51
|
Lee HJ, Kang MJ, Lee EY, Cho SY, Kim H, Paik YK. Application of a peptide-based PF2D platform for quantitative proteomics in disease biomarker discovery. Proteomics 2008; 8:3371-81. [PMID: 18651672 DOI: 10.1002/pmic.200800111] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A peptide-based 2-D liquid phase fractionation (PF2D) system was used in a quantitative proteomic analysis of hepatocellular carcinoma. 2-D liquid maps of peptide specimens showed better resolution than those of proteins, leading to the identification of differentially expressed proteins. Peptide-based PF2D gave well-matched theoretical and experimental pI values and was proven to be a very efficient and versatile analytical tool for both large-scale profiling and quantification of phosphoproteins in disease biomarker discovery.
Collapse
Affiliation(s)
- Hyoung-Joo Lee
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Seoul, Korea
| | | | | | | | | | | |
Collapse
|
52
|
Zubaidah RM, Tan GS, Tan SBE, Lim SG, Lin Q, Chung MCM. 2-D DIGE profiling of hepatocellular carcinoma tissues identified isoforms of far upstream binding protein (FUBP) as novel candidates in liver carcinogenesis. Proteomics 2008; 8:5086-96. [PMID: 19003864 DOI: 10.1002/pmic.200800322] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
53
|
Youn P, Kim S, Ahn JH, Kim Y, Park JD, Ryu DY. Regulation of iron metabolism-related genes in diethylnitrosamine-induced mouse liver tumors. Toxicol Lett 2008; 184:151-8. [PMID: 19061943 DOI: 10.1016/j.toxlet.2008.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 11/05/2008] [Accepted: 11/07/2008] [Indexed: 01/12/2023]
Abstract
BACKGROUND It has been suggested that the altered iron metabolism in liver tumors, characterized by the iron-deficient phenotype, is of importance for tumor growth. AIM This study was performed to elucidate the mechanisms underlying iron deficiency in liver tumors by examining how the liver tumor development affects the expression of iron metabolism-related genes. METHODS Iron metabolism reference values were analyzed in the sera of diethylnitrosamine-induced hepatocellular adenoma-bearing mice. Expression of iron metabolism-related genes was analyzed in adenomas and surrounding non-tumor tissues, and a subgroup of adenoma-bearing mice loaded with iron 72h before sacrifice. RESULTS Iron content of the adenoma tissues was 2.0-2.5-fold lower compared to surrounding and age-matched control tissues. There was no significant difference in serum iron levels between the adenoma-bearing and control mice, while the adenoma-bearing mice exhibited a 2.4-fold lower level of serum transferrin saturation. Expression of iron metabolism-related genes was dysregulated in the adenomas. Iron loading affected protein expression similarly in the adenomas and surrounding tissues suggesting that iron-responsive regulation of the proteins was not impaired. However, the mRNA expression for ceruloplasmin and divalent metal transporter 1 (DMT1) IRE(+) in the adenomas was altered independently of iron status, and the dysregulation may contribute to diminished iron content. CONCLUSION These findings suggest that diethylnitrosamine-induced liver adenoma-bearing mice have abnormal iron metabolism and that dysregulation of iron metabolism-related genes contributes to iron deficiency in the adenomas.
Collapse
Affiliation(s)
- Pilju Youn
- College of Veterinary Medicine, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | | | | | | | | | | |
Collapse
|
54
|
Abstract
At present, studies of hepatocellular carcinoma focus on investigating the molecular mechanism of carcinogenesis, development, metastasis and reccurrence and seeking biological markers for early diagnosis and metastasis prediction and targets for interfering therapy. In the post-genome era, proteomics provides novel insights into the research of hepatocellular carcinoma, which is controlled by multi-genes and multi-proteins. In this paper we reviewed the recent progress in proteomic study of hepatocellular carcinoma.
Collapse
|
55
|
Vivekanandan P, Singh OV. High-dimensional biology to comprehend hepatocellular carcinoma. Expert Rev Proteomics 2008; 5:45-60. [PMID: 18282123 DOI: 10.1586/14789450.5.1.45] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide and is the third leading cause of death from cancer. The diverse etiology, high morbidity/mortality, lack of diagnostic markers for early diagnosis and the highly variable clinical course of HCC have hindered advances in diagnosis and treatment. Microsatellite instability, chromosomal aberrations, mutations in key cell cycle genes and epigenetic changes have been reported in HCC. Availability of modern technologies advance 'high-dimensional biology' (HDB), a term that refers to the simultaneous study of the genetic variants (genome), transcription (mRNA; transcriptome), peptides and proteins (proteomics), and metabolites (metabolomics) for the intermediate products of metabolism of an organ, tissue or organism. The growing interest in omics-based research has enabled the simultaneous examination of thousands of genes, transcripts and proteins of interest, with high-throughput techniques and advanced analytical tools for data analysis. The use of each approach towards functional omics has lead to the classification of HCC into molecular subgroups. Here we review the use of HDB as a tool for the identification of markers for screening, diagnosis, molecular classification and the discovery of new therapeutic drug targets of HCC. With the extensive use of HDB, it may be possible in the near future, to have custom-made therapeutic regimens for HCC based on the molecular subtype, ultimately leading to an improved survival of HCC patients.
Collapse
|
56
|
He M, Qin J, Zhai R, Wei X, Wang Q, Rong M, Jiang Z, Huang Y, Zhang Z. Detection and identification of NAP-2 as a biomarker in hepatitis B-related hepatocellular carcinoma by proteomic approach. Proteome Sci 2008; 6:10. [PMID: 18331625 PMCID: PMC2275230 DOI: 10.1186/1477-5956-6-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 03/10/2008] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND A lack of sensitive and specific biomarkers is a major reason for the high rate of Primary hepatocellular carcinoma (HCC)-related mortality. The aim of this study was to investigate potential proteomic biomarkers specific for HCC. METHODS 81 patients with hepatitis B-related HCC and 33 healthy controls were randomly divided into a training set (33 HCC, 33 controls) and a testing set (48 HCC, 33 controls). Serum proteomic profiles were measured using Surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy (SELDI-TOF-MS).) A classification tree was established by Biomarker Pattern Software (BPS). Candidate SELDI peaks were isolated by tricine-SDS-PAGE, identified by HPLC-MS/MS and validated by immunohistochemistry (IHC) in liver tissues. RESULTS A total of 6 proteomic peaks (3157.33 m/z, 4177.02 m/z, 4284.79 m/z, 4300.80 m/z, 7789.87 m/z, and 7984.14 m/z) were chosen by BPS to establish a classification tree with the highest discriminatory power in the training set. The sensitivity and specificity of this classification tree were 95.92%, and 100% respectively in the testing set. A candidate marker of about 7984 m/z was isolated and identified as neutrophil-activating peptide 2 (NAP-2). IHC staining showed that NAP-2 signals were positive in HCC tissues but negative in adjacent tissues. CONCLUSION The NAP-2 may be a specific proteomic biomarker of hepatitis B-related HCC.
