increased anxiety. Proc Natl Acad Sci U S A 2022; 119:2108768119. [PMID: 35135875 PMCID: PMC8851547 DOI: 10.1073/pnas.2108768119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
The gene CACNA1C encodes for a calcium channel that has been linked to various psychiatric conditions, including schizophrenia and bipolar disorder, through hitherto unknown cellular mechanisms. Here, we report that deletion of Cacna1c in neurons of the developing brain disrupts spontaneous calcium activity and causes abnormal brain development and anxiety. Our results indicate that marginally alterations in the expression level of Cacna1c have major effects on the intrinsic spontaneous calcium activity of neural progenitors that play a crucial role in brain development. Thus, Cacna1c acts as a molecular switch that can increase susceptibility to psychiatric disease. The L-type voltage-gated Ca2+ channel gene CACNA1C is a risk gene for various psychiatric conditions, including schizophrenia and bipolar disorder. However, the cellular mechanism by which CACNA1C contributes to psychiatric disorders has not been elucidated. Here, we report that the embryonic deletion of Cacna1c in neurons destined for the cerebral cortex using an Emx1-Cre strategy disturbs spontaneous Ca2+ activity and causes abnormal brain development and anxiety. By combining computational modeling with electrophysiological membrane potential manipulation, we found that neural network activity was driven by intrinsic spontaneous Ca2+ activity in distinct progenitor cells expressing marginally increased levels of voltage-gated Ca2+ channels. MRI examination of the Cacna1c knockout mouse brains revealed volumetric differences in the neocortex, hippocampus, and periaqueductal gray. These results suggest that Cacna1c acts as a molecular switch and that its disruption during embryogenesis can perturb Ca2+ handling and neural development, which may increase susceptibility to psychiatric disease.
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35
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Singh P, Ahi EP. The importance of alternative splicing in adaptive evolution. Mol Ecol 2022; 31:1928-1938. [DOI: 10.1111/mec.16377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/06/2022] [Accepted: 01/25/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Pooja Singh
- Department of Biological Sciences University of Calgary Calgary Canada
- Institute of Ecology and Evolution University of Bern Bern Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG) Kastanienbaum Switzerland
| | - Ehsan Pashay Ahi
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
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36
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Panagiotakos G, Pasca SP. A matter of space and time: Emerging roles of disease-associated proteins in neural development. Neuron 2022; 110:195-208. [PMID: 34847355 PMCID: PMC8776599 DOI: 10.1016/j.neuron.2021.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/21/2023]
Abstract
Recent genetic studies of neurodevelopmental disorders point to synaptic proteins and ion channels as key contributors to disease pathogenesis. Although many of these proteins, such as the L-type calcium channel Cav1.2 or the postsynaptic scaffolding protein SHANK3, have well-studied functions in mature neurons, new evidence indicates that they may subserve novel, distinct roles in immature cells as the nervous system is assembled in prenatal development. Emerging tools and technologies, including single-cell sequencing and human cellular models of disease, are illuminating differential isoform utilization, spatiotemporal expression, and subcellular localization of ion channels and synaptic proteins in the developing brain compared with the adult, providing new insights into the regulation of developmental processes. We propose that it is essential to consider the temporally distinct and cell-specific roles of these proteins during development and maturity in our framework for understanding neuropsychiatric disorders.
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Affiliation(s)
- Georgia Panagiotakos
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
| | - Sergiu P Pasca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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Wright DJ, Hall NAL, Irish N, Man AL, Glynn W, Mould A, Angeles ADL, Angiolini E, Swarbreck D, Gharbi K, Tunbridge EM, Haerty W. Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes. BMC Genomics 2022; 23:42. [PMID: 35012468 PMCID: PMC8744310 DOI: 10.1186/s12864-021-08261-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains unclear. Long read sequencing allows full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these change with cell state. Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line SH-SY5Y, and to characterise isoform expression and usage across differentiation. RESULTS We identify many previously unannotated features, including a novel transcript of the voltage-gated calcium channel subunit gene, CACNA2D2. We show differential expression and usage of transcripts during differentiation identifying candidates for future research into state change regulation. CONCLUSIONS Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.
