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Wan F, Zhu Y, Wu F, Huang X, Chen Y, Zhou Y, Li H, Liang L, Qin L, Wang Q, He M. Retinol-binding protein 4 as a promising serum biomarker for the diagnosis and prognosis of hepatocellular Carcinoma. Transl Oncol 2024; 45:101979. [PMID: 38728873 PMCID: PMC11107351 DOI: 10.1016/j.tranon.2024.101979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The prognosis of hepatocellular carcinoma (HCC) is universally poor. Early diagnosis plays a pivotal role in determining the outcome of HCC. METHODS We employed a comparative proteomics approach to identify potential biomarkers and validated the application of retinol-binding protein 4 (RBP4) as a biomarker for HCC. RBP4 protein expression was examined in liver tissues from 80 HCC patients through immunohistochemical analysis. Serum RBP4 concentrations were measured by ELISA in a cohort comprising 290 HCC patients, matched 202 chronic hepatitis B patients and 269 healthy controls. Survival data were collected from HCC patients. The diagnostic and prognostic values of RBP4 were evaluated using receiver operating curve (ROC) analysis. RESULTS The validation results demonstrated a significant reduction in RBP4 levels in both liver tissues and serum samples from HCC patients. ROC analysis of the diagnostic value of RBP4 revealed an AUC of 0.879 (95 % CI: 0.854∼0.903) for HCC. When combined with AFP, the AUC increased to 0.919, with a sensitivity of 87.9 % and specificity of 80 %. Survival analysis revealed significantly reduced overall survival time in individuals with low-expression of RBP4 compared to those with high-expression. The joint prognostic model exhibited an AUC of 0.926 (95 % CI: 0.888∼0.964), which was significantly higher than that of AFP alone (AUC=0.809; P <0.0001). CONCLUSIONS RBP4 shows a great potential as a biomarker with appreciable diagnostic value, complementing the AFP in HCC diagnosis. Additionally, it holds promise as a prognostic biomarker that, when integrated into a combined prognostic model, could greatly improve HCC prognosis efficiency.
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Affiliation(s)
- Fengjie Wan
- Guangxi Medical University School of Public Health, Nanning, Guangxi 530021, PR China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, Guangxi 530021, PR China
| | - Yujia Zhu
- Guigang Dermatosis Prevention and Treatment Hospital, Guigang, Guangxi 537100, PR China
| | - Feixiang Wu
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, PR China
| | - Xuejing Huang
- Animal Center of Guangxi Medical University, Nanning, Guangxi 530021, PR China
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT 06520, USA
| | - Yi Zhou
- Guangxi Medical University Life Sciences Institute, Nanning, Guangxi 530021, PR China
| | - Hongtao Li
- Guilin Medical University, Guilin, Guangxi 541001, PR China
| | - Lifang Liang
- Guangxi Medical University School of Public Health, Nanning, Guangxi 530021, PR China
| | - Lirong Qin
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, PR China
| | - Qi Wang
- Guangxi Medical University Cancer Hospital, Nanning, Guangxi 530021, PR China.
| | - Min He
- Guangxi Medical University School of Public Health, Nanning, Guangxi 530021, PR China; Animal Center of Guangxi Medical University, Nanning, Guangxi 530021, PR China; Key Laboratory of High-Incidence-Tumor Prevention & Treatment, Guangxi Medical University, Ministry of Education, Nanning 530021, PR China.
