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Liu Y, Flamier A, Bell GW, Diao AJ, Whitfield TW, Wang HC, Wu Y, Schulte F, Friesen M, Guo R, Mitalipova M, Liu XS, Vos SM, Young RA, Jaenisch R. MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons. Neuron 2024:S0896-6273(24)00245-9. [PMID: 38697112 DOI: 10.1016/j.neuron.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/08/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type (WT) and mutant MECP2 molecules. MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (RNA Pol II). MECP2 directly interacts with RNA Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for RNA Pol II gene expression at many neuronal genes that harbor CpG islands in promoter-proximal regions and that RTT is due, in part, to the loss of gene activity of these genes in neurons.
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Affiliation(s)
- Yi Liu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Anthony Flamier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Annette Jun Diao
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hao-Che Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yizhe Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fabian Schulte
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Max Friesen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ruisi Guo
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Maisam Mitalipova
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - X Shawn Liu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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2
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Dear R, Wagstyl K, Seidlitz J, Markello RD, Arnatkevičiūtė A, Anderson KM, Bethlehem RAI, Raznahan A, Bullmore ET, Vértes PE. Cortical gene expression architecture links healthy neurodevelopment to the imaging, transcriptomics and genetics of autism and schizophrenia. Nat Neurosci 2024:10.1038/s41593-024-01624-4. [PMID: 38649755 DOI: 10.1038/s41593-024-01624-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
Human brain organization involves the coordinated expression of thousands of genes. For example, the first principal component (C1) of cortical transcription identifies a hierarchy from sensorimotor to association regions. In this study, optimized processing of the Allen Human Brain Atlas revealed two new components of cortical gene expression architecture, C2 and C3, which are distinctively enriched for neuronal, metabolic and immune processes, specific cell types and cytoarchitectonics, and genetic variants associated with intelligence. Using additional datasets (PsychENCODE, Allen Cell Atlas and BrainSpan), we found that C1-C3 represent generalizable transcriptional programs that are coordinated within cells and differentially phased during fetal and postnatal development. Autism spectrum disorder and schizophrenia were specifically associated with C1/C2 and C3, respectively, across neuroimaging, differential expression and genome-wide association studies. Evidence converged especially in support of C3 as a normative transcriptional program for adolescent brain development, which can lead to atypical supragranular cortical connectivity in people at high genetic risk for schizophrenia.
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Affiliation(s)
- Richard Dear
- Department of Psychiatry, University of Cambridge, Cambridge, UK.
| | | | - Jakob Seidlitz
- Lifespan Brain Institute, Children's Hospital of Philadelphia and Penn Medicine, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Sciences, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ross D Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Aurina Arnatkevičiūtė
- Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | | | | | - Armin Raznahan
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
| | | | - Petra E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, UK
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3
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Pechmann S. Single-cell expression predicts neuron-specific protein homeostasis networks. Open Biol 2024; 14:230386. [PMID: 38262604 PMCID: PMC10805596 DOI: 10.1098/rsob.230386] [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: 04/22/2023] [Accepted: 11/17/2023] [Indexed: 01/25/2024] Open
Abstract
The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
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Humphries EM, Ahn K, Kember RL, Lopes FL, Mocci E, Peralta JM, Blangero J, Glahn DC, Goes FS, Zandi PP, Kochunov P, Van Hout C, Shuldiner AR, Pollin TI, Mitchell BD, Bucan M, Hong LE, McMahon FJ, Ament SA. Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population. Mol Psychiatry 2023; 28:5262-5271. [PMID: 36882501 PMCID: PMC10483025 DOI: 10.1038/s41380-023-02014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover risk variants with larger effects by conducting a genome-wide association study of mood disorders in a founder population, the Old Order Amish (OOA, n = 1,672). Our analysis revealed four genome-wide significant risk loci, all of which were associated with >2-fold relative risk. Quantitative behavioral and neurocognitive assessments (n = 314) revealed effects of risk variants on sub-clinical depressive symptoms and information processing speed. Network analysis suggested that OOA-specific risk loci harbor novel risk-associated genes that interact with known neuropsychiatry-associated genes via gene interaction networks. Annotation of the variants at these risk loci revealed population-enriched, non-synonymous variants in two genes encoding neurodevelopmental transcription factors, CUX1 and CNOT1. Our findings provide insight into the genetic architecture of mood disorders and a substrate for mechanistic and clinical studies.
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Affiliation(s)
- Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kwangmi Ahn
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabiana L Lopes
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juan M Peralta
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - John Blangero
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | | | - Fernando S Goes
- Departments of Epidemiology and Mental Health, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter P Zandi
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter Kochunov
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cristopher Van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, Mexico
| | - Alan R Shuldiner
- Regeneron Genetics Center, Tarrytown, NY, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - L Elliot Hong
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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5
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Ament SA, Cortes-Gutierrez M, Herb BR, Mocci E, Colantuoni C, McCarthy MM. A single-cell genomic atlas for maturation of the human cerebellum during early childhood. Sci Transl Med 2023; 15:eade1283. [PMID: 37824600 DOI: 10.1126/scitranslmed.ade1283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Inflammation early in life is a clinically established risk factor for autism spectrum disorders and schizophrenia, yet the impact of inflammation on human brain development is poorly understood. The cerebellum undergoes protracted postnatal maturation, making it especially susceptible to perturbations contributing to the risk of developing neurodevelopmental disorders. Here, using single-cell genomics of postmortem cerebellar brain samples, we characterized the postnatal development of cerebellar neurons and glia in 1- to 5-year-old children, comparing individuals who had died while experiencing inflammation with those who had died as a result of an accident. Our analyses revealed that inflammation and postnatal cerebellar maturation are associated with extensive, overlapping transcriptional changes primarily in two subtypes of inhibitory neurons: Purkinje neurons and Golgi neurons. Immunohistochemical analysis of a subset of these postmortem cerebellar samples revealed no change to Purkinje neuron soma size but evidence for increased activation of microglia in those children who had experienced inflammation. Maturation-associated and inflammation-associated gene expression changes included genes implicated in neurodevelopmental disorders. A gene regulatory network model integrating cell type-specific gene expression and chromatin accessibility identified seven temporally specific gene networks in Purkinje neurons and suggested that inflammation may be associated with the premature down-regulation of developmental gene expression programs.
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Affiliation(s)
- Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marcia Cortes-Gutierrez
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian R Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pain Sciences, University of Maryland School of Nursing, Baltimore, MD, USA
| | - Carlo Colantuoni
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Departments of Neurology and Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Margaret M McCarthy
- UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, MD, USA
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6
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Vilela J, Martiniano H, Marques AR, Santos JX, Asif M, Rasga C, Oliveira G, Vicente AM. Identification of Neurotransmission and Synaptic Biological Processes Disrupted in Autism Spectrum Disorder Using Interaction Networks and Community Detection Analysis. Biomedicines 2023; 11:2971. [PMID: 38001974 PMCID: PMC10668950 DOI: 10.3390/biomedicines11112971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by communication deficits and repetitive behavioral patterns. Hundreds of candidate genes have been implicated in ASD, including neurotransmission and synaptic (NS) genes; however, the genetic architecture of this disease is far from clear. In this study, we seek to clarify the biological processes affected by NS gene variants identified in individuals with ASD and the global networks that link those processes together. For a curated list of 1216 NS candidate genes, identified in multiple databases and the literature, we searched for ultra-rare (UR) loss-of-function (LoF) variants in the whole-exome sequencing dataset from the Autism Sequencing Consortium (N = 3938 cases). Filtering for population frequency was carried out using gnomAD (N = 60,146 controls). NS genes with UR LoF variants were used to construct a network of protein-protein interactions, and the network's biological communities were identified by applying the Leiden algorithm. We further explored the expression enrichment of network genes in specific brain regions. We identified 356 variants in 208 genes, with a preponderance of UR LoF variants in the PDE11A and SYTL3 genes. Expression enrichment analysis highlighted several subcortical structures, particularly the basal ganglia. The interaction network defined seven network communities, clustering synaptic and neurotransmitter pathways with several ubiquitous processes that occur in multiple organs and systems. This approach also uncovered biological pathways that are not usually associated with ASD, such as brain cytochromes P450 and brain mitochondrial metabolism. Overall, the community analysis suggests that ASD involves the disruption of synaptic and neurotransmitter pathways but also ubiquitous, but less frequently implicated, biological processes.
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Affiliation(s)
- Joana Vilela
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Hugo Martiniano
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Ana Rita Marques
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - João Xavier Santos
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Muhammad Asif
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Célia Rasga
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo, Serviço do Centro de Desenvolvimento da Criança, Centro de Investigação e Formação Clínica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra (CHUC), 3000-602 Coimbra, Portugal;
- Coimbra Institute for Biomedical Imaging and Translational Research, University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Astrid Moura Vicente
- Departamento de Promoção da Saúde e Doenças Não Transmissíveis, Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, 1649-016 Lisboa, Portugal; (J.V.); (H.M.); (A.R.M.); (J.X.S.); (M.A.); (C.R.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
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7
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Aly A, Laszlo ZI, Rajkumar S, Demir T, Hindley N, Lamont DJ, Lehmann J, Seidel M, Sommer D, Franz-Wachtel M, Barletta F, Heumos S, Czemmel S, Kabashi E, Ludolph A, Boeckers TM, Henstridge CM, Catanese A. Integrative proteomics highlight presynaptic alterations and c-Jun misactivation as convergent pathomechanisms in ALS. Acta Neuropathol 2023; 146:451-475. [PMID: 37488208 PMCID: PMC10412488 DOI: 10.1007/s00401-023-02611-y] [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: 02/17/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease mainly affecting upper and lower motoneurons. Several functionally heterogeneous genes have been associated with the familial form of this disorder (fALS), depicting an extremely complex pathogenic landscape. This heterogeneity has limited the identification of an effective therapy, and this bleak prognosis will only improve with a greater understanding of convergent disease mechanisms. Recent evidence from human post-mortem material and diverse model systems has highlighted the synapse as a crucial structure actively involved in disease progression, suggesting that synaptic aberrations might represent a shared pathological feature across the ALS spectrum. To test this hypothesis, we performed the first comprehensive analysis of the synaptic proteome from post-mortem spinal cord and human iPSC-derived motoneurons carrying mutations in the major ALS genes. This integrated approach highlighted perturbations in the molecular machinery controlling vesicle release as a shared pathomechanism in ALS. Mechanistically, phosphoproteomic analysis linked the presynaptic vesicular phenotype to an accumulation of cytotoxic protein aggregates and to the pro-apoptotic activation of the transcription factor c-Jun, providing detailed insights into the shared pathobiochemistry in ALS. Notably, sub-chronic treatment of our iPSC-derived motoneurons with the fatty acid docosahexaenoic acid exerted a neuroprotective effect by efficiently rescuing the alterations revealed by our multidisciplinary approach. Together, this study provides strong evidence for the central and convergent role played by the synaptic microenvironment within the ALS spinal cord and highlights a potential therapeutic target that counteracts degeneration in a heterogeneous cohort of human motoneuron cultures.
