805
Views
5
CrossRef citations to date
0
Altmetric
Review

Mapping and analyzing the human liver proteome: progress and potential

, , , , , , , , & show all
Pages 833-843 | Received 24 Apr 2016, Accepted 12 Jul 2016, Published online: 02 Aug 2016

References

  • He FC. Systematic deciphering of human liver proteome. J Hepatol. 2008;48:S165–S165.
  • Gao X, Zhang XL, Zheng JJ, et al. Proteomics in China: ready for prime time. Sci China Life Sci. 2010;53(1):22–33.
  • He FC, Chung MCM, Jordan TW. Chinese human liver proteome project: a pathfinder of HUPO human liver proteome project. J Proteome Res. 2010;9(1):1–2.
  • Mato JM, He FC, Beretta L. The 2006 Human Liver Proteome Project (HLPP) workshops. Proteomics Clin Appl. 2007;1(5):442–445.
  • Chen M, Yang B, Ying WT, et al. Annotation of non-synonymous single polymorphisms in human liver proteome by mass spectrometry. Protein Pept Lett. 2010;17(3):277–286.
  • He F. At a glance: proteomics in China. Sci China Life Sci. 2011;54(1):1–2.
  • Sun AH, Jiang Y, Wang X, et al. Liverbase: a comprehensive view of human liver biology. J Proteome Res. 2010;9(1):50–58.
  • Li N, Xu ZW, Zhai LH, et al. Rapid development of proteomics in China: from the perspective of the human liver proteome project and technology development. Sci China Life Sci. 2014;57(12):1162–1171.
  • He FC. The PHOENIX Center: the hub of proteomics in the age of big data. Nature. 2015;527:7576.
  • Leng F. Opportunity and challenge: ten years of proteomics in China. Sci China Life Sci. 2012;55(9):837–839.
  • Choudhary C, Kumar C, Gnad F, et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009;325(5942):834–840.
  • Zhao S, Xu W, Jiang W, et al. Regulation of cellular metabolism by protein lysine acetylation. Science. 2010;327(5968):1000–1004.
  • Kim SC, Sprung R, Chen Y, et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell. 2006;23(4):607–618.
  • Wang Q, Zhang Y, Yang C, et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science. 2010;327(5968):1004–1007.
  • Cao J, Shen C, Wang H, et al. Identification of N-glycosylation sites on secreted proteins of human hepatocellular carcinoma cells with a complementary proteomics approach. J Proteome Res. 2009;8(2):662–672.
  • Ruhaak LR, Zauner G, Huhn C, et al. Glycan labeling strategies and their use in identification and quantification. Anal Bioanal Chem. 2010;397(8):3457–3481.
  • Xiong Z, Qin H, Wan H, et al. Layer-by-layer assembly of multilayer polysaccharide coated magnetic nanoparticles for the selective enrichment of glycopeptides. Chem Commun (Camb). 2013;49(81):9284–9286.
  • Liu J, Wang F, Lin H, et al. Monolithic capillary column based glycoproteomic reactor for high-sensitive analysis of N-glycoproteome. Anal Chem. 2013;85(5):2847–2852.
  • Ma C, Zhao X, Han H, et al. N-linked glycoproteome profiling of human serum using tandem enrichment and multiple fraction concatenation. Electrophoresis. 2013;34(16):2440–2450.
  • Qu Y, Xia S, Yuan H, et al. Integrated sample pretreatment system for N-linked glycosylation site profiling with combination of hydrophilic interaction chromatography and PNGase F immobilized enzymatic reactor via a strong cation exchange precolumn. Anal Chem. 2011;83(19):7457–7463.
  • Zhao Y, Jia W, Wang J, et al. Fragmentation and site-specific quantification of core fucosylated glycoprotein by multiple reaction monitoring-mass spectrometry. Anal Chem. 2011;83(22):8802–8809.
  • Zhang Y, Zhang C, Jiang H, et al. Fishing the PTM proteome with chemical approaches using functional solid phases. Chem Soc Rev. 2015;44(22):8260–8287.
