Large-scale clinical validation of biomarkers for pancreatic cancer using a mass spectrometry-based proteomics approach

// Jisook Park 1 , Eunjung Lee 2 , Kyoung-Jin Park 3 , Hyung-Doo Park 3 , Jong-Won Kim 3 , Hye In Woo 4 , Kwang Hyuck Lee 5 , Kyu-Taek Lee 5 , Jong Kyun Lee 5 , Joon-Oh Park 6 , Young Suk Park 6 , Jin Seok Heo 7 , Seong Ho Choi 7 , Dong Wook Choi 7 , Kee-Taek Jang 8 and Soo-Youn Lee 3, 9 1 Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 2 Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States 3 Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 4 Department of Laboratory Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea 5 Division of Gastroenterology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 6 Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 7 Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 8 Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea 9 Department of Clinical Pharmacology and Therapeutics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea Correspondence to: Soo-Youn Lee, email: suddenbz@skku.edu Keywords: pancreatic cancer, biomarker, validation, proteomics, mass spectrometry Received: October 06, 2016 Accepted: April 15, 2017 Published: April 27, 2017 ABSTRACT We performed an integrated analysis of proteomic and transcriptomic datasets to develop potential diagnostic markers for early pancreatic cancer. In the discovery phase, a multiple reaction monitoring assay of 90 proteins identified by either gene expression analysis or global serum proteome profiling was established and applied to 182 clinical specimens. Nine proteins ( P < 0.05) were selected for the independent validation phase and quantified using stable isotope dilution-multiple reaction monitoring-mass spectrometry in 456 specimens. Of these proteins, four proteins (apolipoprotein A-IV, apolipoprotein CIII, insulin-like growth factor binding protein 2 and tissue inhibitor of metalloproteinase 1) were significantly altered in pancreatic cancer in both the discovery and validation phase ( P < 0.01). Moreover, a panel including carbohydrate antigen 19-9, apolipoprotein A-IV and tissue inhibitor of metalloproteinase 1 showed better performance for distinguishing early pancreatic cancer from pancreatitis (Area under the curve = 0.934, 86% sensitivity at fixed 90% specificity) than carbohydrate antigen 19-9 alone (71% sensitivity). Overall, we present the panel of robust biomarkers for early pancreatic cancer diagnosis through bioinformatics analysis that combined transcriptomic and proteomic data as well as rigorous validation on a large number of independent clinical samples.