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Affiliation(s)
- David J Wright
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Nicola A L Hall
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Naomi Irish
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Angela L Man
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Will Glynn
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Arne Mould
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Alejandro De Los Angeles
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Emily Angiolini
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, Medical Sciences Division, University of Oxford, Oxfordshire, OX3 3JX, UK
- Oxford Health, NHS Foundation Trust, Oxford, Oxfordshire, OX3 7JX, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK.
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38
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Zhang CY, Xiao X, Zhang Z, Hu Z, Li M. An alternative splicing hypothesis for neuropathology of schizophrenia: evidence from studies on historical candidate genes and multi-omics data. Mol Psychiatry 2022; 27:95-112. [PMID: 33686213 DOI: 10.1038/s41380-021-01037-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/08/2021] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
Alternative splicing of schizophrenia risk genes, such as DRD2, GRM3, and DISC1, has been extensively described. Nevertheless, the alternative splicing characteristics of the growing number of schizophrenia risk genes identified through genetic analyses remain relatively opaque. Recently, transcriptomic analyses in human brains based on short-read RNA-sequencing have discovered many "local splicing" events (e.g., exon skipping junctions) associated with genetic risk of schizophrenia, and further molecular characterizations have identified novel spliced isoforms, such as AS3MTd2d3 and ZNF804AE3E4. In addition, long-read sequencing analyses of schizophrenia risk genes (e.g., CACNA1C and NRXN1) have revealed multiple previously unannotated brain-abundant isoforms with therapeutic potentials, and functional analyses of KCNH2-3.1 and Ube3a1 have provided examples for investigating such spliced isoforms in vitro and in vivo. These findings suggest that alternative splicing may be an essential molecular mechanism underlying genetic risk of schizophrenia, however, the incomplete annotations of human brain transcriptomes might have limited our understanding of schizophrenia pathogenesis, and further efforts to elucidate these transcriptional characteristics are urgently needed to gain insights into the illness-correlated brain physiology and pathology as well as to translate genetic discoveries into novel therapeutic targets.
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Affiliation(s)
- Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Eye Center of Xiangya Hospital and Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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Hong JSW, Atkinson LZ, Al-Juffali N, Awad A, Geddes JR, Tunbridge EM, Harrison PJ, Cipriani A. Gabapentin and pregabalin in bipolar disorder, anxiety states, and insomnia: Systematic review, meta-analysis, and rationale. Mol Psychiatry 2022; 27:1339-1349. [PMID: 34819636 PMCID: PMC9095464 DOI: 10.1038/s41380-021-01386-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/29/2022]
Abstract
The gabapentinoids, gabapentin, and pregabalin, target the α2δ subunits of voltage-gated calcium channels. Initially licensed for pain and seizures, they have become widely prescribed drugs. Many of these uses are off-label for psychiatric indications, and there is increasing concern about their safety, so it is particularly important to have good evidence to justify this usage. We conducted a systematic review and meta-analysis of the evidence for three of their common psychiatric uses: bipolar disorder, anxiety, and insomnia. Fifty-five double-blind randomised controlled trials (RCTs) and 15 open-label studies were identified. For bipolar disorder, four double-blind RCTs investigating gabapentin, and no double-blind RCTs investigating pregabalin, were identified. A quantitative synthesis could not be performed due to heterogeneity in the study population, design and outcome measures. Across the anxiety spectrum, a consistent but not universal effect in favour of gabapentinoids compared to placebo was seen (standardised mean difference [SMD] ranging between -2.25 and -0.25). Notably, pregabalin (SMD -0.55, 95% CI -0.92 to -0.18) and gabapentin (SMD -0.92, 95% CI -1.32 to -0.52) were more effective than placebo in reducing preoperative anxiety. In insomnia, results were inconclusive. We conclude that there is moderate evidence of the efficacy of gabapentinoids in anxiety states, but minimal evidence in bipolar disorder and insomnia and they should be used for these disorders only with strong justification. This recommendation applies despite the attractive pharmacological and genetic rationale for targeting voltage-gated calcium channels.
