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Cell type– and brain region–resolved mouse brain proteome

Abstract

Brain transcriptome and connectome maps are being generated, but an equivalent effort on the proteome is currently lacking. We performed high-resolution mass spectrometry–based proteomics for in-depth analysis of the mouse brain and its major brain regions and cell types. Comparisons of the 12,934 identified proteins in oligodendrocytes, astrocytes, microglia and cortical neurons with deep sequencing data of the transcriptome indicated deep coverage of the proteome. Cell type–specific proteins defined as tenfold more abundant than average expression represented about a tenth of the proteome, with an overrepresentation of cell surface proteins. To demonstrate the utility of our resource, we focused on this class of proteins and identified Lsamp, an adhesion molecule of the IgLON family, as a negative regulator of myelination. Our findings provide a framework for a system-level understanding of cell-type diversity in the CNS and serves as a rich resource for analyses of brain development and function.

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Figure 1: Comparison of proteome and RNA-Seq data.
Figure 2: Comparative analysis of cell proteomes.
Figure 3: Quantitative analysis of expressed genes.
Figure 4: Abundant and enriched proteins in the mouse brain and its cell types.
Figure 5: Brain region–resolved proteome (a) PCA.
Figure 6: Comparative pathway enrichment analysis identifies cell adhesion molecules enriched in oligodendrocytes and neurons.
Figure 7: Lsamp interacts with and is expressed on oligodendrocytes and neurons.
Figure 8: Lsamp is a negative regulator of myelination in the fiber tracts of the fimbria-fornix.

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Acknowledgements

We would like to acknowledge the PRIDE Team for upload of proteomics raw data. We thank J. Cox, M.Y. Hein and K. Mayr for helpful discussions, and C. Velte, N. Schwedhelm-Dornmeyer, S. Safaiyan, G. Sowa and M. Dodel for technical assistance. Illumina sequencing was performed by R. Reinhardt at the Max-Planck Genome Center Cologne. The work was supported grants from the German Research Foundation (SI 746/9-1; 10-1; TRR43; RO 4076/3-1), the Tschira-Stiftung, and grants from the Estonian Research Council (IUT20-41 and PUT129). The research leading to these results has received funding from the European Commission under FP7 GA n°ERC-2012-SyG_318987 – ToPAG and MC-ITN IN-SENS (#607616). S.S. received a PhD scholarship from the Boeringer-Ingelheim Fonds and N.K. this recipient of a Marie-Curie fellowship from the INSENS/ FP7-PEOPLE-2013 (607616) framework.

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Authors and Affiliations

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Contributions

K.S., M.M. and M.S. designed the experiments. K.S., S.S., C.G.B., N.K., N.M.-H., L.C. and U.-K.H. performed the experiments. K.S., S.S., S.T., N.K., M.J.R., M.M. and M.S. analyzed the data. K.K. and M.-A.P. provided materials. K.S., M.M. and M.S. wrote the manuscript.

Corresponding authors

Correspondence to Matthias Mann or Mikael Simons.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–14 (PDF 4107 kb)

Supplementary Methods Checklist (PDF 468 kb)

Supplementary Table 1

Protein expression data of adult mouse brain and cultured CNS cell types measured as fractionated samples. (XLSX 7700 kb)

Supplementary Table 2

Protein expression data of mouse brain regions (P60), acutely isolated CNS cell types and cerebellum development (P5, P14, P24) measured by 'single-run' analysis. (XLSX 5694 kb)

Supplementary Table 3

RNA-Seq expression data for the cultured CNS cell types. (XLSX 4139 kb)

Supplementary Table 4

Gene ontology enrichment analysis of the genes expressed exclusively at the transcript level and lack evidence of expression at the protein level. (XLSX 15 kb)

Supplementary Table 5

Protein expression data of cultured CNS cell types for individual replicates and developmental stage. (XLSX 2930 kb)

Supplementary Table 6

Differentially expressed proteins in cultured CNS cell types. (XLSX 2671 kb)

Supplementary Table 7

Differentially expressed proteins in cortical neurons and cerebellar granule neurons. (XLSX 8287 kb)

Supplementary Table 8

Clusters based enrichment analysis for the cultured CNS cell types. (XLSX 68 kb)

Supplementary Table 9

Cluster based enrichment analysis for cerebellar granule neurons. (XLSX 20 kb)

Supplementary Table 10

Comparison of annotation terms (KEGG pathway, GO terms and Corum) between the cultured CNS cell types resolved to individual replicates and developmental stage. (XLSX 375 kb)

Supplementary Table 11

GOCC enrichment of proteins >10 fold enriched in cultured CNS cell types. (XLSX 179 kb)

Supplementary Table 12

GOCC enrichment of transcripts >10 fold enriched in cultured CNS cell types. (XLSX 21 kb)

Supplementary Table 13

Differentially expressed proteins in isolated CNS cell types. (XLSX 3391 kb)

Supplementary Table 14

Comparison of annotation terms (GO terms and Corum) between the cultured and isolated CNS cell types resolved to individual replicates. (XLSX 682 kb)

Supplementary Table 15

A list of the most abundant brain-enriched (>10 fold enrichment as compared to the liver) proteins. (XLSX 51 kb)

Supplementary Table 16

Comparison of annotation terms (KEGG pathways and GO terms) between the mouse brain and liver. (XLSX 100 kb)

Supplementary Table 17

Protein expression in mouse brain regions. (XLSX 5399 kb)

Supplementary Table 18

Differentially expressed 2,901 proteins in mouse brain regions. (XLSX 2152 kb)

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Sharma, K., Schmitt, S., Bergner, C. et al. Cell type– and brain region–resolved mouse brain proteome. Nat Neurosci 18, 1819–1831 (2015). https://doi.org/10.1038/nn.4160

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