Collapse
Affiliation(s)
- Min He
- Medical Scientific Research Center, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Jian Qin
- School of Public Health, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Rihong Zhai
- Department of Environmental Health, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Xiao Wei
- School of Public Health, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Qi Wang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Minhua Rong
- School of Public Health, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Zhihua Jiang
- School of Public Health, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Yuanjiao Huang
- Medical Scientific Research Center, Guangxi Medical University, Nanning, 530021, P. R. China
| | - Zhiyong Zhang
- School of Public Health, Guangxi Medical University, Nanning, 530021, P. R. China
| |
Collapse
|
57
|
Teramoto R, Minagawa H, Honda M, Miyazaki K, Tabuse Y, Kamijo K, Ueda T, Kaneko S. Protein expression profile characteristic to hepatocellular carcinoma revealed by 2D-DIGE with supervised learning. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:764-72. [PMID: 18359300 DOI: 10.1016/j.bbapap.2008.02.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 01/07/2008] [Accepted: 02/20/2008] [Indexed: 12/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and aggressive human malignancies. Although several major risks related to HCC, e.g., hepatitis B and/or hepatitis C virus infection, aflatoxin B1 exposure, alcohol drinking and genetic defects have been revealed, the molecular mechanisms leading to the initiation and progression of HCC have not been clarified. To reduce the mortality and improve the effectiveness of therapy, it is important to detect the proteins which are associated with tumor progression and may be useful as potential therapeutic or diagnosis targets. However, previous studies have not yet revealed the associations among HCC cells, histological grade and AFP. Here, we performed two-dimensional difference gel electrophoresis (2D-DIGE) combined with MS for 18 HCC patients. To focus not on individual proteins but on multiple proteins associated with pathogenesis, we introduce the supervised feature selection based on stochastic gradient boosting (SGB) for identifying protein spots that discriminate HCC/non HCC, histological grade of moderate/well and high alpha-fetoprotein (AFP)/low AFP level without arbitrariness. We detected 18, 25 and 27 protein spots associated with HCC, histological grade and AFP level, respectively. We confirmed that SGB is able to identify the known HCC-related proteins, e.g., heat shock proteins, carbonic anhydrase 2. Moreover, we identified the differentially expressed proteins associated with histological grade of HCC and AFP level and found that aldo-keto reductase 1B10 (AKR1B10) is related to well differentiated HCC, keratin 8 (KRT8) is related to both histological grade and AFP level and protein disulfide isomerase-associated 3 (PDIA3) is associated with both HCC and AFP level. Our pilot study provides new insights on understanding the pathogenesis of HCC, histological grade and AFP level.
Collapse
Affiliation(s)
- Reiji Teramoto
- Bio-IT Center, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki 305-8501, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
58
|
Chen CY, Tsai WL, Wu HC, Syu MJ, Wu CC, Shiesh SC. Diagnostic role of biliary pancreatic elastase for cholangiocarcinoma in patients with cholestasis. Clin Chim Acta 2008; 390:82-9. [PMID: 18252202 DOI: 10.1016/j.cca.2008.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 01/01/2008] [Accepted: 01/02/2008] [Indexed: 01/10/2023]
Abstract
BACKGROUND A wide array of proteins is secreted into the bile and may be associated with biliary tract diseases. We attempted to discover novel biomarker in bile for cholangiocarcinoma. METHODS Bile was collected from patients with bile duct obstruction. Proteins were separated by 2-dimensional electrophoresis and identified by mass spectrometry. Levels of mRNA and protein expression of the candidate biomarker were analyzed by real-time PCR and Western blotting, respectively, whereas enzyme activity was measured by a kinetic method. The diagnostic efficacy was assessed by receiver operating characteristic (ROC) curve analysis. RESULTS Pancreatic elastase (PE) 3B was identified as a biomarker for cholangiocarcinoma. The mRNA of PE 3B was up-regulated in cancerous tissues, compared to non-cancerous tissues. The protein expression and enzyme activity of PE in bile were increased in patients with cholangiocarcinoma, compared to gallstone patients. Biliary amylase activity was used to correct the presence of pancreaticobiliary reflux. Significantly higher PE/amylase ratios in bile were found in patients with cholangiocarcinoma (0.214+/-0.045) than those with gallstone (0.023+/-0.005, p<0.001). The area under the ROC curve of the ratio was 0.877 (95% CI: 0.765 to 0.988). Using 0.065 as a cutoff value, the ratio distinguished malignant from benign causes of biliary obstruction with a sensitivity of 82% and a specificity of 89%. CONCLUSION PE in bile is a biomarker for cholangiocarcinoma and the combination measurement of PE and amylase enhances diagnostic efficacy.
Collapse
Affiliation(s)
- Chiung-Yu Chen
- Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | | | | | | |
Collapse
|
59
|
Li C, Tan YX, Ai JH, Zhou H, Li SJ, Zhang L, Xia QC, Wu JR, Wang HY, Zeng R. Analysis of microdissected cells by two-dimensional LC-MS approaches. Methods Mol Biol 2008; 428:193-208. [PMID: 18287775 DOI: 10.1007/978-1-59745-117-8_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Laser capture microdissection (LCM) is a powerful tool that enables the isolation of specific cell types from tissue sections, overcoming the problem of tissue heterogeneity and contamination. We combined the LCM with isotope-coded affinity tag (ICAT) technology and two-dimensional liquid chromatography to investigate the qualitative and quantitative proteomes of hepatocellular carcinoma (HCC). The effects of three different histochemical stains on tissue sections have been compared, and toluidine blue stain was proved as the most suitable stain for LCM followed by proteomic analysis. The solubilized proteins from microdissected HCC and non-HCC hepatocytes were qualitatively and quantitatively analyzed with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) alone or coupled with cleavable isotope-coded affinity tag (cICAT) labeling technology. A total of 644 proteins were qualitatively identified and 261 proteins were unambiguously quantified. These results showed that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.
Collapse
Affiliation(s)
- Chen Li
- Research Center for Proteome Analysis, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
60
|
Cho SY, Lee EY, Kim HY, Kang MJ, Lee HJ, Kim H, Paik YK. Protein profiling of human plasma samples by two-dimensional electrophoresis. Methods Mol Biol 2008; 428:57-75. [PMID: 18287768 DOI: 10.1007/978-1-59745-117-8_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Human plasma is regarded the most complex and well-known clinical specimen that can be easily obtained; alterations in the levels of plasma proteins or their corresponding enzyme activities may reflect either a healthy or a diseased state. Given that there is no defined genomic information as to the intact protein components in plasma, protein profiling could be the first step toward its molecular characterization. Several problems exist in the analysis of plasma proteins, however. For example, the widest dynamic range of protein concentrations, the presence of high-abundance proteins, and post-translational modifications need to be considered before proteomic studies are undertaken. In particular, efficient depletion or pre-fractionation of high-abundance proteins is crucial for the identification of low-abundance proteins that may contain potential biomarkers. After the removal of high-abundance proteins, protein profiling can be initiated using two-dimensional electrophoresis (2DE), which has been widely used for displaying the differential proteome under specific physiological conditions. Here, we describe a typical 2DE procedure for plasma proteome under either a healthy or a diseased state (e.g., liver cancer) in which pre-fractionation and depletion are integral steps in the search for disease biomarkers.