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Affiliation(s)
- Amr Aly
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Zsofia I Laszlo
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Sandeep Rajkumar
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Tugba Demir
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Nicole Hindley
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Douglas J Lamont
- FingerPrints Proteomics Facility, Discovery Centre, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Johannes Lehmann
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Mira Seidel
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Daniel Sommer
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | | | - Francesca Barletta
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Stefan Czemmel
- Quantitative Biology Center (QBiC), University of Tübingen, 72076, Tübingen, Germany
| | - Edor Kabashi
- Laboratory of Translational Research for Neurological Disorders, Imagine Institute, Université de Paris, INSERM, UMR 1163, 75015, Paris, France
| | - Albert Ludolph
- Department of Neurology, Ulm University School of Medicine, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE), Ulm Site, Germany
| | - Tobias M Boeckers
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE), Ulm Site, Germany
| | - Christopher M Henstridge
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland, UK.
| | - Alberto Catanese
- Institute of Anatomy and Cell Biology, Ulm University, Ulm, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Ulm Site, Germany.
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8
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Ahmed NI, Khandelwal N, Anderson AG, Kulkarni A, Gibson J, Konopka G. Compensation between FOXP transcription factors maintains proper striatal function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546567. [PMID: 37425820 PMCID: PMC10327074 DOI: 10.1101/2023.06.26.546567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Spiny projection neurons (SPNs) of the striatum are critical in integrating neurochemical information to coordinate motor and reward-based behavior. Mutations in the regulatory transcription factors expressed in SPNs can result in neurodevelopmental disorders (NDDs). Paralogous transcription factors Foxp1 and Foxp2, which are both expressed in the dopamine receptor 1 (D1) expressing SPNs, are known to have variants implicated in NDDs. Utilizing mice with a D1-SPN specific loss of Foxp1, Foxp2, or both and a combination of behavior, electrophysiology, and cell-type specific genomic analysis, loss of both genes results in impaired motor and social behavior as well as increased firing of the D1-SPNs. Differential gene expression analysis implicates genes involved in autism risk, electrophysiological properties, and neuronal development and function. Viral mediated re-expression of Foxp1 into the double knockouts was sufficient to restore electrophysiological and behavioral deficits. These data indicate complementary roles between Foxp1 and Foxp2 in the D1-SPNs.
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Affiliation(s)
- Newaz I. Ahmed
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Nitin Khandelwal
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Ashley G. Anderson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Jay Gibson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX 75390-9111, USA
- Lead Contact
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9
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Guo Q, Wang Y, Wang Q, Qian Y, Jiang Y, Dong X, Chen H, Chen X, Liu X, Yu S, Zhu J, Shan S, Wu B, Zhou W, Wang H. In the developing cerebral cortex: axonogenesis, synapse formation, and synaptic plasticity are regulated by SATB2 target genes. Pediatr Res 2023; 93:1519-1527. [PMID: 36028553 DOI: 10.1038/s41390-022-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/23/2022] [Accepted: 07/29/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Special AT-rich sequence-binding protein 2 is essential for the development of cerebral cortex and key molecular node for the establishment of proper neural circuitry and function. Mutations in the SATB2 gene lead to SATB2-associated syndrome, which is characterized by abnormal development of skeleton and central nervous systems. METHODS We generated Satb2 knockout mouse model through CRISPR-Cas9 technology and performed RNA-seq and ChIP-seq of embryonic cerebral cortex. We conducted RT-qPCR, western blot, immunofluorescence staining, luciferase reporter assay and behavioral analysis for experimental verification. RESULTS We identified 1363 downstream effector genes of Satb2 and correlation analysis of Satb2-targeted genes and neurological disease genes showed that Satb2 contribute to cognitive and mental disorders from the early developmental stage. We found that Satb2 directly regulate the expression of Ntng1, Cdh13, Kitl, genes important for axon guidance, synaptic formation, neuron migration, and Satb2 directly activates the expression of Mef2c. We also showed that Satb2 heterozygous knockout mice showed impaired spatial learning and memory. CONCLUSIONS Taken together, our study supportsroles of Satb2 in the regulation of axonogenesis and synaptic formation at the early developmental stage and provides new insights into the complicated regulatory mechanism of Satb2 and new evidence to elucidate the pathogen of SATB2-associated syndrome. IMPACT 1363 downstream effector genes of Satb2 were classified into 5 clusters with different temporal expression patterns. We identified Plxnd1, Ntng1, Efnb2, Ephb1, Plxna2, Epha3, Plxna4, Unc5c, and Flrt2 as axon guidance molecules to regulate axonogenesis. 168 targeted genes of Satb2 were found to regulate synaptic formation in the early development of the cerebral cortex. Transcription factor Mef2c is positively regulated by Satb2, and 28 Mef2c-targeted genes can be directly regulated by Satb2. In the Morris water maze test, Satb2+/- mice showed impaired spatial learning and memory, further strengthening that Satb2 can regulate synaptic functions.
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Affiliation(s)
- Qiufang Guo
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
- Berry Genomics Co, 102206, Beijing, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Qing Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Yinmo Jiang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiang Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Xiuyun Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Shifang Shan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, 201102, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, 201102, Shanghai, China.
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10
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More RP, Warrier V, Brunel H, Buckingham C, Smith P, Allison C, Holt R, Bradshaw CR, Baron-Cohen S. Identifying rare genetic variants in 21 highly multiplex autism families: the role of diagnosis and autistic traits. Mol Psychiatry 2023; 28:2148-2157. [PMID: 36702863 PMCID: PMC10575770 DOI: 10.1038/s41380-022-01938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023]
Abstract
Autism is a highly heritable, heterogeneous, neurodevelopmental condition. Large-scale genetic studies, predominantly focussing on simplex families and clinical diagnoses of autism have identified hundreds of genes associated with autism. Yet, the contribution of these classes of genes to multiplex families and autistic traits still warrants investigation. Here, we conducted whole-genome sequencing of 21 highly multiplex autism families, with at least three autistic individuals in each family, to prioritise genes associated with autism. Using a combination of both autistic traits and clinical diagnosis of autism, we identify rare variants in genes associated with autism, and related neurodevelopmental conditions in multiple families. We identify a modest excess of these variants in autistic individuals compared to individuals without an autism diagnosis. Finally, we identify a convergence of the genes identified in molecular pathways related to development and neurogenesis. In sum, our analysis provides initial evidence to demonstrate the value of integrating autism diagnosis and autistic traits to prioritise genes.
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Affiliation(s)
- Ravi Prabhakar More
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Helena Brunel
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Clara Buckingham
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Paula Smith
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Carrie Allison
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Rosemary Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
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11
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Pinto MJ, Cottin L, Dingli F, Laigle V, Ribeiro LF, Triller A, Henderson F, Loew D, Fabre V, Bessis A. Microglial TNFα orchestrates protein phosphorylation in the cortex during the sleep period and controls homeostatic sleep. EMBO J 2023; 42:e111485. [PMID: 36385434 PMCID: PMC9811617 DOI: 10.15252/embj.2022111485] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
Sleep intensity is adjusted by the length of previous awake time, and under tight homeostatic control by protein phosphorylation. Here, we establish microglia as a new cellular component of the sleep homeostasis circuit. Using quantitative phosphoproteomics of the mouse frontal cortex, we demonstrate that microglia-specific deletion of TNFα perturbs thousands of phosphorylation sites during the sleep period. Substrates of microglial TNFα comprise sleep-related kinases such as MAPKs and MARKs, and numerous synaptic proteins, including a subset whose phosphorylation status encodes sleep need and determines sleep duration. As a result, microglial TNFα loss attenuates the build-up of sleep need, as measured by electroencephalogram slow-wave activity and prevents immediate compensation for loss of sleep. Our data suggest that microglia control sleep homeostasis by releasing TNFα which acts on neuronal circuitry through dynamic control of phosphorylation.
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Affiliation(s)
- Maria J Pinto
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Léa Cottin
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Florent Dingli
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Victor Laigle
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Luís F Ribeiro
- Center for Neuroscience and Cell Biology (CNC), Institute for Interdisciplinary Research (IIIUC)University of CoimbraCoimbraPortugal
| | - Antoine Triller
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Fiona Henderson
- Sorbonne Université, CNRS UMR 8246, INSERM U1130, Neuroscience Paris Seine – Institut de Biologie Paris Seine (NPS – IBPS)ParisFrance
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Véronique Fabre
- Sorbonne Université, CNRS UMR 8246, INSERM U1130, Neuroscience Paris Seine – Institut de Biologie Paris Seine (NPS – IBPS)ParisFrance
| | - Alain Bessis
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
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12
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Laszlo ZI, Hindley N, Sanchez Avila A, Kline RA, Eaton SL, Lamont DJ, Smith C, Spires-Jones TL, Wishart TM, Henstridge CM. Synaptic proteomics reveal distinct molecular signatures of cognitive change and C9ORF72 repeat expansion in the human ALS cortex. Acta Neuropathol Commun 2022; 10:156. [DOI: 10.1186/s40478-022-01455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractIncreasing evidence suggests synaptic dysfunction is a central and possibly triggering factor in Amyotrophic Lateral Sclerosis (ALS). Despite this, we still know very little about the molecular profile of an ALS synapse. To address this gap, we designed a synaptic proteomics experiment to perform an unbiased assessment of the synaptic proteome in the ALS brain. We isolated synaptoneurosomes from fresh-frozen post-mortem human cortex (11 controls and 18 ALS) and stratified the ALS group based on cognitive profile (Edinburgh Cognitive and Behavioural ALS Screen (ECAS score)) and presence of a C9ORF72 hexanucleotide repeat expansion (C9ORF72-RE). This allowed us to assess regional differences and the impact of phenotype and genotype on the synaptic proteome, using Tandem Mass Tagging-based proteomics. We identified over 6000 proteins in our synaptoneurosomes and using robust bioinformatics analysis we validated the strong enrichment of synapses. We found more than 30 ALS-associated proteins in synaptoneurosomes, including TDP-43, FUS, SOD1 and C9ORF72. We identified almost 500 proteins with altered expression levels in ALS, with region-specific changes highlighting proteins and pathways with intriguing links to neurophysiology and pathology. Stratifying the ALS cohort by cognitive status revealed almost 150 specific alterations in cognitively impaired ALS synaptic preparations. Stratifying by C9ORF72-RE status revealed 330 protein alterations in the C9ORF72-RE +ve group, with KEGG pathway analysis highlighting strong enrichment for postsynaptic dysfunction, related to glutamatergic receptor signalling. We have validated some of these changes by western blot and at a single synapse level using array tomography imaging. In summary, we have generated the first unbiased map of the human ALS synaptic proteome, revealing novel insight into this key compartment in ALS pathophysiology and highlighting the influence of cognitive decline and C9ORF72-RE on synaptic composition.
