1
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Fatemi SH, Eschenlauer A, Aman J, Folsom TD, Chekouo T. Quantitative proteomics of dorsolateral prefrontal cortex reveals an early pattern of synaptic dysmaturation in children with idiopathic autism. Cereb Cortex 2024; 34:161-171. [PMID: 38696595 DOI: 10.1093/cercor/bhae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 05/04/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a rising prevalence and unknown etiology presenting with deficits in cognition and abnormal behavior. We hypothesized that the investigation of the synaptic component of prefrontal cortex may provide proteomic signatures that may identify the biological underpinnings of cognitive deficits in childhood ASD. Subcellular fractions of synaptosomes from prefrontal cortices of age-, brain area-, and postmortem-interval-matched samples from children and adults with idiopathic ASD vs. controls were subjected to HPLC-tandem mass spectrometry. Analysis of data revealed the enrichment of ASD risk genes that participate in slow maturation of the postsynaptic density (PSD) structure and function during early brain development. Proteomic analysis revealed down regulation of PSD-related proteins including AMPA and NMDA receptors, GRM3, DLG4, olfactomedins, Shank1-3, Homer1, CaMK2α, NRXN1, NLGN2, Drebrin1, ARHGAP32, and Dock9 in children with autism (FDR-adjusted P < 0.05). In contrast, PSD-related alterations were less severe or unchanged in adult individuals with ASD. Network analyses revealed glutamate receptor abnormalities. Overall, the proteomic data support the concept that idiopathic autism is a synaptopathy involving PSD-related ASD risk genes. Interruption in evolutionarily conserved slow maturation of the PSD complex in prefrontal cortex may lead to the development of ASD in a susceptible individual.
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Affiliation(s)
- S Hossein Fatemi
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Arthur Eschenlauer
- Minnesota Supercomputing Institute, 599 Walter Library, 117 Pleasant Street, Minneapolis, MN 55455, USA
| | - Justin Aman
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Timothy D Folsom
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thierry Chekouo
- University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
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2
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Wang T, Bai Y, Zheng X, Liu X, Xing S, Wang L, Wang H, Feng G, Li C. Sapap4 deficiency leads to postsynaptic defects and abnormal behaviors relevant to hyperkinetic neuropsychiatric disorder in mice. Cereb Cortex 2023; 33:1104-1118. [PMID: 35368073 DOI: 10.1093/cercor/bhac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Postsynaptic proteins play critical roles in synaptic development, function, and plasticity. Dysfunction of postsynaptic proteins is strongly linked to neurodevelopmental and psychiatric disorders. SAP90/PSD95-associated protein 4 (SAPAP4; also known as DLGAP4) is a key component of the PSD95-SAPAP-SHANK excitatory postsynaptic scaffolding complex, which plays important roles at synapses. However, the exact function of the SAPAP4 protein in the brain is poorly understood. Here, we report that Sapap4 knockout (KO) mice have reduced spine density in the prefrontal cortex and abnormal compositions of key postsynaptic proteins in the postsynaptic density (PSD) including reduced PSD95, GluR1, and GluR2 as well as increased SHANK3. These synaptic defects are accompanied by a cluster of abnormal behaviors including hyperactivity, impulsivity, reduced despair/depression-like behavior, hypersensitivity to low dose of amphetamine, memory deficits, and decreased prepulse inhibition, which are reminiscent of mania. Furthermore, the hyperactivity of Sapap4 KO mice could be partially rescued by valproate, a mood stabilizer used for mania treatment in humans. Together, our findings provide evidence that SAPAP4 plays an important role at synapses and reinforce the view that dysfunction of the postsynaptic scaffolding protein SAPAP4 may contribute to the pathogenesis of hyperkinetic neuropsychiatric disorder.