Collapse
Affiliation(s)
- Sang Yun Cho
- Department of Biochemistry, College of Sciences, Yonsei Biomedical Proteome Research Center, Seoul, Korea
| | | | | | | | | | | | | |
Collapse
|
61
|
Paik YK, Kim H, Lee EY, Kwon MS, Cho SY. Overview and introduction to clinical proteomics. Methods Mol Biol 2008; 428:1-31. [PMID: 18287765 DOI: 10.1007/978-1-59745-117-8_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As the field of clinical proteomics progresses, discovery of disease biomarkers becomes paramount. However, the immediate challenges are to establish standard operating procedures for both clinical specimen handling and reduction of sample complexity and to increase the ability to detect proteins and peptides present in low amounts. The traditional concept of a disease biomarker is shifting toward a new paradigm, namely, that an ensemble of proteins or peptides would be more efficient than a single protein/peptide in the diagnosis of disease. Because clinical proteomics usually requires easy access to well-defined fresh clinical specimens (including morphologically consistent tissue and properly pretreated body fluids of sufficient quantity), biorepository systems need to be established. Here, we address these questions and emphasize the necessity of developing various microdissection techniques for tissue specimens, multidimensional fractionation for body fluids, and other related techniques (including bioinformatics), tools which could become integral parts of clinical proteomics for disease biomarker discovery.
Collapse
Affiliation(s)
- Young-Ki Paik
- Department of Biochemistry, Yonsei Proteome Research Center & Biomedical Proteome Research Center, Seoul, Korea
| | | | | | | | | |
Collapse
|
62
|
Sun S, Lee NPY, Poon RTP, Fan ST, He QY, Lau GK, Luk JM. Oncoproteomics of hepatocellular carcinoma: from cancer markers' discovery to functional pathways. Liver Int 2007; 27:1021-38. [PMID: 17845530 DOI: 10.1111/j.1478-3231.2007.01533.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a heterogeneous cancer with no promising treatment and remains one of the most prevailing and lethal malignancies in the world. Researchers in many biological areas now routinely identify and characterize protein markers by a mass spectrometry-based proteomic approach, a method that has been commonly used to discover diagnostic biomarkers for cancer detection. The proteomic research platforms span from the classical two-dimensional polyacrylamide gel electrophoresis (2-DE) to the latest Protein Chip or array technology, which are often integrated with the MALDI (matrix-assisted laser-desorption ionization), SELDI (surface-enhanced laser desorption/ionization) or tandem mass spectrometry (MS/MS). New advances on quantitative proteomic analysis (e.g. SILAC, ICAT, and ITRAQ) and multidimensional protein identification technology (MudPIT) have greatly enhanced the capability of proteomic methods to study the expressions, modifications and functions of protein markers. The present article reviews the latest proteomic development and discovery of biomarkers in HCC that may provide insights into the underlying mechanisms of hepatocarcinogenesis and the readiness of biomarkers for clinical uses.
Collapse
Affiliation(s)
- Stella Sun
- Department of Surgery, LKS Faculty of Medicine, Jockey Club Clinical Research Center, The University of Hong Kong, Pokfulam, Hong Kong
| | | | | | | | | | | | | |
Collapse
|
63
|
Sun W, Xing B, Sun Y, Du X, Lu M, Hao C, Lu Z, Mi W, Wu S, Wei H, Gao X, Zhu Y, Jiang Y, Qian X, He F. Proteome analysis of hepatocellular carcinoma by two-dimensional difference gel electrophoresis: novel protein markers in hepatocellular carcinoma tissues. Mol Cell Proteomics 2007; 6:1798-808. [PMID: 17627933 DOI: 10.1074/mcp.m600449-mcp200] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant tumor, and chronic infection with hepatitis B virus is one of its major risk factors. To identify the proteins involved in HCC carcinogenesis, we used two-dimensional fluorescence DIGE to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples from 12 hepatitis B virus-associated HCC patients were analyzed. A total of 61 spots were significantly up-regulated (ratio >/= 2, p </= 0.01) in tumor samples, whereas 158 spots were down-regulated (ratio </= -2, p </= 0.01). Seventy-one gene products were identified among these spots. Members of the heat shock protein 70 and 90 families were simultaneously up-regulated, whereas metabolism-associated proteins were decreased in HCC samples. The down-regulation of mitochondrial and peroxisomal proteins in these results suggested loss of special organelle functions during HCC carcinogenesis. Four metabolic enzymes involved in the methylation cycle in the liver were down-regulated in HCC tissues, indicating S-adenosylmethionine deficiency in HCC. Two gene products, glyceraldehyde-3-phosphate dehydrogenase and formimidoyltransferase-cyclodeaminase, were identified from inversely altered spots, suggesting that different isoforms or post-translational modifications of these two proteins might play different roles in HCC. For the first time, the overexpression of Hcp70/Hsp90-organizing protein and heterogeneous nuclear ribonucleoproteins C1/C2 in HCC tissues was confirmed by Western blot and then by immunohistochemistry staining in 70 HCC samples, suggesting their potential as protein tumor markers. In summary, we profiled proteome alterations in HCC tissues, and these results may provide useful insights for understanding the mechanism involved in the process of HCC carcinogenesis.
Collapse
MESH Headings
- Adult
- Amino Acid Sequence
- Ammonia-Lyases/metabolism
- Biomarkers, Tumor/analysis
- Blotting, Western
- Carcinoma, Hepatocellular/chemistry
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Down-Regulation
- Electrophoresis, Gel, Two-Dimensional/methods
- Female
- Gene Expression Regulation, Neoplastic
- Heat-Shock Proteins/chemistry
- Heat-Shock Proteins/metabolism
- Heterogeneous-Nuclear Ribonucleoproteins/chemistry
- Heterogeneous-Nuclear Ribonucleoproteins/metabolism
- Humans
- Immunohistochemistry
- Male
- Middle Aged
- Molecular Sequence Data
- Neoplasm Proteins/analysis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/isolation & purification
- Proteome/analysis
- Reproducibility of Results
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Subcellular Fractions
Collapse
Affiliation(s)
- Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, P.R. China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
64
|
Dos Santos A, Thiers V, Sar S, Derian N, Bensalem N, Yilmaz F, Bralet MP, Ducot B, Bréchot C, Demaugre F. Contribution of laser microdissection-based technology to proteomic analysis in hepatocellular carcinoma developing on cirrhosis. Proteomics Clin Appl 2007; 1:545-54. [PMID: 21136705 DOI: 10.1002/prca.200600474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Indexed: 11/10/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major cause of cancer worldwide. Proteomic studies provide opportunities to uncover targets for the diagnosis and treatment of this disease. However, in HCC developing in a setting of cirrhosis, the detection of proteome alterations may be hampered by the increased cellular heterogeneity of tissue when analysing global liver homogenates. The aim of this study was to evaluate whether the identification of proteome alterations in these HCC cases was improved when the differential protein profile between tumour and non-tumour areas of liver was determined using hepatocytes isolated by laser microdissection (LM). Differential profiles established with LM-hepatocytes and liver section homogenates using 2-DE and MS exhibited noticeable differences: 30% of the protein spots with deregulated expression in tumorous LM-samples did not display any modification in homogenates; conversely 15% of proteins altered in tumorous homogenates were not impaired in LM-hepatocytes. These alterations resulted from the presence in cirrhotic liver of fibrotic stroma which displayed a protein pattern different from that determined in LM-hepatocytes. In conclusion, our data demonstrate the interest of LM in distinguishing between fibrotic and hepatocyte proteome alterations and thus the benefit of LM to proteome studies of HCC developing in a context of cirrhosis.
