Integrative Analysis of Brain Region-specific Shank3 Interactomes for Understanding the Heterogeneity of Neuronal Pathophysiology Related to SHANK3 Mutations

Recent molecular genetic studies have identified 100s of risk genes for various neurodevelopmental and neuropsychiatric disorders. As the number of risk genes increases, it is becoming clear that different mutations of a single gene could cause different types of disorders. One of the best examples of such a gene is SHANK3, which encodes a core scaffold protein of the neuronal excitatory post-synapse. Deletions, duplications, and point mutations of SHANK3 are associated with autism spectrum disorders, intellectual disability, schizophrenia, bipolar disorder, and attention deficit hyperactivity disorder. Nevertheless, how the different mutations of SHANK3 can lead to such phenotypic diversity remains largely unknown. In this study, we investigated whether Shank3 could form protein complexes in a brain region-specific manner, which might contribute to the heterogeneity of neuronal pathophysiology caused by SHANK3 mutations. To test this, we generated a medial prefrontal cortex (mPFC) Shank3 in vivo interactome consisting of 211 proteins, and compared this protein list with a Shank3 interactome previously generated from mixed hippocampal and striatal (HP+STR) tissues. Unexpectedly, we found that only 47 proteins (about 20%) were common between the two interactomes, while 164 and 208 proteins were specifically identified in the mPFC and HP+STR interactomes, respectively. Each of the mPFC- and HP+STR-specific Shank3 interactomes represents a highly interconnected network. Upon comparing the brain region-enriched proteomes, we found that the large difference between the mPFC and HP+STR Shank3 interactomes could not be explained by differential protein expression profiles among the brain regions. Importantly, bioinformatic pathway analysis revealed that the representative biological functions of the mPFC- and HP+STR-specific Shank3 interactomes were different, suggesting that these interactors could mediate the brain region-specific functions of Shank3. Meanwhile, the same analysis on the common Shank3 interactors, including Homer and GKAP/SAPAP proteins, suggested that they could mainly function as scaffolding proteins at the post-synaptic density. Lastly, we found that the mPFC- and HP+STR-specific Shank3 interactomes contained a significant number of proteins associated with neurodevelopmental and neuropsychiatric disorders. These results suggest that Shank3 can form protein complexes in a brain region-specific manner, which might contribute to the pathophysiological and phenotypic diversity of disorders related to SHANK3 mutations.

[1]  T. Boeckers,et al.  SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras , 2017, Nature Cell Biology.

[2]  Núria Queralt-Rosinach,et al.  DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants , 2016, Nucleic Acids Res..

[3]  P. Calabresi,et al.  Pharmacological enhancement of mGlu5 receptors rescues behavioral deficits in SHANK3 knock-out mice , 2016, Molecular Psychiatry.

[4]  M. Zoli,et al.  Activity and circadian rhythm influence synaptic Shank3 protein levels in mice , 2016, Journal of neurochemistry.

[5]  R. Weinberg,et al.  The Postsynaptic Density: There Is More than Meets the Eye , 2016, Front. Synaptic Neurosci..

[6]  C. Winters,et al.  Zinc Stabilizes Shank3 at the Postsynaptic Density of Hippocampal Synapses , 2016, PloS one.

[7]  Carlos Prieto,et al.  APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks , 2016, Nucleic Acids Res..

[8]  K. Föhr,et al.  Enlarged dendritic spines and pronounced neophobia in mice lacking the PSD protein RICH2 , 2016, Molecular Brain.

[9]  Neville E. Sanjana,et al.  Mice with Shank3 Mutations Associated with ASD and Schizophrenia Display Both Shared and Distinct Defects , 2016, Neuron.

[10]  Zhandong Liu,et al.  Post-transcriptional regulation of SHANK3 expression by microRNAs related to multiple neuropsychiatric disorders , 2015, Molecular Brain.

[11]  Matthias Mann,et al.  Cell type– and brain region–resolved mouse brain proteome , 2015, Nature Neuroscience.

