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.
At a glance
- Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007). et al.
- A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 83, 309–323 (2014). et al.
- A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J. Neurosci. 28, 264–278 (2008). et al.
- Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135, 749–762 (2008). et al.
- A translational profiling approach for the molecular characterization of CNS cell types. Cell 135, 738–748 (2008). et al.
- An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J. Neurosci. 34, 11929–11947 (2014). et al.
- Spatio-temporal transcriptome of the human brain. Nature 478, 483–489 (2011). et al.
- Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62, 494–509 (2009). et al.
- The microglial sensome revealed by direct RNA sequencing. Nat. Neurosci. 16, 1896–1905 (2013). et al.
- Identification of a unique TGF-beta-dependent molecular and functional signature in microglia. Nat. Neurosci. 17, 131–143 (2014). et al.
- Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 13, 227–232 (2012). &
- Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nat. Neurosci. 17, 1491–1499 (2014). , , &
- Comprehensive proteomics. Curr. Opin. Biotechnol. 22, 3–8 (2011). , &
- The coming age of complete, accurate, and ubiquitous proteomes. Mol. Cell 49, 583–590 (2013). , , &
- Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548 (2011). et al.
- Mass-spectrometry-based draft of the human proteome. Nature 509, 582–587 (2014). et al.
- A draft map of the human proteome. Nature 509, 575–581 (2014). et al.
- Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell Proteomics 11, M111.014050 (2012). , , , &
- Defining the transcriptome and proteome in three functionally different human cell lines. Mol. Syst. Biol. 6, 450 (2010). et al.
- A global view of protein expression in human cells, tissues, and organs. Mol. Syst. Biol. 5, 337 (2009). et al.
- The mystery and magic of glia: a perspective on their roles in health and disease. Neuron 60, 430–440 (2008).
- Mechanisms of axon ensheathment and myelin growth. Nat. Rev. Neurosci. 6, 683–690 (2005). &
- Central nervous system myelin: structure, synthesis and assembly. Trends Cell Biol. 21, 585–593 (2011). , &
- Astrocytes and disease: a neurodevelopmental perspective. Genes Dev. 26, 891–907 (2012). et al.
- Microglia: active sensor and versatile effector cells in the normal and pathologic brain. Nat. Neurosci. 10, 1387–1394 (2007). &
- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008). &
- System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol. Cell Proteomics 11, M111.013722 (2012). et al.
- RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol. Syst. Biol. 7, 497 (2011). et al.
- The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549 (2011). et al.
- Global signatures of protein and mRNA expression levels. Mol. Biosyst. 5, 1512–1526 (2009). , , &
- Correlation of mRNA and protein in complex biological samples. FEBS Lett. 583, 3966–3973 (2009). , &
- MaxLFQ allows accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction. Mol. Cell. Proteomics 13, 2513–2526 (2014). et al.
- Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol. Syst. Biol. 8, 611 (2012). et al.
- Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell 151, 671–683 (2012). et al.
- Clinical and molecular genetics of Stickler syndrome. J. Med. Genet. 36, 353–359 (1999). &
- Negative regulation of central nervous system myelination by polysialylated-neural cell adhesion molecule. Proc. Natl. Acad. Sci. USA 97, 7585–7590 (2000). et al.
- The limbic system-associated membrane protein is an Ig superfamily member that mediates selective neuronal growth and axon targeting. Neuron 15, 287–297 (1995). et al.
- Molecular characterization of a new immunoglobulin superfamily protein with potential roles in opioid binding and cell contact. EMBO J. 8, 489–495 (1989). et al.
- Cloning of neurotrimin defines a new subfamily of differentially expressed neural cell adhesion molecules. J. Neurosci. 15, 2141–2156 (1995). et al.
- Diglons are heterodimeric proteins composed of IgLON subunits, and Diglon-CO inhibits neurite outgrowth from cerebellar granule cells. J. Cell Sci. 117, 3961–3973 (2004). , , , &
- Neurotrimin mediates bifunctional effects on neurite outgrowth via homophilic and heterophilic interactions. J. Neurosci. 18, 9312–9325 (1998). , , &
- A central role for Necl4 (SynCAM4) in Schwann cell-axon interaction and myelination. Nat. Neurosci. 10, 861–869 (2007). et al.
- Nectin-like proteins mediate axon Schwann cell interactions along the internode and are essential for myelination. J. Cell Biol. 178, 861–874 (2007). et al.