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Affiliation(s)
- Tianhua Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Yunxia Bai
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xianjie Zheng
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Xinxia Liu
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Shuang Xing
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Linbin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Huimin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China.,NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 43 Vassar Street, Cambridge, Massachusetts, 02139, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, Massachusetts, 02142, USA
| | - Chunxia Li
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), School of Psychology and Cognitive Science, East China Normal University, 3663 North Zhongshan Road, Shanghai, 200062, China
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3
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Bai Y, Wang H, Li C. SAPAP Scaffold Proteins: From Synaptic Function to Neuropsychiatric Disorders. Cells 2022; 11:cells11233815. [PMID: 36497075 PMCID: PMC9740047 DOI: 10.3390/cells11233815] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Excitatory (glutamatergic) synaptic transmission underlies many aspects of brain activity and the genesis of normal human behavior. The postsynaptic scaffolding proteins SAP90/PSD-95-associated proteins (SAPAPs), which are abundant components of the postsynaptic density (PSD) at excitatory synapses, play critical roles in synaptic structure, formation, development, plasticity, and signaling. The convergence of human genetic data with recent in vitro and in vivo animal model data indicates that mutations in the genes encoding SAPAP1-4 are associated with neurological and psychiatric disorders, and that dysfunction of SAPAP scaffolding proteins may contribute to the pathogenesis of various neuropsychiatric disorders, such as schizophrenia, autism spectrum disorders, obsessive compulsive disorders, Alzheimer's disease, and bipolar disorder. Here, we review recent major genetic, epigenetic, molecular, behavioral, electrophysiological, and circuitry studies that have advanced our knowledge by clarifying the roles of SAPAP proteins at the synapses, providing new insights into the mechanistic links to neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
- Yunxia Bai
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
| | - Huimin Wang
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai 200062, China
| | - Chunxia Li
- Key Laboratory of Brain Functional Genomics (STCSM & MOE), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai 200062, China
- Shanghai Changning Mental Health Center, Shanghai 200335, China
- Correspondence:
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4
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Hsieh MY, Tuan LH, Chang HC, Wang YC, Chen CH, Shy HT, Lee LJ, Gau SSF. Altered synaptic protein expression, aberrant spine morphology, and impaired spatial memory in Dlgap2 mutant mice, a genetic model of autism spectrum disorder. Cereb Cortex 2022; 33:4779-4793. [PMID: 36169576 DOI: 10.1093/cercor/bhac379] [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: 05/24/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
A microdeletion of approximately 2.4 Mb at the 8p23 terminal region has been identified in a Taiwanese autistic boy. Among the products transcribed/translated from genes mapped in this region, the reduction of DLGAP2, a postsynaptic scaffold protein, might be involved in the pathogenesis of autism spectrum disorder (ASD). DLGAP2 protein was detected in the hippocampus yet abolished in homozygous Dlgap2 knockout (Dlgap2 KO) mice. In this study, we characterized the hippocampal phenotypes in Dlgap2 mutant mice. Dlgap2 KO mice exhibited impaired spatial memory, indicating poor hippocampal function in the absence of DLGAP2. Aberrant expressions of postsynaptic proteins, including PSD95, SHANK3, HOMER1, GluN2A, GluR2, mGluR1, mGluR5, βCAMKII, ERK1/2, ARC, BDNF, were noticed in Dlgap2 mutant mice. Further, the spine density was increased in Dlgap2 KO mice, while the ratio of mushroom-type spines was decreased. We also observed a thinner postsynaptic density thickness in Dlgap2 KO mice at the ultrastructural level. These structural changes found in the hippocampus of Dlgap2 KO mice might be linked to impaired hippocampus-related cognitive functions such as spatial memory. Mice with Dlgap2 deficiency, showing signs of intellectual disability, a common co-occurring condition in patients with ASD, could be a promising animal model which may advance our understanding of ASD.
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Affiliation(s)
- Ming-Yen Hsieh
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Heng Tuan
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,School of Medicine, National Tsing Hua University, Hsinchu, Taiwan.,Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ho-Ching Chang
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Chun Wang
- Department of Otolaryngology, Head and Neck Surgery, Chi-Mei Medical Center, Tainan, Taiwan
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Horng-Tzer Shy
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Jen Lee
- Graduate Institute of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan.,Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Susan Shur-Fen Gau
- Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan.,Department of Psychiatry, National Taiwan University Hospital, Taipei, Taiwan
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5
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Novel role of the synaptic scaffold protein Dlgap4 in ventricular surface integrity and neuronal migration during cortical development. Nat Commun 2022; 13:2746. [PMID: 35585091 PMCID: PMC9117333 DOI: 10.1038/s41467-022-30443-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 04/29/2022] [Indexed: 11/08/2022] Open
Abstract
Subcortical heterotopias are malformations associated with epilepsy and intellectual disability, characterized by the presence of ectopic neurons in the white matter. Mouse and human heterotopia mutations were identified in the microtubule-binding protein Echinoderm microtubule-associated protein-like 1, EML1. Further exploring pathological mechanisms, we identified a patient with an EML1-like phenotype and a novel genetic variation in DLGAP4. The protein belongs to a membrane-associated guanylate kinase family known to function in glutamate synapses. We showed that DLGAP4 is strongly expressed in the mouse ventricular zone (VZ) from early corticogenesis, and interacts with key VZ proteins including EML1. In utero electroporation of Dlgap4 knockdown (KD) and overexpression constructs revealed a ventricular surface phenotype including changes in progenitor cell dynamics, morphology, proliferation and neuronal migration defects. The Dlgap4 KD phenotype was rescued by wild-type but not mutant DLGAP4. Dlgap4 is required for the organization of radial glial cell adherens junction components and actin cytoskeleton dynamics at the apical domain, as well as during neuronal migration. Finally, Dlgap4 heterozygous knockout (KO) mice also show developmental defects in the dorsal telencephalon. We hence identify a synapse-related scaffold protein with pleiotropic functions, influencing the integrity of the developing cerebral cortex.