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13
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Casella AM, Colantuoni C, Ament SA. Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies. PLoS Comput Biol 2022; 18:e1010430. [PMID: 36070311 PMCID: PMC9484640 DOI: 10.1371/journal.pcbi.1010430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/19/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
Genetic risk for complex traits is strongly enriched in non-coding genomic regions involved in gene regulation, especially enhancers. However, we lack adequate tools to connect the characteristics of these disruptions to genetic risk. Here, we propose RWAS (Regulome Wide Association Study), a new application of the MAGMA software package to identify the characteristics of enhancers that contribute to genetic risk for disease. RWAS involves three steps: (i) assign genotyped SNPs to cell type- or tissue-specific regulatory features (e.g., enhancers); (ii) test associations of each regulatory feature with a trait of interest for which genome-wide association study (GWAS) summary statistics are available; (iii) perform enhancer-set enrichment analyses to identify quantitative or categorical features of regulatory elements that are associated with the trait. These steps are implemented as a novel application of MAGMA, a tool originally developed for gene-based GWAS analyses. Applying RWAS to interrogate genetic risk for schizophrenia, we discovered a class of risk-associated AT-rich enhancers that are active in the developing brain and harbor binding sites for multiple transcription factors with neurodevelopmental functions. RWAS utilizes open-source software, and we provide a comprehensive collection of annotations for tissue-specific enhancer locations and features, including their evolutionary conservation, AT content, and co-localization with binding sites for hundreds of TFs. RWAS will enable researchers to characterize properties of regulatory elements associated with any trait of interest for which GWAS summary statistics are available. Enhancers are regulatory regions that influence gene expression via the binding of transcription factors. Risk for many heritable diseases is enriched in regulatory regions, including enhancers. In this study, we introduce a novel application of the MAGMA software tool that enables testing for associations between enhancer attributes and risk, and we use this method to determine the enhancer characteristics that are associated with risk for schizophrenia. We found that enhancers associated with schizophrenia risk are both evolutionarily conserved and in physical contact with mutation-intolerant genes, many of which have neurodevelopmental functions. Risk-associated enhancers are also AT-rich and contain binding sites for neurodevelopmental transcription factors.
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Affiliation(s)
- Alex M. Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Medical Scientist Training Program, UMSOM, Baltimore, Maryland, United States of America
| | - Carlo Colantuoni
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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14
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Zhou X, Feliciano P, Shu C, Wang T, Astrovskaya I, Hall JB, Obiajulu JU, Wright JR, Murali SC, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, Snyder LG, Han B, Chang TS, Turner TN, Harvey WT, Nishida A, O'Roak BJ, Geschwind DH, Michaelson JJ, Volfovsky N, Eichler EE, Shen Y, Chung WK. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat Genet 2022; 54:1305-1319. [PMID: 35982159 PMCID: PMC9470534 DOI: 10.1038/s41588-022-01148-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 06/28/2022] [Indexed: 12/16/2022]
Abstract
To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P < 2.5 × 10-6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes (NAV3, ITSN1, SCAF1 and HNRNPUL2; n = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes (CHD8, SCN2A, ADNP, FOXP1 and SHANK3) (59% vs 88%, P = 1.9 × 10-6). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.
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Affiliation(s)
- Xueya Zhou
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Chang Shu
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Neuroscience Research Institute, Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China
| | | | | | - Joseph U Obiajulu
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Taylor R Thomas
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | | | | | | | - Bing Han
- Simons Foundation, New York, NY, USA
| | - Timothy S Chang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tychele N Turner
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew Nishida
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.,Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. .,Simons Foundation, New York, NY, USA. .,Department of Medicine, Columbia University Medical Center, New York, NY, USA.
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15
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Wang Q, Yan S, Zhang J, Du R, Xue L, Li J, Yu C. The differentially expressed proteins related to clinical viral encephalitis revealed by proteomics. IBRAIN 2022; 8:148-164. [PMID: 37786892 PMCID: PMC10528792 DOI: 10.1002/ibra.12036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 02/05/2023]
Abstract
To screen out the prospective biomarkers of viral encephalitis (VE), analyze the biological process and signaling pathways involved by differentially expressed proteins (DEPs). A total of 11 cerebrospinal fluid (CSF) samples with VE and 5 with non-nervous system infection were used to perform label-free proteomic techniques. Then, the bioinformatic analysis of DEPs was applied by Interproscan software. Moreover, 73 CSF samples in the VE group and 53 in the control group were used to verify the changes of some DEPs by enzyme-linked immunosorbent assay (ELISA). Thirty-nine DEPs were identified, including 18 upregulated DEPs and 21 downregulated DEPs. DEPs were mainly enriched in cell adhesion molecules by Kyoto Encyclopedia of Genes and Genomes analysis pathway analysis. The DEPs related to axon tissue were obviously downregulated and the most significant downregulated proteins were neurexin 3, neurofascin, and neuroligin 2 (NLGN2). Moreover, the protein expression of NLGN2 in the VE group was significantly higher than that in the control group by ELISA. The correlation analysis of NLGN2 in the VE group revealed that there was a weak positive correlation with CSF protein and a weak negative correlation with CSF chloride. The clinical VE may be closely related to NLGN2 and the cell adhesion molecule pathway.
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Affiliation(s)
- Qian Wang
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | | | | | - Ruo‐Lan Du
- Institute of Neurological Disease and Department of Anesthesiology, Translational Neuroscience Center, West China HospitalSichuan UniversityChengduChina
| | - Lu‐Lu Xue
- Kunming Medical UniversityKunmingYunnanChina
| | - Juan Li
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Chang‐Yin Yu
- Affiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
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16
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Li W, Lv L, Luo XJ. In vivo study sheds new light on the dendritic spine pathology hypothesis of schizophrenia. Mol Psychiatry 2022; 27:1866-1868. [PMID: 35079121 DOI: 10.1038/s41380-022-01449-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, 453002, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, 453002, China.,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, 453002, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
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17
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Kalman ZE, Dudola D, Mészáros B, Gáspári Z, Dobson L. PSINDB: the postsynaptic protein-protein interaction database. Database (Oxford) 2022; 2022:baac007. [PMID: 35234850 PMCID: PMC9216581 DOI: 10.1093/database/baac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/21/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
The postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein-protein interactions (PPIs) in this network, these data are mostly scattered in the literature or stored in generic databases that are not designed to display aspects that are fundamental to the understanding of postsynaptic functions. To overcome these limitations, we collected postsynaptic PPIs complemented by a high amount of detailed structural and biological information and launched a freely available resource, the Postsynaptic Interaction Database (PSINDB), to make these data and annotations accessible. PSINDB includes tens of thousands of binding regions together with structural features, mediating and regulating the formation of PPIs, annotated with detailed experimental information about each interaction. PSINDB is expected to be useful for various aspects of molecular neurobiology research, from experimental design to network and systems biology-based modeling and analysis of changes in the protein network upon various stimuli. Database URL https://psindb.itk.ppke.hu/.
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Affiliation(s)
- Zsofia E Kalman
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Dániel Dudola
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Laszlo Dobson
- *Corresponding author: Tel: +49 6221 387 8398; Fax: +49 6221 387 8530;
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18
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Ji Y, Chen R, Wang Q, Wei Q, Tao R, Li B. Leveraging Gene-Level Prediction as Informative Covariate in Hypothesis Weighting Improves Power for Rare Variant Association Studies. Genes (Basel) 2022; 13:genes13020381. [PMID: 35205424 PMCID: PMC8872452 DOI: 10.3390/genes13020381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 02/05/2023] Open
Abstract
Gene-based rare variant association studies (RVASs) have low power due to the infrequency of rare variants and the large multiple testing burden. To correct for multiple testing, traditional false discovery rate (FDR) procedures which depend solely on P-values are often used. Recently, Independent Hypothesis Weighting (IHW) was developed to improve the detection power while maintaining FDR control by leveraging prior information for each hypothesis. Here, we present a framework to increase power of gene-based RVASs by incorporating prior information using IHW. We first build supervised machine learning models to assign each gene a prediction score that measures its disease risk, using the input of multiple biological features, fed with high-confidence risk genes and local background genes selected near GWAS significant loci as the training set. Then we use the prediction scores as covariates to prioritize RVAS results via IHW. We demonstrate the effectiveness of this framework through applications to RVASs in schizophrenia and autism spectrum disorder. We found sizeable improvements in the number of significant associations compared to traditional FDR approaches, and independent evidence supporting the relevance of the genes identified by our framework but not traditional FDR, demonstrating the potential of our framework to improve power of gene-based RVASs.
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Affiliation(s)
- Ying Ji
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Rui Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Quan Wang
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Qiang Wei
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Ran Tao
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37203, USA
- Correspondence: (R.T.); (B.L.)
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37232, USA; (Y.J.); (R.C.); (Q.W.); (Q.W.)
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
- Correspondence: (R.T.); (B.L.)