[12]  Kihoon Han,et al.  Emerging role of synaptic actin-regulatory pathway in the pathophysiology of mood disorders , 2015 .

[13]  C. Powell,et al.  Autism-Associated Insertion Mutation (InsG) of Shank3 Exon 21 Causes Impaired Synaptic Transmission and Behavioral Deficits , 2015, The Journal of Neuroscience.

[14]  Laura Inés Furlong,et al.  PsyGeNET: a knowledge platform on psychiatric disorders and their genes , 2015, Bioinform..

[15]  H. Zoghbi,et al.  Fragile X-like behaviors and abnormal cortical dendritic spines in cytoplasmic FMR1-interacting protein 2-mutant mice. , 2015, Human molecular genetics.

[16]  Eunjoon Kim,et al.  Shank3-mutant mice lacking exon 9 show altered excitation/inhibition balance, enhanced rearing, and spatial memory deficit , 2015, Front. Cell. Neurosci..

[17]  M. Owen,et al.  Genetic Risk for Schizophrenia: Convergence on Synaptic Pathways Involved in Plasticity , 2015, Biological Psychiatry.

[18]  A. Smit,et al.  Interaction proteomics reveals brain region-specific AMPA receptor complexes. , 2014, Journal of proteome research.

[19]  Christopher S. Poultney,et al.  Synaptic, transcriptional, and chromatin genes disrupted in autism , 2014, Nature.

[20]  D. Baehrens,et al.  Regional Diversity and Developmental Dynamics of the AMPA-Receptor Proteome in the Mammalian Brain , 2014, Neuron.

[21]  T. Maniatis,et al.  An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex , 2014, The Journal of Neuroscience.

[22]  Elodie Ey,et al.  Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments , 2014, PLoS genetics.

[23]  A. Need,et al.  One gene, many neuropsychiatric disorders: lessons from Mendelian diseases , 2014, Nature Neuroscience.

[24]  Yoonji Lee,et al.  Transcriptional and functional complexity of Shank3 provides a molecular framework to understand the phenotypic heterogeneity of SHANK3 causing autism and Shank3 mutant mice , 2014, Molecular Autism.

[25]  Thomas Bourgeron,et al.  The emerging role of SHANK genes in neuropsychiatric disorders , 2014, Developmental neurobiology.

[26]  E. Banks,et al.  De novo mutations in schizophrenia implicate synaptic networks , 2014, Nature.

[27]  T. Boeckers,et al.  Zinc deficiency dysregulates the synaptic ProSAP/Shank scaffold and might contribute to autism spectrum disorders. , 2014, Brain : a journal of neurology.

[28]  P. Worley,et al.  Loss of Predominant Shank3 Isoforms Results in Hippocampus-Dependent Impairments in Behavior and Synaptic Transmission , 2013, The Journal of Neuroscience.

[29]  A. Breman,et al.  SHANK3 overexpression causes manic-like behavior with unique pharmacogenetic properties , 2013, Nature.

[30]  T. Boeckers,et al.  SHANK3 Gene Mutations Associated with Autism Facilitate Ligand Binding to the Shank3 Ankyrin Repeat Region* , 2013, The Journal of Biological Chemistry.

[31]  P. Worley,et al.  Shank3-Rich2 Interaction Regulates AMPA Receptor Recycling and Synaptic Long-Term Potentiation , 2013, The Journal of Neuroscience.

[32]  Tobias Grossmann,et al.  The role of medial prefrontal cortex in early social cognition , 2013, Front. Hum. Neurosci..

[33]  M. Ehlers,et al.  Modeling Autism by SHANK Gene Mutations in Mice , 2013, Neuron.

[34]  D. R. Euston,et al.  The Role of Medial Prefrontal Cortex in Memory and Decision Making , 2012, Neuron.

[35]  James Y. Zhang,et al.  Reduced Excitatory Neurotransmission and Mild Autism-Relevant Phenotypes in Adolescent Shank3 Null Mutant Mice , 2012, The Journal of Neuroscience.

[36]  Anne-Marie Le Sourd,et al.  Autistic-like behaviours and hyperactivity in mice lacking ProSAP1/Shank2 , 2012, Nature.