  • Liu L, Zhang Y, Zhang L, et al. Highly specific revelation of rat serum glycopeptidome by boronic acid-functionalized mesoporous silica. Anal Chim Acta. 2012;753:64–72.
  • Zhang L, Xu Y, Yao H, et al. Boronic acid functionalized core-satellite composite nanoparticles for advanced enrichment of glycopeptides and glycoproteins. Chemistry. 2009;15(39):10158–10166.
  • Wang Y, Liu M, Xie L, et al. Highly efficient enrichment method for glycopeptide analyses: using specific and nonspecific nanoparticles synergistically. Anal Chem. 2014;86(4):2057–2064.
  • Liu L, Yu M, Zhang Y, et al. Hydrazide functionalized core-shell magnetic nanocomposites for highly specific enrichment of N-glycopeptides. ACS Appl Mater Interfaces. 2014;6(10):7823–7832.
  • Zhang Y, Kuang M, Zhang L, et al. An accessible protocol for solid-phase extraction of N-linked glycopeptides through reductive amination by amine-functionalized magnetic nanoparticles. Anal Chem. 2013;85(11):5535–5541.
  • Zhang Y, Yu M, Zhang C, et al. Highly selective and ultra fast solid-phase extraction of N-glycoproteome by oxime click chemistry using aminooxy-functionalized magnetic nanoparticles. Anal Chem. 2014;86(15):7920–7924.
  • Zhang W, Wang H, Zhang L, et al. Large-scale assignment of N-glycosylation sites using complementary enzymatic deglycosylation. Talanta. 2011;85(1):499–505.
  • Zhang W, Wang H, Tang H, et al. Endoglycosidase-mediated incorporation of 18O into glycans for relative glycan quantitation. Anal Chem. 2011;83(12):4975–4981.
  • Wang H, Li H, Zhang W, et al. Multiplex profiling of glycoproteins using a novel bead-based lectin array. Proteomics. 2014;14(1):78–86.
  • Wang H, Zhang W, Zhao J, et al. N-Glycosylation pattern of recombinant human CD82 (KAI1), a tumor-associated membrane protein. J Proteomics. 2012;75(4):1375–1385.
  • Li H, Shen H, Yan G, et al. Site-specific structural characterization of O-glycosylation and identification of phosphorylation sites of recombinant osteopontin. Biochim Biophys Acta. 2015;1854(6):581–591.
  • Liu Z, Cao J, He Y, et al. Tandem 18O stable isotope labeling for quantification of N-glycoproteome. J Proteome Res. 2010;9(1):227–236.
  • Zhang W, Cao W, Huang J, et al. PNGase F-mediated incorporation of (18)O into glycans for relative glycan quantitation. Analyst. 2015;140(4):1082–1089.
  • Cao W, Zhang W, Huang J, et al. Glycan reducing end dual isotopic labeling (GREDIL) for mass spectrometry-based quantitative N-glycomics. Chem Commun (Camb). 2015;51(71):13603–13606.
  • Liu M, Zhang Y, Chen Y, et al. Efficient and accurate glycopeptide identification pipeline for high-throughput site-specific N-glycosylation analysis. J Proteome Res. 2014;13(6):3121–3129.
  • Cao W, Cao J, Huang J, et al. Enhanced N-glycosylation site exploitation of sialoglycopeptides by peptide IPG-IEF assisted TiO2 chromatography. Glycoconj J. 2012;29(5–6):433–443.
  • Kaji H, Saito H, Yamauchi Y, et al. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol. 2003;21(6):667–672.
  • Segu ZM, Hussein A, Novotny MV, et al. Assigning N-glycosylation sites of glycoproteins using LC/MSMS in conjunction with endo-M/exoglycosidase mixture. J Proteome Res. 2010;9(7):3598–3607.
  • Andre M, Morelle W, Planchon S, et al. Glycosylation status of the membrane protein CD9P-1. Proteomics. 2007;7(21):3880–3895.
  • Tie JK, Zheng MY, Pope RM, et al. Identification of the N-linked glycosylation sites of vitamin K-dependent carboxylase and effect of glycosylation on carboxylase function. Biochemistry. 2006;45(49):14755–14763.