Collapse
|
65
|
Clifton JG, Li X, Reutter W, Hixson DC, Josic D. Comparative proteomics of rat liver and Morris hepatoma 7777 plasma membranes. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:293-301. [PMID: 16987716 DOI: 10.1016/j.jchromb.2006.08.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 08/16/2006] [Accepted: 08/21/2006] [Indexed: 01/01/2023]
Abstract
Plasma membranes from normal rat liver and hepatocellular carcinoma Morris hepatoma 7777 were selectively solubilized by use of different reagents. After selective solubilization, proteins were identified by nano-HPLC-electrospray ionization tandem mass spectrometry (LC-ESI MS/MS). Using simple software, the patterns of proteins identified in membrane solubilizates from liver and hepatoma were compared. Proteins identified in Morris hepatoma 7777 and not in the corresponding membrane solubilizate from liver, mostly members of the annexin and heat shock protein families, are discussed as potential candidate markers for hepatocellular carcinomas.
Collapse
Affiliation(s)
- James G Clifton
- Proteomics Core, COBRE Center for Cancer Research Development, Rhode Island Hospital, 1 Hoppin Street, Providence, RI 02903, USA
| | | | | | | | | |
Collapse
|
66
|
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics 2007; 8:66. [PMID: 17326819 PMCID: PMC1828168 DOI: 10.1186/1471-2105-8-66] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 02/27/2007] [Indexed: 02/02/2023] Open
Abstract
Background The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Results Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO , to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. Conclusion This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment.
Collapse
|
67
|
Kuramitsu Y, Nakamura K. Proteomic analysis of cancer tissues: shedding light on carcinogenesis and possible biomarkers. Proteomics 2007; 6:5650-61. [PMID: 16972299 DOI: 10.1002/pmic.200600218] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Lung, gastric, colorectal, pancreatic, and esophageal cancers, as well as hepatocellular carcinoma (HCC), were the six most common and highly fatal cancers for Japanese men in Japan in 2003, while for women uterine cervical cancer could also be added to this list. To identify diagnostic or therapeutic biomarkers for these cancers, investigators are nowadays performing proteomic analyses of cancer tissues and cells, and revealing a large number of molecules which are diagnostic, prognostic and informative of carcinogenesis. From reports of proteomic analyses of cancerous tissues and noncancerous tissues sampled from HCC, and pancreatic, esophageal, gastric, colorectal, lung and uterine cervical cancers, we classified the proteins into digestive enzymes, growth factors, cell adhesion molecules, calcium-binding proteins, proteases, protease inhibitors, transporter proteins, structural molecules, apoptosis inhibitor, molecular chaperone, as well as proteins related to cell growth, cell differentiation, cell transformation, tumor invasion, carcinogen metabolism, and others. The aim of this study was to understand carcinogenesis of major cancers from a proteomics perspective using samples from cancer patients, and to elucidate their tumor biomarkers.
Collapse
Affiliation(s)
- Yasuhiro Kuramitsu
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | | |
Collapse
|
68
|
Kuramitsu Y, Nakamura K. Current progress in proteomic study of hepatitis C virus-related human hepatocellular carcinoma. Expert Rev Proteomics 2007; 2:589-601. [PMID: 16097891 DOI: 10.1586/14789450.2.4.589] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Chronic infection with hepatitis C virus (HCV) is known to be a risk factor for not only cirrhosis and steatosis but also hepatocellular carcinoma (HCC). A number of diagnostic and prognostic molecular markers are being identified by transcriptomic and proteomic analysis of HCC today. However, the analyses are performed on HCC in general, and the studied tissues are HCV infected, HBV infected, infected with both or neither, or the infection status may be unknown. The authors performed proteomic analysis of cancerous and noncancerous tissues from HCC patients with HCV infection, and determined that, in the cancerous tissues, HSP70 family proteins such as GRP78, HSC70, GRP75 and HSP70.1, glutaine synthetase isoforms, HSP60, alpha-enolase, phosphoglycerate mutase 1, ATP synthetase beta chain and triosephosphate isomerase were increased whereas albumin, ferritin light chain, smoothelin, tropomyosin beta chain, arginase 1, aldolase B and kietohexokinase were decreased. The aim of this study is to understand the pathogenesis of HCV-HCC using proteomic analysis of samples from HCV-HCC patients on which transcriptomics has already been performed.
Collapse
Affiliation(s)
- Yasuhiro Kuramitsu
- Department of Biochemistry and Biomolecular Recognition, Yamaguchi University School of Medicine, Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan.
| | | |
Collapse
|
69
|
Göbel T, Vorderwülbecke S, Hauck K, Fey H, Häussinger D, Erhardt A. New multi protein patterns differentiate liver fibrosis stages and hepatocellular carcinoma in chronic hepatitis C serum samples. World J Gastroenterol 2006; 12:7604-12. [PMID: 17171788 PMCID: PMC4088041 DOI: 10.3748/wjg.v12.i47.7604] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify a multi serum protein pattern as well as single protein markers using surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) for detection and differentiation of liver fibrosis (F1-F2), liver cirrhosis (F4) and hepatocellular carcinoma (HCC) in patients with chronic hepatitis C virus (HCV).
METHODS: Serum samples of 39 patients with F1/F2 fibrosis, 44 patients with F4 fibrosis, 34 patients with HCC were applied to CM10 arrays and analyzed using the SELDI-TOF ProteinChip System (PBS-IIc; Ciphergen Biosystems) after anion-exchange fractionation. All patients had chronic hepatitis C and histologically confirmed fibrosis stage/HCC. Data were analyzed for protein patterns by multivariate statistical techniques and artificial neural networks.
RESULTS: A 4 peptide/protein multimarker panel (7486, 12 843, 44 293 and 53 598 Da) correctly identified HCCs with a sensitivity of 100% and specificity of 85% in a two way-comparison of HCV-cirrhosis versus HCV-HCC training samples (AUROC 0.943). Sensitivity and specificity for identification of HCC were 68% and 80% for random test samples. Cirrhotic patients could be discriminated against patients with F1 or F2 fibrosis using a 5 peptide/protein multimarker pattern (2873, 6646, 7775, 10 525 and 67 867 Da) with a specificity of 100% and a sensitivity of 85% in training samples (AUROC 0.976) and a sensitivity and specificity of 80% and 67% for random test samples. Combination of the biomarker classifiers with APRI score and alfa-fetopotein (AFP) improved the diagnostic performance. The 6646 Da marker protein for liver fibrosis was identified as apolipoprotein C-I.
CONCLUSION: SELDI-TOF-MS technology combined with protein pattern analysis seems a valuable approach for the identification of liver cirrhosis and hepatocellular carcinoma in patients with chronic hepatitis C. Most probably a combination of different serum markers will help to identify liver cirrhosis and early-stage hepatocellular carcinomas in the future.