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19
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Schiapparelli LM, Sharma P, He HY, Li J, Shah SH, McClatchy DB, Ma Y, Liu HH, Goldberg JL, Yates JR, Cline HT. Proteomic screen reveals diverse protein transport between connected neurons in the visual system. Cell Rep 2022; 38:110287. [PMID: 35081342 PMCID: PMC8906846 DOI: 10.1016/j.celrep.2021.110287] [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] [Received: 02/23/2021] [Revised: 11/22/2021] [Accepted: 12/28/2021] [Indexed: 11/20/2022] Open
Abstract
Intercellular transfer of toxic proteins between neurons is thought to contribute to neurodegenerative disease, but whether direct interneuronal protein transfer occurs in the healthy brain is not clear. To assess the prevalence and identity of transferred proteins and the cellular specificity of transfer, we biotinylated retinal ganglion cell proteins in vivo and examined biotinylated proteins transported through the rodent visual circuit using microscopy, biochemistry, and mass spectrometry. Electron microscopy demonstrated preferential transfer of biotinylated proteins from retinogeniculate inputs to excitatory lateral geniculate nucleus (LGN) neurons compared with GABAergic neurons. An unbiased mass spectrometry-based screen identified 200 transneuronally transported proteins (TNTPs) isolated from the visual cortex. The majority of TNTPs are present in neuronal exosomes, and virally expressed TNTPs, including tau and β-synuclein, were detected in isolated exosomes and postsynaptic neurons. Our data demonstrate transfer of diverse endogenous proteins between neurons in the healthy intact brain and suggest that TNTP transport may be mediated by exosomes. Schiapparelli et al. show that diverse endogenous proteins are transported anterogradely across synapses in the rat visual system. About 200 transneuronally transported proteins (TNTPs) were identified by MS/MS, and selected TNTPs, including β-synuclein and tau, were validated using biochemical and histological methods. TNTP transport may be mediated by exosomes.
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Affiliation(s)
- Lucio M Schiapparelli
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pranav Sharma
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Xosomix, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Hai-Yan He
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jianli Li
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sahil H Shah
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Neuroscience Graduate Program and Medical Scientist Training Program, University of California, San Diego, La Jolla, CA 92093, USA; Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - Daniel B McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Han-Hsuan Liu
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey L Goldberg
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hollis T Cline
- Neuroscience Department and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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20
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Distinct gene-set burden patterns underlie common generalized and focal epilepsies. EBioMedicine 2021; 72:103588. [PMID: 34571366 PMCID: PMC8479647 DOI: 10.1016/j.ebiom.2021.103588] [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] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/04/2021] [Accepted: 09/06/2021] [Indexed: 01/02/2023] Open
Abstract
Background Analyses of few gene-sets in epilepsy showed a potential to unravel key disease associations. We set out to investigate the burden of ultra-rare variants (URVs) in a comprehensive range of biologically informed gene-sets presumed to be implicated in epileptogenesis. Methods The burden of 12 URV types in 92 gene-sets was compared between cases and controls using whole exome sequencing data from individuals of European descent with developmental and epileptic encephalopathies (DEE, n = 1,003), genetic generalized epilepsy (GGE, n = 3,064), or non-acquired focal epilepsy (NAFE, n = 3,522), collected by the Epi25 Collaborative, compared to 3,962 ancestry-matched controls. Findings Missense URVs in highly constrained regions were enriched in neuron-specific and developmental genes, whereas genes not expressed in brain were not affected. GGE featured a higher burden in gene-sets derived from inhibitory vs. excitatory neurons or associated receptors, whereas the opposite was found for NAFE, and DEE featured a burden in both. Top-ranked susceptibility genes from recent genome-wide association studies (GWAS) and gene-sets derived from generalized vs. focal epilepsies revealed specific enrichment patterns of URVs in GGE vs. NAFE. Interpretation Missense URVs affecting highly constrained sites differentially impact genes expressed in inhibitory vs. excitatory pathways in generalized vs. focal epilepsies. The excess of URVs in top-ranked GWAS risk-genes suggests a convergence of rare deleterious and common risk-variants in the pathogenesis of generalized and focal epilepsies. Funding DFG Research Unit FOR-2715 (Germany), FNR (Luxembourg), NHGRI (US), NHLBI (US), DAAD (Germany).
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21
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Carlyle BC, Kandigian SE, Kreuzer J, Das S, Trombetta BA, Kuo Y, Bennett DA, Schneider JA, Petyuk VA, Kitchen RR, Morris R, Nairn AC, Hyman BT, Haas W, Arnold SE. Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiol Aging 2021; 105:99-114. [PMID: 34052751 PMCID: PMC8338777 DOI: 10.1016/j.neurobiolaging.2021.04.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is defined by the presence of abundant amyloid-β (Aβ) and tau neuropathology. While this neuropathology is necessary for AD diagnosis, it is not sufficient for causing cognitive impairment. Up to one third of community dwelling older adults harbor intermediate to high levels of AD neuropathology at death yet demonstrate no significant cognitive impairment. Conversely, there are individuals who exhibit dementia with no gross explanatory neuropathology. In prior studies, synapse loss correlated with cognitive impairment. To understand how synaptic composition changes in relation to neuropathology and cognition, multiplexed liquid chromatography mass-spectrometry was used to quantify enriched synaptic proteins from the parietal association cortex of 100 subjects with contrasting levels of AD pathology and cognitive performance. 123 unique proteins were significantly associated with diagnostic category. Functional analysis showed enrichment of serotonin release and oxidative phosphorylation categories in normal (cognitively unimpaired, low neuropathology) and "resilient" (unimpaired despite AD pathology) individuals. In contrast, frail individuals, (low pathology, impaired cognition) showed a metabolic shift towards glycolysis and increased presence of proteasome subunits.
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Affiliation(s)
- Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Savannah E Kandigian
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Johannes Kreuzer
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Sudeshna Das
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Yikai Kuo
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | | | | | | | - Robert R Kitchen
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | - Robert Morris
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | | | - Bradley T Hyman
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Wilhelm Haas
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
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22
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Chau KK, Zhang P, Urresti J, Amar M, Pramod AB, Chen J, Thomas A, Corominas R, Lin GN, Iakoucheva LM. Full-length isoform transcriptome of the developing human brain provides further insights into autism. Cell Rep 2021; 36:109631. [PMID: 34469739 PMCID: PMC8437376 DOI: 10.1016/j.celrep.2021.109631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 04/23/2021] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing plays an important role in brain development, but its global contribution to human neurodevelopmental diseases (NDDs) requires further investigation. Here we examine the relationships between splicing isoform expression in the brain and de novo loss-of-function mutations from individuals with NDDs. We analyze the full-length isoform transcriptome of the developing human brain and observe differentially expressed isoforms and isoform co-expression modules undetectable by gene-level analyses. These isoforms are enriched in loss-of-function mutations and microexons, are co-expressed with a unique set of partners, and have higher prenatal expression. We experimentally test the effect of splice-site mutations and demonstrate exon skipping in five NDD risk genes, including SCN2A, DYRK1A, and BTRC. Our results suggest that the splice site mutation in BTRC reduces translational efficiency, likely affecting Wnt signaling through impaired degradation of β-catenin. We propose that functional effects of mutations should be investigated at the isoform- rather than gene-level resolution.
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Affiliation(s)
- Kevin K Chau
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA; Department of Biology, University of California, San Diego, La Jolla, CA, USA
| | - Pan Zhang
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Jorge Urresti
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Megha Amar
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Akula Bala Pramod
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Jiaye Chen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Amy Thomas
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Roser Corominas
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Guan Ning Lin
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
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23
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Amar M, Pramod AB, Yu NK, Herrera VM, Qiu LR, Moran-Losada P, Zhang P, Trujillo CA, Ellegood J, Urresti J, Chau K, Diedrich J, Chen J, Gutierrez J, Sebat J, Ramanathan D, Lerch JP, Yates JR, Muotri AR, Iakoucheva LM. Autism-linked Cullin3 germline haploinsufficiency impacts cytoskeletal dynamics and cortical neurogenesis through RhoA signaling. Mol Psychiatry 2021; 26:3586-3613. [PMID: 33727673 PMCID: PMC8443683 DOI: 10.1038/s41380-021-01052-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/12/2021] [Accepted: 02/12/2021] [Indexed: 01/01/2023]
Abstract
E3-ubiquitin ligase Cullin3 (Cul3) is a high confidence risk gene for autism spectrum disorder (ASD) and developmental delay (DD). To investigate how Cul3 mutations impact brain development, we generated a haploinsufficient Cul3 mouse model using CRISPR/Cas9 genome engineering. Cul3 mutant mice exhibited social and cognitive deficits and hyperactive behavior. Brain MRI found decreased volume of cortical regions and changes in many other brain regions of Cul3 mutant mice starting from early postnatal development. Spatiotemporal transcriptomic and proteomic profiling of embryonic, early postnatal and adult brain implicated neurogenesis and cytoskeletal defects as key drivers of Cul3 functional impact. Specifically, dendritic growth, filamentous actin puncta, and spontaneous network activity were reduced in Cul3 mutant mice. Inhibition of small GTPase RhoA, a molecular substrate of Cul3 ligase, rescued dendrite length and network activity phenotypes. Our study identified defects in neuronal cytoskeleton and Rho signaling as the primary targets of Cul3 mutation during brain development.
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Affiliation(s)
- Megha Amar
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Akula Bala Pramod
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nam-Kyung Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Lily R Qiu
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON, Canada
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, The University of Oxford, Oxford, UK
| | | | - Pan Zhang
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Cleber A Trujillo
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, CA, USA
| | - Jacob Ellegood
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON, Canada
| | - Jorge Urresti
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Kevin Chau
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jolene Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jiaye Chen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jessica Gutierrez
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
| | - Dhakshin Ramanathan
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jason P Lerch
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, ON, Canada
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neuroscience, The University of Oxford, Oxford, UK
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Alysson R Muotri
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, CA, USA.
- Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, CA, USA.
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA, USA.
