An Anatomically Resolved Mouse Brain Proteome Reveals Parkinson Disease-relevant Pathways

Here, we present a mouse brain protein atlas that covers 17 surgically distinct neuroanatomical regions of the adult mouse brain, each less than 1 mm3 in size. The protein expression levels are determined for 6,500 to 7,500 gene protein products from each region and over 12,000 gene protein products for the entire brain, documenting the physiological repertoire of mouse brain proteins in an anatomically resolved and comprehensive manner. We explored the utility of our spatially defined protein profiling methods in a mouse model of Parkinson's disease. We compared the proteome from a vulnerable region (substantia nigra pars compacta) of wild type and parkinsonian mice with that of an adjacent, less vulnerable, region (ventral tegmental area) and identified several proteins that exhibited both spatiotemporal- and genotype-restricted changes. We validated the most robustly altered proteins using an alternative profiling method and found that these modifications may highlight potential new pathways for future studies. This proteomic atlas is a valuable resource that offers a practical framework for investigating the molecular intricacies of normal brain function as well as regional vulnerability in neurological diseases. All of the mouse regional proteome profiling data are published on line at http://mbpa.bprc.ac.cn/. Here, we present a mouse brain protein atlas that covers 17 surgically distinct neuroanatomical regions of the adult mouse brain, each less than 1 mm3 in size. The protein expression levels are determined for 6,500 to 7,500 gene protein products from each region and over 12,000 gene protein products for the entire brain, documenting the physiological repertoire of mouse brain proteins in an anatomically resolved and comprehensive manner. We explored the utility of our spatially defined protein profiling methods in a mouse model of Parkinson's disease. We compared the proteome from a vulnerable region (substantia nigra pars compacta) of wild type and parkinsonian mice with that of an adjacent, less vulnerable, region (ventral tegmental area) and identified several proteins that exhibited both spatiotemporal- and genotype-restricted changes. We validated the most robustly altered proteins using an alternative profiling method and found that these modifications may highlight potential new pathways for future studies. This proteomic atlas is a valuable resource that offers a practical framework for investigating the molecular intricacies of normal brain function as well as regional vulnerability in neurological diseases. All of the mouse regional proteome profiling data are published on line at http://mbpa.bprc.ac.cn/. Recently, Allen Brain Atlas reported genome-wide gene expression patterns in the brains of adult and developing mice using high throughput in situ hybridization (ISH) 1The abbreviations used are: ISH, in situ hybridization; AUC, area under the curve; FDR, false discovery rate; HD, Huntington's disease; iBAQ, intensity-based absolute quantification; iFOT, fraction of total; iPAC, integrated peak alignment corrector; PD, Parkinson's disease; PD1.4, Proteome Discoverer 1.4 interface; PRM, parallel reaction monitoring; RMA, restful model access; RP, reverse phase; RSOP, region-specific outlier proteins; RT, retention time; SNc, substantia nigra pars compacta; sRP, small scale reverse phase; TG, transgenic; VTA, ventral tegmental area; XIC, extracted ion chromatogram; GP, gene protein product; XIC, extracted ion chromatogram; α-syn, α-synuclein; ACN, acetonitrile; Gldn, gliomedin; Ndn, necdin; HCD, High-energy collisional dissociation; OLF, Olfactory bulb; MY, Medulla; STR, Striatum; PSM, Peptide-spectrum match. 1The abbreviations used are: ISH, in situ hybridization; AUC, area under the curve; FDR, false discovery rate; HD, Huntington's disease; iBAQ, intensity-based absolute quantification; iFOT, fraction of total; iPAC, integrated peak alignment corrector; PD, Parkinson's disease; PD1.4, Proteome Discoverer 1.4 interface; PRM, parallel reaction monitoring; RMA, restful model access; RP, reverse phase; RSOP, region-specific outlier proteins; RT, retention time; SNc, substantia nigra pars compacta; sRP, small scale reverse phase; TG, transgenic; VTA, ventral tegmental area; XIC, extracted ion chromatogram; GP, gene protein product; XIC, extracted ion chromatogram; α-syn, α-synuclein; ACN, acetonitrile; Gldn, gliomedin; Ndn, necdin; HCD, High-energy collisional dissociation; OLF, Olfactory bulb; MY, Medulla; STR, Striatum; PSM, Peptide-spectrum match. 