Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker
Parkinson’s disease (PD) is a prevalent neurodegenerative disease for which robust biomarkers are needed. Because protein structure reflects function, we tested whether global, in situ analysis of protein structural changes provides insight into PD pathophysiology and could inform a new concept of s...
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Veröffentlicht in: | Nature structural & molecular biology 2022-10, Vol.29 (10), p.978-989 |
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creator | Mackmull, Marie-Therese Nagel, Luise Sesterhenn, Fabian Muntel, Jan Grossbach, Jan Stalder, Patrick Bruderer, Roland Reiter, Lukas van de Berg, Wilma D. J. de Souza, Natalie Beyer, Andreas Picotti, Paola |
description | Parkinson’s disease (PD) is a prevalent neurodegenerative disease for which robust biomarkers are needed. Because protein structure reflects function, we tested whether global, in situ analysis of protein structural changes provides insight into PD pathophysiology and could inform a new concept of structural disease biomarkers. Using limited proteolysis–mass spectrometry (LiP–MS), we identified 76 structurally altered proteins in cerebrospinal fluid (CSF) of individuals with PD relative to healthy donors. These proteins were enriched in processes misregulated in PD, and some proteins also showed structural changes in PD brain samples. CSF protein structural information outperformed abundance information in discriminating between healthy participants and those with PD and improved the discriminatory performance of CSF measures of the hallmark PD protein α-synuclein. We also present the first analysis of inter-individual variability of a structural proteome in healthy individuals, identifying biophysical features of variable protein regions. Although independent validation is needed, our data suggest that global analyses of the human structural proteome will guide the development of novel structural biomarkers of disease and enable hypothesis generation about underlying disease processes.
This study identifies protein structural changes in cerebrospinal fluid of people with Parkinson’s disease relative to healthy individuals and proposes the concept of structural disease biomarkers. It also analyzes proteome structural variability in healthy people. |
doi_str_mv | 10.1038/s41594-022-00837-0 |
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This study identifies protein structural changes in cerebrospinal fluid of people with Parkinson’s disease relative to healthy individuals and proposes the concept of structural disease biomarkers. It also analyzes proteome structural variability in healthy people.</description><identifier>ISSN: 1545-9993</identifier><identifier>EISSN: 1545-9985</identifier><identifier>DOI: 10.1038/s41594-022-00837-0</identifier><identifier>PMID: 36224378</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>101/58 ; 631/337/475 ; 631/80/470/2284 ; 692/699 ; 82/58 ; alpha-Synuclein - metabolism ; Biochemistry ; Biological Microscopy ; Biomarkers ; Biomedical and Life Sciences ; Cerebrospinal fluid ; Humans ; Life Sciences ; Mass spectrometry ; Mass spectroscopy ; Membrane Biology ; Movement disorders ; Neurodegenerative Diseases ; Parkinson Disease ; Parkinson's disease ; Protein Structure ; Proteins ; Proteolysis ; Proteome - metabolism ; Proteomes ; Structure-function relationships ; Synuclein ; Variability</subject><ispartof>Nature structural & molecular biology, 2022-10, Vol.29 (10), p.978-989</ispartof><rights>The Author(s), under exclusive licence to Springer Nature America, Inc. 2022. Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2022. The Author(s), under exclusive licence to Springer Nature America, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-8fb258a9a0610df8de348e04d1cdf629c34fbd61620929547d4e6bbddc617b43</citedby><cites>FETCH-LOGICAL-c375t-8fb258a9a0610df8de348e04d1cdf629c34fbd61620929547d4e6bbddc617b43</cites><orcidid>0000-0002-9394-5665 ; 0000-0003-2928-1144 ; 0000-0002-4109-3552 ; 0000-0002-3891-2123 ; 0000-0003-2320-5829</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41594-022-00837-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41594-022-00837-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36224378$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mackmull, Marie-Therese</creatorcontrib><creatorcontrib>Nagel, Luise</creatorcontrib><creatorcontrib>Sesterhenn, Fabian</creatorcontrib><creatorcontrib>Muntel, Jan</creatorcontrib><creatorcontrib>Grossbach, Jan</creatorcontrib><creatorcontrib>Stalder, Patrick</creatorcontrib><creatorcontrib>Bruderer, Roland</creatorcontrib><creatorcontrib>Reiter, Lukas</creatorcontrib><creatorcontrib>van de Berg, Wilma D. J.</creatorcontrib><creatorcontrib>de Souza, Natalie</creatorcontrib><creatorcontrib>Beyer, Andreas</creatorcontrib><creatorcontrib>Picotti, Paola</creatorcontrib><title>Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker</title><title>Nature structural & molecular biology</title><addtitle>Nat Struct Mol Biol</addtitle><addtitle>Nat Struct Mol Biol</addtitle><description>Parkinson’s disease (PD) is a prevalent neurodegenerative disease for which robust biomarkers are needed. Because protein structure reflects function, we tested whether global, in situ analysis of protein structural changes provides insight into PD pathophysiology and could inform a new concept of structural disease biomarkers. Using limited proteolysis–mass spectrometry (LiP–MS), we identified 76 structurally altered proteins in cerebrospinal fluid (CSF) of individuals with PD relative to healthy donors. These proteins were enriched in processes misregulated in PD, and some proteins also showed structural changes in PD brain samples. CSF protein structural information outperformed abundance information in discriminating between healthy participants and those with PD and improved the discriminatory performance of CSF measures of the hallmark PD protein α-synuclein. We also present the first analysis of inter-individual variability of a structural proteome in healthy individuals, identifying biophysical features of variable protein regions. Although independent validation is needed, our data suggest that global analyses of the human structural proteome will guide the development of novel structural biomarkers of disease and enable hypothesis generation about underlying disease processes.
