Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors.
Identifieur interne : 002244 ( PubMed/Checkpoint ); précédent : 002243; suivant : 002245Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors.
Auteurs : Christopher M. Overall [Canada] ; Eric M. Tam ; Reinhild Kappelhoff ; Andrea Connor ; Tom Ewart ; Charlotte J. Morrison ; Xose Puente ; Carlos L Pez-Otín ; Arun SethSource :
- Biological chemistry [ 1431-6730 ] ; 2004.
Descripteurs français
- KwdFr :
- Catalyse, Coloration et marquage, Femelle, Glandes mammaires humaines (enzymologie), Humains, Inhibiteurs de protéases (métabolisme), Lignée cellulaire, Lignée cellulaire tumorale, Matrix metalloproteinases (métabolisme), Peptide hydrolases (analyse), Peptide hydrolases (génétique), Peptide hydrolases (métabolisme), Protéomique (), Protéomique (instrumentation), Secreted matrix metalloproteinases, Spectrométrie de masse (), Spécificité du substrat (physiologie), Structure tertiaire des protéines (physiologie), Séquençage par oligonucléotides en batterie (), Séquençage par oligonucléotides en batterie (instrumentation), Techniques de double hybride, Tumeurs du sein (enzymologie).
- MESH :
- analyse : Peptide hydrolases.
- enzymologie : Glandes mammaires humaines, Tumeurs du sein.
- génétique : Peptide hydrolases.
- métabolisme : Inhibiteurs de protéases, Matrix metalloproteinases, Peptide hydrolases, Protéomique, Séquençage par oligonucléotides en batterie.
- physiologie : Spécificité du substrat, Structure tertiaire des protéines.
- Catalyse, Coloration et marquage, Femelle, Humains, Lignée cellulaire, Lignée cellulaire tumorale, Protéomique, Secreted matrix metalloproteinases, Spectrométrie de masse, Séquençage par oligonucléotides en batterie, Techniques de double hybride.
English descriptors
- KwdEn :
- Breast Neoplasms (enzymology), Catalysis, Cell Line, Cell Line, Tumor, Female, Humans, Mammary Glands, Human (enzymology), Mass Spectrometry (methods), Matrix Metalloproteinases (metabolism), Matrix Metalloproteinases, Secreted, Oligonucleotide Array Sequence Analysis (instrumentation), Oligonucleotide Array Sequence Analysis (methods), Peptide Hydrolases (analysis), Peptide Hydrolases (genetics), Peptide Hydrolases (metabolism), Protease Inhibitors (metabolism), Protein Structure, Tertiary (physiology), Proteomics (instrumentation), Proteomics (methods), Staining and Labeling, Substrate Specificity (physiology), Two-Hybrid System Techniques.
- MESH :
- chemical , analysis : Peptide Hydrolases.
- chemical , genetics : Peptide Hydrolases.
- chemical , metabolism : Matrix Metalloproteinases, Peptide Hydrolases, Protease Inhibitors.
- enzymology : Breast Neoplasms, Mammary Glands, Human.
- instrumentation : Oligonucleotide Array Sequence Analysis, Proteomics.
- methods : Mass Spectrometry, Oligonucleotide Array Sequence Analysis, Proteomics.
- physiology : Protein Structure, Tertiary, Substrate Specificity.
- Catalysis, Cell Line, Cell Line, Tumor, Female, Humans, Matrix Metalloproteinases, Secreted, Staining and Labeling, Two-Hybrid System Techniques.