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Simons M. Cell type- and brain region-resolved mouse brain proteome.Nat. Neurosci. 2015; PubMed Scopus Google reported a mouse cell type and brain regional proteome that 12,000 gene products in as as of This an profiling and the for to this profiling. of a region-specific proteome from the that most brain are to a brain Parkinson's and Huntington's are both by protein and in PD, in HD, in the S. vulnerability in from to 2011; Full Text Full Text PDF PubMed Scopus Google Scholar). The proteins for regional and vulnerability in most to proteome profiling of the brain with a that surgically to regions most by neurological valuable information and pathways for In this we to proteomic profiling is in as as of tissue with 1 of and we this to from a mouse model of used in this were in a with a with to and in an mice to All mice were by the and for of and The wild type mice were used for brain regional proteome profiling the Parkinson's mice line were a from and S.M. J. 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J. J. Liu W. W. Liu M. T. T. L. W. C. Y. J. L. A. et al.A for and of Full Text Full Text PDF PubMed Scopus Google Scholar). The of the to the of the high to distribution of the entire to coverage spectrometry and are under label-free fraction of an to be than B. D. N. J. J. Chen W. 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Kannaiyan N. Manrique-Hoyos N. Kongi K. Cantuti L. Hanisch U.K. Philips M.A. Rossner M.J. Mann M. Simons M. Cell type- and brain region-resolved mouse brain proteome.Nat. Neurosci. 2015; PubMed Scopus Google in a the and We found a high of of these and this the of we abundance with a analysis PRM, using a type of mass M.S. reaction for high and high mass 2012; 11: Full Text Full Text PDF PubMed Scopus Google Scholar). data with proteomic profiling we by at each protein over data were in from to and data were in the a of of identified by profiling with of and these data of to this for label-free proteome profiling. Brain regions in their and to these been (1.Lein E.S. Hawrylycz M.J. Ao N. Ayres M. Bensinger A. Bernard A. Boe A.F. Boguski M.S. Brockway K.S. Byrnes E.J. Chen L. Chen L. Chen T.M. Chin M.C. Chong J. et al.Genome-wide atlas of gene expression in the adult mouse brain.Nature. 2007; 445: 168-176Crossref PubMed Scopus (3669) Google Scholar, M.J. E.S. Ng L. van de A. C. Bernard A. D. Boe A.F. et anatomically comprehensive atlas of the adult brain 2012; PubMed Scopus Google Scholar, A.I. T. S. D. J. R. M. gene atlas of the mouse and PubMed Scopus Google Scholar). these to protein abundance in correlation mRNA and protein we compared our profiling to the Allen Brain Atlas (1.Lein E.S. Hawrylycz M.J. Ao N. Ayres M. Bensinger A. Bernard A. Boe A.F. Boguski M.S. Brockway K.S. Byrnes E.J. Chen L. Chen L. Chen T.M. Chin M.C. Chong J. et al.Genome-wide atlas of gene expression in the adult mouse brain.Nature. 2007; 445: 168-176Crossref PubMed Scopus (3669) Google Scholar). we in methods and these studies, we were to for regions and This not to be expression to as for expression a brain are This analysis a method to to of and protein We of gene products found both in our profiling and Allen Brain Atlas We based the on the of and distributions and on their that not be We found that of correlation and proteins the of correlation a expression and protein abundance for region-specific proteins. 