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J Proteome Res DOI:10.1021/acs.jproteome.5b01119

Targeted MS Assay Predicting Tamoxifen Resistance in Estrogen-Receptor-Positive Breast Cancer Tissues and Sera.

Publication TypeJournal Article
Year of Publication2016
AuthorsDe Marchi, T, Kuhn, E, Dekker, LJ, Stingl, C, Braakman, RBH, Opdam, M, Linn, SC, Sweep, FCGJ, Span, PN, Luider, TM, Foekens, JA, Martens, JWM, Carr, SA, Umar, A
JournalJ Proteome Res
Date Published2016 Apr 01
KeywordsAntineoplastic Agents, Hormonal, Apoptosis Regulatory Proteins, Biomarkers, Tumor, Breast Neoplasms, Carbon Isotopes, Carrier Proteins, Drug Resistance, Neoplasm, Female, Gene Expression, High-Throughput Screening Assays, Humans, Immunoprecipitation, Indicator Dilution Techniques, Membrane Proteins, Microfilament Proteins, Neoplasm Proteins, Nitrogen Isotopes, Prognosis, Receptors, Estrogen, RNA-Binding Proteins, Survival Analysis, Tamoxifen, Tandem Mass Spectrometry, Treatment Outcome

We recently reported on the development of a 4-protein-based classifier (PDCD4, CGN, G3BP2, and OCIAD1) capable of predicting outcome to tamoxifen treatment in recurrent, estrogen-receptor-positive breast cancer based on high-resolution MS data. A precise and high-throughput assay to measure these proteins in a multiplexed, targeted fashion would be favorable to measure large numbers of patient samples to move these findings toward a clinical setting. By coupling immunoprecipitation to multiple reaction monitoring (MRM) MS and stable isotope dilution, we developed a high-precision assay to measure the 4-protein signature in 38 primary breast cancer whole tissue lysates (WTLs). Furthermore, we evaluated the presence and patient stratification capabilities of our signature in an independent set of 24 matched (pre- and post-therapy) sera. We compared the performance of immuno-MRM (iMRM) with direct MRM in the absence of fractionation and shotgun proteomics in combination with label-free quantification (LFQ) on both WTL and laser capture microdissected (LCM) tissues. Measurement of the 4-proteins by iMRM showed not only higher accuracy in measuring proteotypic peptides (Spearman r: 0.74 to 0.93) when compared with MRM (Spearman r: 0.0 to 0.76) but also significantly discriminated patient groups based on treatment outcome (hazard ratio [HR]: 10.96; 95% confidence interval [CI]: 4.33 to 27.76; Log-rank P < 0.001) when compared with LCM (HR: 2.85; 95% CI: 1.24 to 6.54; Log-rank P = 0.013) and WTL (HR: 1.16; 95% CI: 0.57 to 2.33; Log-rank P = 0.680) LFQ-based predictors. Serum sample analysis by iMRM confirmed the detection of the four proteins in these samples. We hereby report that iMRM outperformed regular MRM, confirmed our previous high-resolution MS results in tumor tissues, and has shown that the 4-protein signature is measurable in serum samples.


Alternate JournalJ. Proteome Res.
PubMed ID26958999
Grant ListU24CA160034 / CA / NCI NIH HHS / United States