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Yang Y, Ma Y, Yuan M, Peng Y, Fang Z, Wang J. Identifying the biomarkers and pathways associated with hepatocellular carcinoma based on an integrated analysis approach. Liver Int 2021; 41:2485-2498. [PMID: 34033190 DOI: 10.1111/liv.14972] [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] [Received: 09/26/2019] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 02/13/2023]
Abstract
BACKGROUND AND AIMS Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. The molecular mechanism underlying HCC is still unclear. In this study, we conducted a comprehensive analysis to explore the genes, pathways and their interactions involved in HCC. METHODS We analysed the gene expression datasets corresponding to 488 samples from 10 studies on HCC and identified the genes differentially expressed in HCC samples. Then, the genes were compared against Phenolyzer and GeneCards to screen those potentially associated with HCC. The features of the selected genes were explored by mapping them onto the human protein-protein interaction network, and a subnetwork related to HCC was constructed. Hub genes in this HCC specific subnetwork were identified, and their relevance with HCC was investigated by survival analysis. RESULTS We identified 444 differentially expressed genes (177 upregulated and 267 downregulated) related to HCC. Functional enrichment analysis revealed that pathways like p53 signalling and chemical carcinogenesis were eriched in HCC genes. In the subnetwork related to HCC, five disease modules were detected. Further analysis identified six hub genes from the HCC specific subnetwork. Survival analysis showed that the expression levels of these genes were negatively correlated with survival rate of HCC patients. CONCLUSIONS Based on a systems biology framework, we identified the genes, pathways, as well as the disease specific network related to HCC. We also found novel biomarkers whose expression patterns were correlated with progression of HCC, and they could be candidates for further investigation.
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Affiliation(s)
- Yichen Yang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China.,Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Yuequn Ma
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Meng Yuan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Yonglin Peng
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Zhonghai Fang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
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Multiplexed Proteomic Approach for Identification of Serum Biomarkers in Hepatocellular Carcinoma Patients with Normal AFP. J Clin Med 2020; 9:jcm9020323. [PMID: 31979338 PMCID: PMC7074125 DOI: 10.3390/jcm9020323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023] Open
Abstract
Alpha fetoprotein (AFP) has been used as a serologic indicator of hepatocellular carcinoma (HCC). We aimed to identify an HCC-specific serum biomarker for diagnosis using a multiplexed proteomic technique in HCC patients with normal AFP levels. A total of 152 patients were included from Guro Hospital, Korea University. Among 267 identified proteins, 28 and 86 proteins showed at least a two-fold elevation or reduction in expression, respectively. Multiple reaction monitoring (MRM) analysis of 41 proteins revealed 10 proteins were differentially expressed in patients with liver cirrhosis and HCC patients with normal AFP. A combination of tripartite motif22 (Trim22), seprase, and bone morphogenetic protein1 had an area under receiver operating characteristic of 0.957 for HCC diagnosis. Real-time PCR and western blot analysis of the paired tumor/non-tumor liver tissue in HCC revealed a reduced expression of Trim22 in the tumor tissue. Also, serum levels of Trim22 were significantly reduced in HCC patients with normal AFP compared to those with liver cirrhosis (p = 0.032). Inhibition of Trim22 increased cellular proliferation in human hepatoma cell lines, whereas overexpression of Trim22 decreased cellular proliferation in hepatoma cell lines. In conclusion, the combination of three serum markers improved the chance of diagnosing HCC. MRM-based quantification of the serum protein in patients with normal AFP provides the potential for early diagnosis of HCC.
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Yang J, Xie Q, Zhou H, Chang L, Wei W, Wang Y, Li H, Deng Z, Xiao Y, Wu J, Xu P, Hong X. Proteomic Analysis and NIR-II Imaging of MCM2 Protein in Hepatocellular Carcinoma. J Proteome Res 2018; 17:2428-2439. [DOI: 10.1021/acs.jproteome.8b00181] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing Yang
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Qi Xie
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Center for Experimental Basic Medical Education, School of Basic Medical Sciences, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan 430071, China
| | - Hui Zhou
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yin Wang
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hong Li
- Pathology Department, Binzhou Medical University Hospital, Binzhou 256600, China
| | - Zixin Deng
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Yuling Xiao
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Junzhu Wu
- Center for Experimental Basic Medical Education, School of Basic Medical Sciences, Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals and Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan University, Wuhan 430071, China
| | - Ping Xu
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
- Anhui Medical University, Hefei 230032, China
| | - Xuechuan Hong
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Zhongnan Hospital of Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Medical College, Tibet University, Lasa 850000, China
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Sahab ZJ, Semaan SM, Sang QXA. Methodology and Applications of Disease Biomarker Identification in Human Serum. Biomark Insights 2017. [DOI: 10.1177/117727190700200034] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biomarkers are biomolecules that serve as indicators of biological and pathological processes, or physiological and pharmacological responses to a drug treatment. Because of the high abundance of albumin and heterogeneity of plasma lipoproteins and glycoproteins, biomarkers are difficult to identify in human serum. Due to the clinical significance the identification of disease biomarkers in serum holds great promise for personalized medicine, especially for disease diagnosis and prognosis. This review summarizes some common and emerging proteomics techniques utilized in the separation of serum samples and identification of disease signatures. The practical application of each protein separation or identification technique is analyzed using specific examples. Biomarkers of cancers of prostate, breast, ovary, and lung in human serum have been reviewed, as well as those of heart disease, arthritis, asthma, and cystic fibrosis. Despite the advancement of technology few biomarkers have been approved by the Food and Drug Administration for disease diagnosis and prognosis due to the complexity of structure and function of protein biomarkers and lack of high sensitivity, specificity, and reproducibility for those putative biomarkers. The combination of different types of technologies and statistical analysis may provide more effective methods to identify and validate new disease biomarkers in blood.
