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.

Human-specific features of spatial gene expression and regulation in eight brain regions

“…3C). An analysis based on 585 published cell-type marker genes contained in the modules (Sharma et al 2015) showed the strong enrichment of modules 6, 12, and 20 in microglial markers (hypergeometric test, BH-corrected P-value <0.05) (Fig. 3D,E).…”

“…Among the 63 module 22 genes reported to be expressed in mouse neurons and astrocytes (Sharma et al 2015), we selected seven genes highly expressed in the human hippocampus (average RPKM >50) and covering most of the human-specificity ratio range: RSPH1, PDLIM4, FOLR1, CNN3, F3, PBXIP1, and RGMA (Fig. 4A).…”

“…PBXIP1 and F3 staining revealed morphology compatible with astrocyte projections, and F3 signal partially colocalized with GFAP staining marking the majority of astrocytes and their projections. Notably, the localization of CNN3, PBXIP1, and F3 in astrocytes and their projections was reported in both mice and humans (Darmanis et al 2015;Sharma et al 2015;Zhang et al 2016), whereas the localization of RSPH1 and RGMA in neurons was reported in humans (Zhang et al 2016) and mice (Sharma et al 2015), respectively (Supplemental Table S9). …”

“…Cold Spring Harbor Laboratory Press on April 27, 2019 -Published by genome.cshlp.org Downloaded from Cell-type marker genes from a previously published paper (Sharma et al 2015) were used to determine the enriched celltype markers in genes of each module by means of a hypergeometric test. The BH-corrected hypergeometric test P-value of <0.05 was used as the judging boundary of enrichment.…”

Organellar Proteomics: Tissue Specificity, Absolute Quantity, Posttranslational Modifications and Protein-Protein Interactions

“…Mass spectrometry analyses of different cell lines and multiple tissues have been carried out to address how tissues differ in gene and protein expression and how this contributes to tissue-specific biological functions [5][6][7]. Particularly important to subcellular organelles, existing proteomics studies indicated that mitochondria are functionally specialized in different tissues, which is crucial to its involvement in normal physiology and diseases [8][9][10].…”