Project description:Electrophysiological features of excitatory synapses vary widely throughout the brain, granting neuronal circuits the ability to decode and store diverse patterns of information. Synapses formed by the same neurons have similar electrophysiological characteristics, belonging to the same type. However, these are generally confined to microscopic brain regions, precluding their proteomic analysis. This has greatly limited our ability to investigate the molecular basis of synaptic physiology. Here we introduce a procedure to characterise the proteome of individual synaptic types. We reveal a remarkable proteomic diversity among the synaptic types of the trisynaptic circuit. Differentially expressed proteins participate in well-known synaptic processes, controlling the signalling pathways preferentially used among diverse synapses. Noteworthy, all synaptic types differentially express proteins directly involved in the function of glutamate receptors. Moreover, neuron-specific gene expression programs would participate in their regulation. Indeed, genes coding for these proteins exhibit such distinct expression profiles between neuronal types that they greatly contribute to their classification. Our data is an important resource for exploring the molecular mechanisms behind electrophysiological properties of different hippocampal synaptic types. Our combined analysis of proteomics and transcriptomics data uncovers a previously unrecognised neuron-specific transcriptomic control of synaptic proteome diversity, directed towards the regulation of glutamate receptors and their regulatory proteins.
Project description:Electrophysiological features of excitatory synapses vary widely throughout the brain, granting neuronal circuits the ability to decode and store diverse patterns of information. Synapses formed by the same neurons have similar electrophysiological characteristics, belonging to the same type. However, these are generally confined to microscopic brain regions, precluding their proteomic analysis. This has greatly limited our ability to investigate the molecular basis of synaptic physiology. Here we introduce a procedure to characterise the proteome of individual synaptic types. We reveal a remarkable proteomic diversity among the synaptic types of the trisynaptic circuit. Differentially expressed proteins participate in well-known synaptic processes, controlling the signalling pathways preferentially used among diverse synapses. Noteworthy, all synaptic types differentially express proteins directly involved in the function of glutamate receptors. Moreover, neuron-specific gene expression programs would participate in their regulation. Indeed, genes coding for these proteins exhibit such distinct expression profiles between neuronal types that they greatly contribute to their classification. Our data is an important resource for exploring the molecular mechanisms behind electrophysiological properties of different hippocampal synaptic types. Our combined analysis of proteomics and transcriptomics data uncovers a previously unrecognised neuron-specific transcriptomic control of synaptic proteome diversity, directed towards the regulation of glutamate receptors and their regulatory proteins.
Project description:Brain function relies on communication via neuronal synapses. Neurons build and diversify synaptic contacts using different protein combinations that define the specificity, function and plasticity potential of synapses. More than a thousand proteins have been globally identified in both pre- and postsynaptic compartments, providing substantial potential for synaptic diversity. While there is ample evidence of diverse synaptic structures, states or functional properties, the diversity of the underlying individual synaptic proteomes remains largely unexplored. Here we used 7 different Cre-driver mouse lines crossed with a floxed mouse line in which the presynaptic terminals were fluorescently labeled (SypTOM) to identify the proteomes that underlie synaptic diversity. We combined microdissection of 5 different brain regions with fluorescent-activated synaptosome sorting to isolate and analyze using quantitative mass spectrometry 18 types of synapses and their underlying synaptic proteomes. We discovered ~1’800 unique synapse type-enriched proteins and allocated thousands of proteins to different types of synapses. We identify commonly shared synaptic protein modules and highlight the hotspots for proteome specialization. A protein-protein correlation network classifies proteins into modules and their association with synaptic traits reveals synaptic protein communities that correlate with either neurotransmitter glutamate or GABA. Finally, we reveal specializations and commonalities of the striatal dopaminergic proteome and outline the proteome diversity of synapses formed by parvalbumin, somatostatin and vasoactive intestinal peptide-expressing cortical interneuron subtypes, highlighting proteome signatures that relate to their functional properties. This study opens the door for molecular systems-biology analysis of synapses and provides a framework to integrate proteomic information for synapse subtypes of interest with cellular or circuit-level experiments.
Project description:current synapse proteomics are restricted to “average” composition of abundant synaptic proteins. Here we performed a subcellular proteomic workflow that could identify and quantify the deep proteome of synaptic vesicles purified from rat whole brain, including previously missing proteins present in a small percentage of central synapses. This synaptic vesicle proteome newly detected many proteins of physiological and pathological relevance particularly in low abundance range, thus providing a resource for future investigations on diversified synaptic functions and neuronal dysfunctions.
Raw data from 3 replicates of synaptosomes (P2') and 3 replicates of SV are deposited here. Each replicate coming from 24 fractions from a peptide fractionation step in the workflow.
Project description:There are very few studies exploring the genetic diversity of tick-borne encephalitis complex viruses. Most of the viruses have been sequenced using capillary electrophoresis, however, very few viruses have been analyzed using deep sequencing to look at the genotypes in each virus population. In this study, different viruses and strains belonging to the tick-borne encephalitis complex were sequenced and genetic diversity was analyzed. Shannon entropy and single nucleotide variants were used to compare the viruses. Then genetic diversity was compared to the phylogenetic relationship of the viruses.
Project description:Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differen-tiation of stem cells toward particular neural cell fates in vitro often relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain incomplete. Here, we developed an arrayed screen of 14 morphogen modulators in human neu-ral organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and anno-tated single cell references of the human fetal brain we discovered that this screening approach generated consid-erable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neurotransmitter identities. Tuning GABAergic neural sub-type diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards an in vitro morphogen atlas of human neural cell differentiation that will bring insights into hu-man development, evolution, and disease.
Project description:As part of the PhenoGen Project (https://phenogen.org), whole brain RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.