Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry
The aim of this study was to uncover the membrane protein profile differences between colorectal carcinoma and neighboring normal mucosa from colorectal cancer patients. Information from cellular membrane proteomes can be used not only to study the roles of membrane proteins in fundamental biologica...
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| creator | Chen, Jinn-Shiun Chen, Kuei-Tien Fan, Chung-Wei Han, Chia-Li Chen, Yu-Ju Yu, Jau-Song Chang, Yu-Sun Chien, Chih-Wei Wu, Chien-Peng Hung, Ray-Ping Chan, Err-Cheng |
| description | The aim of this study was to uncover the membrane protein profile differences between colorectal carcinoma and neighboring normal mucosa from colorectal cancer patients. Information from cellular membrane proteomes can be used not only to study the roles of membrane proteins in fundamental biological processes, but also to discover novel targets for improving the management of colorectal cancer patients. We used solvent extraction and a gel-assisted digestion method, together with isobaric tags with related and absolute quantitation (iTRAQ) reagents to label tumoral and adjacent normal tissues in a pairwise manner (n = 8). For high-throughput quantification, these digested labeled peptides were combined and simultaneously analyzed using LC-MS/MS. Using the shotgun approach, we identified a total of 438 distinct proteins from membrane fractions of all eight patients. After comparing protein expression between cancerous and corresponding normal tissue, we identified 34 upregulated and eight downregulated proteins with expression changes greater than twofold (Student's t-test, P < 0.05). Among these, the overexpression of well-established biomarkers such as carcinoembryonic antigens (CEACAM5, CEACAM6), as well as claudin-3, HLA class I histocompatibility antigen A-1, tapasin and mitochondrial solute carrier family 25A4 were confirmed by western blotting. We conclude that gel-assisted digestion and iTRAQ labeling MS is a potential approach for uncovering and comparing membrane protein profiles of tissue samples that has the potential to identify novel biomarkers. |
| doi_str_mv | 10.1111/j.1742-4658.2010.07712.x |
| format | Article |
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Information from cellular membrane proteomes can be used not only to study the roles of membrane proteins in fundamental biological processes, but also to discover novel targets for improving the management of colorectal cancer patients. We used solvent extraction and a gel-assisted digestion method, together with isobaric tags with related and absolute quantitation (iTRAQ) reagents to label tumoral and adjacent normal tissues in a pairwise manner (n = 8). For high-throughput quantification, these digested labeled peptides were combined and simultaneously analyzed using LC-MS/MS. Using the shotgun approach, we identified a total of 438 distinct proteins from membrane fractions of all eight patients. After comparing protein expression between cancerous and corresponding normal tissue, we identified 34 upregulated and eight downregulated proteins with expression changes greater than twofold (Student's t-test, P < 0.05). Among these, the overexpression of well-established biomarkers such as carcinoembryonic antigens (CEACAM5, CEACAM6), as well as claudin-3, HLA class I histocompatibility antigen A-1, tapasin and mitochondrial solute carrier family 25A4 were confirmed by western blotting. We conclude that gel-assisted digestion and iTRAQ labeling MS is a potential approach for uncovering and comparing membrane protein profiles of tissue samples that has the potential to identify novel biomarkers.