Collapse
Affiliation(s)
- Thomas Göbel
- Klinik für Gastroenterologie, Hepatologie und Infektiologie, Heinrich-Heine-Universität Düsseldorf, Moorenstr. 5, D-40225 Düsseldorf, Germany
| | | | | | | | | | | |
Collapse
|
70
|
Holmström P, Gåfvels M, Eriksson LC, Dzikaite V, Hultcrantz R, Eggertsen G, Stål P. Expression of iron regulatory genes in a rat model of hepatocellular carcinoma. Liver Int 2006; 26:976-85. [PMID: 16953838 DOI: 10.1111/j.1478-3231.2006.01316.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
BACKGROUND/AIMS The altered iron metabolism in hepatocellular carcinomas (HCCs), characterized by the iron-deficient phenotype, is suggested to be of importance for tumour growth. However, the underlying molecular mechanisms remain poorly understood. We asked whether these iron perturbations would involve altered expression of genes controlling iron homeostasis. METHODS HCCs were induced in rats by the Solt and Farber protocol of chemical hepatocarcinogenesis, and to evaluate the effects of iron loading, one group of animals were supplemented with dietary iron during tumour progression. Tissue iron contents were determined, labelling indices of S-phase nuclei were calculated, and mRNA levels of iron-regulatory genes were quantitated. Protein levels of ferroportin1 were determined with Western blot. RESULTS HCCs displayed reduced amount of tissue iron and lack of histologically stainable iron. HCCs expressed significantly higher mRNA levels of genes involved in iron uptake (transferrin receptor-1, divalent metal ion transporter-1), ferroxidase activity (Ferritin-H), and iron extrusion (ferroportin1). The protein levels of ferroportin1 in iron-deficient HCCs were similar as in control livers, and did not increase in HCCs exposed to iron. Hepcidin mRNA levels were decreased in iron-deficient HCCs, rose in response to iron loading and correlated to the tissue iron content. CONCLUSIONS Taken together, the altered expressions of iron-regulatory genes in HCCs possibly reflect an increased demand for bioavailable iron and a high iron turnover in neoplastic cells.
Collapse
Affiliation(s)
- Petra Holmström
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | |
Collapse
|
71
|
Lee IN, Chen CH, Sheu JC, Lee HS, Huang GT, Chen DS, Yu CY, Wen CL, Lu FJ, Chow LP. Identification of complement C3a as a candidate biomarker in human chronic hepatitis C and HCV-related hepatocellular carcinoma using a proteomics approach. Proteomics 2006; 6:2865-73. [PMID: 16586433 DOI: 10.1002/pmic.200500488] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Although the significant risk factors for hepatocellular carcinoma (HCC) are well known from epidemiological studies, diagnosis of this disease at an early stage is difficult, and HCC remains one of the leading causes of cancer death worldwide. Thus, to identify any useful HCC-related biomarkers is still a need. We performed SELDI-TOF MS to identify differentially expressed proteins in HCC serum using weak cation exchange protein chips. Protein characterization was performed by 2-DE separation and nano flow LC-MS/MS. A total of 55 sera were collected from HCC patients and compared with those from 48 patients with chronic hepatitis and 9 healthy individuals. A candidate marker of about 8900 Da was detected as differentially expressed in patients with chronic hepatitis C and hepatitis C virus (HCV)-related HCC. We identified this differentially expressed protein as complement C3a. The expression of C3a in HCC sera was further validated by PS20 chip immunoassay and Western blotting. Complement C3a was found to be elevated in patients with chronic hepatitis C and HCV-related HCC. The combination of SELDI-TOF MS and 2-DE provides a solution to identify disease-associated serum biomarkers.
Collapse
MESH Headings
- Aged
- Biomarkers, Tumor/blood
- Blotting, Western
- Carcinoma, Hepatocellular/blood
- Carcinoma, Hepatocellular/diagnosis
- Complement C3a/analysis
- Complement C3a/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Hepatitis C, Chronic/blood
- Hepatitis C, Chronic/diagnosis
- Humans
- Middle Aged
- Protein Array Analysis
- Proteomics
- Reference Values
- Reproducibility of Results
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Collapse
Affiliation(s)
- I-Neng Lee
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
72
|
Feng JT, Shang S, Beretta L. Proteomics for the early detection and treatment of hepatocellular carcinoma. Oncogene 2006; 25:3810-7. [PMID: 16799622 DOI: 10.1038/sj.onc.1209551] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The prognosis for hepatocellular carcinoma (HCC) is poor and has not improved in recent years, largely owing to lack of early diagnosis, frequent recurrence after surgery and resistance to chemotherapy. Proteomics holds the promise of improving our understanding of HCC carcinogenesis and progression as well as of discovering novel diagnostics and therapeutics. Proteomic analyses of HCC cell lines, animal models and serum and tumor tissue from patients with HCC have been performed to date. Proteomic technologies have greatly improved in the past few years as reviewed here. It is anticipated that with the recent development of protein tagging, protein separation methods and mass spectrometry sensitivity, proteomic studies of HCC will allow the identification of diagnostic and prognostic biomarkers as well as therapeutic targets, which could greatly improve the clinical management of HCC patients.
Collapse
Affiliation(s)
- J T Feng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | |
Collapse
|
73
|
Kim H, Kang HJ, You KT, Kim SH, Lee KY, Kim TI, Kim C, Song SY, Kim HJ, Lee C, Kim H. Suppression of human selenium-binding protein 1 is a late event in colorectal carcinogenesis and is associated with poor survival. Proteomics 2006; 6:3466-76. [PMID: 16645984 DOI: 10.1002/pmic.200500629] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The purpose of this study was to analyze altered protein expression in cancer tissues and determine its relationship to prognosis in colorectal carcinomas. We performed proteomic expression analysis on 14 colorectal carcinomas and matched nontumorous colonic mucosa by 2-DE and MALDI-TOF-MS. Comparative analysis of the respective spot patterns on 2-DE showed 14 spots that were markedly changed in the colorectal carcinomas. Among them, selenium-binding protein 1 (SELENBP1) was markedly decreased in 12 (85%) carcinomas. The reduced expression of SELENBP1 was further supported by Western blot analysis and immunohistochemistry. Suppression of SELENBP1 was further analyzed in another eight-paired adenomas and carcinomas from the same patients using Western blot analysis and immunohistochemistry, and revealed that one adenoma and seven carcinomas exhibited markedly reduced SELENBP1 expression. Patients with low levels of SELENBP1 expression had significantly lower overall survival rates (72 vs. 85%, p = 0.021) among the 240 stages II and III colorectal carcinomas by using tissue microarray analysis. Our findings indicate that suppression of SELENBP1 is a frequent and late event in colorectal carcinogenesis, and may contribute to the rapid progression of colorectal carcinoma.