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Affiliation(s)
- Ziad J. Sahab
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, U.S.A
| | - Suzan M. Semaan
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, U.S.A
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, U.S.A
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Nie W, Yan L, Lee YH, Guha C, Kurland IJ, Lu H. Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma. MASS SPECTROMETRY REVIEWS 2016; 35:331-349. [PMID: 24890331 DOI: 10.1002/mas.21439] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 04/17/2014] [Accepted: 04/17/2014] [Indexed: 06/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.
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Affiliation(s)
- Wenna Nie
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Leyu Yan
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
| | - Yie H Lee
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology, Singapore, 138602, Singapore
| | - Chandan Guha
- Department of Radiation Oncology, Montefiore Medical Center, New York, New York, 10461
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research and Training Center, Department of Medicine, Albert Einstein College of Medicine, New York, New York, 10461
| | - Haitao Lu
- Chongqing University Innovative Drug Research Centre, School of Chemistry and Chemical Engineering, Chongqing, 401331, PR China
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 4059, Australia
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Borlak J, Singh P, Gazzana G. Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events. BMC Genomics 2015; 16:124. [PMID: 25872475 PMCID: PMC4357185 DOI: 10.1186/s12864-015-1312-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/03/2015] [Indexed: 02/06/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is on the rise and the sixth most common cancer worldwide. To combat HCC effectively research is directed towards its early detection and the development of targeted therapies. Given the fact that epidermal growth factor (EGF) is an important mitogen for hepatocytes we searched for disease regulated proteins to improve an understanding of the molecular pathogenesis of EGF induced HCC. Disease regulated proteins were studied by 2DE MALDI-TOF/TOF and a transcriptomic approach, by immunohistochemistry and advanced bioinformatics. Results Mapping of EGF induced liver cancer in a transgenic mouse model identified n = 96 (p < 0.05) significantly regulated proteins of which n = 54 were tumour-specific. To unravel molecular circuits linked to aberrant EGFR signalling diverse computational approaches were employed and this defined n = 7 key nodes using n = 82 disease regulated proteins for network construction. STRING analysis revealed protein-protein interactions of > 70% disease regulated proteins with individual proteins being validated by immunohistochemistry. The disease regulated network proteins were mapped to distinct pathways and bioinformatics provided novel insight into molecular circuits associated with significant changes in either glycolysis and gluconeogenesis, argine and proline metabolism, protein processing in endoplasmic reticulum, Hif- and MAPK signalling, lipoprotein metabolism, platelet activation and hemostatic control as a result of aberrant EGF signalling. The biological significance of the findings was corroborated with gene expression data derived from tumour tissues to evntually define a rationale by which tumours embark on intriguing changes in metabolism that is of utility for an understanding of tumour growth. Moreover, among the EGF tumour specific proteins n = 11 were likewise uniquely expressed in human HCC and for n = 49 proteins regulation in human HCC was confirmed using the publically available Human Protein Atlas depository, therefore demonstrating clinical significance. Conclusion Novel insight into the molecular pathogenesis of EGF induced liver cancer was obtained and among the 37 newly identified proteins several are likely candidates for the development of molecularly targeted therapies and include the nucleoside diphosphate kinase A, bifunctional ATP-dependent dihydroyacetone kinase and phosphatidylethanolamine-binding protein1, the latter being an inhibitor of the Raf-1 kinase. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1312-z) contains supplementary material, which is available to authorized users.