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Affiliation(s)
- James S. W. Hong
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK
| | - Lauren Z. Atkinson
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.497865.10000 0004 0427 1035Oxford Centre for Human Brain Activity, University of Oxford, Oxford, UK ,grid.416938.10000 0004 0641 5119Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Noura Al-Juffali
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.416938.10000 0004 0641 5119Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Amine Awad
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.32224.350000 0004 0386 9924Department of Neurology, Massachusetts General Hospital, Boston, MA 02114 USA
| | - John R. Geddes
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.416938.10000 0004 0641 5119Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Elizabeth M. Tunbridge
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.416938.10000 0004 0641 5119Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Paul J. Harrison
- grid.416938.10000 0004 0641 5119Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX UK ,grid.416938.10000 0004 0641 5119Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK
| | - Andrea Cipriani
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX3 7JX, UK. .,Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford, UK.
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40
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Abstract
The cognitive dysfunction experienced by patients with schizophrenia represents a major unmet clinical need. We believe that enhancing synaptic function and plasticity by targeting kalirin may provide a novel means to remediate these symptoms. Karilin (a protein encoded by the KALRN gene) has multiple functional domains, including two Dbl homology (DH) guanine exchange factor (GEF) domains, which act to enhance the activity of the Rho family guanosine triphosphate (GTP)-ases. Here, we provide an overview of kalirin's roles in brain function and its therapeutic potential in schizophrenia. We outline how it mediates diverse effects via a suite of distinct isoforms that couple to members of the Rho GTPase family to regulate synapse formation and stabilisation, and how genomic and post-mortem data implicate it in schizophrenia. We then review the current state of knowledge about the influence of kalirin on brain function at a systems level, based largely on evidence from transgenic mouse models, which support its proposed role in regulating dendritic spine function and plasticity. We demonstrate that, whilst the GTPases are classically considered to be 'undruggable', targeting kalirin and other Rho GEFs provides a means to indirectly modulate their activity. Finally, we integrate across the information presented to assess the therapeutic potential of kalirin for schizophrenia and highlight the key outstanding questions required to advance it in this capacity; namely, the need for more information about the diversity and function of its isoforms, how these change across neurodevelopment, and how they affect brain function in vivo.
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42
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Allemand E, Ango F. Analysis of Splicing Regulation by Third-Generation Sequencing. Methods Mol Biol 2022; 2537:81-95. [PMID: 35895260 DOI: 10.1007/978-1-0716-2521-7_6] [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] [Indexed: 06/15/2023]
Abstract
In Metazoa, the diversity of transcripts produced by the RNA Polymerase II is generated essentially through post-transcriptional processing of the nascent transcripts. The regulation of exon inclusion by alternative splicing is one of the main sources of this diversity, which leads to the expansion of the proteome. The portfolio of alternative transcripts remains largely underestimated. Improvement of the sequencing technologies has enhanced the characterization of RNA isoforms and led to the perpetual incrementation of gene expression diversity. Here, we describe a high throughput approach to assess in-depth the splicing regulation of target gene(s) using the third-generation sequencing (TGS) technologies.
