A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing.
Identifieur interne : 000188 ( Main/Exploration ); précédent : 000187; suivant : 000189A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing.
Auteurs : Rémi Longuespée [Allemagne] ; Deborah Alberts [Belgique] ; Charles Pottier [Belgique] ; Nicolas Smargiasso [Belgique] ; Gabriel Mazzucchelli [Belgique] ; Dominique Baiwir [Belgique] ; Mark Kriegsmann [Allemagne] ; Michael Herfs [Belgique] ; Jörg Kriegsmann [Allemagne] ; Philippe Delvenne [Belgique] ; Edwin De Pauw [Belgique]Source :
- Methods (San Diego, Calif.) [ 1095-9130 ] ; 2016.
Abstract
Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest.
DOI: 10.1016/j.ymeth.2015.12.008
PubMed: 26690073
Affiliations:
- Allemagne, Belgique
- Bade-Wurtemberg, District de Karlsruhe, Province de Liège, Région wallonne
- Heidelberg, Liège
- Université de Liège
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Proteopath GmbH, Trier, Germany. Electronic address: r.longuespee@molekularpatho-trier.de.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium; Proteopath GmbH, Trier</wicri:regionArea><wicri:noRegion>Trier</wicri:noRegion><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author><author><name sortKey="Alberts, Deborah" sort="Alberts, Deborah" uniqKey="Alberts D" first="Deborah" last="Alberts">Deborah Alberts</name><affiliation wicri:level="4"><nlm:affiliation>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège</wicri:regionArea><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author><author><name sortKey="Pottier, Charles" sort="Pottier, Charles" uniqKey="Pottier C" first="Charles" last="Pottier">Charles Pottier</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège</wicri:regionArea><wicri:noRegion>Liège</wicri:noRegion></affiliation></author><author><name sortKey="Smargiasso, Nicolas" sort="Smargiasso, Nicolas" uniqKey="Smargiasso N" first="Nicolas" last="Smargiasso">Nicolas Smargiasso</name><affiliation wicri:level="4"><nlm:affiliation>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège</wicri:regionArea><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author><author><name sortKey="Mazzucchelli, Gabriel" sort="Mazzucchelli, Gabriel" uniqKey="Mazzucchelli G" first="Gabriel" last="Mazzucchelli">Gabriel Mazzucchelli</name><affiliation wicri:level="4"><nlm:affiliation>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège</wicri:regionArea><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author><author><name sortKey="Baiwir, Dominique" sort="Baiwir, Dominique" uniqKey="Baiwir D" first="Dominique" last="Baiwir">Dominique Baiwir</name><affiliation wicri:level="4"><nlm:affiliation>GIGA Proteomic Facility, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>GIGA Proteomic Facility, University of Liège, Liège</wicri:regionArea><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author><author><name sortKey="Kriegsmann, Mark" sort="Kriegsmann, Mark" uniqKey="Kriegsmann M" first="Mark" last="Kriegsmann">Mark Kriegsmann</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Pathology, University of Heidelberg, Heidelberg, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Pathology, University of Heidelberg, Heidelberg</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Karlsruhe</region><settlement type="city">Heidelberg</settlement></placeName></affiliation></author><author><name sortKey="Herfs, Michael" sort="Herfs, Michael" uniqKey="Herfs M" first="Michael" last="Herfs">Michael Herfs</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège</wicri:regionArea><wicri:noRegion>Liège</wicri:noRegion></affiliation></author><author><name sortKey="Kriegsmann, Jorg" sort="Kriegsmann, Jorg" uniqKey="Kriegsmann J" first="Jörg" last="Kriegsmann">Jörg Kriegsmann</name><affiliation wicri:level="1"><nlm:affiliation>Proteopath GmbH, Trier, Germany; MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Proteopath GmbH, Trier, Germany; MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier</wicri:regionArea><wicri:noRegion>Trier</wicri:noRegion><wicri:noRegion>Trier</wicri:noRegion><wicri:noRegion>Trier</wicri:noRegion></affiliation></author><author><name sortKey="Delvenne, Philippe" sort="Delvenne, Philippe" uniqKey="Delvenne P" first="Philippe" last="Delvenne">Philippe Delvenne</name><affiliation wicri:level="1"><nlm:affiliation>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Pathology, University of Liège Hospital, Liege, Belgium; GIGA Cancer, University of Liège, Liège</wicri:regionArea><wicri:noRegion>Liège</wicri:noRegion></affiliation></author><author><name sortKey="De Pauw, Edwin" sort="De Pauw, Edwin" uniqKey="De Pauw E" first="Edwin" last="De Pauw">Edwin De Pauw</name><affiliation wicri:level="4"><nlm:affiliation>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>Mass Spectrometry Laboratory, Systems Biology and Chemical Biology, GIGA-Research, University of Liège, Liège</wicri:regionArea><orgName type="university">Université de Liège</orgName><placeName><settlement type="city">Liège</settlement><region type="region" nuts="1">Région wallonne</region><region type="province" nuts="1">Province de Liège</region></placeName></affiliation></author></analytic><series><title level="j">Methods (San Diego, Calif.)</title><idno type="eISSN">1095-9130</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest.</div></front></TEI><affiliations><list><country><li>Allemagne</li><li>Belgique</li></country><region><li>Bade-Wurtemberg</li><li>District de Karlsruhe</li><li>Province de Liège</li><li>Région wallonne</li></region><settlement><li>Heidelberg</li><li>Liège</li></settlement><orgName><li>Université de Liège</li></orgName></list><tree><country name="Allemagne"><region name="Région wallonne"><name sortKey="Longuespee, Remi" sort="Longuespee, Remi" uniqKey="Longuespee R" first="Rémi" last="Longuespée">Rémi Longuespée</name></region><name sortKey="Kriegsmann, Jorg" sort="Kriegsmann, Jorg" uniqKey="Kriegsmann J" first="Jörg" last="Kriegsmann">Jörg Kriegsmann</name><name sortKey="Kriegsmann, Mark" sort="Kriegsmann, Mark" uniqKey="Kriegsmann M" first="Mark" last="Kriegsmann">Mark Kriegsmann</name></country><country name="Belgique"><region name="Région wallonne"><name sortKey="Alberts, Deborah" sort="Alberts, Deborah" uniqKey="Alberts D" first="Deborah" last="Alberts">Deborah Alberts</name></region><name sortKey="Baiwir, Dominique" sort="Baiwir, Dominique" uniqKey="Baiwir D" first="Dominique" last="Baiwir">Dominique Baiwir</name><name sortKey="De Pauw, Edwin" sort="De Pauw, Edwin" uniqKey="De Pauw E" first="Edwin" last="De Pauw">Edwin De Pauw</name><name sortKey="Delvenne, Philippe" sort="Delvenne, Philippe" uniqKey="Delvenne P" first="Philippe" last="Delvenne">Philippe Delvenne</name><name sortKey="Herfs, Michael" sort="Herfs, Michael" uniqKey="Herfs M" first="Michael" last="Herfs">Michael Herfs</name><name sortKey="Mazzucchelli, Gabriel" sort="Mazzucchelli, Gabriel" uniqKey="Mazzucchelli G" first="Gabriel" last="Mazzucchelli">Gabriel Mazzucchelli</name><name sortKey="Pottier, Charles" sort="Pottier, Charles" uniqKey="Pottier C" first="Charles" last="Pottier">Charles Pottier</name><name sortKey="Smargiasso, Nicolas" sort="Smargiasso, Nicolas" uniqKey="Smargiasso N" first="Nicolas" last="Smargiasso">Nicolas Smargiasso</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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