MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting.
Identifieur interne : 000812 ( Ncbi/Merge ); précédent : 000811; suivant : 000813MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting.
Auteurs : J. Stauber [France] ; R. Lemaire ; J. Franck ; D. Bonnel ; D. Croix ; R. Day ; M. Wisztorski ; I. Fournier ; M. SalzetSource :
- Journal of proteome research [ 1535-3893 ] ; 2008.
English descriptors
- KwdEn :
- Animals, Biomarkers (metabolism), Chromatography, Liquid, Disease Models, Animal, Formaldehyde (chemistry), Male, Paraffin Embedding, Parkinson Disease (metabolism), Rats, Rats, Wistar, Spectrometry, Mass, Electrospray Ionization, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization (methods).
- MESH :
- chemical , chemistry : Formaldehyde.
- chemical , metabolism : Biomarkers.
- metabolism : Parkinson Disease.
- methods : Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization.
- Animals, Chromatography, Liquid, Disease Models, Animal, Male, Paraffin Embedding, Rats, Rats, Wistar, Spectrometry, Mass, Electrospray Ionization.
Abstract
A common technique for the long-term storage of tissues in hospitals and clinical laboratories is preservation in formalin-fixed paraffin-embedded (FFPE) blocks. Such tissues stored for more than five years have not been useful for proteomic studies focused on biomarker discovery. Recently, MS-based proteomic analyses of FFPE showed positive results on blocks stored for less than 2 days. However, most samples are stored for more than one year, and thus our objective was to establish a novel strategy using as a model system 6-hydroxydopamine (6-OHDA) treated rat brain tissues stored in FFPE blocks for more than 9 years. We examined MALDI tissue profiling combining the use of automatic spotting of the MALDI matrix with in situ tissue enzymatic digestion. On adjacent sections, the identification of compounds is carried out by tissue digestion followed by nanoLC/MS-MS analysis. The combination of these approaches provides MALDI direct analysis, MALDI/MS imaging, as well as the localization of a large number of proteins. This method is validated since the analyses confirmed that ubiquitin, trans-elongation factor 1, hexokinase, and the Neurofilament M are down-regulated as previously shown in human or Parkinson animal models. In contrast, peroxidoredoxin 6, F1 ATPase, and alpha-enolase are up-regulated. In addition, we uncovered three novel putative biomarkers, the trans-elongation factor 1 (eEF1) and the collapsin response mediator 1 and 2 from protein libraries. Finally, we validate the CRMP-2 protein using immunocytochemistry and MALDI imaging based on the different ions from trypsic digestion of the protein. The access to archived FFPE tissue using MALDI profiling and imaging opens a whole new area in clinical studies and biomarker discovery from hospital biopsy libraries.
DOI: 10.1021/pr070464x
PubMed: 18247558
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Stauber</name><affiliation wicri:level="3"><nlm:affiliation>Université des Sciences et Technologies de Lille, FRE-CNRS 2933, MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, IFR 147, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université des Sciences et Technologies de Lille, FRE-CNRS 2933, MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, IFR 147, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Villeneuve d'Ascq</settlement></placeName></affiliation></author><author><name sortKey="Lemaire, R" sort="Lemaire, R" uniqKey="Lemaire R" first="R" last="Lemaire">R. Lemaire</name></author><author><name sortKey="Franck, J" sort="Franck, J" uniqKey="Franck J" first="J" last="Franck">J. 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Stauber</name><affiliation wicri:level="3"><nlm:affiliation>Université des Sciences et Technologies de Lille, FRE-CNRS 2933, MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, IFR 147, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université des Sciences et Technologies de Lille, FRE-CNRS 2933, MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, IFR 147, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Villeneuve d'Ascq</settlement></placeName></affiliation></author><author><name sortKey="Lemaire, R" sort="Lemaire, R" uniqKey="Lemaire R" first="R" last="Lemaire">R. Lemaire</name></author><author><name sortKey="Franck, J" sort="Franck, J" uniqKey="Franck J" first="J" last="Franck">J. Franck</name></author><author><name sortKey="Bonnel, D" sort="Bonnel, D" uniqKey="Bonnel D" first="D" last="Bonnel">D. Bonnel</name></author><author><name sortKey="Croix, D" sort="Croix, D" uniqKey="Croix D" first="D" last="Croix">D. Croix</name></author><author><name sortKey="Day, R" sort="Day, R" uniqKey="Day