Pathway-based biomarker search by high-throughput proteomics profiling of secretomes Journal Article
| Authors: | Lawlor, K.; Nazarian, A.; Lacomis, L.; Tempst, P.; Villanueva, J. |
| Article Title: | Pathway-based biomarker search by high-throughput proteomics profiling of secretomes |
| Abstract: | An efficient means for the identification of prognostic and predictive biomarkers is essential in today's cancer management. A new approach toward biomarker discovery has therefore been proposed, where pathways instead of individual proteins would be monitored and targeted. Recently, the 'secretome', a biological fluid that may be enriched with secreted and/or shed proteins from adjacent disease-relevant cancer cells, has been targeted for biomarker discovery. We describe a novel method for secretome analysis using "stacking gels", label-free relative quantitation, and pathway analysis. The protocol presented here increases the throughput of secretome analysis by approximately 1 order of magnitude compared to earlier methodologies. In the first application, six cancer cell lines from three different tissues were studied. The global secretome data sets obtained were analyzed using pathway analysis software to attempt integrating the experimental findings into a cellular signaling context. This suggested that several secretome proteins might be interconnected with intracellular canonical pathways. This, in turn, may eventually allow the use of secretomes for discovery of pathway-based biomarkers. When this strategy was applied to two breast cancer cell lines, it appeared that the IGF signaling and the plasminogen activating system may be differentially regulated in invasive breast cancer, but this remains speculative until it is verified in a clinical setting. In summary, the methodology proposed optimizes cell culture with sample fractionation and LC-MS to obtain the highest yield from cultured cell secretomes, with a focus on rational biomarker discovery through putative linkage with cancer relevant pathways. © 2009 American Chemical Society. |
| Keywords: | signal transduction; mitogen activated protein kinase; unclassified drug; human cell; mass spectrometry; biological marker; breast cancer; gene expression profiling; computational biology; protein targeting; epidermal growth factor receptor 2; neoplasm proteins; tumor markers, biological; cancer cell culture; high throughput screening; cell line, tumor; breast neoplasms; proteomics; urinary bladder neoplasms; cancer invasion; prostatic neoplasms; membrane antigen; serine proteinase; signal peptide; cancer cell; western blotting; vasculotropin a; interleukin 6; protein secretion; fractionation; bioinformatics; computer program; cancer biomarker; lc-ms/ms; pathways analysis; secretome; axl receptor tyrosine kinase; cd51 antigen; collagen alpha1 chain; collagen alpha2 chain; colony stimulating factor 1; cystatin; cysteine rich protein 61; galectin 1; galectin 3 binding protein; insulin like growth factor binding protein 7; laminin; laminin b1 subunit; laminin gamma2 subunit; lysyl oxidase like 2; n acetylglucosamine 6 sulfatase; neutrophil gelatinase associated lipocalin; pentraxin related protein; plasminogen activator inhibitor 1; protein cathepsin z; protein prss2; somatomedin binding protein; tissue plasminogen activator; body fluid; pathway analysis; plasminogen activation |
| Journal Title: | Journal of Proteome Research |
| Volume: | 8 |
| Issue: | 3 |
| ISSN: | 1535-3893 |
| Publisher: | American Chemical Society |
| Date Published: | 2009-03-06 |
| Start Page: | 1489 |
| End Page: | 1503 |
| Language: | English |
| DOI: | 10.1021/pr8008572 |
| PUBMED: | 19199430 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 16" - "Export Date: 30 November 2010" - "CODEN: JPROB" - "Source: Scopus" |
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24Villanueva -
324Tempst -
9Lawlor -
11
Gettings -
21
Lacomis
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