</description><identifier>ISSN: 1742-464X</identifier><identifier>EISSN: 1742-4658</identifier><identifier>DOI: 10.1111/j.1742-4658.2010.07712.x</identifier><identifier>PMID: 20546304</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Adenine Nucleotide Translocator 1 - metabolism ; Biochemistry ; biomarker ; Biomarkers - metabolism ; Blotting, Western ; Carcinoembryonic Antigen - metabolism ; Cell Membrane - metabolism ; Claudin-3 ; Cluster Analysis ; Colon - metabolism ; Colorectal cancer ; colorectal neoplasms ; Colorectal Neoplasms - metabolism ; Comparative studies ; Down-Regulation - genetics ; Extracellular Space - metabolism ; HLA-A1 Antigen - metabolism ; Humans ; Intracellular Membranes - metabolism ; mass spectrometry ; membrane protein ; Membrane Proteins - genetics ; Membrane Proteins - metabolism ; Membrane Transport Proteins - metabolism ; Membranes ; Peptide Fragments - analysis ; proteomic profile ; Proteomics ; Proteomics - methods ; Rectum - metabolism ; Tandem Mass Spectrometry - methods ; Trypsin - metabolism ; Up-Regulation - genetics</subject><ispartof>The FEBS journal, 2010-07, Vol.277 (14), p.3028-3038</ispartof><rights>2010 The Authors Journal compilation © 2010 FEBS</rights><rights>Journal compilation © 2010 Federation of European Biochemical Societies</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5022-351d9fa60a5f6ee63f0a831785e6757c4f79c8626b6f216d8731e4ce898e195f3</citedby><cites>FETCH-LOGICAL-c5022-351d9fa60a5f6ee63f0a831785e6757c4f79c8626b6f216d8731e4ce898e195f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1742-4658.2010.07712.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1742-4658.2010.07712.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27903,27904,45553,45554,46387,46811</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20546304$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Jinn-Shiun</creatorcontrib><creatorcontrib>Chen, Kuei-Tien</creatorcontrib><creatorcontrib>Fan, Chung-Wei</creatorcontrib><creatorcontrib>Han, Chia-Li</creatorcontrib><creatorcontrib>Chen, Yu-Ju</creatorcontrib><creatorcontrib>Yu, Jau-Song</creatorcontrib><creatorcontrib>Chang, Yu-Sun</creatorcontrib><creatorcontrib>Chien, Chih-Wei</creatorcontrib><creatorcontrib>Wu, Chien-Peng</creatorcontrib><creatorcontrib>Hung, Ray-Ping</creatorcontrib><creatorcontrib>Chan, Err-Cheng</creatorcontrib><title>Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry</title><title>The FEBS journal</title><addtitle>FEBS J</addtitle><description>The aim of this study was to uncover the membrane protein profile differences between colorectal carcinoma and neighboring normal mucosa from colorectal cancer patients. Information from cellular membrane proteomes can be used not only to study the roles of membrane proteins in fundamental biological processes, but also to discover novel targets for improving the management of colorectal cancer patients. We used solvent extraction and a gel-assisted digestion method, together with isobaric tags with related and absolute quantitation (iTRAQ) reagents to label tumoral and adjacent normal tissues in a pairwise manner (n = 8). For high-throughput quantification, these digested labeled peptides were combined and simultaneously analyzed using LC-MS/MS. Using the shotgun approach, we identified a total of 438 distinct proteins from membrane fractions of all eight patients. After comparing protein expression between cancerous and corresponding normal tissue, we identified 34 upregulated and eight downregulated proteins with expression changes greater than twofold (Student's t-test, P < 0.05). Among these, the overexpression of well-established biomarkers such as carcinoembryonic antigens (CEACAM5, CEACAM6), as well as claudin-3, HLA class I histocompatibility antigen A-1, tapasin and mitochondrial solute carrier family 25A4 were confirmed by western blotting. We conclude that gel-assisted digestion and iTRAQ labeling MS is a potential approach for uncovering and comparing membrane protein profiles of tissue samples that has the potential to identify novel biomarkers.