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Affiliation(s)
- Eric Allemand
- Laboratory of cellular and molecular mechanisms of hematological disorders and therapeutic implications, Institut IMAGINE, INSERM, Paris, France.
| | - Fabrice Ango
- INM, University of Montpellier, INSERM, Montpellier, France
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Heck J, Palmeira Do Amaral AC, Weißbach S, El Khallouqi A, Bikbaev A, Heine M. More than a pore: How voltage-gated calcium channels act on different levels of neuronal communication regulation. Channels (Austin) 2021; 15:322-338. [PMID: 34107849 PMCID: PMC8205089 DOI: 10.1080/19336950.2021.1900024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Voltage-gated calcium channels (VGCCs) represent key regulators of the calcium influx through the plasma membrane of excitable cells, like neurons. Activated by the depolarization of the membrane, the opening of VGCCs induces very transient and local changes in the intracellular calcium concentration, known as calcium nanodomains, that in turn trigger calcium-dependent signaling cascades and the release of chemical neurotransmitters. Based on their central importance as concierges of excitation-secretion coupling and therefore neuronal communication, VGCCs have been studied in multiple aspects of neuronal function and malfunction. However, studies on molecular interaction partners and recent progress in omics technologies have extended the actual concept of these molecules. With this review, we want to illustrate some new perspectives of VGCCs reaching beyond their function as calcium-permeable pores in the plasma membrane. Therefore, we will discuss the relevance of VGCCs as voltage sensors in functional complexes with ryanodine receptors, channel-independent actions of auxiliary VGCC subunits, and provide an insight into how VGCCs even directly participate in gene regulation. Furthermore, we will illustrate how structural changes in the intracellular C-terminus of VGCCs generated by alternative splicing events might not only affect the biophysical channel characteristics but rather determine their molecular environment and downstream signaling pathways.
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Affiliation(s)
- Jennifer Heck
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
| | - Ana Carolina Palmeira Do Amaral
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
| | - Stephan Weißbach
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
- Computational Genomics and Bioinformatics, Johannes Gutenberg-University Mainz, University Medical Center Mainz, Institute for Human Genetics, Mainz, Germany
| | - Abderazzaq El Khallouqi
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
| | - Arthur Bikbaev
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
| | - Martin Heine
- Functional Neurobiology, Johannes Gutenberg-University Mainz, Institute for Developmental Biology and Neurobiology, Mainz, Germany
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Hofer NT, Pinggera A, Nikonishyna YV, Tuluc P, Fritz EM, Obermair GJ, Striessnig J. Stabilization of negative activation voltages of Cav1.3 L-Type Ca 2+-channels by alternative splicing. Channels (Austin) 2021; 15:38-52. [PMID: 33380256 PMCID: PMC7781618 DOI: 10.1080/19336950.2020.1859260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022] Open
Abstract
-->Low voltage-activated Cav1.3 L-type Ca2+-channels are key regulators of neuronal excitability controlling neuronal development and different types of learning and memory. Their physiological functions are enabled by their negative activation voltage-range, which allows Cav1.3 to be active at subthreshold voltages. Alternative splicing in the C-terminus of their pore-forming α1-subunits gives rise to C-terminal long (Cav1.3L) and short (Cav1.3S) splice variants allowing Cav1.3S to activate at even more negative voltages than Cav1.3L. We discovered that inclusion of exons 8b, 11, and 32 in Cav1.3S further shifts activation (-3 to -4 mV) and inactivation (-4 to -6 mV) to more negative voltages as revealed by functional characterization in tsA-201 cells. We found transcripts of these exons in mouse chromaffin cells, the cochlea, and the brain. Our data further suggest that Cav1.3-containing exons 11 and 32 constitute a significant part of native channels in the brain. We therefore investigated the effect of these splice variants on human disease variants. Splicing did not prevent the gating defects of the previously reported human pathogenic variant S652L, which further shifted the voltage-dependence of activation of exon 11-containing channels by more than -12 mV. In contrast, we found no evidence for gating changes of the CACNA1D missense variant R498L, located in exon 11, which has recently been identified in a patient with an epileptic syndrome. Our data demonstrate that alternative splicing outside the C-terminus involving exons 11 and 32 contributes to channel fine-tuning by stabilizing negative activation and inactivation gating properties of wild-type and mutant Cav1.3 channels.
