TY - JOUR
T1 - De Novo biosynthetic profiling of high abundance proteins in cystic fibrosis lung epithelial cells
AU - Pollard, Harvey B.
AU - Eidelman, Ofer
AU - Jozwik, Catherine
AU - Huang, Wei
AU - Srivastava, Meera
AU - Ji, Xia D.
AU - McGowan, Brighid
AU - Norris, Christine Formas
AU - Todo, Tsuyoshi
AU - Darling, Thomas
AU - Mogayzel, Peter J.
AU - Zeitlin, Pamela L.
AU - Wright, Jerry
AU - Guggino, William B.
AU - Metcalf, Eleanore
AU - Driscoll, William J.
AU - Mueller, Greg
AU - Paweletz, Cloud
AU - Jacobowitz, David M.
PY - 2006/9
Y1 - 2006/9
N2 - In previous studies with cystic fibrosis (CF) IB3-1 lung epithelial cells in culture, we identified 194 unique high abundance proteins by conventional two-dimensional gel electrophoresis and mass spectrometry (Pollard, H. B., Ji, X.-D., Jozwik, C. J., and Jacobowitz, D. M. (2005) High abundance protein profiling of cystic fibrosis lung epithelial cells. Proteomics 5, 2210-2226). In the present work we compared the IB3-1 cells with IB3-1/S9 daughter cells repaired by gene transfer with AAV-(wild type)CFTR. We report that gene transfer resulted in significant changes in silver stain intensity of only 20 of the 194 proteins. However, simultaneous measurement of de novo biosynthetic rates with [35S]methionine of all 194 proteins in both cell types resulted in the identification of an additional 31 CF-specific proteins. Of the 51 proteins identified by this hybrid approach, only six proteins changed similarly in both the mass and kinetics categories. This kinetic portion of the high abundance CF proteome, hidden from direct analysis of abundance, included proteins from transcription and signaling pathways such as NFκB, chaperones such as HSC70, cytoskeletal proteins, and others. Connectivity analysis indicated that ∼30% of the 51-member hybrid high abundance CF proteome interacts with the NFκB signaling pathway. In conclusion, measurement of biosynthetic rates on a global scale can be used to identify disease-specific differences within the high abundance cystic fibrosis proteome. Most of these kinetically defined proteins are unaffected in expression level when using conventional silver stain analysis. We anticipate that this novel hybrid approach to discovery of the high abundance CF proteome will find general application to other proteomic problems in biology and medicine.
AB - In previous studies with cystic fibrosis (CF) IB3-1 lung epithelial cells in culture, we identified 194 unique high abundance proteins by conventional two-dimensional gel electrophoresis and mass spectrometry (Pollard, H. B., Ji, X.-D., Jozwik, C. J., and Jacobowitz, D. M. (2005) High abundance protein profiling of cystic fibrosis lung epithelial cells. Proteomics 5, 2210-2226). In the present work we compared the IB3-1 cells with IB3-1/S9 daughter cells repaired by gene transfer with AAV-(wild type)CFTR. We report that gene transfer resulted in significant changes in silver stain intensity of only 20 of the 194 proteins. However, simultaneous measurement of de novo biosynthetic rates with [35S]methionine of all 194 proteins in both cell types resulted in the identification of an additional 31 CF-specific proteins. Of the 51 proteins identified by this hybrid approach, only six proteins changed similarly in both the mass and kinetics categories. This kinetic portion of the high abundance CF proteome, hidden from direct analysis of abundance, included proteins from transcription and signaling pathways such as NFκB, chaperones such as HSC70, cytoskeletal proteins, and others. Connectivity analysis indicated that ∼30% of the 51-member hybrid high abundance CF proteome interacts with the NFκB signaling pathway. In conclusion, measurement of biosynthetic rates on a global scale can be used to identify disease-specific differences within the high abundance cystic fibrosis proteome. Most of these kinetically defined proteins are unaffected in expression level when using conventional silver stain analysis. We anticipate that this novel hybrid approach to discovery of the high abundance CF proteome will find general application to other proteomic problems in biology and medicine.
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U2 - 10.1074/mcp.M600091-MCP200
DO - 10.1074/mcp.M600091-MCP200
M3 - Article
C2 - 16829594
AN - SCOPUS:33749256500
SN - 1535-9476
VL - 5
SP - 1628
EP - 1637
JO - Molecular and Cellular Proteomics
JF - Molecular and Cellular Proteomics
IS - 9
ER -