</description><subject>Adenine Nucleotide Translocator 1 - metabolism</subject><subject>Biochemistry</subject><subject>biomarker</subject><subject>Biomarkers - metabolism</subject><subject>Blotting, Western</subject><subject>Carcinoembryonic Antigen - metabolism</subject><subject>Cell Membrane - metabolism</subject><subject>Claudin-3</subject><subject>Cluster Analysis</subject><subject>Colon - metabolism</subject><subject>Colorectal cancer</subject><subject>colorectal neoplasms</subject><subject>Colorectal Neoplasms - metabolism</subject><subject>Comparative studies</subject><subject>Down-Regulation - genetics</subject><subject>Extracellular Space - metabolism</subject><subject>HLA-A1 Antigen - metabolism</subject><subject>Humans</subject><subject>Intracellular Membranes - metabolism</subject><subject>mass spectrometry</subject><subject>membrane protein</subject><subject>Membrane Proteins - genetics</subject><subject>Membrane Proteins - metabolism</subject><subject>Membrane Transport Proteins - metabolism</subject><subject>Membranes</subject><subject>Peptide Fragments - analysis</subject><subject>proteomic profile</subject><subject>Proteomics</subject><subject>Proteomics - methods</subject><subject>Rectum - metabolism</subject><subject>Tandem Mass Spectrometry - methods</subject><subject>Trypsin - metabolism</subject><subject>Up-Regulation - genetics</subject><issn>1742-464X</issn><issn>1742-4658</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNks1uEzEUhUcIREvhFcBiwyrBHv_NbJBK1BakSgjaSuwsx3OdOhqPgz1Rm_fhQXunKVmwAW98df2dI18fVxVhdM5wfVzPmRb1TCjZzGuKXao1q-f3z6rjw8HzQy1-HlWvSllTyqVo25fVUU2lUJyK4-r3IsWNzaGkgSRPIsRltgMQn60bAzY3OY2QYnBT5UMPZeKGlKPtiR064uzgIKdtIbfbaAfiUp8yuBGPx1DKFgV3YbwlK-hntpRQRuhIF1ZQHv0ni3D94_Q76e0S-jCsSESMlA165BRhzLvX1Qtv-wJvnvaT6ub87HrxZXb57eLr4vRy5iSt6xmXrGu9VdRKrwAU99Q2nOlGgtJSO-F16xpVq6XyNVNdozkD4aBpG2Ct9Pyk-rD3xVF_4cVHE0Nx0Pf4Ijig0UKgmmr2b5Jz2SraKiTf_0Wu0zYPOIaRWstWM0ERavaQy6mUDN5scog27wyjZkrcrM0UppmCNVPi5jFxc4_St0_-22WE7iD8EzECn_bAHYa3-29jc372-Woq0eDd3sDbZOwK_4q5uUKUU9YoJlrJHwAGCMYK</recordid><startdate>201007</startdate><enddate>201007</enddate><creator>Chen, Jinn-Shiun</creator><creator>Chen, Kuei-Tien</creator><creator>Fan, Chung-Wei</creator><creator>Han, Chia-Li</creator><creator>Chen, Yu-Ju</creator><creator>Yu, Jau-Song</creator><creator>Chang, Yu-Sun</creator><creator>Chien, Chih-Wei</creator><creator>Wu, Chien-Peng</creator><creator>Hung, Ray-Ping</creator><creator>Chan, Err-Cheng</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7QO</scope></search><sort><creationdate>201007</creationdate><title>Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry</title><author>Chen, Jinn-Shiun ; Chen, Kuei-Tien ; Fan, Chung-Wei ; Han, Chia-Li ; Chen, Yu-Ju ; Yu, Jau-Song ; Chang, Yu-Sun ; Chien, Chih-Wei ; Wu, Chien-Peng ; Hung, Ray-Ping ; Chan, Err-Cheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5022-351d9fa60a5f6ee63f0a831785e6757c4f79c8626b6f216d8731e4ce898e195f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Adenine Nucleotide Translocator 1 - metabolism</topic><topic>Biochemistry</topic><topic>biomarker</topic><topic>Biomarkers - metabolism</topic><topic>Blotting, Western</topic><topic>Carcinoembryonic Antigen - metabolism</topic><topic>Cell Membrane - metabolism</topic><topic>Claudin-3</topic><topic>Cluster Analysis</topic><topic>Colon - metabolism</topic><topic>Colorectal cancer</topic><topic>colorectal neoplasms</topic><topic>Colorectal Neoplasms - metabolism</topic><topic>Comparative studies</topic><topic>Down-Regulation - genetics</topic><topic>Extracellular Space - metabolism</topic><topic>HLA-A1 Antigen - metabolism</topic><topic>Humans</topic><topic>Intracellular Membranes - metabolism</topic><topic>mass spectrometry</topic><topic>membrane protein</topic><topic>Membrane Proteins - genetics</topic><topic>Membrane Proteins - metabolism</topic><topic>Membrane Transport Proteins - metabolism</topic><topic>Membranes</topic><topic>Peptide Fragments - analysis</topic><topic>proteomic profile</topic><topic>Proteomics</topic><topic>Proteomics - methods</topic><topic>Rectum - metabolism</topic><topic>Tandem Mass Spectrometry - methods</topic><topic>Trypsin - metabolism</topic><topic>Up-Regulation - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Jinn-Shiun</creatorcontrib><creatorcontrib>Chen, Kuei-Tien</creatorcontrib><creatorcontrib>Fan, Chung-Wei</creatorcontrib><creatorcontrib>Han, Chia-Li</creatorcontrib><creatorcontrib>Chen, Yu-Ju</creatorcontrib><creatorcontrib>Yu, Jau-Song</creatorcontrib><creatorcontrib>Chang, Yu-Sun</creatorcontrib><creatorcontrib>Chien, Chih-Wei</creatorcontrib><creatorcontrib>Wu, Chien-Peng</creatorcontrib><creatorcontrib>Hung, Ray-Ping</creatorcontrib><creatorcontrib>Chan, Err-Cheng</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><jtitle>The FEBS journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Jinn-Shiun</au><au>Chen, Kuei-Tien</au><au>Fan, Chung-Wei</au><au>Han, Chia-Li</au><au>Chen, Yu-Ju</au><au>Yu, Jau-Song</au><au>Chang, Yu-Sun</au><au>Chien, Chih-Wei</au><au>Wu, Chien-Peng</au><au>Hung, Ray-Ping</au><au>Chan, Err-Cheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry</atitle><jtitle>The FEBS journal</jtitle><addtitle>FEBS J</addtitle><date>2010-07</date><risdate>2010</risdate><volume>277</volume><issue>14</issue><spage>3028</spage><epage>3038</epage><pages>3028-3038</pages><issn>1742-464X</issn><eissn>1742-4658</eissn><abstract>The aim of this study was to uncover the membrane protein profile differences between colorectal carcinoma and neighboring normal mucosa from colorectal cancer patients. Information from cellular membrane proteomes can be used not only to study the roles of membrane proteins in fundamental biological processes, but also to discover novel targets for improving the management of colorectal cancer patients. We used solvent extraction and a gel-assisted digestion method, together with isobaric tags with related and absolute quantitation (iTRAQ) reagents to label tumoral and adjacent normal tissues in a pairwise manner (n = 8). For high-throughput quantification, these digested labeled peptides were combined and simultaneously analyzed using LC-MS/MS. Using the shotgun approach, we identified a total of 438 distinct proteins from membrane fractions of all eight patients. After comparing protein expression between cancerous and corresponding normal tissue, we identified 34 upregulated and eight downregulated proteins with expression changes greater than twofold (Student's t-test, P < 0.05). Among these, the overexpression of well-established biomarkers such as carcinoembryonic antigens (CEACAM5, CEACAM6), as well as claudin-3, HLA class I histocompatibility antigen A-1, tapasin and mitochondrial solute carrier family 25A4 were confirmed by western blotting. We conclude that gel-assisted digestion and iTRAQ labeling MS is a potential approach for uncovering and comparing membrane protein profiles of tissue samples that has the potential to identify novel biomarkers.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>20546304</pmid><doi>10.1111/j.1742-4658.2010.07712.x</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adenine Nucleotide Translocator 1 - metabolism Biochemistry biomarker Biomarkers - metabolism Blotting, Western Carcinoembryonic Antigen - metabolism Cell Membrane - metabolism Claudin-3 Cluster Analysis Colon - metabolism Colorectal cancer colorectal neoplasms Colorectal Neoplasms - metabolism Comparative studies Down-Regulation - genetics Extracellular Space - metabolism HLA-A1 Antigen - metabolism Humans Intracellular Membranes - metabolism mass spectrometry membrane protein Membrane Proteins - genetics Membrane Proteins - metabolism Membrane Transport Proteins - metabolism Membranes Peptide Fragments - analysis proteomic profile Proteomics Proteomics - methods Rectum - metabolism Tandem Mass Spectrometry - methods Trypsin - metabolism Up-Regulation - genetics |
| title | Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry |
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