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.
Subject(s)
Dorsolateral Prefrontal Cortex , Proteomics , Humans , Child , Male , Female , Adult , Dorsolateral Prefrontal Cortex/metabolism , Child, Preschool , Autism Spectrum Disorder/metabolism , Autism Spectrum Disorder/genetics , Synapses/metabolism , Adolescent , Young Adult , Autistic Disorder/metabolism , Autistic Disorder/genetics , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Synaptosomes/metabolism , Prefrontal Cortex/metabolism , Post-Synaptic Density/metabolismABSTRACT
Down syndrome (DS) is the most common form of inherited intellectual disability caused by trisomy of chromosome 21, presenting with intellectual impairment, craniofacial abnormalities, cardiac defects, and gastrointestinal disorders. The Ts65Dn mouse model replicates many abnormalities of DS. We hypothesized that investigation of the cerebral cortex of fluoxetine-treated trisomic mice may provide proteomic signatures that identify therapeutic targets for DS. Subcellular fractionation of synaptosomes from cerebral cortices of age- and brain-area-matched samples from fluoxetine-treated vs. water-treated trisomic and euploid male mice were subjected to HPLC-tandem mass spectrometry. Analysis of the data revealed enrichment of trisomic risk genes that participate in regulation of synaptic vesicular traffic, pre-synaptic and post-synaptic development, and mitochondrial energy pathways during early brain development. Proteomic analysis of trisomic synaptic fractions revealed significant downregulation of proteins involved in synaptic vesicular traffic, including vesicular endocytosis (CLTA, CLTB, CLTC), synaptic assembly and maturation (EXOC1, EXOC3, EXOC8), anterograde axonal transport (EXOC1), neurotransmitter transport to PSD (SACM1L), endosomal-lysosomal acidification (ROGDI, DMXL2), and synaptic signaling (NRXN1, HIP1, ITSN1, YWHAG). Additionally, trisomic proteomes revealed upregulation of several trafficking proteins, involved in vesicular exocytosis (Rab5B), synapse elimination (UBE3A), scission of endocytosis (DBN1), transport of ER in dendritic spines (MYO5A), presynaptic activity-dependent bulk endocytosis (FMR1), and NMDA receptor activity (GRIN2A). Chronic fluoxetine treatment of Ts65Dn mice rescued synaptic vesicular abnormalities and prevented abnormal proteomic changes in adult Ts65Dn mice, pointing to therapeutic targets for potential treatment of DS.
Subject(s)
Down Syndrome , Fluoxetine , Proteomics , Synaptic Vesicles , Animals , Fluoxetine/pharmacology , Mice , Down Syndrome/metabolism , Down Syndrome/drug therapy , Down Syndrome/genetics , Down Syndrome/pathology , Male , Proteomics/methods , Synaptic Vesicles/metabolism , Synaptic Vesicles/drug effects , Disease Models, Animal , Proteome/metabolism , Cerebral Cortex/metabolism , Cerebral Cortex/drug effects , Synaptosomes/metabolism , Synaptosomes/drug effects , Trisomy/geneticsABSTRACT
O-GlcNAc transferase (OGT), a nutrient sensor sensitive to glucose flux, is highly expressed in the pancreas. However, the role of OGT in the mitochondria of ß-cells is unexplored. In this study, we identified the role of OGT in mitochondrial function in ß-cells. Constitutive deletion of OGT (ßOGTKO) or inducible ablation in mature ß-cells (ißOGTKO) causes distinct effects on mitochondrial morphology and function. Islets from ßOGTKO, but not ißOGTKO, mice display swollen mitochondria, reduced glucose-stimulated oxygen consumption rate, ATP production, and glycolysis. Alleviating endoplasmic reticulum stress by genetic deletion of Chop did not rescue the mitochondrial dysfunction in ßOGTKO mice. We identified altered islet proteome between ßOGTKO and ißOGTKO mice. Pancreatic and duodenal homeobox 1 (Pdx1) was reduced in in ßOGTKO islets. Pdx1 overexpression increased insulin content and improved mitochondrial morphology and function in ßOGTKO islets. These data underscore the essential role of OGT in regulating ß-cell mitochondrial morphology and bioenergetics. In conclusion, OGT couples nutrient signal and mitochondrial function to promote normal ß-cell physiology.
Subject(s)
Diabetes Mellitus, Type 2/genetics , Homeodomain Proteins/metabolism , Mitochondria/metabolism , N-Acetylglucosaminyltransferases/metabolism , Trans-Activators/metabolism , Animals , Electron Transport , Electron Transport Chain Complex Proteins/genetics , Electron Transport Chain Complex Proteins/metabolism , Genetic Predisposition to Disease , Glucose Tolerance Test , Homeodomain Proteins/genetics , Insulin Secretion , Mice , Mice, Knockout , N-Acetylglucosaminyltransferases/genetics , Proteomics , Trans-Activators/geneticsABSTRACT
Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise. Applications of such sophisticated workflows are many, including those which integrate software from different 'omic domains (e.g. genomics, proteomics, metabolomics). In these complex workflows, intermediate outputs are often generated as tabular text files, which must be transformed into customized formats which are compatible with the next software tools in the pipeline. Consequently, many text manipulation steps are added to an already complex workflow, overly complicating the process. In some cases, limitations to existing text manipulation are such that desired analyses can only be carried out using highly sophisticated processing steps beyond the reach of even advanced users and developers. For users with some SQL knowledge, these text operations could be combined into single, concise query on a relational database. As a solution, we have developed the Query Tabular Galaxy tool, which leverages a SQLite database generated from tabular input data. This database can be queried and manipulated to produce transformed and customized tabular outputs compatible with downstream processing steps. Regular expressions can also be utilized for even more sophisticated manipulations, such as find and replace and other filtering actions. Using several Galaxy-based multi-omic workflows as an example, we demonstrate how the Query Tabular tool dramatically streamlines and simplifies the creation of multi-step analyses, efficiently enabling complicated textual manipulations and processing. This tool should find broad utility for users of the Galaxy platform seeking to develop and use sophisticated workflows involving text manipulation on tabular outputs.
