Abstract 4788: A focused proteomics technology QUEST-MS identified a novel plasma prostate cancer biomarker polypeptide complementing PSA test
Authors: Ueda Koji , Tatsuguchi Ayako , Tamura Kenji , Shuin Taro , Nakayama Masato , Sato Taka-Aki , Nakamura Yusuke , Nakagawa Hidewaki 
Published: August 2012

Abstract
Prostate cancer accounted for more than 250,000 death worldwide in 2009, which was the 9th highest cause of cancer related death in Japan (The Population Survey Report 2010, the Ministry of Health, Labor and Welfare). Although the widespread use of PSA test has contributed to the early diagnosis of prostate cancer, expanding overdiagnosis cases and unnecessary biopsies have emerged as a big issue. To identify novel plasma biomarkers that could complement the specificity of PSA test and improve diagnostic accuracy, especially in the early stage of prostate cancer, we employed a focused proteomic technology QUEST-MS (Quick Enrichment of Small Targets for Mass Spectrometry). The rapid 96-well format preparation method QUEST was simply based on sequential reversed phase chromatography purifications which allowed efficient enrichment of less than 20 kDa proteins from 116 plasma samples in a half of day, prior to LC/MS/MS analysis. In this biomarker screening experiment, plasma from 24 healthy controls, 19 benign prostate hypertrophy (BPH) patients, and 73 prostate cancer patients (Gleason score 5-10) were analyzed with LTQ-Orbitrap-Velos mass spectrometer. The 116 LC/MS/MS raw data were directly loaded onto the Expressionist proteome server platform (Genedata AG) and subjected to data processing, label-free quantification analysis, and the following biomarker discovery analysis. We extracted peptides demonstrating prostate cancer-specific expression patterns by Absent-Present Search algorithm on the Expressionist Analyst module, which searched all-or-nothing peptides between two clinical groups (healthy control + BPH vs. prostate cancer). Finally 108 peptides were selected from over 100,000 peptides with the criteria; detection in at most 1 case among 43 controls and at least 12 cases among 73 prostate cancer patients. Simultaneously, protein identification analysis was processed on the Proteome Discoverer 1.3 software (Thermo Scientific) using the Sequest program, resulting in 1,126 non-redundant plasma protein identifications with false discovery rate &lt; 1%. The list included the identification of PSA with 4 distinct high-confidence level peptides. Here we would like to show a successful identification of a new prostate cancer biomarker candidate polypeptide which displayed the Gleason score-dependent escalation of its plasma level among 12 prostate cancer samples, and only low level detection in 1 control sample. Although the prostate-specific expression feature of this polypeptide was quite similar with PSA, the pattern of positive cases was independent. Thus, the integration of biomarker focusing technology QUEST-MS and the high-end mass spectrometer analysis might be able to reach lots of unidentified low abundant (around 100 pg/ml) serum/plasma biomarkers.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4788. doi:1538-7445.AM2012-4788