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Colijn MA, Carrion P, Poirier-Morency G, Rogic S, Torres I, Menon M, Lisonek M, Cook C, DeGraaf A, Thammaiah SP, Neelakant H, Willaeys V, Leonova O, White RF, Yip S, Mungall AJ, MacLeod PM, Gibson WT, Sullivan PF, Honer WG, Pavlidis P, Stowe RM. SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110888. [PMID: 37918557 DOI: 10.1016/j.pnpbp.2023.110888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
OBJECTIVE SETD1A encodes a histone methyltransferase involved in various cell cycle regulatory processes. Loss-of-function SETD1A variants have been associated with numerous neurodevelopmental phenotypes, including intellectual disability and schizophrenia. While the association between rare coding variants in SETD1A and schizophrenia has achieved genome-wide significance by rare variant burden testing, only a few studies have described the psychiatric phenomenology of such individuals in detail. This systematic review and case report aims to characterize the neurodevelopmental and psychiatric phenotypes of SETD1A variant-associated schizophrenia. METHODS A PubMed search was completed in July 2022 and updated in May 2023. Only studies that reported individuals with a SETD1A variant as well as a primary psychotic disorder were ultimately included. Additionally, another two previously unpublished cases of SETD1A variant-associated psychosis from our own sequencing cohort are described. RESULTS The search yielded 32 articles. While 15 articles met inclusion criteria, only five provided case descriptions. In total, phenotypic information was available for 11 individuals, in addition to our own two unpublished cases. Our findings suggest that although individuals with SETD1A variant-associated schizophrenia may share a number of common features, phenotypic variability nonetheless exists. Moreover, although such individuals may exhibit numerous other neurodevelopmental features suggestive of the syndrome, their psychiatric presentations appear to be similar to those of general schizophrenia populations. CONCLUSIONS Loss-of-function SETD1A variants may underlie the development of psychosis in a small percentage of individuals with schizophrenia. Identifying such individuals may become increasingly important, given the potential for advances in precision medicine treatment approaches.
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Affiliation(s)
- Mark A Colijn
- Department of Psychiatry, Hotchkiss Brain Institute, and Mathison Centre for Mental Health Research & Education, University of Calgary, Calgary, AB, Canada.
| | - Prescilla Carrion
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Sanja Rogic
- Department of Psychiatry and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ivan Torres
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services, Vancouver, BC, Canada
| | - Mahesh Menon
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Courtney Cook
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ashley DeGraaf
- Heart Centre, St. Paul's Hospital and Providence Health, Vancouver, BC, Canada
| | | | - Harish Neelakant
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Veerle Willaeys
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada
| | - Olga Leonova
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Randall F White
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Patrick M MacLeod
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia and BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Patrick F Sullivan
- Psychiatry and Genetics, University of North Carolina at Chapel Hill, NC, USA; Karolinska Institut, Stockholm, Sweden
| | - William G Honer
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services Research Institute, Vancouver, BC, Canada
| | - Paul Pavlidis
- Department of Psychiatry, Michael Smith Laboratories, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- Departments of Psychiatry and Neurology (Medicine), BC Neuropsychiatry Program, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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Harnish JM, Li L, Rogic S, Poirier-Morency G, Kim SY, Boycott KM, Wangler MF, Bellen HJ, Hieter P, Pavlidis P, Liu Z, Yamamoto S. ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. Hum Mutat 2022; 43:743-759. [PMID: 35224820 PMCID: PMC9133126 DOI: 10.1002/humu.24364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/12/2022] [Accepted: 02/23/2022] [Indexed: 11/08/2022]
Abstract
Next-generation sequencing is a prevalent diagnostic tool for undiagnosed diseases and has played a significant role in rare disease gene discovery. Although this technology resolves some cases, others are given a list of possibly damaging genetic variants necessitating functional studies. Productive collaborations between scientists, clinicians, and patients (affected individuals) can help resolve such medical mysteries and provide insights into in vivo function of human genes. Furthermore, facilitating interactions between scientists and research funders, including nonprofit organizations or commercial entities, can dramatically reduce the time to translate discoveries from bench to bedside. Several systems designed to connect clinicians and researchers with a shared gene of interest have been successful. However, these platforms exclude some stakeholders based on their role or geography. Here we describe ModelMatcher, a global online matchmaking tool designed to facilitate cross-disciplinary collaborations, especially between scientists and other stakeholders of rare and undiagnosed disease research. ModelMatcher is integrated into the Rare Diseases Models and Mechanisms Network and Matchmaker Exchange, allowing users to identify potential collaborators in other registries. This living database decreases the time from when a scientist or clinician is making discoveries regarding their genes of interest, to when they identify collaborators and sponsors to facilitate translational and therapeutic research.
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Affiliation(s)
- J. Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
| | - Lucian Li
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
| | | | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Graduate Program, BCM, Houston, TX, 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital (TCH), Houston, TX, 77030, USA
- Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX, 77030, USA
- Department of Neuroscience, BCM, Houston, TX, 77030, USA
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Lim N, Tesar S, Belmadani M, Poirier-Morency G, Mancarci BO, Sicherman J, Jacobson M, Leong J, Tan P, Pavlidis P. Curation of over 10 000 transcriptomic studies to enable data reuse. Database (Oxford) 2021; 2021:6143045. [PMID: 33599246 PMCID: PMC7904053 DOI: 10.1093/database/baab006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/09/2020] [Accepted: 01/28/2021] [Indexed: 01/07/2023]
Abstract
Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html.
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Affiliation(s)
- Nathaniel Lim
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Stepan Tesar
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Manuel Belmadani
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Guillaume Poirier-Morency
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Burak Ogan Mancarci
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Jordan Sicherman
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Justin Leong
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
| | - Patrick Tan
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T1Z4, Canada
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