title: Large-scale proteome quantification of hepatocellular carcinoma tissues by a three-dimensional liquid chromatography strategy integrated with sample preparation.
abstract: Hepatocellular carcinoma is one of the most fatal cancers worldwide. In this study, a reversed-phase-strong cation exchange-reversed-phase three-dimensional liquid chromatography strategy was established and coupled with mass spectrometry to investigate the differential proteome expression of HCC and normal liver tissues. In total, 2759 proteins were reliably quantified, of which, 648 proteins were dysregulated more than 3-fold in HCC liver tissues. Some important proteins that relate to HCC pathology were significantly dysregulated, such as NAT2 and AKR1B10. Furthermore, 2307 phosphorylation sites from 1264 phosphoproteins were obtained in our previous phosphoproteome quantification, and the nonphosphorylated counterparts of 445 phosphoproteins with 983 phosphorylation sites were reliably quantified in this work. It was observed that 337 (34%) phosphorylation sites exhibit significantly different expression trends from that of their corresponding nonphosphoproteins. Some novel phosphorylation sites with important biological functions in the progression of HCC were reliably quantified, such as the significant downregulation of pT185 for ERK2 and pY204 for ERK1.
authors: Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.
authors: Bo
authors: B
authors: Xu
authors: Fangjun
authors: F
authors: Wang
authors: Chunxia
authors: C
authors: Song
authors: Zhen
authors: Z
authors: Sun
authors: Kai
authors: K
authors: Cheng
authors: Yexiong
authors: Y
authors: Tan
authors: Hongyang
authors: H
authors: Wang
authors: Hanfa
authors: H
authors: Zou
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000378:metabolism*; D002852:Chromatography, Ion Exchange; D002853:Chromatography, Liquid / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D008113:Liver Neoplasms / Q000378:metabolism*; D013058:Mass Spectrometry; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods
chemical_list: D010750:Phosphoproteins