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
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24
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Toriumi K, Berto S, Koike S, Usui N, Dan T, Suzuki K, Miyashita M, Horiuchi Y, Yoshikawa A, Asakura M, Nagahama K, Lin HC, Sugaya Y, Watanabe T, Kano M, Ogasawara Y, Miyata T, Itokawa M, Konopka G, Arai M. Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex. Redox Biol 2021; 45:102057. [PMID: 34198071 PMCID: PMC8253914 DOI: 10.1016/j.redox.2021.102057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Methylglyoxal (MG) is a reactive and cytotoxic α-dicarbonyl byproduct of glycolysis. Our bodies have several bio-defense systems to detoxify MG, including an enzymatic system by glyoxalase (GLO) 1 and GLO2. We identified a subtype of schizophrenia patients with novel mutations in the GLO1 gene that results in reductions of enzymatic activity. Moreover, we found that vitamin B6 (VB6) levels in peripheral blood of the schizophrenia patients with GLO1 dysfunction are significantly lower than that of healthy controls. However, the effects of GLO1 dysfunction and VB6 deficiency on the pathophysiology of schizophrenia remains poorly understood. Here, we generated a novel mouse model for this subgroup of schizophrenia patients by feeding Glo1 knockout mice VB6-deficent diets (KO/VB6(−)) and evaluated the combined effects of GLO1 dysfunction and VB6 deficiency on brain function. KO/VB6(−) mice accumulated homocysteine in plasma and MG in the prefrontal cortex (PFC), hippocampus, and striatum, and displayed behavioral deficits, such as impairments of social interaction and cognitive memory and a sensorimotor deficit in the prepulse inhibition test. Furthermore, we found aberrant gene expression related to mitochondria function in the PFC of the KO/VB6(−) mice by RNA-sequencing and weighted gene co-expression network analysis (WGCNA). Finally, we demonstrated abnormal mitochondrial respiratory function and subsequently enhanced oxidative stress in the PFC of KO/VB6(−) mice in the PFC. These findings suggest that the combination of GLO1 dysfunction and VB6 deficiency may cause the observed behavioral deficits via mitochondrial dysfunction and oxidative stress in the PFC. A combination of Glo1 KO and VB6 deficiency induces MG accumulation in the brain. Glo1 KO/VB6(−) mice exhibit schizophrenia-like behavioral deficits. Gene expression related to mitochondria is impaired in the PFC of the Glo1 KO/VB6(−). Mitochondria in the PFC of the Glo1 KO/VB6(−) mice show respiratory dysfunction. Oxidative stress is enhanced in the PFC of the Glo1 KO/VB6(−).
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Affiliation(s)
- Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29403, USA
| | - Shin Koike
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Center for Medical Research and Education, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka, 565-0871, Japan
| | - Takashi Dan
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry, Graduate School of Medicine, Shinshu University, Nagano, 390-8621, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Yasue Horiuchi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Akane Yoshikawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Mai Asakura
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hsiao-Chun Lin
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Sugaya
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takaki Watanabe
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Ogasawara
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Toshio Miyata
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.
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25
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Clifford BRE. The bewitched ear: State of the art genomics research on tinnitus. EBioMedicine 2021; 67:103349. [PMID: 33906065 PMCID: PMC8099621 DOI: 10.1016/j.ebiom.2021.103349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- By Royce E Clifford
- Division of Otolaryngology - Head and Neck Surgery, School of Health Sciences, University of California San Diego, La Jolla, CA, USA; Department of Research, Veteran Administration Hospital San Diego, CA, USA; Visiting Scientist, Department of Environmental Science, Harvard School of Public Health, Boston MA, USA.
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26
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van Gelder CAGH, Altelaar M. Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics. Mol Cell Proteomics 2021; 20:100087. [PMID: 33933679 PMCID: PMC8167277 DOI: 10.1016/j.mcpro.2021.100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/21/2023] Open
Abstract
One of the most fascinating features of the brain is its ability to adapt to its surroundings. Synaptic plasticity, the dynamic mechanism of functional and structural alterations in synaptic strength, is essential for brain functioning and underlies a variety of processes such as learning and memory. Although the molecular mechanisms underlying such rapid plasticity are not fully understood, a consensus exists on the important role of proteins. The study of these neuronal proteins using neuroproteomics has increased rapidly in the last decades, and advancements in MS-based proteomics have broadened our understanding of neuroplasticity exponentially. In this review, we discuss the trends in MS-based neuroproteomics for the study of synaptic protein-protein interactions and protein signaling dynamics, with a focus on sample types, different labeling and enrichment approaches, and data analysis and interpretation. We highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.
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Affiliation(s)
- Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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27
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Amanat S, Gallego-Martinez A, Sollini J, Perez-Carpena P, Espinosa-Sanchez JM, Aran I, Soto-Varela A, Batuecas-Caletrio A, Canlon B, May P, Cederroth CR, Lopez-Escamez JA. Burden of rare variants in synaptic genes in patients with severe tinnitus: An exome based extreme phenotype study. EBioMedicine 2021; 66:103309. [PMID: 33813136 PMCID: PMC8047463 DOI: 10.1016/j.ebiom.2021.103309] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND tinnitus is a heterogeneous condition associated with audiological and/or mental disorders. Chronic, severe tinnitus is reported in 1% of the population and it shows a relevant heritability, according to twins, adoptees and familial aggregation studies. The genetic contribution to severe tinnitus is unknown since large genomic studies include individuals with self-reported tinnitus and large heterogeneity in the phenotype. The aim of this study was to identify genes for severe tinnitus in patients with extreme phenotype. METHODS for this extreme phenotype study, we used three different cohorts with European ancestry (Spanish with Meniere disease (MD), Swedes tinnitus and European generalized epilepsy). In addition, four independent control datasets were also used for comparisons. Whole-exome sequencing was performed for the MD and epilepsy cohorts and whole-genome sequencing was carried out in Swedes with tinnitus. FINDINGS we found an enrichment of rare missense variants in 24 synaptic genes in a Spanish cohort, the most significant being PRUNE2, AKAP9, SORBS1, ITGAX, ANK2, KIF20B and TSC2 (p < 2E-04), when they were compared with reference datasets. This burden was replicated for ANK2 gene in a Swedish cohort with 97 tinnitus individuals, and in a subset of 34 Swedish patients with severe tinnitus for ANK2, AKAP9 and TSC2 genes (p < 2E-02). However, these associations were not significant in a third cohort of 701 generalized epilepsy individuals without tinnitus. Gene ontology (GO) and gene-set enrichment analyses revealed several pathways and biological processes involved in severe tinnitus, including membrane trafficking and cytoskeletal protein binding in neurons. INTERPRETATION a burden of rare variants in ANK2, AKAP9 and TSC2 is associated with severe tinnitus. ANK2, encodes a cytoskeleton scaffolding protein that coordinates the assembly of several proteins, drives axonal branching and influences connectivity in neurons.
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Affiliation(s)
- Sana Amanat
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain
| | - Joseph Sollini
- Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK
| | - Patricia Perez-Carpena
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Juan M Espinosa-Sanchez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Ismael Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Andres Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, Santiago de Compostela, Spain
| | | | - Barbara Canlon
- Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for System Biomedicine, University of Luxemburg, Esch-sur-Alzette, Luxembourg
| | - Christopher R Cederroth
- Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, UK; Laboratory of Experimental Audiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Ropewalk House, Nottingham, UK
| | - Jose A Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/ Junta de Andalucía, PTS, Granada, Spain; Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.Granada, Hospital Universitario Virgen de las Nieves, Granada, Spain; Department of Surgery, Division of Otolaryngology, University of Granada, Granada, Spain.
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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29
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He D, Fan C, Qi M, Yang Y, Cooper DN, Zhao H. Prioritization of schizophrenia risk genes from GWAS results by integrating multi-omics data. Transl Psychiatry 2021; 11:175. [PMID: 33731678 PMCID: PMC7969765 DOI: 10.1038/s41398-021-01294-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/09/2021] [Accepted: 02/03/2021] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia (SCZ) is a polygenic disease with a heritability approaching 80%. Over 100 SCZ-related loci have so far been identified by genome-wide association studies (GWAS). However, the risk genes associated with these loci often remain unknown. We present a new risk gene predictor, rGAT-omics, that integrates multi-omics data under a Bayesian framework by combining the Hotelling and Box-Cox transformations. The Bayesian framework was constructed using gene ontology, tissue-specific protein-protein networks, and multi-omics data including differentially expressed genes in SCZ and controls, distance from genes to the index single-nucleotide polymorphisms (SNPs), and de novo mutations. The application of rGAT-omics to the 108 loci identified by a recent GWAS study of SCZ predicted 103 high-risk genes (HRGs) that explain a high proportion of SCZ heritability (Enrichment = 43.44 and [Formula: see text]). HRGs were shown to be significantly ([Formula: see text]) enriched in genes associated with neurological activities, and more likely to be expressed in brain tissues and SCZ-associated cell types than background genes. The predicted HRGs included 16 novel genes not present in any existing databases of SCZ-associated genes or previously predicted to be SCZ risk genes by any other method. More importantly, 13 of these 16 genes were not the nearest to the index SNP markers, and them would have been difficult to identify as risk genes by conventional approaches while ten out of the 16 genes are associated with neurological functions that make them prime candidates for pathological involvement in SCZ. Therefore, rGAT-omics has revealed novel insights into the molecular mechanisms underlying SCZ and could provide potential clues to future therapies.
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Affiliation(s)
- Dan He
- grid.412536.70000 0004 1791 7851Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China ,grid.484195.5Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Cong Fan
- grid.412536.70000 0004 1791 7851Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China ,grid.484195.5Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Mengling Qi
- grid.412536.70000 0004 1791 7851Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China ,grid.484195.5Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Yuedong Yang
- grid.12981.330000 0001 2360 039XSchool of Data and Computer Science, Sun Yat-Sen University, 510006 Guangzhou, China
| | - David N. Cooper
- grid.5600.30000 0001 0807 5670Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China.
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30
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Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons. Mol Psychiatry 2021; 26:6125-6148. [PMID: 34188164 PMCID: PMC8760061 DOI: 10.1038/s41380-021-01179-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
While the transcription factor NEUROD2 has recently been associated with epilepsy, its precise role during nervous system development remains unclear. Using a multi-scale approach, we set out to understand how Neurod2 deletion affects the development of the cerebral cortex in mice. In Neurod2 KO embryos, cortical projection neurons over-migrated, thereby altering the final size and position of layers. In juvenile and adults, spine density and turnover were dysregulated in apical but not basal compartments in layer 5 neurons. Patch-clamp recordings in layer 5 neurons of juvenile mice revealed increased intrinsic excitability. Bulk RNA sequencing showed dysregulated expression of many genes associated with neuronal excitability and synaptic function, whose human orthologs were strongly associated with autism spectrum disorders (ASD). At the behavior level, Neurod2 KO mice displayed social interaction deficits, stereotypies, hyperactivity, and occasionally spontaneous seizures. Mice heterozygous for Neurod2 had similar defects, indicating that Neurod2 is haploinsufficient. Finally, specific deletion of Neurod2 in forebrain excitatory neurons recapitulated cellular and behavioral phenotypes found in constitutive KO mice, revealing the region-specific contribution of dysfunctional Neurod2 in symptoms. Informed by these neurobehavioral features in mouse mutants, we identified eleven patients from eight families with a neurodevelopmental disorder including intellectual disability and ASD associated with NEUROD2 pathogenic mutations. Our findings demonstrate crucial roles for Neurod2 in neocortical development, whose alterations can cause neurodevelopmental disorders including intellectual disability and ASD.
