Regional Diversity in the Postsynaptic Proteome of the Mouse Brain

Roy, Marcia; Sorokina, Oksana; McLean, Colin; Tapia-González, Silvia; DeFelipe, Javier; Armstrong, J. Douglas; Grant, Seth G. N.

doi:10.3390/proteomes6030031

Cited by 44 publications

(46 citation statements)

References 67 publications

(97 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…IgSF8 (Fig. 3A) has previously been detected in excitatory 15 postsynaptic densities (PSDs) (14) and active zone (AZ) membrane preparations (23), but not in synaptic cleft proteomes (24,25). IgSF8 is highly expressed in the nervous system (26) and localizes to axons and presynaptic terminals of olfactory sensory neurons during synaptogenesis To test whether IgSF8 and TenR interact directly, we mixed equimolar amounts of 10 Fc control protein, TenR-Fc, or Brevican-Fc, another brain ECM protein, with His-IgSF8 recombinant protein and precipitated Fc proteins.…”

Section: Main Textmentioning

confidence: 85%

“…This synaptic diversity is essential for information processing in pyramidal neurons (9). Recent studies reveal a synapse type-specific localization and function of postsynaptic adhesion molecules in hippocampal pyramidal neuron dendrites (10-12), suggesting that compartmentalized distributions of CSPs contribute to the specification of synaptic structure and 15 function. Analogous to single-cell sequencing, probing the mechanisms underlying synaptic diversity requires dissecting the molecular composition of specific synapse types.…”

Section: Main Textmentioning

confidence: 99%

“…Using the UniProt database to query our results for transmembrane, membrane-anchored, and secreted proteins among the MF-CA3 synaptic proteome, we identified a rich repertoire of 15 CSPs that includes adhesion proteins, receptors, secreted glycoproteins, receptor protein tyrosine phosphatases and tyrosine kinases ( Fig. 2A and table S2).…”

Section: Main Textmentioning

confidence: 99%

“…2C and table S2), indicating that our approach is capable of isolating both receptor and ligand at MF-CA3 synapses. 15 To determine the functional significance of IgSF8 for MF-CA3 synapse development, we removed IgSF8 presynaptically by crossing Igsf8 conditional knockout (cKO) mice with the dentate granule cell-specific Rbp4-Cre line. This selectively abolished IgSF8 immunoreactivity in CA3 SL, without affecting gross MF-CA3 tract morphology (Fig.…”

Section: Main Textmentioning

confidence: 99%

“…Dissecting the molecular composition of specific synapse types will be an essential step toward molecular connectomics (39). 15 The authors declare no competing interests. Data and materials availability: MS raw files and search results can be accessed via Proteome Exchange at PXD013492.…”

Section: Main Textmentioning

confidence: 99%

See 4 more Smart Citations

Synapse type-specific proteomic dissection identifies IgSF8 as a hippocampal CA3 microcircuit organizer

