title: Onco-proteogenomics identifies urinary S100A9 and GRN as potential combinatorial biomarkers for early diagnosis of hepatocellular carcinoma.
abstract: Hepatocellular carcinoma (HCC), the major type of liver cancer, is among the most lethal cancers owing to its aggressive nature and frequently late detection. Therefore, the possibility to identify early diagnostic markers could be of significant benefit. Urine has especially become one of the most attractive body fluids in biomarker discovery as it can be obtained non-invasively in large quantities and is stable as compared with other body fluids. To identify potential protein biomarker for early diagnosis of HCC, we explored protein expression profiles in urine from HCC patients and normal controls (n = 44) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry (nanoLC-MS/MS) and stable isotope dimethyl labeling. We have systematically mapped 91 proteins with differential expressions (p < 0.05), which included 8 down-regulated microtubule proteins and 83 up-regulated proteins involved in signal and inflammation response. Further integrated proteogenomic approach composed of proteomic, genomic and transcriptomic analysis identified that S100A9 and GRN were co-amplified (p < 0.001) and co-expressed (p < 0.01) in HCC tumors and urine samples. In addition, the amplifications of S100A9 or GRN were found to be associated with poor survival in HCC patients, and their co-amplification was also prognosed worse overall survival than individual ones. Our results suggest that urinary S100A9 and GRN as potential combinatorial biomarkers can be applied to early diagnosis of hepatocellular carcinoma and highlight the utility of onco-proteogenomics for identifying protein markers that can be applied to disease-oriented translational medicine.
authors.affiliation: Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan ; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Chun-Hao
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: Chao-Jen
authors.initials: CJ
authors.lastname: Kuo
authors.affiliation: Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: Shih-Shin
authors.initials: SS
authors.lastname: Liang
authors.affiliation: Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: Shu-Wen
authors.initials: SW
authors.lastname: Chi
authors.affiliation: Department of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: Edward
authors.initials: E
authors.lastname: Hsi
authors.affiliation: Physiology Biophysics and Systems Biology Program, Weill Graduate School of Medical Sciences, Cornell University, NY 10065, USA.
authors.forename: Chi-Chao
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Division of Hepatobiliary Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: King-Teh
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Quantitative Proteomics Center and Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan ; Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan ; Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
authors.forename: Shyh-Horng
authors.initials: SH
authors.lastname: Chiou
keywords: D/H, deuterium/hydrogen labeling; GRN, granulins; Granulin; HCC, hepatocellular carcinoma; HILIC, hydrophilic interaction chromatography; Hepatocellular carcinoma; Protein S100-A9; Proteogenomics; Quantitative proteomics; S100A9, protein S100-A9; Urinary biomarkers; nanoLC–MS/MS, nano-liquid chromatography coupled tandem mass spectrometry