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WIREs Syst Biol Med
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Integration of proteomics into systems biology of cancer

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Abstract Deciphering the complexity and heterogeneity of cancer, benefits from integration of proteomic level data into systems biology efforts. The opportunities available as a result of advances in proteomic technologies, the successes to date, and the challenges involved in integrating diverse datasets are addressed in this review. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1169 This article is categorized under: Translational, Genomic, and Systems Medicine > Diagnostic Methods Laboratory Methods and Technologies > Proteomics Methods Translational, Genomic, and Systems Medicine > Translational Medicine

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Proteomic profiling of cancer cells. Freshly isolated tumor cells or cancer cell lines to be compared are cultured in the presence of isotopically labeled amino acids. Media, biotinylated cell‐surface proteins, and whole lysates are isolated separately and analyzed. Cell lysates may be further fractionated for separate analysis of subcompartments (e.g. nuclear proteins), or protein subgroups (e.g. phosphoproteins).

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Plasma protein signatures of lung cancer derived from analysis of mouse models of cancer. The heat map displays clustering together of lung cancer mouse models' plasma proteome data. Below is a comparison between human lung adenocarcinoma plasmas and human lung nonadenocarcinoma plasmas of levels of proteins associated with an NKX2.1 signature identified in lung adenocarcinoma. An EGFR‐related protein network identified in plasma from an EGFR mutant lung cancer mouse model is shown. A list of proteins associated with a neuroendocrine signature in small cell lung cancer (SCLC) plasma is presented. Numbers refer to plasma protein case/control ratios and corresponding gene expression ratios in tumor tissue from the SCLC mouse model compared to controls.

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Conceptual framework for the contribution of proteomics to the systems biology of cancer.

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The wide world of protein modifications that affect function and yield biomarkers and therapeutic targets.

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Translational, Genomic, and Systems Medicine > Diagnostic Methods
Translational, Genomic, and Systems Medicine > Translational Medicine
Laboratory Methods and Technologies > Proteomics Methods

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