  • Wedepohl S, Kaup M, Riese SB, et al. N-glycan analysis of recombinant L-Selectin reveals sulfated GalNAc and GalNAc-GalNAc motifs. J Proteome Res. 2010;9(7):3403–3411.
  • Tonoli H, Barrett JC. CD82 metastasis suppressor gene: a potential target for new therapeutics? Trends Mol Med. 2005;11(12):563–570.
  • Rodrigues LR, Teixeira JA, Schmitt FL, et al. The role of osteopontin in tumor progression and metastasis in breast cancer. Cancer Epidemiol Biomarkers Prev. 2007;16(6):1087–1097.
  • Minai-Tehrani A, Chang SH, Park SB, et al. The oglycosylation mutant osteopontin alters lung cancer cell growth and migration in vitro and in vivo. Int J Mol Med. 2013;32(5):1137–1149.
  • Sun W, Zhong F, Zhi LT, et al. Systematic -omics analysis of HBV-associated liver diseases. Cancer Lett. 2009;286(1):89–95.
  • Coleman O, Henry M, McVey G, et al. Proteomic strategies in the search for novel pancreatic cancer biomarkers and drug targets: recent advances and clinical impact. Expert Rev Proteomics. 2016;13(4):383–394.
  • Long X, Zhang J, Zhang Y, et al. Nano-LC-MS/MS based proteomics of hepatocellular carcinoma cells compared to Chang liver cells and tanshinone IIA induction. Mol Biosyst. 2011;7(5):1728–1741.
  • Yu Y, Shen H, Yu H, et al. Systematic proteomic analysis of human hepotacellular carcinoma cells reveals molecular pathways and networks involved in metastasis. Mol Biosyst. 2011;7(6):1908–1916.
  • Li Y, Tang ZY, Ye SL, et al. Establishment of cell clones with different metastatic potential from the metastatic hepatocellular carcinoma cell line MHCC97. World J Gastroenterol. 2001;7(5):630–636.
  • Li Y, Tang Y, Ye L, et al. Establishment of a hepatocellular carcinoma cell line with unique metastatic characteristics through in vivo selection and screening for metastasis-related genes through cDNA microarray. J Cancer Res Clin Oncol. 2003;129(1):43–51.
  • Shen C, Yu Y, Li H, et al. Global profiling of proteolytically modified proteins in human metastatic hepatocellular carcinoma cell lines reveals CAPN2 centered network. Proteomics. 2012;12(12):1917–1927.
  • Cao J, Shen C, Zhang J, et al. Comparison of alternative extraction methods for secretome profiling in human hepatocellular carcinoma cells. Sci China Life Sci. 2011;54(1):34–38.
  • Yu Y, Pan X, Ding Y, et al. An iTRAQ based quantitative proteomic strategy to explore novel secreted proteins in metastatic hepatocellular carcinoma cell lines. Analyst. 2013;138(16):4505–4511.
  • Zhang HY, Wu P, Chen FY, et al. SILAC-based quantitative proteomic analysis of secretome between activated and reverted hepatic stellate cells. Proteomics. 2014;14(17–18):1977–1986.
  • Yin X, Zhang Y, Liu X, et al. Systematic comparison between SDS-PAGE/RPLC and high-/low-pH RPLC coupled tandem mass spectrometry strategies in a whole proteome analysis. Analyst. 2015;140(4):1314–1322.
  • Shen H, Zhong F, Zhang Y, et al. Transcriptome and proteome of human hepatocellular carcinoma reveal shared metastatic pathways with significant genes. Proteomics. 2015;15(11):1793–1800.
  • Feng L, Li H, Zhang Y, et al. Metastasis-related genes in hepatocellular carcinoma cell-lines are clustered on chromosome territories predicted by transcriptome and proteome. Sci China-Chemistry. 2016;59(3):380–382.
  • Lu Y, Liu J, Lin C, et al. Peroxiredoxin 2: a potential biomarker for early diagnosis of hepatitis B virus related liver fibrosis identified by proteomic analysis of the plasma. BMC Gastroenterol. 2010;10:115.