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31
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Urresti J, Zhang P, Moran-Losada P, Yu NK, Negraes PD, Trujillo CA, Antaki D, Amar M, Chau K, Pramod AB, Diedrich J, Tejwani L, Romero S, Sebat J, Yates III JR, Muotri AR, Iakoucheva LM. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Mol Psychiatry 2021; 26:7560-7580. [PMID: 34433918 PMCID: PMC8873019 DOI: 10.1038/s41380-021-01243-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 11/09/2022]
Abstract
Reciprocal deletion and duplication of the 16p11.2 region is the most common copy number variation (CNV) associated with autism spectrum disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV dosage affects neuronal maturation, proliferation, and synapse number, in addition to its effect on organoid size. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with a significant excess of neurons and depletion of neural progenitors observed in deletions. Transcriptomic and proteomic profiling revealed multiple pathways dysregulated by the 16p11.2 CNV, including neuron migration, actin cytoskeleton, ion channel activity, synaptic-related functions, and Wnt signaling. The level of the active form of small GTPase RhoA was increased in both, deletions and duplications. Inhibition of RhoA activity rescued migration deficits, but not neurite outgrowth. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.
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Affiliation(s)
- Jorge Urresti
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Pan Zhang
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Patricia Moran-Losada
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Nam-Kyung Yu
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Priscilla D. Negraes
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Cleber A. Trujillo
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Danny Antaki
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Megha Amar
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Kevin Chau
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Akula Bala Pramod
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Jolene Diedrich
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Leon Tejwani
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Sarah Romero
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Jonathan Sebat
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Beyster Center for Psychiatric Genomics, La Jolla, CA USA
| | - John R. Yates III
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Kavli Institute for Brain and Mind, La Jolla, CA USA ,Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA USA
| | - Lilia M. Iakoucheva
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
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Escalera-Balsera A, Roman-Naranjo P, Lopez-Escamez JA. Systematic Review of Sequencing Studies and Gene Expression Profiling in Familial Meniere Disease. Genes (Basel) 2020; 11:E1414. [PMID: 33260921 PMCID: PMC7761472 DOI: 10.3390/genes11121414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Familial Meniere Disease (FMD) is a rare inner ear disorder characterized by episodic vertigo associated with sensorineural hearing loss, tinnitus and/or aural fullness. We conducted a systematic review to find sequencing studies segregating rare variants in FMD to obtain evidence to support candidate genes for MD. After evaluating the quality of the retrieved records, eight studies were selected to carry out a quantitative synthesis. These articles described 20 single nucleotide variants (SNVs) in 11 genes (FAM136A, DTNA, PRKCB, COCH, DPT, SEMA3D, STRC, HMX2, TMEM55B, OTOG and LSAMP), most of them in singular families-the exception being the OTOG gene. Furthermore, we analyzed the pathogenicity of each SNV and compared its allelic frequency with reference datasets to evaluate its role in the pathogenesis of FMD. By retrieving gene expression data in these genes from different databases, we could classify them according to their gene expression in neural or inner ear tissues. Finally, we evaluated the pattern of inheritance to conclude which genes show an autosomal dominant (AD) or autosomal recessive (AR) inheritance in FMD.
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Affiliation(s)
- Alba Escalera-Balsera
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Pablo Roman-Naranjo
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
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33
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Gulyássy P, Puska G, Györffy BA, Todorov-Völgyi K, Juhász G, Drahos L, Kékesi KA. Proteomic comparison of different synaptosome preparation procedures. Amino Acids 2020; 52:1529-1543. [PMID: 33211194 PMCID: PMC7695668 DOI: 10.1007/s00726-020-02912-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/05/2020] [Indexed: 01/10/2023]
Abstract
Synaptosomes are frequently used research objects in neurobiology studies focusing on synaptic transmission as they mimic several aspects of the physiological synaptic functions. They contain the whole apparatus for neurotransmission, the presynaptic nerve ending with synaptic vesicles, synaptic mitochondria and often a segment of the postsynaptic membrane along with the postsynaptic density is attached to its outer surface. As being artificial functional organelles, synaptosomes are viable for several hours, retain their activity, membrane potential, and capable to store, release, and reuptake neurotransmitters. Synaptosomes are ideal subjects for proteomic analysis. The recently available separation and protein detection techniques can cope with the reduced complexity of the organelle and enable the simultaneous qualitative and quantitative analysis of thousands of proteins shaping the structural and functional characteristics of the synapse. Synaptosomes are formed during the homogenization of nervous tissue in the isoosmotic milieu and can be isolated from the homogenate by various approaches. Each enrichment method has its own benefits and drawbacks and there is not a single method that is optimal for all research purposes. For a proper proteomic experiment, it is desirable to preserve the native synaptic structure during the isolation procedure and keep the degree of contamination from other organelles or cell types as low as possible. In this article, we examined five synaptosome isolation methods from a proteomic point of view by the means of electron microscopy, Western blot, and liquid chromatography-mass spectrometry to compare their efficiency in the isolation of synaptosomes and depletion of contaminating subcellular structures. In our study, the different isolation procedures led to a largely overlapping pool of proteins with a fairly similar distribution of presynaptic, active zone, synaptic vesicle, and postsynaptic proteins; however, discrete differences were noticeable in individual postsynaptic proteins and in the number of identified transmembrane proteins. Much pronounced variance was observed in the degree of contamination with mitochondrial and glial structures. Therefore, we suggest that in selecting the appropriate isolation method for any neuroproteomics experiment carried out on synaptosomes, the degree and sort/source of contamination should be considered as a primary aspect.
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Affiliation(s)
- Péter Gulyássy
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
| | - Gina Puska
- Department of Anatomy, Cell and Development Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Ecology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary.,MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Balázs A Györffy
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,ELTE-NAP Neuroimmunology Research Group, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Katalin Todorov-Völgyi
- MTA-ELTE NAP Laboratory of Molecular and Systems Neurobiology, Institute of Biology, Hungarian Academy of Sciences and ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - Gábor Juhász
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
| | - László Drahos
- MTA-TTK NAP B MS Neuroproteomics Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary.,MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - Katalin Adrienna Kékesi
- Laboratory of Proteomics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary.,Department of Physiology and Neurobiology, ELTE Eötvös Loránd University, Budapest, 1117, Hungary
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Lachén-Montes M, Mendizuri N, Ausín K, Pérez-Mediavilla A, Azkargorta M, Iloro I, Elortza F, Kondo H, Ohigashi I, Ferrer I, de la Torre R, Robledo P, Fernández-Irigoyen J, Santamaría E. Smelling the Dark Proteome: Functional Characterization of PITH Domain-Containing Protein 1 (C1orf128) in Olfactory Metabolism. J Proteome Res 2020; 19:4826-4843. [PMID: 33185454 DOI: 10.1021/acs.jproteome.0c00452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer's disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1-/- mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Alberto Pérez-Mediavilla
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, 31008 Pamplona, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Isidre Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28029 Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, 08908 Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain.,School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CB06/03), CIBEROBN, 28029 Madrid, Spain
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
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Schiapparelli LM, Shah SH, Ma Y, McClatchy DB, Sharma P, Li J, Yates JR, Goldberg JL, Cline HT. The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo. Cell Rep 2020; 28:1935-1947.e5. [PMID: 31412257 PMCID: PMC6707540 DOI: 10.1016/j.celrep.2019.07.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/03/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022] Open
Abstract
The brain processes information and generates cognitive and motor outputs through functions of spatially organized proteins in different types of neurons. More complete knowledge of proteins and their distributions within neuronal compartments in intact circuits would help in the understanding of brain function. We used unbiased in vivo protein labeling with intravitreal NHS-biotin for discovery and analysis of endogenous axonally transported proteins in the visual system using tandem mass spectrometric proteomics, biochemistry, and both light and electron microscopy. Purification and proteomic analysis of biotinylated peptides identified ~1,000 proteins transported from retinal ganglion cells into the optic nerve and ~575 biotinylated proteins recovered from presynaptic compartments of lateral geniculate nucleus and superior colliculus. Approximately 360 biotinylated proteins were differentially detected in the two retinal targets. This study characterizes axonally transported proteins in the healthy adult visual system by analyzing proteomes from multiple compartments of retinal ganglion cell projections in the intact brain. Axonal protein transport is essential for circuit function. Schiapparelli et al. use unbiased in vivo protein labeling and mass spectrometry to identify ~1,000 proteins in the “RGC axonal transportome.” About 350 retinal proteins are differentially transported to the lateral geniculate nucleus or the superior colliculus, indicating target-specific diversity in presynaptic protein content.
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Affiliation(s)
- Lucio M Schiapparelli
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sahil H Shah
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA; Neuroscience Graduate Program and Medical Scientist Training Program, University of California, San Diego, La Jolla, CA 92093, USA; Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel B McClatchy
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pranav Sharma
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jianli Li
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey L Goldberg
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - Hollis T Cline
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA.
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36
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Sierksma A, Lu A, Mancuso R, Fattorelli N, Thrupp N, Salta E, Zoco J, Blum D, Buée L, De Strooper B, Fiers M. Novel Alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology. EMBO Mol Med 2020; 12:e10606. [PMID: 31951107 PMCID: PMC7059012 DOI: 10.15252/emmm.201910606] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Polygenic risk scores have identified that genetic variants without genome-wide significance still add to the genetic risk of developing Alzheimer's disease (AD). Whether and how subthreshold risk loci translate into relevant disease pathways is unknown. We investigate here the involvement of AD risk variants in the transcriptional responses of two mouse models: APPswe/PS1L166P and Thy-TAU22. A unique gene expression module, highly enriched for AD risk genes, is specifically responsive to Aβ but not TAU pathology. We identify in this module 7 established AD risk genes (APOE, CLU, INPP5D, CD33, PLCG2, SPI1, and FCER1G) and 11 AD GWAS genes below the genome-wide significance threshold (GPC2, TREML2, SYK, GRN, SLC2A5, SAMSN1, PYDC1, HEXB, RRBP1, LYN, and BLNK), that become significantly upregulated when exposed to Aβ. Single microglia sequencing confirms that Aβ, not TAU, pathology induces marked transcriptional changes in microglia, including increased proportions of activated microglia. We conclude that genetic risk of AD functionally translates into different microglia pathway responses to Aβ pathology, placing AD genetic risk downstream of the amyloid pathway but upstream of TAU pathology.
