NDLI: Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles.

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Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Deeb, Sally J. D'Souza, Rochelle C. J. Cox, Jürgen Schmidt-Supprian, Marc Mann, Matthias
Description	Country affiliation: Germany Author Affiliation: Deeb SJ ( Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.)
Abstract	Correct classification of cancer patients into subtypes is a prerequisite for acute diagnosis and effective treatment. Currently this classification relies mainly on histological assessment, but gene expression analysis by microarrays has shown great promise. Here we show that high accuracy, quantitative proteomics can robustly segregate cancer subtypes directly at the level of expressed proteins. We investigated two histologically indistinguishable subtypes of diffuse large B-cell lymphoma (DLBCL): activated B-cell-like (ABC) and germinal-center B-cell-like (GCB) subtypes, by first developing a general lymphoma stable isotope labeling with amino acids in cell culture (SILAC) mix from heavy stable isotope-labeled cell lines. This super-SILAC mix was combined with cell lysates from five ABC-DLBCL and five GCB-DLBCL cell lines. Shotgun proteomic analysis on a linear ion trap Orbitrap mass spectrometer with high mass accuracy at the MS and MS/MS levels yielded a proteome of more than 7,500 identified proteins. High accuracy of quantification allowed robust separation of subtypes by principal component analysis. The main contributors to the classification included proteins known to be differentially expressed between the subtypes such as the transcription factors IRF4 and SPI1/PU.1, cell surface markers CD44 and CD27, as well as novel candidates. We extracted a signature of 55 proteins that segregated subtypes and contained proteins connected to functional differences between the ABC and GCB-DLBCL subtypes, including many NF-κB-regulated genes. Shortening the analysis time to single-shot analysis combined with use of the new linear quadrupole Orbitrap analyzer (Q Exactive) also clearly differentiated between the subtypes. These results show that high resolution shotgun proteomics combined with super-SILAC-based quantification is a promising new technology for tumor characterization and classification.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.M111.015362
Journal	Molecular & Cellular Proteomics
Issue Number	5
Volume Number	11
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2012-05-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Gene Expression Profiling Lymphoma, Large B-cell, Diffuse Classification Proteome Metabolism Amino Acids Chemistry Cell Line, Tumor Cluster Analysis Isotope Labeling Pathology Peptide Fragments Principal Component Analysis Genetics Proteomics Tandem Mass Spectrometry Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

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Super-SILAC Allows Classification of Diffuse Large B-cell Lymphoma Subtypes by Their Protein Expression Profiles*

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Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles.