A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Nature Biotechnology (Impact Factor: 41.51). 06/2011; 29(7):635-43. DOI: 10.1038/nbt.1899
Source: PubMed


We developed a pipeline to integrate the proteomic technologies used from the discovery to the verification stages of plasma biomarker identification and applied it to identify early biomarkers of cardiac injury from the blood of patients undergoing a therapeutic, planned myocardial infarction (PMI) for treatment of hypertrophic cardiomyopathy. Sampling of blood directly from patient hearts before, during and after controlled myocardial injury ensured enrichment for candidate biomarkers and allowed patients to serve as their own biological controls. LC-MS/MS analyses detected 121 highly differentially expressed proteins, including previously credentialed markers of cardiovascular disease and >100 novel candidate biomarkers for myocardial infarction (MI). Accurate inclusion mass screening (AIMS) qualified a subset of the candidates based on highly specific, targeted detection in peripheral plasma, including some markers unlikely to have been identified without this step. Analyses of peripheral plasma from controls and patients with PMI or spontaneous MI by quantitative multiple reaction monitoring mass spectrometry or immunoassays suggest that the candidate biomarkers may be specific to MI. This study demonstrates that modern proteomic technologies, when coherently integrated, can yield novel cardiovascular biomarkers meriting further evaluation in large, heterogeneous cohorts.

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Available from: Dongxiao Shen
    • "For example, Addona et al. developed an approach to bridge shotgun proteomics and MRM-based targeted proteomics that they called accurate inclusion mass screening. The authors claimed that over 60% of the candidates from the discovery stage were qualified for MRM verification [14]. Muraoka et al. identified 61 prognostic protein candidates from individual breast cancer tissue samples using quantitative screening with iTRAQ, and they further quantified over 80% of these potential biomarkers in individual tissues using MRM [15]. "
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    • "The large number of putative protein biomarkers that exist in the literature needs to be validated, something which requires high precision, robust assays with high throughput, appropriate for the analysis of thousands of patient samples. Quantitative mass spectrometric assays, like MRM (multiple reaction monitoring), have a huge potential in both the validation of newly discovered biomarker candidates and in the measurements of known markers within a multiplex assay format in the clinical routine [2] [3] [4] [5] [6]. Thanks to the SISCAPA (stable isotope standards and capture by antipeptide antibodies ) technique [7] [8] [9], the sensitivity of mass spectrometry based methods is not a limiting factor anymore in comparison with the classical immune-based assays; nevertheless the capability to multiplexing has enormous advantage. "

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