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Affiliation(s)
- Annerieke Sierksma
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Ashley Lu
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Renzo Mancuso
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Nicola Fattorelli
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Nicola Thrupp
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Evgenia Salta
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - Jesus Zoco
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
| | - David Blum
- INSERM, CHU Lille, LabEx DISTALZ, UMR‐S 1172, Alzheimer & TauopathiesUniversité LilleLilleFrance
| | - Luc Buée
- INSERM, CHU Lille, LabEx DISTALZ, UMR‐S 1172, Alzheimer & TauopathiesUniversité LilleLilleFrance
| | - Bart De Strooper
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
- UK Dementia Research InstituteUniversity College LondonLondonUK
| | - Mark Fiers
- VIB Center for Brain & Disease ResearchLeuvenBelgium
- Laboratory for the Research of Neurodegenerative DiseasesDepartment of NeurosciencesLeuven Brain Institute (LBI)KU Leuven (University of Leuven)LeuvenBelgium
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37
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McNeill EM, Warinner C, Alkins S, Taylor A, Heggeness H, DeLuca TF, Fulga TA, Wall DP, Griffith LC, Van Vactor D. The conserved microRNA miR-34 regulates synaptogenesis via coordination of distinct mechanisms in presynaptic and postsynaptic cells. Nat Commun 2020; 11:1092. [PMID: 32107390 PMCID: PMC7046720 DOI: 10.1038/s41467-020-14761-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/31/2020] [Indexed: 01/30/2023] Open
Abstract
Micro(mi)RNA-based post-transcriptional regulatory mechanisms have been broadly implicated in the assembly and modulation of synaptic connections required to shape neural circuits, however, relatively few specific miRNAs have been identified that control synapse formation. Using a conditional transgenic toolkit for competitive inhibition of miRNA function in Drosophila, we performed an unbiased screen for novel regulators of synapse morphogenesis at the larval neuromuscular junction (NMJ). From a set of ten new validated regulators of NMJ growth, we discovered that miR-34 mutants display synaptic phenotypes and cell type-specific functions suggesting distinct downstream mechanisms in the presynaptic and postsynaptic compartments. A search for conserved downstream targets for miR-34 identified the junctional receptor CNTNAP4/Neurexin-IV (Nrx-IV) and the membrane cytoskeletal effector Adducin/Hu-li tai shao (Hts) as proteins whose synaptic expression is restricted by miR-34. Manipulation of miR-34, Nrx-IV or Hts-M function in motor neurons or muscle supports a model where presynaptic miR-34 inhibits Nrx-IV to influence active zone formation, whereas, postsynaptic miR-34 inhibits Hts to regulate the initiation of bouton formation from presynaptic terminals. Although micro(mi)RNA-based post-transcriptional regulatory mechanisms have been implicated in the assembly and modulation of synaptic connections, few miRNAs have been identified that control synapse formation. Here, authors performed an unbiased screen for novel regulators of synapse morphogenesis at the Drosophila larval neuromuscular junction and discovered that miR-34 inhibits Nrx-IV to influence active zone formation, whereas, postsynaptic miR-34 inhibits Hts to regulate the initiation of bouton formation from presynaptic terminals.
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Affiliation(s)
- Elizabeth M McNeill
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - Chloe Warinner
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen Alkins
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, 02454, USA
| | - Alicia Taylor
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - Hansine Heggeness
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Todd F DeLuca
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Tudor A Fulga
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Weatherall Institute, Oxford University, Oxford, UK
| | - Dennis P Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Leslie C Griffith
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, 02454, USA
| | - David Van Vactor
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.
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38
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Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel-Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ. Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Mol Cell 2020; 77:1176-1192.e16. [PMID: 31999954 DOI: 10.1016/j.molcel.2020.01.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/15/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022]
Abstract
Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.
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Affiliation(s)
| | - Rieko Niibori
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Eric W Salter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Brian Tsang
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xinyi Liang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | | | - Jonathan Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Tyler Henderson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eesha Sharma
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mathieu Quesnel-Vallières
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona 08003, Spain
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John Georgiou
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; ICREA, Barcelona 08010, Spain
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Graham L Collingridge
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Melanie A Woodin
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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39
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Gamble KL, Silver R. Circadian rhythmicity and the community of clockworkers. Eur J Neurosci 2019; 51:2314-2328. [PMID: 31814204 DOI: 10.1111/ejn.14626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/17/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Karen L Gamble
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rae Silver
- Department of Neuroscience, Barnard College, New York, NY, USA.,Department of Psychology, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Health Sciences, New York, NY, USA
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40
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Ratnakumar A, Zimmerman SE, Jordan BA, Mar JC. Estrogen activates Alzheimer's disease genes. ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2019; 5:906-917. [PMID: 31890855 PMCID: PMC6926344 DOI: 10.1016/j.trci.2019.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Introduction Women are at increased risk for Alzheimer's disease (AD), but the reason why remains unknown. One hypothesis is that low estrogen levels at menopause increases vulnerability to AD, but this remains unproven. Methods We compared neuronal genes upregulated by estrogen in ovariectomized female rhesus macaques with a database of >17,000 diverse gene sets and applied a rare variant burden test to exome sequencing data from 1208 female AD patients with the age of onset < 75 years and 2162 female AD controls. Results We found a striking overlap between genes upregulated by estrogen in macaques and genes downregulated in the human postmortem AD brain, and we found that estrogen upregulates the APOE gene and that progesterone acts antagonistically to estrogen genome-wide. We also found that female patients with AD have excess rare mutations in the early menopause gene MCM8. Discussion We show with genomic data that the menopausal loss of estrogen could underlie the increased risk for AD in women.
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Affiliation(s)
- Abhirami Ratnakumar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Samuel E Zimmerman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.,Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Australia
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41
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Pirooznia M, Niranjan T, Chen YC, Tunc I, Goes FS, Avramopoulos D, Potash JB, Huganir RL, Zandi PP, Wang T. Affected Sib-Pair Analyses Identify Signaling Networks Associated With Social Behavioral Deficits in Autism. Front Genet 2019; 10:1186. [PMID: 31827489 PMCID: PMC6892440 DOI: 10.3389/fgene.2019.01186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/25/2019] [Indexed: 11/29/2022] Open
Abstract
Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. Several hundreds of risk genes for autism have been identified, however, it remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n = 1,886) in affected male sib-pairs (n = 274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF ≤ 1%) and predicted functional variants. We selected affected sib-pairs with a large (≥10; n = 92 pairs) or a small (≤4; n = 108 pairs) difference in total cumulative Autism Diagnostic Interview-Revised (ADI-R) social scores (SOCT_CS). We compared burdens of unshared variants present only in sibs with severe social deficits and found a higher burden in SOCT_CS≥10 compared to SOCT_CS ≤ 4 (SOCT_CS≥10: 705.1 ± 16.2; SOCT_CS ≤ 4, 668.3 ± 9.0; p = 0.025). Unshared SOCT_CS≥10 genes only in sibs with severe social deficits are significantly enriched in the SFARI gene set. Network analyses of these genes using InWeb_IM, molecular signatures database (MSigDB), and GeNetMeta identified enrichment for phosphoinositide 3-kinase (PI3K)-AKT-mammalian target of rapamycin (mTOR) (Enrichment Score [eScore] p value = 3.36E−07; n = 8 genes) and Nerve growth factor (NGF) (eScore p value = 8.94E−07; n = 9 genes) networks. These studies support a key role for these signaling networks in social behavioral deficits and present a novel approach to associate risk genes and signaling networks with core behavioral domains in autism.
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Affiliation(s)
- Mehdi Pirooznia
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejasvi Niranjan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Ilker Tunc
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dimitrios Avramopoulos
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health and Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, United States
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Zareba-Koziol M, Bartkowiak-Kaczmarek A, Figiel I, Krzystyniak A, Wojtowicz T, Bijata M, Wlodarczyk J. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins. Mol Cell Proteomics 2019; 18:1916-1938. [PMID: 31311849 PMCID: PMC6773552 DOI: 10.1074/mcp.ra119.001581] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Indexed: 11/06/2022] Open
Abstract
The precise regulation of synaptic integrity is critical for neuronal network connectivity and proper brain function. Essential aspects of the activity and localization of synaptic proteins are regulated by posttranslational modifications. S-palmitoylation is a reversible covalent modification of the cysteine with palmitate. It modulates affinity of the protein for cell membranes and membranous compartments. Intracellular palmitoylation dynamics are regulated by crosstalk with other posttranslational modifications, such as S-nitrosylation. S-nitrosylation is a covalent modification of cysteine thiol by nitric oxide and can modulate protein functions. Therefore, simultaneous identification of endogenous site-specific proteomes of both cysteine modifications under certain biological conditions offers new insights into the regulation of functional pathways. Still unclear, however, are the ways in which this crosstalk is affected in brain pathology, such as stress-related disorders. Using a newly developed mass spectrometry-based approach Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni), we analyzed the endogenous S-palmitoylation and S-nitrosylation of postsynaptic density proteins at the level of specific single cysteine in a mouse model of chronic stress. Among a total of 813 S-PALM and 620 S-NO cysteine sites that were characterized on 465 and 360 proteins, respectively, we sought to identify those that were differentially affected by stress. Our data show involvement of S-palmitoylation and S-nitrosylation crosstalk in the regulation of 122 proteins including receptors, scaffolding proteins, regulatory proteins and cytoskeletal components. Our results suggest that atypical crosstalk between the S-palmitoylation and S-nitrosylation interplay of proteins involved in synaptic transmission, protein localization and regulation of synaptic plasticity might be one of the main events associated with chronic stress disorder, leading to destabilization in synaptic networks.
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Affiliation(s)
- Monika Zareba-Koziol
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland.
| | - Anna Bartkowiak-Kaczmarek
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Izabela Figiel
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Adam Krzystyniak
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Tomasz Wojtowicz
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Monika Bijata
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Jakub Wlodarczyk
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland.