Collapse
Affiliation(s)
- Hyunki Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
74
|
Chignard N, Shang S, Wang H, Marrero J, Bréchot C, Hanash S, Beretta L. Cleavage of endoplasmic reticulum proteins in hepatocellular carcinoma: Detection of generated fragments in patient sera. Gastroenterology 2006; 130:2010-22. [PMID: 16762624 DOI: 10.1053/j.gastro.2006.02.058] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 02/15/2006] [Indexed: 02/02/2023]
Abstract
BACKGROUND & AIMS In the past decade, there has been a rising incidence of hepatocellular carcinoma (HCC) and a progressive increase in HCC-related mortality in the United States and Western Europe. The poor survival of patients with HCC is largely related to the lack of reliable tools for early diagnosis. METHODS We have applied proteomics tools to the comparative analysis of protein profiles between HCC and adjacent nontumor tissues as a means for discovering novel molecular markers. RESULTS Forty-seven protein spots that showed reproducible variation were identified by mass spectrometry, corresponding to 23 distinct genes. A positive correlation between transcript and protein level variations was observed for only 7 out of the 23 genes. Proteolytic cleavage accounted for the discrepancies between messenger RNA and protein level changes for 7 genes including calreticulin, PDIA3, PDI, and GRP78. We detected a fragment of each of these 4 endoplasmic reticulum proteins in the culture supernatant of the PLC-PRF5 hepatoma cell line, suggesting that their cleavage leads to release of selected cleaved products in the extracellular compartment. We also detected calreticulin and PDIA3 cleavage products in sera of patients with HCC. A statistically highly significant difference in calreticulin and PDIA3 fragment serum levels between patients with HCC and healthy individuals was observed. Amounts of calreticulin and PDIA3 fragments were also significantly different between patients with HCC and at-risk patients (patients with chronic hepatitis or cirrhosis). CONCLUSIONS Specific isoforms in general and cleavage products in particular should therefore be further evaluated as new markers for HCC.
Collapse
Affiliation(s)
- Nicolas Chignard
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | | | | | | | | | | |
Collapse
|
75
|
Shen H, Cheng G, Fan H, Zhang J, Zhang X, Lu H, Liu C, Sun F, Jin H, Xu X, Xu G, Wang S, Fang C, Bao H, Wang Y, Wang J, Zhong H, Yu Z, Liu Y, Tang Z, Yang P. Expressed proteome analysis of human hepatocellular carcinoma in nude mice (LCI-D20) with high metastasis potential. Proteomics 2006; 6:528-37. [PMID: 16372266 DOI: 10.1002/pmic.200500232] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report for the first time an expressed proteome for human hepatocellular carcinoma (HCC) in nude mice model. Most cases of human liver cancer are HCC with highly metastatic ability. Therefore, the early prediction or diagnosis and effective treatment are the key points of research. We have previously successfully established a human HCC nude mice model (LCI-D20) with high metastasis potential. To understand better the tumor biology of HCC it is worth to explore the relativity of all expressed protein profiles in the LCI-D20 HCC nude mice model. With advanced proteomics technologies, we have carried out a proteomic analysis with following stages: protein sample preparation of cancer tissue, including total cellular extraction and sequential fractionation, 2-DE and 2-D LC separation, ESI/MALDI-MS/MS identification, as well as data-dependent bioinformatics. The identified proteins were classified bioinformatically respective to their function, biological process and intracellular localization. Some important proteins found in HCC, e.g. metabolism enzymes, proteins regulating cell motility, signaling proteins, and heat shock proteins, are discussed in terms of their metastasis.
Collapse
MESH Headings
- Animals
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/secondary
- Electrophoresis, Gel, Two-Dimensional
- Humans
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/pathology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasm Proteins/metabolism
- Proteome
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Huali Shen
- Institutes for Biomedical Sciences, Fudan University, Shanghai, P R China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
76
|
Blanc JF, Lalanne C, Plomion C, Schmitter JM, Bathany K, Gion JM, Bioulac-Sage P, Balabaud C, Bonneu M, Rosenbaum J. Proteomic analysis of differentially expressed proteins in hepatocellular carcinoma developed in patients with chronic viral hepatitis C. Proteomics 2006; 5:3778-89. [PMID: 16097030 DOI: 10.1002/pmic.200401194] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major complication of chronic viral hepatitis C. Therapy for HCC is still disappointing. It is thus of great importance to identify novel HCC markers for early detection of the disease, and tumor-specific proteins as potential therapeutic targets. We have used a proteomic approach to identify new proteins involved in HCC development. Four cases of HCC developing from chronic viral hepatitis C were analyzed by two-dimensional electrophoresis (2-DE), and results were compared to those of paired adjacent non-tumorous liver tissues. For MS fingerprinting, protein spots with differential intensity between HCC and non-tumorous liver were directly cut out of gels and processed for MALDI-MS and nano-LC-ESI-MS/MS analysis. Approximately 850 spots were visualized in each gel. The comparative analysis of paired samples indicated that 345 protein spots showed significant differences in expression level between non-tumor and tumor tissue. Among the 345 protein spots analyzed, 238 spots corresponding to 155 different proteins were identified; 49 proteins were up-regulated, whereas 106 proteins were down-regulated. Among these 155 proteins, 91 proteins were regulated in at least three cases. Although 52 out of these 91 proteins have been already described by previous proteomic or transcriptomic studies, or are already known to be involved in hepatocarcinogenesis, this experiment revealed 39 new proteins differentially expressed in HCC developing from viral hepatitis C. Variations in protein accumulation were confirmed for two selected proteins (apolipoprotein E, chloride intracellular channel 1) by Western blotting in ten additional cases of HCC developing in patients with viral hepatitis C.
Collapse
Affiliation(s)
- Jean-Frédéric Blanc
- INSERM, E362, IFR66 Bordeaux, Université Victor Segalen Bordeaux 2, Bordeaux, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
77
|
Li C, Tan YX, Zhou H, Ding SJ, Li SJ, Ma DJ, Man XB, Hong Y, Zhang L, Li L, Xia QC, Wu JR, Wang HY, Zeng R. Proteomic analysis of hepatitis B virus-associated hepatocellular carcinoma: Identification of potential tumor markers. Proteomics 2005; 5:1125-39. [PMID: 15759316 DOI: 10.1002/pmic.200401141] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is a malignancy of both underdeveloped and developing countries. Proteomes of ten pairs of clinical hepatitis B virus associated HCC tissue samples were obtained by high resolution two-dimensional gel electrophoresis. Comprehensive analyses of proteins associated with B-type HCC were focused on total differentially expressed proteins (> or = two-fold increase or decrease, Student's t-test, p < 0.05) from one pair of samples. Protein identification was done by peptide mass fingerprinting with matrix assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography-tandem mass spectrometry. Comparative analyses of proteins associated with B-type HCC included repeat statistics in ten cases. A total of 100 protein spots, corresponding to 80 different gene products, were identified. Proteins whose expression levels were different by more than 2-fold in at least 50% of the cases (five of ten cases) were further analyzed and 45 proteins were selected out as candidates for HCC-associated proteins. Western blotting further validated up-regulated expressions of two candidate proteins in tumor tissues: proliferating cell antigen and stathmin 1. This comprehensive and comparative analyses of proteins associated with B-type HCC could provide useful molecular markers for diagnostics and prognostics and for therapeutic targets. The physiological significance of the differential expressions for several candidate proteins are discussed.
Collapse
MESH Headings
- Adult
- Amino Acid Sequence
- Biomarkers, Tumor
- Blotting, Western
- Carcinoma, Hepatocellular/complications
- Carcinoma, Hepatocellular/virology
- Cell Line, Tumor
- Chromatography, Liquid
- Computational Biology/methods
- Electrophoresis, Gel, Two-Dimensional
- Female
- Gene Expression Regulation, Neoplastic
- Gene Expression Regulation, Viral
- Hepatitis B/complications
- Hepatitis B virus/metabolism
- Humans
- Image Processing, Computer-Assisted
- Male
- Mass Spectrometry/methods
- Microtubule Proteins/biosynthesis
- Middle Aged
- Molecular Sequence Data
- Phosphoproteins/biosynthesis
- Proliferating Cell Nuclear Antigen/biosynthesis
- Protein Isoforms
- Proteomics/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Stathmin
- Up-Regulation
Collapse
Affiliation(s)
- Chen Li
- Research Center for Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
78
|
Takashima M, Kuramitsu Y, Yokoyama Y, Iizuka N, Fujimoto M, Nishisaka T, Okita K, Oka M, Nakamura K. Overexpression of alpha enolase in hepatitis C virus-related hepatocellular carcinoma: association with tumor progression as determined by proteomic analysis. Proteomics 2005; 5:1686-92. [PMID: 15800975 DOI: 10.1002/pmic.200401022] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To identify proteins that could be molecular targets for diagnosis and treatment of hepatitis C virus-related hepatocellular carcinoma (HCV-related HCC), we used a proteomic approach to analyze protein expression in samples of human liver. Twenty-six pairs of tumorous and corresponding nontumorous liver samples from patients with HCV-related HCC and six normal liver samples were analyzed by two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry. One of the numerous spots that showed stronger intensity in tumorous than in nontumorous samples was identified as alpha enolase, a key enzyme in the glycolytic pathway. Expression of this protein increased with tumor dedifferentiation and was significantly higher in poorly differentiated HCC than in well-differentiated HCC. This pattern was reproduced by immunoblot analysis and immunohistochemistry. Expression of alpha enolase also correlated positively with tumor size and venous invasion. These results suggest that alpha enolase is one of the candidates for biomarkers for tumor progression that deserves further investigation in HCV-related HCC.
Collapse
Affiliation(s)
- Motonari Takashima
- Department of Surgery II, Yamaguchi University School of Medicine, Ube, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
79
|
Cho SY, Lee EY, Lee JS, Kim HY, Park JM, Kwon MS, Park YK, Lee HJ, Kang MJ, Kim JY, Yoo JS, Park SJ, Cho JW, Kim HS, Paik YK. Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map. Proteomics 2005; 5:3386-96. [PMID: 16047310 DOI: 10.1002/pmic.200401310] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human plasma is the most clinically valuable specimen, containing not only a dynamic concentration range of protein components, but also several groups of high-abundance proteins that seriously interfere with the detection of low-abundance potential biomarker proteins. To establish a high-throughput method for efficient depletion of high-abundance proteins and subsequent fractionation, prior to molecular analysis of proteins, we explored how coupled immunoaffinity columns, commercially available as multiple affinity removal columns (MARC) and free flow electrophoresis (FFE), could apply to the HUPO plasma proteome project. Here we report identification of proteins and construction of a human plasma 2-DE map devoid of six major abundance proteins (albumin, transferrin, IgG, IgA, haptoglobin, and antitrypsin) using MARC. The proteins were identified by PMF, matching with various internal 2-DE maps, resulting in a total of 144 nonredundant proteins that were identified from 398 spots. Tissue plasminogen activator, usually present at 10-60 ng/mL plasma, was also identified, indicative of a potentially low-abundance biomarker. Comparison of representative 2-D gel images of three ethnic groups (Caucasian, Asian-American, African-American) plasma exhibited minor differences in certain proteins between races and sample pretreatment. To establish a throughput fractionation of plasma samples by FFE, either MARC flow-through fractions or untreated samples of Korean serum were subjected to FFE. After separation of samples on FFE, an aliquot of each fraction was analyzed by 1-D gel, in which MARC separation was a prerequisite for FFE work. Thus, a working scheme of MARC --> FFE --> 1-D PAGE --> 2-D-nanoLC-MS/MS may be considered as a widely applicable standard platform technology for fractionation of complex samples like plasma.
Collapse
Affiliation(s)
- Sang Yun Cho
- Department of Biochemistry, Yonsei Proteome Research Center and Biomedical Proteome Research Center, Yonsei University, Seoul, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
80
|
Affiliation(s)
- Romain Parent
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M5-A864, P.O. Box 19024, Seattle, WA 98109-1024, USA
| | | |
Collapse
|
81
|
Jacobs JM, Diamond DL, Chan EY, Gritsenko MA, Qian W, Stastna M, Baas T, Camp DG, Carithers RL, Smith RD, Katze MG. Proteome analysis of liver cells expressing a full-length hepatitis C virus (HCV) replicon and biopsy specimens of posttransplantation liver from HCV-infected patients. J Virol 2005; 79:7558-69. [PMID: 15919910 PMCID: PMC1143647 DOI: 10.1128/jvi.79.12.7558-7569.2005] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The development of a reproducible model system for the study of hepatitis C virus (HCV) infection has the potential to significantly enhance the study of virus-host interactions and provide future direction for modeling the pathogenesis of HCV. While there are studies describing global gene expression changes associated with HCV infection, changes in the proteome have not been characterized. We report the first large-scale proteome analysis of the highly permissive Huh-7.5 cell line containing a full-length HCV replicon. We detected >4,200 proteins in this cell line, including HCV replicon proteins, using multidimensional liquid chromatographic (LC) separations coupled to mass spectrometry. Consistent with the literature, a comparison of HCV replicon-positive and -negative Huh-7.5 cells identified expression changes of proteins involved in lipid metabolism. We extended these analyses to liver biopsy material from HCV-infected patients where a total of >1,500 proteins were detected from only 2 mug of liver biopsy protein digest using the Huh-7.5 protein database and the accurate mass and time tag strategy. These findings demonstrate the utility of multidimensional proteome analysis of the HCV replicon model system for assisting in the determination of proteins/pathways affected by HCV infection. Our ability to extend these analyses to the highly complex proteome of small liver biopsies with limiting protein yields offers the unique opportunity to begin evaluating the clinical significance of protein expression changes associated with HCV infection.
Collapse
Affiliation(s)
- Jon M Jacobs
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195-8070, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Hayat M. Liver Carcinoma. HANDBOOK OF IMMUNOHISTOCHEMISTRY AND IN SITU HYBRIDIZATION OF HUMAN CARCINOMAS 2005:131-151. [DOI: 10.1016/s1874-5784(05)80018-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
|
83
|
Abstract
Refinements of serological markers and screening of patients at high risk for developing hepatocellular carcinoma (HCC) may lead to better HCC detection, earlier intervention, and successful treatment, improving long-term outcomes. Proteomics promises the discovery of biomarkers for early HCC detection and diagnosis. Proteomic-based profiling uniquely allows delineation of global changes in expression patterns resulting from transcriptional and posttranscriptional control, posttranslational modifications, and shifts in proteins between cellular compartments. Approaches to that effect include direct serum protein profiling and comparative analysis of protein expression in normal, precancerous, and early-stage tumor tissues. Identification of panels of tumor antigens that elicit a humoral response also may contribute to the discovery of new markers for HCC screening and diagnosis. Today, 2-dimensional polyacrylamide gel electrophoresis, multidimensional liquid chromatography, mass spectrometry, and protein microarrays are among the proteomic tools available for biomarker and drug target discovery. We review these technologies and their application to the study of HCC. Our objective is to provide a framework for appreciating the promise, while at the same time understanding the challenges behind translating proteomics discovery into novel diagnostic tests.
Collapse
Affiliation(s)
- Nicolas Chignard
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | |
Collapse
|
84
|
Shen X, Lin JS, Kong XJ. Maxizyme against mtp53 transfected by adenovirus enhanced transferrin receptor-mediated gene delivery systeminduced apoptosis of hepatoma cells. Shijie Huaren Xiaohua Zazhi 2004; 12:1539-1542. [DOI: 10.11569/wcjd.v12.i7.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the influence of introduction of maxizyme against mtp53 by adenovirus enhanced transferrin receptor-mediated gene delivery system on MHCC97 cells.
METHODS: Hepatoma cell line MHCC97 containing mutated p53 gene was served as a model. The maxizyme against mtp53 was transfected to the cells by adenovirus enhanced transferrin receptor-mediated gene delivery system. The level of mtp53-mRNA was detected by means of semi-quantitative reverse transcription polymerase chain reaction (RT-PCR). The apoptosis of the hepatoma cells was measured by DNA ladder assay and FCM.
RESULTS: After 48 hours of transfection by AVET system, RT-PCR results indicated the expression of mtp53 mRNA in pEGFP-Maxizyme group was significantly lower than that in control group. And DNA "ladder" with agarose gel electrophoresis was observed in pEGFP-maxizyme group. The result of flow cytometry exhibited apoptotic index in pEGFP-maxizyme group was 22.95%, which was higher than those in blank control group and pEGFP group.
CONCLUSION: The recombinant ribozyme cDNA eukaryotic expression vector pEGFP-maxizyme can be efficiently transfected into MHCC97 cell by adenovirus enhanced transferrin receptor-mediated gene delivery system and the expression of maxizyme may inhibit the mtp53 gene expression and promote apoptosis of MHCC97 cells. The AVET system may be a useful tool in gene delivery for gene therapy of human HCC.
Collapse
|
85
|
Zeindl-Eberhart E, Haraida S, Liebmann S, Jungblut PR, Lamer S, Mayer D, Jäger G, Chung S, Rabes HM. Detection and identification of tumor-associated protein variants in human hepatocellular carcinomas. Hepatology 2004; 39:540-9. [PMID: 14768008 DOI: 10.1002/hep.20060] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The proteomic approach is a valuable tool to detect and identify proteins that are associated with cancer. In previous investigations on experimentally induced rat hepatomas, we detected aldose reductase-like protein (ARLP) as a highly significant marker protein. Our present study was intended to look for the presence of similar tumor-associated marker proteins on human hepatocellular carcinomas (HCC). We found several novel tumor-associated protein variants that represent members of the aldo-keto reductase (AKR) superfamily. Human aldose reductase-like protein-1 (hARLP-1) was the most prominent tumor-associated AKR member detected in HCC by 2-dimensional electrophoresis (2-DE) and identified by mass spectrometric fingerprinting. The enzyme was found in 4 distinct forms (hARLP-1, 36/7.4 (kd/pI); hARLP-2, 36/7.2; hARLP-3, 36/6.4; and hARLP-4, 33/7.35). In addition, a human aldose reductase-like protein (hARLP-5, 36/7.6) was identified that differed from hARLP-1 by 1 amino acid (D313N), indicating 2 allelic forms of the human aldose reductase-like gene. A novel antibody directed against common parts of the hARLPs revealed hARLP reactivity in human HCC by immunohistochemistry. Furthermore, aldose reductase (AR) was identified and characterized as a tumor-associated variant. In conclusion, in all investigated human HCCs at least one of the various types of the described tumor-associated proteins of the AKR superfamily was clearly present. Of these HCC samples, 95% were positive for hARLPs as proven by 2-DE analysis and/or by use of the antibody directed against hARLP. Thus, hARLP is a strong candidate for use as an immunohistochemical diagnostic marker of human HCC.
Collapse
|
86
|
Wang Y, Cui F, Lv Y, Li C, Xu X, Deng C, Wang D, Sun Y, Hu G, Lang Z, Huang C, Yang X. HBsAg and HBx knocked into the p21 locus causes hepatocellular carcinoma in mice. Hepatology 2004; 39:318-24. [PMID: 14767984 DOI: 10.1002/hep.20076] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hepatocellular carcinoma (HCC) affects males in a significantly higher proportion than females and is one of the human cancers etiologically related to viral factors. Many studies provide strong evidence of the direct role that hepatitis B virus (HBV) plays in hepatic carcinogenesis, but the functions of HBV surface antigen (HBsAg) and X protein (HBx) in hepatocarcinogenesis through direct or indirect mechanisms are still being debated. We generated two HBV gene knock-in transgenic mouse lines by homologous recombination. HBsAg and HBx genes were integrated into the mouse p21 locus. Both male and female p21-HBx transgenic mice developed HCC after the age of 18 months; however, male p21-HBsAg transgenic mice began to develop HCC 3 months earlier. The expression of a number of genes related to metabolism and genomic instability largely resembled the molecular changes during the development of HCC in humans. ER-beta (estrogen receptor-beta) was extremely up-regulated only in tumor tissues of male p21-HBsAg mice, providing genetic evidence that HBsAg might be the major risk factor affecting the gender difference in the causes of HCC. In conclusion, these mice might serve as good models for studying the different roles of HBsAg and HBx in early events of HBV-related hepatocarcinogenesis.
Collapse
MESH Headings
- Animals
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/physiopathology
- Cyclin-Dependent Kinase Inhibitor p21
- Cyclins/genetics
- Estrogen Receptor beta
- Female
- Gene Expression Regulation, Neoplastic
- Hepatitis B Surface Antigens/genetics
- Liver/pathology
- Liver/physiopathology
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/pathology
- Liver Neoplasms, Experimental/physiopathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Pregnancy
- Receptors, Estrogen/genetics
- Sex Characteristics
- Trans-Activators/genetics
- Viral Regulatory and Accessory Proteins
Collapse
Affiliation(s)
- Youliang Wang
- Genetic Laboratory of Development and Diseases, Institute of Biotechnology, Beijing, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
87
|
Li C, Hong Y, Tan YX, Zhou H, Ai JH, Li SJ, Zhang L, Xia QC, Wu JR, Wang HY, Zeng R. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mol Cell Proteomics 2004; 3:399-409. [PMID: 14726492 DOI: 10.1074/mcp.m300133-mcp200] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Laser capture microdissection (LCM) is a powerful tool that enables the isolation of specific cell types from tissue sections, overcoming the problem of tissue heterogeneity and contamination. This study combined the LCM with isotope-coded affinity tag (ICAT) technology and two-dimensional liquid chromatography to investigate the qualitative and quantitative proteomes of hepatocellular carcinoma (HCC). The effects of three different histochemical stains on tissue sections have been compared, and toluidine blue stain was proved as the most suitable stain for LCM followed by proteomic analysis. The solubilized proteins from microdissected HCC and non-HCC hepatocytes were qualitatively and quantitatively analyzed with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) alone or coupled with cleavable ICAT labeling technology. A total of 644 proteins were qualitative identified, and 261 proteins were unambiguously quantitated. These results show that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.
Collapse
Affiliation(s)
- Chen Li
- Research Center for Proteome Analysis, Key Lab of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|