R" first="R" last="Day">R. Day</name></author><author><name sortKey="Wisztorski, M" sort="Wisztorski, M" uniqKey="Wisztorski M" first="M" last="Wisztorski">M. Wisztorski</name></author><author><name sortKey="Fournier, I" sort="Fournier, I" uniqKey="Fournier I" first="I" last="Fournier">I. Fournier</name></author><author><name sortKey="Salzet, M" sort="Salzet, M" uniqKey="Salzet M" first="M" last="Salzet">M. Salzet</name></author></analytic><series><title level="j">Journal of proteome research</title><idno type="ISSN">1535-3893</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Biomarkers (metabolism)</term><term>Chromatography, Liquid</term><term>Disease Models, Animal</term><term>Formaldehyde (chemistry)</term><term>Male</term><term>Paraffin Embedding</term><term>Parkinson Disease (metabolism)</term><term>Rats</term><term>Rats, Wistar</term><term>Spectrometry, Mass, Electrospray Ionization</term><term>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Formaldehyde</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Biomarkers</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Parkinson Disease</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Chromatography, Liquid</term><term>Disease Models, Animal</term><term>Male</term><term>Paraffin Embedding</term><term>Rats</term><term>Rats, Wistar</term><term>Spectrometry, Mass, Electrospray Ionization</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A common technique for the long-term storage of tissues in hospitals and clinical laboratories is preservation in formalin-fixed paraffin-embedded (FFPE) blocks. Such tissues stored for more than five years have not been useful for proteomic studies focused on biomarker discovery. Recently, MS-based proteomic analyses of FFPE showed positive results on blocks stored for less than 2 days. However, most samples are stored for more than one year, and thus our objective was to establish a novel strategy using as a model system 6-hydroxydopamine (6-OHDA) treated rat brain tissues stored in FFPE blocks for more than 9 years. We examined MALDI tissue profiling combining the use of automatic spotting of the MALDI matrix with in situ tissue enzymatic digestion. On adjacent sections, the identification of compounds is carried out by tissue digestion followed by nanoLC/MS-MS analysis. The combination of these approaches provides MALDI direct analysis, MALDI/MS imaging, as well as the localization of a large number of proteins. This method is validated since the analyses confirmed that ubiquitin, trans-elongation factor 1, hexokinase, and the Neurofilament M are down-regulated as previously shown in human or Parkinson animal models. In contrast, peroxidoredoxin 6, F1 ATPase, and alpha-enolase are up-regulated. In addition, we uncovered three novel putative biomarkers, the trans-elongation factor 1 (eEF1) and the collapsin response mediator 1 and 2 from protein libraries. Finally, we validate the CRMP-2 protein using immunocytochemistry and MALDI imaging based on the different ions from trypsic digestion of the protein. The access to archived FFPE tissue using MALDI profiling and imaging opens a whole new area in clinical studies and biomarker discovery from hospital biopsy libraries.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18247558</PMID><DateCreated><Year>2008</Year><Month>03</Month><Day>10</Day></DateCreated><DateCompleted><Year>2008</Year><Month>06</Month><Day>03</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1535-3893</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><Issue>3</Issue><PubDate><Year>2008</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Journal of proteome research</Title><ISOAbbreviation>J. Proteome Res.</ISOAbbreviation></Journal><ArticleTitle>MALDI imaging of formalin-fixed paraffin-embedded tissues: application to model animals of Parkinson disease for biomarker hunting.</ArticleTitle><Pagination><MedlinePgn>969-78</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/pr070464x</ELocationID><Abstract><AbstractText>A common technique for the long-term storage of tissues in hospitals and clinical laboratories is preservation in formalin-fixed paraffin-embedded (FFPE) blocks. Such tissues stored for more than five years have not been useful for proteomic studies focused on biomarker discovery. Recently, MS-based proteomic analyses of FFPE showed positive results on blocks stored for less than 2 days. However, most samples are stored for more than one year, and thus our objective was to establish a novel strategy using as a model system 6-hydroxydopamine (6-OHDA) treated rat brain tissues stored in FFPE blocks for more than 9 years. We examined MALDI tissue profiling combining the use of automatic spotting of the MALDI matrix with in situ tissue enzymatic