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Abstract
Liver cancer is the fifth most common cancer, but the second leading cause of cancer death, in the world, with more than 700,000 fatalities annually. The major etiology of liver cancer is infection with an hepatotropic virus such as hepatitis B virus or hepatitis C virus infection. While chronic viral infection remains the main cause of liver disease and risk of hepatocellular carcinoma (HCC), rates of nonviral-associated HCC are occurring at an alarmingly increasing rate. Like many cancers, survival rates are closely associated with time of detection. If HCC is caught early, survival rates can be as high as 50%. Regrettably, most cases of HCC are caught late where survival rates can be as low as 2-7%. Thus, there has been great interest in discovering serum biomarkers that could be used to identify those with HCC. To this end, many groups have examined the N-linked glycans to identify changes that occur with HCC. As the liver secretes the vast majority of proteins into the serum, this has often been a starting point for study. In serum, alterations in core fucosylation, outer-arm fucosylation, increased sialylation, and glycan branching have been observed in patients with HCC. Similar findings have been found directly in HCC tissue suggesting that these glycan changes may play a role in tumor formation and development.
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Affiliation(s)
- Anand Mehta
- Department of Microbiology and Immunology, Drexel University College of Medicine, Doylestown, Pennsylvania, USA
| | - Harmin Herrera
- Department of Microbiology and Immunology, Drexel University College of Medicine, Doylestown, Pennsylvania, USA
| | - Timothy Block
- Department of Microbiology and Immunology, Drexel University College of Medicine, Doylestown, Pennsylvania, USA
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Identification and validation of potential new biomarkers for prostate cancer diagnosis and prognosis using 2D-DIGE and MS. BIOMED RESEARCH INTERNATIONAL 2015; 2015:454256. [PMID: 25667921 PMCID: PMC4312578 DOI: 10.1155/2015/454256] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 12/14/2022]
Abstract
This study was designed to identify and validate potential new biomarkers for prostate cancer and to distinguish patients with and without biochemical relapse. Prostate tissue samples analyzed by 2D-DIGE (two-dimensional difference in gel electrophoresis) and mass spectrometry (MS) revealed downregulation of secernin-1 (P < 0.044) in prostate cancer, while vinculin showed significant upregulation (P < 0.001). Secernin-1 overexpression in prostate tissue was validated using Western blot and immunohistochemistry while vinculin expression was validated using immunohistochemistry. These findings indicate that secernin-1 and vinculin are potential new tissue biomarkers for prostate cancer diagnosis and prognosis, respectively. For validation, protein levels in urine were also examined by Western blot analysis. Urinary vinculin levels in prostate cancer patients were significantly higher than in urine from nontumor patients (P = 0.006). Using multiple reaction monitoring-MS (MRM-MS) analysis, prostatic acid phosphatase (PAP) showed significant higher levels in the urine of prostate cancer patients compared to controls (P = 0.012), while galectin-3 showed significant lower levels in the urine of prostate cancer patients with biochemical relapse, compared to those without relapse (P = 0.017). Three proteins were successfully differentiated between patients with and without prostate cancer and patients with and without relapse by using MRM. Thus, this technique shows promise for implementation as a noninvasive clinical diagnostic technique.
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Knudsen ES, Gopal P, Singal AG. The changing landscape of hepatocellular carcinoma: etiology, genetics, and therapy. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:574-83. [PMID: 24388934 PMCID: PMC3936328 DOI: 10.1016/j.ajpath.2013.10.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) represents one of the leading causes of cancer death and has proved to be highly refractory to treatment. Extensive analysis of the disease has demonstrated that it arises predominantly in response to high-risk etiological challenges, most notably hepatitis virus. However, with evolving vaccination and the obesity epidemic, progressively more cases are associated with underlying metabolic dysfunction. Pathologically diverse forms of HCC are observed, and recent sequencing analysis has defined common events that target well-known cancer pathways including β-catenin/Axin, TP53, and RB/CDKN2A, as well as frequent aberrations in chromatin remodeling factors. However, there are a myriad of low frequency genetic events that make each HCC case unique. Gene expression profiling approaches have successfully been deployed for prognostic assessment of hepatocellular carcinoma and to detect the earliest stages of disease. Despite more extensive research, systemic treatment for HCC is exceedingly limited, with only a handful of drugs providing benefit. Ongoing clinical trials are attempting to exploit specific biological dependencies of HCC to improve the dismal prognosis. Overall, the future of HCC treatment will rely on an understanding of the interplay between etiological factors, molecular features of disease, and rational therapeutic intervention.