Abstract
The biological role of most proteases in vivo is largely unknown. Therefore, to develop robust techniques to analyze the protease degradome in cells and tissues and to elucidate their substrate degradomes we have developed a dedicated and complete human protease and inhibitor microarray that we have called the CLIP-CHIP Oligonucleotides (70-mers) for identifying all 715 human proteases, inactive homologs and inhibitors were spotted in triplicate onto glass slides with a dedicated subarray containing oligonucleotides for specific human breast carcinoma genes. Initial analyses revealed the elevated expression of a number of proteases in invasive ductal cell carcinoma including ADAMTS17, carboxypeptidases A5 and M, tryptase-gamma and matriptase-2. Matrix metalloproteinases (MMPs) showed a restricted expression pattern in both normal and cancerous breast tissues with most expressed at low levels. However, of the several MMPs expressed in significant quantities, the carcinoma samples showed only slightly elevated amounts other than for MMP-28 which was strongly elevated. To discover new protease substrates we developed a novel yeast two-hybrid approach we term 'inactive catalytic domain capture' (ICDC). Here, an inactive mutant protease catalytic domain lacking the propeptide was used as a yeast two hybrid bait to screen a human fibroblast cDNA library for interactor proteins as a substrate trap. Wnt-induced signaling protein-2 (WISP-2) was identified by ICDC and was biochemically confirmed as a new MMP substrate. In another approach we used isotope-coded affinity tag (ICAT) labeling with tandem mass spectrometry to quantitate the levels of secreted or shed extracellular proteins in MDA-MB-231 breast carcinoma cell cultures in the presence or absence of membrane type 1-MMP (MT1-MMP) overexpression. By this proteomic approach we identified and biochemically confirmed that IL-8, the serine protease inhibitor SLPI, the death receptor-6, pro-TNF-alpha and CTGF are novel substrates of MT1-MMP. The utility and quantitative nature of ICAT with MS/MS analysis as a new screen for protease substrate discovery based on detection of cleaved or shed substrate products should be readily adaptable to other classes of protease for assessing proteolytic function in a cellular context.
DOI: 10.1515/BC.2004.058
PubMed: 15255181
Affiliations:
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pubmed:15255181Le document en format XML
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<term>Female</term>
<term>Humans</term>
<term>Mammary Glands, Human (enzymology)</term>
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<term>Matrix Metalloproteinases (metabolism)</term>
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<term>Femelle</term>
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<term>Humains</term>
<term>Inhibiteurs de protéases (métabolisme)</term>
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<term>Lignée cellulaire tumorale</term>
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<term>Peptide hydrolases (génétique)</term>
<term>Peptide hydrolases (métabolisme)</term>
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<term>Spectrométrie de masse ()</term>
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<term>Structure tertiaire des protéines (physiologie)</term>
<term>Séquençage par oligonucléotides en batterie ()</term>
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<term>Peptide hydrolases</term>
<term>Protéomique</term>
<term>Séquençage par oligonucléotides en batterie</term>
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<term>Structure tertiaire des protéines</term>
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<term>Cell Line, Tumor</term>
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<term>Staining and Labeling</term>
<term>Two-Hybrid System Techniques</term>
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<term>Coloration et marquage</term>
<term>Femelle</term>
<term>Humains</term>
<term>Lignée cellulaire</term>
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<front><div type="abstract" xml:lang="en">The biological role of most proteases in vivo is largely unknown. Therefore, to develop robust techniques to analyze the protease degradome in cells and tissues and to elucidate their substrate degradomes we have developed a dedicated and complete human protease and inhibitor microarray that we have called the CLIP-CHIP Oligonucleotides (70-mers) for identifying all 715 human proteases, inactive homologs and inhibitors were spotted in triplicate onto glass slides with a dedicated subarray containing oligonucleotides for specific human breast carcinoma genes. Initial analyses revealed the elevated expression of a number of proteases in invasive ductal cell carcinoma including ADAMTS17, carboxypeptidases A5 and M, tryptase-gamma and matriptase-2. Matrix metalloproteinases (MMPs) showed a restricted expression pattern in both normal and cancerous breast tissues with most expressed at low levels. However, of the several MMPs expressed in significant quantities, the carcinoma samples showed only slightly elevated amounts other than for MMP-28 which was strongly elevated. To discover new protease substrates we developed a novel yeast two-hybrid approach we term 'inactive catalytic domain capture' (ICDC). Here, an inactive mutant protease catalytic domain lacking the propeptide was used as a yeast two hybrid bait to screen a human fibroblast cDNA library for interactor proteins as