- Expression of cellular adhesion molecule 'OPCML' is down-regulated in gliomas and other brain tumours. Neuropathol. Appl. Neurobiol. 33, 77–85 (2007). et al.
- Global proteome analysis of the NCI-60 cell line panel. Cell Rep. 4, 609–620 (2013). et al.
- Cell type–resolved quantitative proteomics of murine liver. Cell Metab. 20, 1076–1087 (2014). , , &
- Characterization of the proteome, diseases and evolution of the human postsynaptic density. Nat. Neurosci. 14, 19–21 (2011). et al.
- Complementary expression and heterophilic interactions between IgLON family members neurotrimin and LAMP. J. Neurobiol. 51, 190–204 (2002). et al.
- White matter in learning, cognition and psychiatric disorders. Trends Neurosci. 31, 361–370 (2008).
- Limbic system associated membrane protein as a potential target for neuropsychiatric disorders. Front. Pharmacol 4, 32 (2013). , , &
- Neuron to glia signaling triggers myelin membrane exocytosis from endosomal storage sites. J. Cell Biol. 172, 937–948 (2006). et al.
- Myelin basic protein-dependent plasma membrane reorganization in the formation of myelin. EMBO J. 25, 5037–5048 (2006). et al.
- CD14 and TRIF govern distinct responsiveness and responses in mouse microglial TLR4 challenges by structural variants of LPS. Brain Behav. Immun. 25, 957–970 (2011). et al.
- In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856–2860 (2006). , , , &
- Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007). , &
- Universal sample preparation method for proteome analysis. Nat. Methods 6, 359–362 (2009). , , &
- Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794–1805 (2011). et al.
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013). et al.
- Software for computing and annotating genomic ranges. PLOS Comput. Biol. 9, e1003118 (2013). et al.
- The multispecific thyroid hormone transporter OATP1C1 mediates cell-specific sulforhodamine 101-labeling of hippocampal astrocytes. Brain Struct. Funct. 220, 193–203 (2015). et al.
- Myelin membrane wrapping of CNS axons by PI(3,4,5)P3-dependent polarized growth at the inner tongue. Cell 156, 277–290 (2014). et al.
- Supplementary Text and Figures (4,206 KB)
Supplementary Figures 1–14
- Supplementary Table 1 (7,885 KB)
Protein expression data of adult mouse brain and cultured CNS cell types measured as fractionated samples.
- Supplementary Table 2 (5830 KB)
Protein expression data of mouse brain regions (P60), acutely isolated CNS cell types and cerebellum development (P5, P14, P24) measured by 'single-run' analysis.
- Supplementary Table 3 (4,239 KB)
RNA-Seq expression data for the cultured CNS cell types.
- Supplementary Table 4 (15 KB)
Gene ontology enrichment analysis of the genes expressed exclusively at the transcript level and lack evidence of expression at the protein level.
- Supplementary Table 5 (3,000 KB)
Protein expression data of cultured CNS cell types for individual replicates and developmental stage.
- Supplementary Table 6 (2,735 KB)
Differentially expressed proteins in cultured CNS cell types.
- Supplementary Table 7 (8,486 KB)
Differentially expressed proteins in cortical neurons and cerebellar granule neurons.
- Supplementary Table 8 (69 KB)
Clusters based enrichment analysis for the cultured CNS cell types.
- Supplementary Table 9 (21 KB)
Cluster based enrichment analysis for cerebellar granule neurons.
- Supplementary Table 10 (384 KB)
Comparison of annotation terms (KEGG pathway, GO terms and Corum) between the cultured CNS cell types resolved to individual replicates and developmental stage.
- Supplementary Table 11 (184 KB)
GOCC enrichment of proteins >10 fold enriched in cultured CNS cell types.
- Supplementary Table 12 (21 KB)
GOCC enrichment of transcripts >10 fold enriched in cultured CNS cell types.
- Supplementary Table 13 (3472 KB)
Differentially expressed proteins in isolated CNS cell types.
- Supplementary Table 14 (699 KB)
Comparison of annotation terms (GO terms and Corum) between the cultured and isolated CNS cell types resolved to individual replicates.
- Supplementary Table 15 (52 KB)
A list of the most abundant brain-enriched (>10 fold enrichment as compared to the liver) proteins.
- Supplementary Table 16 (103 KB)
Comparison of annotation terms (KEGG pathways and GO terms) between the mouse brain and liver.
- Supplementary Table 17 (5538 KB)
Protein expression in mouse brain regions.
- Supplementary Table 18 (2203 KB)
Differentially expressed 2,901 proteins in mouse brain regions.