digestion. On adjacent sections, the identification of compounds is carried out by tissue digestion followed by nanoLC/MS-MS analysis. The combination of these approaches provides MALDI direct analysis, MALDI/MS imaging, as well as the localization of a large number of proteins. This method is validated since the analyses confirmed that ubiquitin, trans-elongation factor 1, hexokinase, and the Neurofilament M are down-regulated as previously shown in human or Parkinson animal models. In contrast, peroxidoredoxin 6, F1 ATPase, and alpha-enolase are up-regulated. In addition, we uncovered three novel putative biomarkers, the trans-elongation factor 1 (eEF1) and the collapsin response mediator 1 and 2 from protein libraries. Finally, we validate the CRMP-2 protein using immunocytochemistry and MALDI imaging based on the different ions from trypsic digestion of the protein. The access to archived FFPE tissue using MALDI profiling and imaging opens a whole new area in clinical studies and biomarker discovery from hospital biopsy libraries.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stauber</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Université des Sciences et Technologies de Lille, FRE-CNRS 2933, MALDI Imaging Team, Laboratoire de Neuroimmunologie des Annélides, IFR 147, Cité Scientifique, 59655 Villeneuve d'Ascq Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lemaire</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Franck</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Bonnel</LastName><ForeName>D</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Croix</LastName><ForeName>D</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Day</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Wisztorski</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Fournier</LastName><ForeName>I</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Salzet</LastName><ForeName>M</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>02</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Proteome Res</MedlineTA><NlmUniqueID>101128775</NlmUniqueID><ISSNLinking>1535-3893</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015415">Biomarkers</NameOfSubstance></Chemical><Chemical><RegistryNumber>1HG84L3525</RegistryNumber><NameOfSubstance UI="D005557">Formaldehyde</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015415" MajorTopicYN="N">Biomarkers</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002853" MajorTopicYN="N">Chromatography, Liquid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004195" MajorTopicYN="Y">Disease Models, Animal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005557" MajorTopicYN="N">Formaldehyde</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016612" MajorTopicYN="Y">Paraffin Embedding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010300" MajorTopicYN="N">Parkinson Disease</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D051381" MajorTopicYN="N">Rats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017208" MajorTopicYN="N">Rats, Wistar</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021241" MajorTopicYN="N">Spectrometry, Mass, Electrospray Ionization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019032" MajorTopicYN="N">Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>2</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>6</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>2</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18247558</ArticleId><ArticleId IdType="doi">10.1021/pr070464x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Hauts-de-France</li><li>Nord-Pas-de-Calais</li></region><settlement><li>Villeneuve d'Ascq</li></settlement></list><tree><noCountry><name sortKey="Bonnel, D" sort="Bonnel, D" uniqKey="Bonnel D" first="D" last="Bonnel">D. Bonnel</name><name sortKey="Croix, D" sort="Croix, D" uniqKey="Croix D" first="D" last="Croix">D. Croix</name><name sortKey="Day, R" sort="Day, R" uniqKey="Day R" first="R" last="Day">R. Day</name><name sortKey="Fournier, I" sort="Fournier, I" uniqKey="Fournier I" first="I" last="Fournier">I. Fournier</name><name sortKey="Franck, J" sort="Franck, J" uniqKey="Franck J" first="J" last="Franck">J. Franck</name><name sortKey="Lemaire, R" sort="Lemaire, R" uniqKey="Lemaire R" first="R" last="Lemaire">R. Lemaire</name><name sortKey="Salzet, M" sort="Salzet, M" uniqKey="Salzet M" first="M" last="Salzet">M. Salzet</name><name sortKey="Wisztorski, M" sort="Wisztorski, M" uniqKey="Wisztorski M" first="M" last="Wisztorski">M. Wisztorski</name></noCountry><country name="France"><region name="Hauts-de-France"><name sortKey="Stauber, J" sort="Stauber, J" uniqKey="Stauber J" first="J" last="Stauber">J. 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