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43
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Chabbert D, Caubit X, Roubertoux PL, Carlier M, Habermann B, Jacq B, Salin P, Metwaly M, Frahm C, Fatmi A, Garratt AN, Severac D, Dubois E, Kerkerian-Le Goff L, Fasano L, Gubellini P. Postnatal Tshz3 Deletion Drives Altered Corticostriatal Function and Autism Spectrum Disorder-like Behavior. Biol Psychiatry 2019; 86:274-285. [PMID: 31060802 DOI: 10.1016/j.biopsych.2019.03.974] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Heterozygous deletion of the TSHZ3 gene, encoding for the teashirt zinc-finger homeobox family member 3 (TSHZ3) transcription factor that is highly expressed in cortical projection neurons (CPNs), has been linked to an autism spectrum disorder (ASD) syndrome. Similarly, mice with Tshz3 haploinsufficiency show ASD-like behavior, paralleled by molecular changes in CPNs and corticostriatal synaptic dysfunctions. Here, we aimed at gaining more insight into "when" and "where" TSHZ3 is required for the proper development of the brain, and its deficiency crucial for developing this ASD syndrome. METHODS We generated and characterized a novel mouse model of conditional Tshz3 deletion, obtained by crossing Tshz3flox/flox with CaMKIIalpha-Cre mice, in which Tshz3 is deleted in CPNs from postnatal day 2 to 3 onward. We characterized these mice by a multilevel approach combining genetics, cell biology, electrophysiology, behavioral testing, and bioinformatics. RESULTS These conditional Tshz3 knockout mice exhibit altered cortical expression of more than 1000 genes, ∼50% of which have their human orthologue involved in ASD, in particular genes encoding for glutamatergic synapse components. Consistently, we detected electrophysiological and synaptic changes in CPNs and impaired corticostriatal transmission and plasticity. Furthermore, these mice showed strong ASD-like behavioral deficits. CONCLUSIONS Our study reveals a crucial postnatal role of TSHZ3 in the development and functioning of the corticostriatal circuitry and provides evidence that dysfunction in these circuits might be determinant for ASD pathogenesis. Our conditional Tshz3 knockout mouse constitutes a novel ASD model, opening the possibility for an early postnatal therapeutic window for the syndrome linked to TSHZ3 haploinsufficiency.
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Affiliation(s)
| | | | | | | | - Bianca Habermann
- Aix Marseille Univ, CNRS, IBDM, Marseille, France; Aix Marseille Univ, INSERM, TAGC, Marseille, France
| | - Bernard Jacq
- Aix Marseille Univ, CNRS, IBDM, Marseille, France
| | - Pascal Salin
- Aix Marseille Univ, CNRS, IBDM, Marseille, France
| | | | | | - Ahmed Fatmi
- Aix Marseille Univ, CNRS, IBDM, Marseille, France
| | - Alistair N Garratt
- Institute of Cell Biology and Neurobiology, Center for Anatomy, Charité University Hospital Berlin, Berlin, Germany
| | - Dany Severac
- Univ Montpellier, CNRS, INSERM, MGX, Montpellier, France
| | - Emeric Dubois
- Univ Montpellier, CNRS, INSERM, MGX, Montpellier, France
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Kiss-Tóth A, Dobson L, Péterfia B, Ángyán AF, Ligeti B, Lukács G, Gáspári Z. Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. ENTROPY (BASEL, SWITZERLAND) 2019; 21:E761. [PMID: 33267475 PMCID: PMC7515291 DOI: 10.3390/e21080761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
The human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, and this duality is also imprinted in the amino acid sequence. We introduce Diversity of Potential Interactions (DPI), a structure and regulation based descriptor to assess the diversity of interactions. Our approach reveals that the postsynaptic proteome has its own characteristic features and these properties reliably discriminate them from other proteins of the human proteome. Our results suggest that postsynaptic proteins are especially susceptible to forming diverse interactions with each other, which might be key in the reorganization of the postsynaptic density (PSD) in molecular processes related to learning and memory.
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Affiliation(s)
- Annamária Kiss-Tóth
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
- 3in-PPCU Research Group, 2500 Esztergom, Hungary
| | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Annamária F. Ángyán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Gergely Lukács
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
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45
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Shi L, Luo X, Jiang J, Chen Y, Liu C, Hu T, Li M, Lin Q, Li Y, Huang J, Wang H, Niu Y, Shi Y, Styner M, Wang J, Lu Y, Sun X, Yu H, Ji W, Su B. Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development. Natl Sci Rev 2019; 6:480-493. [PMID: 34691896 PMCID: PMC8291473 DOI: 10.1093/nsr/nwz043] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/06/2019] [Accepted: 03/23/2019] [Indexed: 12/16/2022] Open
Abstract
Brain size and cognitive skills are the most dramatically changed traits in humans during evolution and yet the genetic mechanisms underlying these human-specific changes remain elusive. Here, we successfully generated 11 transgenic rhesus monkeys (8 first-generation and 3 second-generation) carrying human copies of MCPH1, an important gene for brain development and brain evolution. Brain-image and tissue-section analyses indicated an altered pattern of neural-cell differentiation, resulting in a delayed neuronal maturation and neural-fiber myelination of the transgenic monkeys, similar to the known evolutionary change of developmental delay (neoteny) in humans. Further brain-transcriptome and tissue-section analyses of major developmental stages showed a marked human-like expression delay of neuron differentiation and synaptic-signaling genes, providing a molecular explanation for the observed brain-developmental delay of the transgenic monkeys. More importantly, the transgenic monkeys exhibited better short-term memory and shorter reaction time compared with the wild-type controls in the delayed-matching-to-sample task. The presented data represent the first attempt to experimentally interrogate the genetic basis of human brain origin using a transgenic monkey model and it values the use of non-human primates in understanding unique human traits.
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Affiliation(s)
- Lei Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jin Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yongchang Chen
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translation Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Cirong Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ting Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Min Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qiang Lin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yanjiao Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jun Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong Wang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translation Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Yuyu Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translation Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Yundi Shi
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - Martin Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - Jianhong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yi Lu
- Department of Medical Imaging, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Xuejin Sun
- Department of Medical Imaging, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Hualin Yu
- Department of Minimally Invasive Neurosurgery, the First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translation Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data. Nat Neurosci 2019; 22:691-699. [PMID: 30988527 PMCID: PMC6646046 DOI: 10.1038/s41593-019-0382-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Genome-wide association studies (GWAS) have identified >100 schizophrenia (SCZ)-associated loci, but using these findings to illuminate disease biology remains a challenge. Here, we present integrative RIsk Gene Selector (iRIGS), a Bayesian framework that integrates multi-omics data and gene networks to infer risk genes in GWAS loci. By applying iRIGS to SCZ GWAS data, we predicted a set of high-confidence risk genes (HRGs), most of which are not the nearest genes to the GWAS index variants. HRGs account for a significantly enriched heritability estimated by stratified LD-score regression. Moreover, HRGs are predominantly expressed in brain tissues, especially prenatally, and are enriched for targets of approved drugs, suggesting opportunities to reposition existing drugs for SCZ. Thus, iRIGS can leverage accumulating functional genomics and GWAS data to advance understanding of SCZ etiology and potential therapeutics.
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Weissenkampen JD, Jiang Y, Eckert S, Jiang B, Li B, Liu DJ. Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits. ACTA ACUST UNITED AC 2019; 101:e83. [PMID: 30849219 DOI: 10.1002/cphg.83] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With the advent of Next Generation Sequencing (NGS) technologies, whole genome and whole exome DNA sequencing has become affordable for routine genetic studies. Coupled with improved genotyping arrays and genotype imputation methodologies, it is increasingly feasible to obtain rare genetic variant information in large datasets. Such datasets allow researchers to gain a more complete understanding of the genetic architecture of complex traits caused by rare variants. State-of-the-art statistical methods for the statistical genetics analysis of sequence-based association, including efficient algorithms for association analysis in biobank-scale datasets, gene-association tests, meta-analysis, fine mapping methods that integrate functional genomic dataset, and phenome-wide association studies (PheWAS), are reviewed here. These methods are expected to be highly useful for next generation statistical genetics analysis in the era of precision medicine. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- J Dylan Weissenkampen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Scott Eckert
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania
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Neurexins - versatile molecular platforms in the synaptic cleft. Curr Opin Struct Biol 2019; 54:112-121. [PMID: 30831539 DOI: 10.1016/j.sbi.2019.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 01/05/2023]
Abstract
Neurexins constitute a large family of synaptic organizers. Their extracellular domains protrude into the synaptic cleft where they can form transsynaptic bridges with different partners. A unique constellation of structural elements within their ectodomains enables neurexins to create molecular platforms within the synaptic cleft that permit a large portfolio of partners to be recruited, assembled and their interactions to be dynamically regulated. Neurexins and their partners are implicated in neuropsychiatric diseases including autism spectrum disorder and schizophrenia. Detailed understanding of the mechanisms that underlie neurexin interactions may in future guide the design of tools to manipulate synaptic connections and their function, in particular those involved in the pathogenesis of neuropsychiatric disease.
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49
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Hannou L, Roy P, Ballester Roig MN, Mongrain V. Transcriptional control of synaptic components by the clock machinery. Eur J Neurosci 2019; 51:241-267. [DOI: 10.1111/ejn.14294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/01/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Lydia Hannou
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of PsychiatryUniversité de Montréal Montreal Quebec Canada
| | - Pierre‐Gabriel Roy
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
| | - Maria Neus Ballester Roig
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research CenterHôpital du Sacré‐Cœur de Montréal (CIUSSS‐NIM) Montreal Quebec Canada
- Department of NeuroscienceUniversité de Montréal Montreal Quebec Canada
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50
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Polygenic risk score for schizophrenia is not strongly associated with the expression of specific genes or gene sets. Psychiatr Genet 2018; 28:59-65. [PMID: 29672343 DOI: 10.1097/ypg.0000000000000197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The polygenic risk score (PRS) is derived from single nucleotide polymorphisms (SNPs) including those that are genome-wide significant and also including a large number of others more weakly associated with schizophrenia. Such variants are widely dispersed, though concentrated near genes expressed in the brain, and it has been proposed that these SNP associations result from impacts on cell regulatory networks that ultimately affect the expression or function of a modest number of 'core' genes. A previous study showed association of some genome-wide association study-significant variants with expression of a number of genes, by examining pairwise correlations of gene expression with SNP genotypes. METHODS The present study used data downloaded from the CommonMind Consortium site, consisting of SNP genotypes and RNAseq expression data from the dorsolateral prefrontal cortex, to examine whether the expression of individual genes or sets of genes correlated with PRS in 207 controls and 209 schizophrenia cases. RESULTS Although the PRS was significantly associated with phenotype, the correlations with genes and gene sets followed distributions expected by chance. Thus, this analysis failed to show that the PRS captures a cumulative effect of multiple variants impacting the expression of a small number of genes and it failed to focus attention on a small number of genes of biological relevance. CONCLUSION The multiple SNP associations observed in schizophrenia may result from other mechanisms, including effects mediated indirectly through environmental risk factors.
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