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Affiliation(s)
- Erik S Knudsen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Amit G Singal
- Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas; Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.
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Cao XL, Li H, Yu XL, Liang P, Dong BW, Fan J, Li M, Liu FY. Predicting early intrahepatic recurrence of hepatocellular carcinoma after microwave ablation using SELDI-TOF proteomic signature. PLoS One 2013; 8:e82448. [PMID: 24349287 PMCID: PMC3862627 DOI: 10.1371/journal.pone.0082448] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 11/03/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND/AIMS Despite great progress in the treatment of hepatocellular carcinoma (HCC) over the last-decade, intrahepatic recurrence is still the most frequent serious adverse event after all the treatments including microwave ablation. This study aimed to predict early recurrence of HCC after microwave ablation using serum proteomic signature. METHODS After curative microwave ablation of HCC, 86 patients were followed-up for 1 year. Serum samples were collected before microwave ablation. The mass spectra of proteins were generated using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Serum samples from 50 patients were randomly selected as a training set and for biomarkers discovery and model development. The remaining serum samples were categorized for validation of the algorithm. RESULTS According to preablation serum protein profiling obtained from the 50 HCC samples in the training set, nine significant differentially-expressed proteins were detected in the serum samples between recurrent and non-recurrent patients. Decision classification tree combined with three candidate proteins with m/z values of 7787, 6858 and 6646 was produced using Biomarker Patterns Software with sensitivity of 85.7% and specificity of 88.9% in the training set. When the SELDI marker pattern was tested with the blinded testing set, it yielded a sensitivity of 80.0%, a specificity of 88.5% and a positive predictive value of 86.1%. CONCLUSIONS Differentially-expressed protein peaks in preablation serum screened by SELDI are associated with prognosis of HCC. The decision classification tree is a potential tool in predicting early intrahepatic recurrence in HCC patients after microwave ablation.
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Affiliation(s)
- Xiao-lin Cao
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
- Department of Ultrasound, Southern Building Clinic Division, General Hospital of People's Liberation Army, Beijing, China
| | - Hua Li
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
- Department of Ultrasound, the 306 Hospital of Chinese People's Liberation Army, Beijing, China
| | - Xiao-ling Yu
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
- * E-mail: (XlY); (PL)
| | - Ping Liang
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
- * E-mail: (XlY); (PL)
| | - Bao-wei Dong
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
| | - Jin Fan
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
| | - Meng Li
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
| | - Fang-yi Liu
- Department of Interventional Ultrasound, General Hospital of People's Liberation Army, Beijing, China
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Proteomic analysis of pleural effusion from lung adenocarcinoma patients by shotgun strategy. Clin Transl Oncol 2013; 16:153-7. [PMID: 23907289 DOI: 10.1007/s12094-013-1054-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
PURPOSE To construct a protein catalogue of malignant pleural effusion from lung adenocarcinoma patients and to screen the potential candidates of biomarkers for diagnostic value in human lung adenocarcinoma. METHOD Five malignant pleural effusion samples of lung adenocarcinoma patients were collected from January 2009 to September. A composite sample was analyzed using shotgun strategy. Pleural effusion samples were separated by means of SDS-PAGE. Proteomic analysis was performed by 1D-LC-MS/MS, and then the proteins were identified using SEQUEST software and protein database search. RESULTS Among 230 unique proteins, 123 proteins were identified with higher confidence levels (at least two unique peptide sequences matched). Most of these proteins have been reported in plasma. However, there are 7 proteins, including JUP protein, suprabasin, annexin A2, transforming growth factor-beta-induced protein ig-h3 (βig-h3), V-set and immunoglobulin domain-containing protein 4 precursor, ifapsoriasin 2 and actin, cytoplasmic 1 have not been reported in serum. CONCLUSIONS Seven proteins may represent potential candidates of biomarkers. Annexin A2 is of special interest since it may play a role in the regulation of intercellular adhesion and cell proliferation.
