Region-Specific PSD-95 Interactomes Contribute to Functional Diversity of Excitatory Synapses in Human Brain

Abstract

Running title -PSD-95 protein-protein interactions in human brainThe overarching goal of this exploratory study is to link subcellular microdomain specific protein-protein interactomes with big data analytics. We isolated postsynaptic density-95 (PSD-95) complexes from four human brain regions and compared their protein interactomes using multiple bioinformatics techniques. We demonstrate that human brain regions have unique postsynaptic protein signatures that may be used to interrogate perturbagen databases. Assessment of our hippocampal signature using the iLINCS database yielded several compounds with recently characterized "off target" effects on protein-protein interactions in the posynaptic density compartment. Acknowledgments:We would like to thank all those that have supported this research: the L.I.F.E. Foundation, UCNI pilot award, Lindsay Brinkmeyer Schizophrenia Research Fund, Center for Clinical and Translational Science Training (CCTST), and NIH grant MH107916. The MS data was acquired in the University of Cincinnati Proteomics Laboratory on a mass spectrometer funded in part through the NIH S10 shared instrumentation grant RR027015.Altering the expression of PSD-95 protein significantly changes synaptic structure and function, including molecular correlates of learning and memory, long-term potentiation (LTP) and long-term depression (LTD). For example, PSD-95 overexpression increases the amplitude of excitatory postsynaptic currents (EPSCs), to the extent that additional stimulus is unable to further strengthen LTP [13][14][15][16][17]. In contrast, PSD-95 knockdown disrupts postsynaptic density structure and suppresses EPSCs, consistent with a role for PSD-95 in synaptic fidelity [18][19][20]. Further highlighting the importance of PSD-95 in the synapse, knockout of PSD-95 in mice and genomic variants within postsynaptic density hub proteins are particularly implicated in neuropsychiatric disorders such as schizophrenia and autism [21,22].To investigate excitatory postsynaptic protein hubs, we targeted PSD-95 due to its high level of localization to the postsynaptic density (~95%), its well-characterized role as a hub protein, and the large number of constituents in its protein interactome (~1000) [23][24][25]. We designed a series of experiments to examine brain region-specific excitatory postsynaptic proteomes to answer the following questions. 1) Do postsynaptic protein-protein interactions differ by brain region? 2) Can we accurately detect and separate samples based on these differences? and 3) Can region-specific protein interactomes inform functional differences? For these experiments we used four human brain regions (anterior cingulate cortex (ACC), dorsolateral prefrontal cortex (DLPFC), hippocampus (HPC), and superior temporal gyrus (STG)) from 3 well-matched control male subjects from the Alabama Brain Collection. A total of 289 proteins were identified as part of a PSD-95 protein interactome that were present across all four brain regions.We hypothesize that there is region-specific ...

Systems-based proteomics to resolve the biology of Alzheimer’s disease beyond amyloid and tau

“…For instance, sequential window acquisition of all theoretical mass spectra (SWATH-MS), a relatively userfriendly technology capable of deep proteome coverage and high quantitative accuracy [72,83], stands to significantly advance the application of DIA to complex tissue analyses. Efforts to adapt this strategy for the quantification of bulk brain proteomes are already underway [84].…”