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6
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Schob C, Hempel M, Safka Brozkova D, Jiang H, Kim SY, Batzir NA, Orenstein N, Bierhals T, Johannsen J, Uhrova Meszarosova A, Chae JH, Seeman P, Woidy M, Fang F, Kubisch C, Kindler S, Denecke J. Dominant KPNA3 Mutations Cause Infantile-Onset Hereditary Spastic Paraplegia. Ann Neurol 2021; 90:738-750. [PMID: 34564892 DOI: 10.1002/ana.26228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Hereditary spastic paraplegia (HSP) is a highly heterogeneous neurologic disorder characterized by lower-extremity spasticity. Here, we set out to determine the genetic basis of an autosomal dominant, pure, and infantile-onset form of HSP in a cohort of 8 patients with a uniform clinical presentation. METHODS Trio whole-exome sequencing was used in 5 index patients with infantile-onset pure HSP to determine the genetic cause of disease. The functional impact of identified genetic variants was verified using bioinformatics and complementary cellular and biochemical assays. RESULTS Distinct heterozygous KPNA3 missense variants were found to segregate with the clinical phenotype in 8 patients; in 4 of them KPNA3 variants had occurred de novo. Mutant karyopherin-α3 proteins exhibited a variable pattern of altered expression level, subcellular distribution, and protein interaction. INTERPRETATION Our genetic findings implicate heterozygous variants in KPNA3 as a novel cause for autosomal dominant, early-onset, and pure HSP. Mutant karyopherin-α3 proteins display varying deficits in molecular and cellular functions, thus, for the first time, implicating dysfunctional nucleocytoplasmic shuttling as a novel pathomechanism causing HSP. ANN NEUROL 2021;90:738-750.
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Affiliation(s)
- Claudia Schob
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dana Safka Brozkova
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Huafang Jiang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Soo Yeon Kim
- Department of Genomics Medicine, Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea
| | - Nurit Assia Batzir
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel
| | - Naama Orenstein
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Uhrova Meszarosova
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jong-Hee Chae
- Department of Genomics Medicine, Rare Disease Center, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pavel Seeman
- Neurogenetic Laboratory, Department of Pediatric Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Mathias Woidy
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kindler
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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7
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Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence. Mol Psychiatry 2021; 26:4367-4382. [PMID: 31745236 DOI: 10.1038/s41380-019-0588-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 10/22/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
Alcohol misuse is a major public health problem originating from genetic and environmental risk factors. Alterations in the brain epigenome may orchestrate changes in gene expression that lead to alcohol misuse and dependence. Through epigenome-wide association analysis of DNA methylation from human brain tissues, we identified a differentially methylated region, DMR-DLGAP2, associated with alcohol dependence. Methylation within DMR-DLGAP2 was found to be genotype-dependent, allele-specific and associated with reward processing in brain. Methylation at the DMR-DLGAP2 regulated expression of DLGAP2 in vitro, and Dlgap2-deficient mice showed reduced alcohol consumption compared with wild-type controls. These results suggest that DLGAP2 may be an interface for genetic and epigenetic factors controlling alcohol use and dependence.
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8
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Wang X, Yang Z, Fang S, Zhang Y, Guo J, Gou L. Declining Levels of Specialized Synaptic Surface Proteins in nNOS-Expressing Interneurons in Mice Treated Prenatally with Valproic Acid. Neurochem Res 2021; 46:1794-1800. [PMID: 33876374 DOI: 10.1007/s11064-021-03326-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/12/2021] [Accepted: 04/09/2021] [Indexed: 11/27/2022]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorder characterized by impaired social interaction, and repetitive or restricted interests and behaviors. Membrane proteins are a significant part of the proteins in cell and play key functions in synaptic transmission. We have recently shown that neuronal nitric oxide synthase (nNOS) expression was reduced in the basolateral amygdala (BLA) of mice following postnatal valproic acid (VPA) exposure. In the current study, we utilized a label-free proteomics approach to identify and quantify surface protein expression in nNOS-positive interneurons between VPA-treated and control mice. Western blot was used to confirm the expression of selected membrane proteins. Our proteomics data revealed differentially expressed surface proteins in nNOS interneurons, e.g. Narp, AMPA-type glutamate (AMPA) receptor subunit GluA4 and Protein kinase C gamma (PKCγ), which were validated by Western blotting in mice treated with VPA. This work will pave the way for further elucidation of the mechanisms of these differentially membrane proteins in nNOS interneurons-medicated ASD.
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Affiliation(s)
- Xiaona Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Henan Engineering Research Center of Childhood Neurodevelopment, Children's Hospital Affiliated to Zhengzhou University, 33 Longhu Outer Circle Dong Road, Zhengzhou, 450018, Henan, China.
| | - Zhigang Yang
- Department of Neurology, Children's Hospital Affiliated to Zhengzhou University, 33 Longhu Outer Circle Dong Road, Zhengzhou, 450018, Henan, China
| | - Shuanfeng Fang
- Healthcare Department, Children's Hospital Affiliated to Zhengzhou University, 33 Longhu Outer Circle Dong Road, Zhengzhou, 450018, Henan, China
| | - Yaodong Zhang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Henan Engineering Research Center of Childhood Neurodevelopment, Children's Hospital Affiliated to Zhengzhou University, 33 Longhu Outer Circle Dong Road, Zhengzhou, 450018, Henan, China
| | - Jisheng Guo
- School of Basic Medical Sciences, Yantai Campus of Binzhou Medical University, 346 Guanhai Road, Laishan District, Yantai City, 264003, Shandong, China
| | - Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital, Xuzhou, China
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9
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Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU. A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun 2021; 12:463. [PMID: 33469025 PMCID: PMC7815907 DOI: 10.1038/s41467-020-20343-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/27/2020] [Indexed: 01/19/2023] Open
Abstract
Splicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a single-cell investigation of differential isoform expression (DIE) between brain regions using single-cell long-read sequencing in mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7 ( www.isoformAtlas.com ). Isoform tests for DIE show better performance than exon tests. We detect hundreds of DIE events traceable to cell types, often corresponding to functionally distinct protein isoforms. Mostly, one cell type is responsible for brain-region specific DIE. However, for fewer genes, multiple cell types influence DIE. Thus, regional identity can, although rarely, override cell-type specificity. Cell types indigenous to one anatomic structure display distinctive DIE, e.g. the choroid plexus epithelium manifests distinct transcription-start-site usage. Spatial transcriptomics and long-read sequencing yield a spatially resolved splicing map. Our methods quantify isoform expression with cell-type and spatial resolution and it contributes to further our understanding of how the brain integrates molecular and cellular complexity.
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Affiliation(s)
- Anoushka Joglekar
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Andrey Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, 2628 XE, The Netherlands
| | - Paul Collier
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Susan Lin
- Graduate Program in Neuroscience, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Anna Katharina Schlusche
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Jordan Marrocco
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | | | - Bettina Haase
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY, USA
| | | | | | | | - Man Ying Wong
- Brain and Mind Research Institute and Appel Alzheimer's Research Institute, Weill Cornell Medicine, New York, NY, USA
| | | | - Simon A Hardwick
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Qi Wang
- Section of Bioinformatics and Systems Cardiology, University Hospital, 96120, Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital, 96120, Heidelberg, Germany
| | | | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Erich D Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Wenjie Luo
- Brain and Mind Research Institute and Appel Alzheimer's Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Geoffrey S Pitt
- Graduate Program in Neuroscience, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - M Elizabeth Ross
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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10
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Wilkinson B, Coba MP. Molecular architecture of postsynaptic Interactomes. Cell Signal 2020; 76:109782. [PMID: 32941943 DOI: 10.1016/j.cellsig.2020.109782] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 01/02/2023]
Abstract
The postsynaptic density (PSD) plays an essential role in the organization of the synaptic signaling machinery. It contains a set of core scaffolding proteins that provide the backbone to PSD protein-protein interaction networks (PINs). These core scaffolding proteins can be seen as three principal layers classified by protein family, with DLG proteins being at the top, SHANKs along the bottom, and DLGAPs connecting the two layers. Early studies utilizing yeast two hybrid enabled the identification of direct protein-protein interactions (PPIs) within the multiple layers of scaffolding proteins. More recently, mass-spectrometry has allowed the characterization of whole interactomes within the PSD. This expansion of knowledge has further solidified the centrality of core scaffolding family members within synaptic PINs and provided context for their role in neuronal development and synaptic function. Here, we discuss the scaffolding machinery of the PSD, their essential functions in the organization of synaptic PINs, along with their relationship to neuronal processes found to be impaired in complex brain disorders.
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Affiliation(s)
- Brent Wilkinson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Marcelo P Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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11
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Kim K, Shin W, Kang M, Lee S, Kim D, Kang R, Jung Y, Cho Y, Yang E, Kim H, Bae YC, Kim E. Presynaptic PTPσ regulates postsynaptic NMDA receptor function through direct adhesion-independent mechanisms. eLife 2020; 9:54224. [PMID: 32142410 PMCID: PMC7069723 DOI: 10.7554/elife.54224] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
Synaptic adhesion molecules regulate synapse development and function. However, whether and how presynaptic adhesion molecules regulate postsynaptic NMDAR function remains largely unclear. Presynaptic LAR family receptor tyrosine phosphatases (LAR-RPTPs) regulate synapse development through mechanisms that include trans-synaptic adhesion; however, whether they regulate postsynaptic receptor functions remains unknown. Here we report that presynaptic PTPσ, a LAR-RPTP, enhances postsynaptic NMDA receptor (NMDAR) currents and NMDAR-dependent synaptic plasticity in the hippocampus. This regulation does not involve trans-synaptic adhesions of PTPσ, suggesting that the cytoplasmic domains of PTPσ, known to have tyrosine phosphatase activity and mediate protein-protein interactions, are important. In line with this, phosphotyrosine levels of presynaptic proteins, including neurexin-1, are strongly increased in PTPσ-mutant mice. Behaviorally, PTPσ-dependent NMDAR regulation is important for social and reward-related novelty recognition. These results suggest that presynaptic PTPσ regulates postsynaptic NMDAR function through trans-synaptic and direct adhesion-independent mechanisms and novelty recognition in social and reward contexts.
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Affiliation(s)
- Kyungdeok Kim
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Wangyong Shin
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Muwon Kang
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Doyoun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
| | - Ryeonghwa Kang
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Yewon Jung
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Yisul Cho
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, Republic of Korea
| | - Esther Yang
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Yong Chul Bae
- Department of Anatomy and Neurobiology, School of Dentistry, Kyungpook National University, Daegu, Republic of Korea
| | - Eunjoon Kim
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, Republic of Korea
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Trushina NI, Mulkidjanian AY, Brandt R. The microtubule skeleton and the evolution of neuronal complexity in vertebrates. Biol Chem 2020; 400:1163-1179. [PMID: 31116700 DOI: 10.1515/hsz-2019-0149] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022]
Abstract
The evolution of a highly developed nervous system is mirrored by the ability of individual neurons to develop increased morphological complexity. As microtubules (MTs) are crucially involved in neuronal development, we tested the hypothesis that the evolution of complexity is driven by an increasing capacity of the MT system for regulated molecular interactions as it may be implemented by a higher number of molecular players and a greater ability of the individual molecules to interact. We performed bioinformatics analysis on different classes of components of the vertebrate neuronal MT cytoskeleton. We show that the number of orthologs of tubulin structure proteins, MT-binding proteins and tubulin-sequestering proteins expanded during vertebrate evolution. We observed that protein diversity of MT-binding and tubulin-sequestering proteins increased by alternative splicing. In addition, we found that regions of the MT-binding protein tau and MAP6 displayed a clear increase in disorder extent during evolution. The data provide evidence that vertebrate evolution is paralleled by gene expansions, changes in alternative splicing and evolution of coding sequences of components of the MT system. The results suggest that in particular evolutionary changes in tubulin-structure proteins, MT-binding proteins and tubulin-sequestering proteins were prominent drivers for the development of increased neuronal complexity.
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Affiliation(s)
- Nataliya I Trushina
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastraße 7, D-49076 Osnabrück, Germany.,A.N. Belozersky Institute of Physico-Chemical Biology and School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Center for Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Institute of Cognitive Science, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
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13
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Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019; 10:E976. [PMID: 31783652 PMCID: PMC6947233 DOI: 10.3390/genes10120976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 01/12/2023] Open
Abstract
The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.
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Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sasha Tetu
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Åsa Viklund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
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