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Affiliation(s)
- Nadja T. Hofer
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, University of Innsbruck, Austria
| | - Alexandra Pinggera
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yuliia V. Nikonishyna
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, University of Innsbruck, Austria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, University of Innsbruck, Austria
| | - Eva M. Fritz
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, University of Innsbruck, Austria
| | - Gerald J. Obermair
- Institute of Physiology, Medical University Innsbruck, Innsbruck, Austria
- Division Physiology, Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Centre for Molecular Biosciences, University of Innsbruck, Austria
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45
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Hall NAL, Carlyle BC, Haerty W, Tunbridge EM. Roadblock: improved annotations do not necessarily translate into new functional insights. Genome Biol 2021; 22:320. [PMID: 34809684 PMCID: PMC8607653 DOI: 10.1186/s13059-021-02542-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Nicola A L Hall
- Department of Psychiatry, University of Oxford, Oxford, UK.
- Oxford Health NHS Foundation Trust, Oxford, UK.
| | | | - Wilfried Haerty
- The Earlham Institute, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Foundation Trust, Oxford, UK
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46
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Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing. Sci Rep 2021; 11:22372. [PMID: 34785703 PMCID: PMC8595663 DOI: 10.1038/s41598-021-01749-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/26/2021] [Indexed: 01/31/2023] Open
Abstract
More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
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Wookey P, Gupta P, Bittencourt L, Cheung S, Hare D, Furness S. Methods to measure calcitonin receptor activity, up-regulated in cell stress, apoptosis and autophagy. F1000Res 2021; 10:1019. [PMID: 34745567 PMCID: PMC8543166 DOI: 10.12688/f1000research.72845.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 11/24/2022] Open
Abstract
The expression of the calcitonin receptor (CT Receptor) is widespread throughout the life cycle of mammals and in many diseases, and in these contexts the functions of the common isoforms is largely unknown. The relatively recent development of anti-CT Receptor antibodies that bind separate epitopes on the CT
a Receptor and CT
b Receptor isoforms has advanced our knowledge and understanding of these events. CT Receptor at the protein level is upregulated in programmed cell death including apoptosis (as described in a previous publication) and autophagy, which is discussed in our upcoming, unpublished review. Incomplete data sets are cited in this review on the upregulation of CACLR (encoding CT Receptor) mRNA, in particular the insert-positive isoform (CT
b Receptor), in response to cell stress. Cell stress is induced by growth in depleted foetal bovine serum (dFBS) or without FBS, both of which induce degrees of starvation and autophagy, or dFBS plus staurosporine, which induces apoptosis. Details of the methods deployed to generate these data are described here including measurement of the upregulation of CT
b Receptor mRNA with qPCR and nanopore long range sequencing. An anti-CT Receptor antibody also known as CalRexin
TM, which binds an epitope in the N-terminal domain, was conjugated to either fluorophore 568, which is accumulated into apoptotic cells as previously reported, or pHrodo Red, a pH dependent fluorescent dye, which is accumulated into autophagic and apoptotic cells. These conjugates are under development to image programmed cell death. The methods for conjugation and high content imaging on the Operetta platform are described. The high fluorescence intensity at low pH of CalRexin:pHrodo Red in both autophagic and apoptotic cells suggests localisation in autophago-lysosomes and lysosomes respectively. Overall, these observations and the methods that underpin them have contributed to our understanding of the widespread expression of CT Receptor isoforms.
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Affiliation(s)
- Peter Wookey
- Medicine, University of Melbourne, Heidelberg, Victoria, 3084, Australia
| | - Pragya Gupta
- Medicine, University of Melbourne, Heidelberg, Victoria, 3084, Australia
| | - Lucas Bittencourt
- Medicine, University of Melbourne, Heidelberg, Victoria, 3084, Australia
| | - Shane Cheung
- BOMP, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - David Hare
- Medicine, University of Melbourne, Heidelberg, Victoria, 3084, Australia
| | - Sebastian Furness
- Drug Discovery Biology and Department of Pharmacology, Monash University, Parkville, Victoria, 3052, Australia.,School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, St Lucia, Queensland, 4067, Australia
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Liu Y, Rosikiewicz W, Pan Z, Jillette N, Wang P, Taghbalout A, Foox J, Mason C, Carroll M, Cheng A, Li S. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biol 2021; 22:295. [PMID: 34663425 PMCID: PMC8524990 DOI: 10.1186/s13059-021-02510-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/04/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads. Here, we assess the performance of different methylation-calling tools to provide a systematic evaluation to guide researchers performing human epigenome-wide studies. RESULTS We compare seven analytic tools for detecting DNA methylation from nanopore long-read sequencing data generated from human natural DNA at a whole-genome scale. We evaluate the per-read and per-site performance of CpG methylation prediction across different genomic contexts, CpG site coverage, and computational resources consumed by each tool. The seven tools exhibit different performances across the evaluation criteria. We show that the methylation prediction at regions with discordant DNA methylation patterns, intergenic regions, low CG density regions, and repetitive regions show room for improvement across all tools. Furthermore, we demonstrate that 5hmC levels at least partly contribute to the discrepancy between bisulfite and nanopore sequencing. Lastly, we provide an online DNA methylation database ( https://nanome.jax.org ) to display the DNA methylation levels detected by nanopore sequencing and bisulfite sequencing data across different genomic contexts. CONCLUSIONS Our study is the first systematic benchmark of computational methods for detection of mammalian whole-genome DNA modifications in nanopore sequencing. We provide a broad foundation for cross-platform standardization and an evaluation of analytical tools designed for genome-scale modified base detection using nanopore sequencing.
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Affiliation(s)
- Yang Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Wojciech Rosikiewicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Present address: Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ziwei Pan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA
| | | | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Aziz Taghbalout
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Martin Carroll
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Albert Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health Center, Farmington, CT, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA.
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49
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Al-Juffali N. Critical Developmental Windows of Voltage-Gated Cation Channel Expression in Psychiatric Disorders. Biol Psychiatry 2021; 90:e31-e32. [PMID: 34446155 DOI: 10.1016/j.biopsych.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Noura Al-Juffali
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom.
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50
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De Los Angeles A, Fernando MB, Hall NAL, Brennand KJ, Harrison PJ, Maher BJ, Weinberger DR, Tunbridge EM. Induced Pluripotent Stem Cells in Psychiatry: An Overview and Critical Perspective. Biol Psychiatry 2021; 90:362-372. [PMID: 34176589 PMCID: PMC8375580 DOI: 10.1016/j.biopsych.2021.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 02/08/2023]
Abstract
A key challenge in psychiatry research is the development of high-fidelity model systems that can be experimentally manipulated to explore and test pathophysiological mechanisms of illness. In this respect, the emerging capacity to derive neural cells and circuits from human induced pluripotent stem cells (iPSCs) has generated significant excitement. This review aims to provide a critical appraisal of the potential for iPSCs in illuminating pathophysiological mechanisms in the context of other available technical approaches. We discuss the selection of iPSC phenotypes relevant to psychiatry, the information that researchers can draw on to help guide these decisions, and how researchers choose between the use of 2-dimensional cultures and the use of more complex 3-dimensional model systems. We discuss the strengths and limitations of current models and the challenges and opportunities that they present. Finally, we discuss the potential of iPSC-based model systems for clarifying the mechanisms underlying genetic risk for psychiatry and the steps that will be needed to ensure that robust and reliable conclusions can be drawn. We argue that while iPSC-based models are ideally placed to study fundamental processes occurring within and between neural cells, they are often less well suited for case-control studies, given issues relating to statistical power and the challenges in identifying which cellular phenotypes are meaningful at the level of the whole individual. Our aim is to highlight the importance of considering the hypotheses of a given study to guide decisions about which, if any, iPSC-based system is most appropriate to address it.
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Affiliation(s)
- Alejandro De Los Angeles
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, New York; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicola A L Hall
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Brady J Maher
- Lieber Institute for Brain Development, Baltimore, Maryland; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, Maryland; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom.
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