PreprintCited by 22Neuroscience and Neuropharmacology ResearchSingle-cell and spatial transcriptomicsMemory and Neural Mechanisms

The molecular diversity of hippocampal regions and strata at synaptic resolution revealed by integrated transcriptomic and proteomic profiling

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Kaulich, Eva, Waselenchuk, Quinn, Fürst, Nicole, Desch, Kristina, Mosbacher, Janus, Ciirdaeva, Elena, Juengling, Marcel, Tushev, Georgi +2 more·2024·Nature Communications

Preprint — published as 10.1038/s41467-025-63119-5

Abstract

The molecular diversity of neurons and their synapses underlies the different responses and plasticity profiles that drive all neural circuits and behavior. While the extent of this diversity has been partially revealed by transcriptomic and proteomic profiling, combined studies of neuronal transcripts and proteins are limited. Here, we used microdissection of mouse hippocampal subregions and CA1 strata and fluorescence-activated synaptosome sorting (FASS) to characterize the transcripts and proteins from different hippocampal neurons and their compartments with synaptic resolution. Parallel RNA-seq and LC-MS/MS of microdissections identified over 15,000 mRNA transcripts and 10,000 proteins, revealing thousands with local enrichment such as classes of glutamate receptors and voltage-gated potassium channels, myelin-associated molecules, and adhesion molecules. Synaptosome analysis further identified specific enrichment of molecules from collagen, ribosome, solute carrier, and receptor families at different synapses formed along CA1 neurons. By integrating mRNA and protein data, we defined clusters of co-regulated molecules such as adhesion and neurofilament proteins and transporter mRNAs, and found subsets of mRNA-protein pairs with strong correlation and anti-correlation in their abundance variation. Our findings comprise a rich resource on the molecular landscape of the hippocampus and its synapses that is accessible at syndive.org , and highlight the coordinated organization of transcripts and proteins between regions, neuronal compartments, and synapses.

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Authors
Kaulich, E., Waselenchuk, Q., Fürst, N., Desch, K., Mosbacher, J., Ciirdaeva, E., Juengling, M., Tushev, G., Langer, J., & Schuman, E. M.
Affiliations
  • Max Planck Institute for Brain Research (DE)
  • Max Planck Institute of Biophysics (DE)
  • Radboud University Nijmegen (NL)
Corresponding author
Schuman, Erin M.
Venue
Nature Communications
Publisher
openRxiv
Published
2024-08-05
Volume
16
Issue
1
Pages
7942-7942
ISSN
2041-1723 (ISSN-L)
OpenAlex
W4413698594
Cited by
22
References
242
Citations by year
2026: 18 · 2025: 4
FWCI
8.63
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Radboud Repository (Radboud University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
Funders
  • US-UK Fulbright Commission
  • European Commission
  • Max-Planck-Gesellschaft
  • HORIZON EUROPE European Research Council (101054512)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Memory and Neural Mechanisms
Keywords
hippocampus, synapses, spatial transcriptomics, spatial proteomics, local protein synthesis, translatome, pyramidal neurons, CA1, synaptic specificity, adhesion molecules, cytoskeletal proteins, kinases, protein half-life, mice
MeSH terms
Animals, Hippocampus, Male, Mice, Inbred C57BL, RNA, Messenger, Synapses, Synaptosomes, Pyramidal Cells, Proteome, Gene Expression Profiling, Proteomics, Mice, Transcriptome

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