Apóstolo

Smukowski²,

Vanderlinden

et al. 2019

Preprint

View full text Add to dashboard Cite

Synaptic diversity is a key feature of neural circuits. Its underlying molecular basis is largely unknown, due to the challenge of analyzing the protein composition of specific synapse types.Here, we isolate the hippocampal mossy fiber (MF) synapse, taking advantage of its unique size and architecture, and dissect its proteome. We identify a rich cell-surface repertoire that includes 5 adhesion proteins, guidance cue receptors, extracellular matrix (ECM) proteins, and proteins of unknown function. Among the latter, we find IgSF8, a previously uncharacterized neuronal receptor, and uncover its role in regulating MF synapse architecture and feedforward inhibition on CA3 pyramidal neurons. Our findings reveal a diverse MF synapse surface proteome and highlight the role of neuronal surface-ECM interactions in the specification of synapse identity and circuit 10 formation. One Sentence Summary:Proteomic dissection of a specific synapse 15 3 Main Text:Neural circuits are composed of distinct neuronal cell types connected in highly specific patterns.Establishing these patterns of connectivity critically relies on cell-surface proteins (CSPs) expressed in cell type-specific combinations. CSPs, including transmembrane, membraneanchored, and secreted proteins, engage in networks of interactions that control neurite guidance, 5 target selection, and synapse development required for the formation of functional circuits (1).Single-cell RNA sequencing has enabled the characterization of cell type-specific CSP repertoires (2-6), but determining how these dictate complex patterns of connectivity (7, 8) poses a major challenge.This challenge is exemplified by pyramidal neurons, which receive different types of 10 synapses on their dendritic arbor, each with a distinct architecture, subcellular location, and functional properties. This synaptic diversity is essential for information processing in pyramidal neurons (9). Recent studies reveal a synapse type-specific localization and function of postsynaptic adhesion molecules in hippocampal pyramidal neuron dendrites (10-12), suggesting that compartmentalized distributions of CSPs contribute to the specification of synaptic structure and 15 function. Analogous to single-cell sequencing, probing the mechanisms underlying synaptic diversity requires dissecting the molecular composition of specific synapse types. This has remained challenging, as microdissection or chemical labeling strategies combined with mass spectrometry (MS) (13-15) average different synapse types, and affinity purification of synapse type-specific protein complexes (16) requires genetically engineered mice. Here, we isolate the 20 hippocampal mossy fiber (MF) synapse, a large and morphologically complex excitatory synapse (17) connecting dentate granule cell axons (mossy fibers) and CA3 pyramidal neuron dendrites in stratum lucidum (SL) (Fig. 1A, B), from wild-type (WT) tissue and map its CSP landscape. 4To isolate a specific synapse type from the hippocampus, we started with a previously published approach (18) ...

show abstract

Section: Main Textmentioning

confidence: 85%

Section: Main Textmentioning

confidence: 99%

Section: Main Textmentioning

confidence: 99%

Section: Main Textmentioning

confidence: 99%

Section: Main Textmentioning

confidence: 99%

See 3 more Smart Citations

Synapse type-specific proteomic dissection identifies IgSF8 as a hippocampal CA3 microcircuit organizer

Apóstolo

Smukowski²,

Vanderlinden

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

Prediction of a Cell-Class-Specific Mouse Mesoconnectome Using Gene Expression Data

2020

View full text Add to dashboard Cite

Reconstructing brain connectivity at sufficient resolution for computational models designed to study the biophysical mechanisms underlying cognitive processes is extremely challenging. For such a purpose, a mesoconnectome that includes laminar and cell-class specificity would be a major step forward. We analyzed the ability of gene expression patterns to predict cell-class and layer-specific projection patterns and assessed the functional annotations of the most predictive groups of genes. To achieve our goal we used publicly available volumetric gene expression and connectivity data and we trained computational models to learn and predict cell-class and layer-specific axonal projections using gene expression data. Predictions were done in two ways, namely predicting projection strengths using the expression of individual genes and using the co-expression of genes organized in spatial modules, as well as predicting binary forms of projection. For predicting the strength of projections, we found that ridge (L2-regularized) regression had the highest cross-validated accuracy with a median r2 score of 0.54 which corresponded for binarized predictions to a median area under the ROC value of 0.89. Next, we identified 200 spatial gene modules using a dictionary learning and sparse coding approach. We found that these modules yielded predictions of comparable accuracy, with a median r2 score of 0.51. Finally, a gene ontology enrichment analysis of the most predictive gene groups resulted in significant annotations related to postsynaptic function. Taken together, we have demonstrated a prediction workflow that can be used to perform multimodal data integration to improve the accuracy of the predicted mesoconnectome and support other neuroscience use cases.

show abstract

Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

2021

View full text Add to dashboard Cite

Finding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.

show abstract

Regional Diversity in the Postsynaptic Proteome of the Mouse Brain

Cited by 44 publications

References 67 publications

Synapse type-specific proteomic dissection identifies IgSF8 as a hippocampal CA3 microcircuit organizer

Synapse type-specific proteomic dissection identifies IgSF8 as a hippocampal CA3 microcircuit organizer

Prediction of a Cell-Class-Specific Mouse Mesoconnectome Using Gene Expression Data

Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

Contact Info

Product

Resources

About