This study identifies protein structural changes in cerebrospinal fluid of people with Parkinson’s disease relative to healthy individuals and proposes the concept of structural disease biomarkers. It also analyzes proteome structural variability in healthy people.</description><subject>101/58</subject><subject>631/337/475</subject><subject>631/80/470/2284</subject><subject>692/699</subject><subject>82/58</subject><subject>alpha-Synuclein - metabolism</subject><subject>Biochemistry</subject><subject>Biological Microscopy</subject><subject>Biomarkers</subject><subject>Biomedical and Life Sciences</subject><subject>Cerebrospinal fluid</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Membrane Biology</subject><subject>Movement disorders</subject><subject>Neurodegenerative Diseases</subject><subject>Parkinson Disease</subject><subject>Parkinson's disease</subject><subject>Protein Structure</subject><subject>Proteins</subject><subject>Proteolysis</subject><subject>Proteome - metabolism</subject><subject>Proteomes</subject><subject>Structure-function relationships</subject><subject>Synuclein</subject><subject>Variability</subject><issn>1545-9993</issn><issn>1545-9985</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9kc1qFjEUhoMotlZvwIUE3LhwNP-TWUrRKhR00X3ITM7Y1PmSmpOxfDvxLrw9r8S0Uyu4cJVAnvcN5zyEPOXsFWfSvkbF9aA6JkTHmJV9x-6RQ66V7obB6vt390EekEeIF4wJrXv5kBxII4SSvT0kP06WPPrlJY2JYqwr9ckve4xI80zrOVCsZZ3qWvxCL0uukHdwzcYU4rcYVr8gvYr1nH7y5UtMmNOv7z-RhojgEWjNNAZINc576mmCKzotHm_Kx5h3LQPlMXkwtxp4cnsekbN3b8-O33enH08-HL857SbZ69rZeRTa-sEzw1mYbQCpLDAV-BRmI4ZJqnkMhhvBBjFo1QcFZhxDmAzvRyWPyIutto3xdQWsbhdxgmXxCfKKTvRCaauE4g19_g96kdfSFrNR_WCM0I0SGzWVjFhgdpcltpH2jjN3LchtglwT5G4EOdZCz26r13EH4S7yx0gD5AZge0qfofz9-z-1vwGf8J4O</recordid><startdate>20221001</startdate><enddate>20221001</enddate><creator>Mackmull, Marie-Therese</creator><creator>Nagel, Luise</creator><creator>Sesterhenn, Fabian</creator><creator>Muntel, Jan</creator><creator>Grossbach, Jan</creator><creator>Stalder, Patrick</creator><creator>Bruderer, Roland</creator><creator>Reiter, Lukas</creator><creator>van de Berg, Wilma D. 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J.</au><au>de Souza, Natalie</au><au>Beyer, Andreas</au><au>Picotti, Paola</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker</atitle><jtitle>Nature structural & molecular biology</jtitle><stitle>Nat Struct Mol Biol</stitle><addtitle>Nat Struct Mol Biol</addtitle><date>2022-10-01</date><risdate>2022</risdate><volume>29</volume><issue>10</issue><spage>978</spage><epage>989</epage><pages>978-989</pages><issn>1545-9993</issn><eissn>1545-9985</eissn><abstract>Parkinson’s disease (PD) is a prevalent neurodegenerative disease for which robust biomarkers are needed. Because protein structure reflects function, we tested whether global, in situ analysis of protein structural changes provides insight into PD pathophysiology and could inform a new concept of structural disease biomarkers. Using limited proteolysis–mass spectrometry (LiP–MS), we identified 76 structurally altered proteins in cerebrospinal fluid (CSF) of individuals with PD relative to healthy donors. These proteins were enriched in processes misregulated in PD, and some proteins also showed structural changes in PD brain samples. CSF protein structural information outperformed abundance information in discriminating between healthy participants and those with PD and improved the discriminatory performance of CSF measures of the hallmark PD protein α-synuclein. We also present the first analysis of inter-individual variability of a structural proteome in healthy individuals, identifying biophysical features of variable protein regions. Although independent validation is needed, our data suggest that global analyses of the human structural proteome will guide the development of novel structural biomarkers of disease and enable hypothesis generation about underlying disease processes.
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subjects | 101/58 631/337/475 631/80/470/2284 692/699 82/58 alpha-Synuclein - metabolism Biochemistry Biological Microscopy Biomarkers Biomedical and Life Sciences Cerebrospinal fluid Humans Life Sciences Mass spectrometry Mass spectroscopy Membrane Biology Movement disorders Neurodegenerative Diseases Parkinson Disease Parkinson's disease Protein Structure Proteins Proteolysis Proteome - metabolism Proteomes Structure-function relationships Synuclein Variability |
title | Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker |
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