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J. in mice wild type 2012; PubMed Scopus Google Scholar, de M. C.A. A. J. Sharma A. L. N. L. J. the and of both and 5: PubMed Scopus Google Scholar). we to we our data and to identify that may be for We for that may be to the in the region of the mice over We found that and their levels increased in the over in the of and We to may in the and are In this we found that as and are in the mice are in of and and these that are spatiotemporal that in mice and that the events may be as novel pathways for the events to In this we a spatially defined proteomic of the mouse brain and used this to and disease. We the for proteome profiling in than of mass to 6,500 to 7,500 gene protein products from brain the of this we of a that at cell type- and brain region-resolved mouse brain proteome (9.Sharma K. Schmitt S. Bergner C.G. Tyanova S. Kannaiyan N. Manrique-Hoyos N. Kongi K. Cantuti L. Hanisch U.K. Philips M.A. Rossner M.J. Mann M. Simons M. Cell type- and brain region-resolved mouse brain proteome.Nat. Neurosci. 2015; PubMed Scopus Google Scholar). In that (9.Sharma K. Schmitt S. Bergner C.G. Tyanova S. Kannaiyan N. Manrique-Hoyos N. Kongi K. Cantuti L. Hanisch U.K. Philips M.A. Rossner M.J. Mann M. Simons M. Cell type- and brain region-resolved mouse brain proteome.Nat. Neurosci. 2015; PubMed Scopus Google Scholar), the mouse brain surgically distinct and used these as a for protein profiling. of 12,000 proteins each brain on their we of 17 distinct brain regions and the our studies. The throughput of proteome for scale In to high throughput our label-free a high that as as of tissue The high of this for proteome profiling of small from and complex is we found that the of the proteins we identified of This well with most of the published proteome profiling of of proteome with N. J. Mann M. of murine 2014; Full Text Full Text PDF PubMed Scopus Google Scholar, M. A. J. M. A. A. J. R. The proteome of a cell 2011; PubMed Scopus Google Scholar). This our method to proteins of a of for the our method to proteins from to and Because our protein compared with using (9.Sharma K. Schmitt S. Bergner C.G. Tyanova S. Kannaiyan N. Manrique-Hoyos N. Kongi K. Cantuti L. Hanisch U.K. Philips M.A. Rossner M.J. Mann M. Simons M. Cell type- and brain region-resolved mouse brain proteome.Nat. Neurosci. 2015; PubMed Scopus Google Scholar), is to of proteins. We found of of from the Cell Atlas D. A. T. A. C. R. A. A. et al.A mass cell protein One. 2015; PubMed Scopus Google Scholar). of the reported proteins be identified using this This that our to proteins. this in the of a spatially of the entire mouse brain 1 be in the future Lee L. J. in mice wild type 2012; PubMed Scopus Google Scholar, de M. C.A. A. J. Sharma A. L. N. L. J. the and of both and 5: PubMed Scopus Google Scholar). The of proteomic in the the of the of the brain regions sampled in this provides an and to identify proteins that are region-specific and to and function The utility of the mouse brain proteome be in of and to as the by the Allen Brain to our both and the identified in our the that were not found in the brain region by that are by cell that of the of that and that are with in the brain these new as well as of the of a gene in the of and disease. we our to the biological are brain regions to in our in and we to the proteome spatially and are and have regions that are in Parkinson's the and the the of this we were to a to this by at of disease. this we were to several of proteins abundance altered in the over the the we for by at markers of as and The identified as a resource to the and a for in the of vulnerability in at spatiotemporal in gene products the and the VTA, we found that proteins as and were altered at an are with the that is with and the proteins to a in may be D. D. function and on 2014; PubMed Google Scholar). these proteins in the and be a in studies that a of these altered proteins the of we at we found that proteomic were gene over to a of we found that the of and proteins at the of the This is with the by the and the in the of a that of the proteins in our in and the of of C. J. to the proteins of and PubMed Scopus Google Scholar, R. D. K. A. M. of in a model for the and of in brain.Neuron. Full Text PDF PubMed Scopus Google Scholar). we to identify that may be to in a spatiotemporal and manner. We found that and as as exhibited an in the over and as as exhibited an in the over the function of these proteins in the of are not at this of their in function in the of of in the of our mouse brain proteome the for proteins of gene products to new pathways for of that are in brain regions in the vulnerability of in of neurological disease. We for and of the with

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