a substrate trap. Wnt-induced signaling protein-2 (WISP-2) was identified by ICDC and was biochemically confirmed as a new MMP substrate. In another approach we used isotope-coded affinity tag (ICAT) labeling with tandem mass spectrometry to quantitate the levels of secreted or shed extracellular proteins in MDA-MB-231 breast carcinoma cell cultures in the presence or absence of membrane type 1-MMP (MT1-MMP) overexpression. By this proteomic approach we identified and biochemically confirmed that IL-8, the serine protease inhibitor SLPI, the death receptor-6, pro-TNF-alpha and CTGF are novel substrates of MT1-MMP. The utility and quantitative nature of ICAT with MS/MS analysis as a new screen for protease substrate discovery based on detection of cleaved or shed substrate products should be readily adaptable to other classes of protease for assessing proteolytic function in a cellular context.</div>
</front>
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<ArticleTitle>Protease degradomics: mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors.</ArticleTitle>
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<Abstract><AbstractText>The biological role of most proteases in vivo is largely unknown. Therefore, to develop robust techniques to analyze the protease degradome in cells and tissues and to elucidate their substrate degradomes we have developed a dedicated and complete human protease and inhibitor microarray that we have called the CLIP-CHIP Oligonucleotides (70-mers) for identifying all 715 human proteases, inactive homologs and inhibitors were spotted in triplicate onto glass slides with a dedicated subarray containing oligonucleotides for specific human breast carcinoma genes. Initial analyses revealed the elevated expression of a number of proteases in invasive ductal cell carcinoma including ADAMTS17, carboxypeptidases A5 and M, tryptase-gamma and matriptase-2. Matrix metalloproteinases (MMPs) showed a restricted expression pattern in both normal and cancerous breast tissues with most expressed at low levels. However, of the several MMPs expressed in significant quantities, the carcinoma samples showed only slightly elevated amounts other than for MMP-28 which was strongly elevated. To discover new protease substrates we developed a novel yeast two-hybrid approach we term 'inactive catalytic domain capture' (ICDC). Here, an inactive mutant protease catalytic domain lacking the propeptide was used as a yeast two hybrid bait to screen a human fibroblast cDNA library for interactor proteins as a substrate trap. Wnt-induced signaling protein-2 (WISP-2) was identified by ICDC and was biochemically confirmed as a new MMP substrate. In another approach we used isotope-coded affinity tag (ICAT) labeling with tandem mass spectrometry to quantitate the levels of secreted or shed extracellular proteins in MDA-MB-231 breast carcinoma cell cultures in the presence or absence of membrane type 1-MMP (MT1-MMP) overexpression. By this proteomic approach we identified and biochemically confirmed that IL-8, the serine protease inhibitor SLPI, the death receptor-6, pro-TNF-alpha and CTGF are novel substrates of MT1-MMP. The utility and quantitative nature of ICAT with MS/MS analysis as a new screen for protease substrate discovery based on detection of cleaved or shed substrate products should be readily adaptable to other classes of protease for assessing proteolytic function in a cellular context.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Overall</LastName>
<ForeName>Christopher M</ForeName>
<Initials>CM</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada. chris.overall@ubc.ca</Affiliation>
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<Author ValidYN="Y"><LastName>Tam</LastName>
<ForeName>Eric M</ForeName>
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<Author ValidYN="Y"><LastName>Kappelhoff</LastName>
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<ArticleIdList><ArticleId IdType="pubmed">15255181</ArticleId>
<ArticleId IdType="doi">10.1515/BC.2004.058</ArticleId>
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<affiliations><list><country><li>Canada</li>
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<tree><noCountry><name sortKey="Connor, Andrea" sort="Connor, Andrea" uniqKey="Connor A" first="Andrea" last="Connor">Andrea Connor</name>
<name sortKey="Ewart, Tom" sort="Ewart, Tom" uniqKey="Ewart T" first="Tom" last="Ewart">Tom Ewart</name>
<name sortKey="Kappelhoff, Reinhild" sort="Kappelhoff, Reinhild" uniqKey="Kappelhoff R" first="Reinhild" last="Kappelhoff">Reinhild Kappelhoff</name>
<name sortKey="L Pez Otin, Carlos" sort="L Pez Otin, Carlos" uniqKey="L Pez Otin C" first="Carlos" last="L Pez-Otín">Carlos L Pez-Otín</name>
<name sortKey="Morrison, Charlotte J" sort="Morrison, Charlotte J" uniqKey="Morrison C" first="Charlotte J" last="Morrison">Charlotte J. Morrison</name>
<name sortKey="Puente, Xose" sort="Puente, Xose" uniqKey="Puente X" first="Xose" last="Puente">Xose Puente</name>
<name sortKey="Seth, Arun" sort="Seth, Arun" uniqKey="Seth A" first="Arun" last="Seth">Arun Seth</name>
<name sortKey="Tam, Eric M" sort="Tam, Eric M" uniqKey="Tam E" first="Eric M" last="Tam">Eric M. Tam</name>
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<country name="Canada"><noRegion><name sortKey="Overall, Christopher M" sort="Overall, Christopher M" uniqKey="Overall C" first="Christopher M" last="Overall">Christopher M. Overall</name>
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