[37]  Mark F Bear,et al.  Synaptic dysfunction in neurodevelopmental disorders associated with autism and intellectual disabilities. , 2012, Cold Spring Harbor perspectives in biology.

[38]  Bradley P. Coe,et al.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations , 2012, Nature.

[39]  M. Sheng,et al.  The postsynaptic organization of synapses. , 2011, Cold Spring Harbor perspectives in biology.

[40]  T. Boeckers,et al.  Postsynaptic ProSAP/Shank scaffolds in the cross-hair of synaptopathies. , 2011, Trends in cell biology.

[41]  Ann K. Shinn,et al.  Abnormal Medial Prefrontal Cortex Resting-State Connectivity in Bipolar Disorder and Schizophrenia , 2011, Neuropsychopharmacology.

[42]  A. Beaudet,et al.  Synaptic dysfunction and abnormal behaviors in mice lacking major isoforms of Shank3. , 2011, Human molecular genetics.

[43]  D. Licatalosi,et al.  FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism , 2011, Cell.

[44]  Diana V. Dugas,et al.  Protein Interactome Reveals Converging Molecular Pathways Among Autism Disorders , 2011, Science Translational Medicine.

[45]  G. Feng,et al.  Shank3 mutant mice display autistic-like behaviours and striatal dysfunction , 2011, Nature.

[46]  Mark J. Harris,et al.  Haploinsufficiency of the autism-associated Shank3 gene leads to deficits in synaptic function, social interaction, and social communication , 2010, Molecular autism.

[47]  C. Gillberg,et al.  The genetics of autism spectrum disorders and related neuropsychiatric disorders in childhood. , 2010, The American journal of psychiatry.

[48]  Jonathan G. Lees,et al.  Transient protein-protein interactions: structural, functional, and network properties. , 2010, Structure.

[49]  Marie-Pierre Dubé,et al.  De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia , 2010, Proceedings of the National Academy of Sciences.

[50]  C. Hoogenraad,et al.  Synapse Pathology in Psychiatric and Neurologic Disease , 2010, Current neurology and neuroscience reports.

[51]  M. Sheng,et al.  Regulated RalBP1 Binding to RalA and PSD-95 Controls AMPA Receptor Endocytosis and LTD , 2009, PLoS biology.

[52]  M. Furey,et al.  Brain structural and functional abnormalities in mood disorders: implications for neurocircuitry models of depression , 2008, Brain Structure and Function.

[53]  Xiaobing Chen,et al.  Organization of the core structure of the postsynaptic density , 2008, Proceedings of the National Academy of Sciences.

[54]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[55]  Christian R Marshall,et al.  Contribution of SHANK3 mutations to autism spectrum disorder. , 2007, American journal of human genetics.

[56]  C. Hoogenraad,et al.  The postsynaptic architecture of excitatory synapses: a more quantitative view. , 2007, Annual review of biochemistry.

[57]  S. Buono,et al.  Schizophrenia in a patient with subtelomeric duplication of chromosome 22q , 2007, Clinical genetics.

[58]  Thomas Bourgeron,et al.  Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders , 2007, Nature Genetics.

[59]  Eckart D Gundelfinger,et al.  An Architectural Framework That May Lie at the Core of the Postsynaptic Density , 2006, Science.

[60]  R. Weinberg,et al.  Regulation of Dendritic Spine Morphogenesis by Insulin Receptor Substrate 53, a Downstream Effector of Rac1 and Cdc42 Small GTPases , 2005, The Journal of Neuroscience.

[61]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[62]  H. McDermid,et al.  Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsufficiency of SHANK3/PROSAP2 in the major neurological symptoms , 2003, Journal of medical genetics.

[63]  J. Yates,et al.  DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. , 2002, Journal of proteome research.

[64]  M. Sheng,et al.  The Shank family of scaffold proteins. , 2000, Journal of cell science.

[65]  T. Tzschentke,et al.  The medial prefrontal cortex as a part of the brain reward system , 2000, Amino Acids.