  • Li SL, Liu X, Wei L, et al. Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy. Sci China-Life Sci. 2011;54(5):393–402.
  • Kang XN, Sun L, Guo K, et al. Serum protein biomarkers screening in HCC patients with liver cirrhosis by ICAT-LC-MS/MS. J Cancer Res Clin Oncol. 2010;136(8):1151–1159.
  • Shu H, Kang XN, Guo K, et al. Diagnostic value of serum haptoglobin protein as hepatocellular carcinoma candidate marker complementary to alpha fetoprotein. Oncol Rep. 2010;24(5):1271–1276.
  • Zhang S, Jiang K, Sun C, et al. Quantitative analysis of site-specific N-glycans on sera haptoglobin beta chain in liver diseases. Acta Biochim Biophys Sin. 2013;45(12):1021–1029.
  • Zhang S, Shu H, Luo KX, et al. N-linked glycan changes of serum haptoglobin beta chain in liver disease patients. Mol Biosyst. 2011;7(5):1621–1628.
  • Jin GZ, Li Y, Cong WM, et al. iTRAQ-2DLC-ESI-MS/MS based identification of a new set of immunohistochemical biomarkers for classification of dysplastic nodules and small hepatocellular carcinoma. J Proteome Res. 2011;10(8):3418–3428.
  • Yu H, Zhao J, Lin L, et al. Proteomic study explores AGR2 as pro-metastatic protein in HCC. Mol Biosyst. 2012;8(10):2710–2718.
  • Lin L, Han MM, Wang F, et al. CXCR7 stimulates MAPK signaling to regulate hepatocellular carcinoma progression. Cell Death Dis. 2014;5:e1488.
  • Sun C, Sun L, Li Y, et al. Sox2 expression predicts poor survival of hepatocellular carcinoma patients and it promotes liver cancer cell invasion by activating Slug. Med Oncol. 2013;30(2):1–10.
  • Sun C, Sun L, Jiang K, et al. NANOG promotes liver cancer cell invasion by inducing epithelial-mesenchymal transition through NODAL/SMAD3 signaling pathway. Int J Biochem Cell Biol. 2013;45(6):1099–1108.
  • Yu H, Shen H, Zhang Y, et al. CAV1 promotes HCC cell progression and metastasis through Wnt/beta-catenin pathway. PLoS One. 2014;9(9):e106451.
  • Zhang S, Jiang K, Zhang QL, et al. Serum fucosylated paraoxonase 1 as a potential glycobiomarker for clinical diagnosis of early hepatocellular carcinoma using ELISA index. Glycoconj J. 2015;32(3–4):119–125.
  • Jiang K, Shang SX, Li W, et al. Multiple lectin assays for detecting glyco-alteration of serum GP73 in liver diseases. Glycoconj J. 2015;32(9):657–664.
  • Zhang QL, Jiang K, Li Y, et al. Histidine-rich glycoprotein function in hepatocellular carcinoma depends on its N-glycosylation status, and it regulates cell proliferation by inhibiting Erk1/2 phosphorylation. Oncotarget. 2015;6(30):30222–30231.
  • Wu SF, Li N, Ma J, et al. First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon. J Proteome Res. 2013;12(1):67–80.
  • Zhang CP, Li N, Zhai LH, et al. Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1. J Proteome Res. 2014;13(1):114–125.
  • Zhang Y, Yan GQ, Zhai LH, et al. Proteome atlas of human chromosome 8 and its multiple 8p deficiencies in tumorigenesis of the stomach, colon, and liver. J Proteome Res. 2013;12(1):81–88.
  • Chang C, Li LW, Zhang CP, et al. Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP. J Proteome Res. 2014;13(1):38–49.
  • Liu Y, Ying WT, Ren Z, et al. Chromosome-8-coded proteome of Chinese Chromosome Proteome Data Set (CCPD) 2.0 with partial immunohistochemical verifications. J Proteome Res. 2014;13(1):126–136.
  • Chen C, Liu X, Zheng W, et al. Screening of missing proteins in the human liver proteome by improved MRM-approach-based targeted proteomics. J Proteome Res. 2014;13(4):1969–1978.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.