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Patel M, Shariff MIF, Ladep NG, Thillainayagam AV, Thomas HC, Khan SA, Taylor-Robinson SD. Hepatocellular carcinoma: diagnostics and screening. J Eval Clin Pract 2012; 18:335-42. [PMID: 21114800 DOI: 10.1111/j.1365-2753.2010.01599.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the commonest primary hepatic malignancy and the third most common cause of cancer-related death worldwide. Incidence remains highest in the developing world and is steadily increasing across the developed world. The majority of HCC occurs on a background of cirrhosis, principally caused by two major risk factors, chronic hepatitis B and hepatitis C infection. Current diagnostic modalities, of ultrasound and α-fetoprotein, are expensive and lack sensitivity in tumour detection. Early diagnosis is integral to improved survival rates and there have been recent advances in technology that have enabled early identification of the process of hepatocarcinogenesis. This review outlines the epidemiological trends and risk factors for HCC; diagnostic techniques and current guidelines for screening and surveillance; and newer methods of screening.
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Affiliation(s)
- Madhvi Patel
- Division of Diabetes Endocrinology and Metabolism, Department of Medicine, Imperial College London, London, UK
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14
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Chen HS, Liu M, Shi LJ, Zhao JL, Zhang CP, Lin LQ, Liu Y, Zhang SJ, Jin JC, Wang L, Shen BZ, Liu JR. Effects of Raspberry Phytochemical Extract on Cell Proliferation, Apoptosis, and Serum Proteomics in a Rat Model. J Food Sci 2011; 76:T192-8. [PMID: 22417609 DOI: 10.1111/j.1750-3841.2011.02373.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hong-Sheng Chen
- Treatment Center of Oncology, the Fourth Affiliated Hospital of Harbin Medical Univ., 37 YiYuan Street, NanGang District, Harbin 150001, PR China
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15
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Lee YY, McKinney KQ, Ghosh S, Iannitti DA, Martinie JB, Caballes FR, Russo MW, Ahrens WA, Lundgren DH, Han DK, Bonkovsky HL, Hwang SI. Subcellular tissue proteomics of hepatocellular carcinoma for molecular signature discovery. J Proteome Res 2011; 10:5070-83. [PMID: 21913717 DOI: 10.1021/pr2005204] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading causes of mortality from solid organ malignancy worldwide. Because of the complexity of proteins within liver cells and tissues, the discovery of therapeutic targets of HCC has been difficult. To investigate strategies for decreasing the complexity of tissue samples for detecting meaningful protein mediators of HCC, we employed subcellular fractionation combined with 1D-gel electrophoresis and liquid chromatography-tandem mass spectrometry analysis. Moreover, we utilized a statistical method, namely, the Power Law Global Error Model (PLGEM), to distinguish differentially expressed proteins in a duplicate proteomic data set. Mass spectrometric analysis identified 3045 proteins in nontumor and HCC from cytosolic, membrane, nuclear, and cytoskeletal fractions. The final lists of highly differentiated proteins from the targeted fractions were searched for potentially translocated proteins in HCC from soluble compartments to the nuclear or cytoskeletal compartments. This analysis refined our targets of interest to include 21 potential targets of HCC from these fractions. Furthermore, we validated the potential molecular targets of HCC, MATR3, LETM1, ILF2, and IQGAP2 by Western blotting, immunohistochemisty, and immunofluorescent microscopy. Here we demonstrate an efficient strategy of subcellular tissue proteomics toward molecular target discovery of one of the most complicated human disease, HCC.
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Affiliation(s)
- Yong-Yook Lee
- Department of Research, Carolinas HealthCare System , Charlotte, NC, USA
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16
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Gou L, Wang W, Tong A, Yao Y, Zhou Y, Yi C, Yang J. Proteomic identification of RhoA as a potential biomarker for proliferation and metastasis in hepatocellular carcinoma. J Mol Med (Berl) 2011; 89:817-27. [PMID: 21475975 DOI: 10.1007/s00109-011-0753-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 03/20/2011] [Accepted: 03/21/2011] [Indexed: 02/05/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies in the world, and there is an urgent need to discover novel factors that can act as biomarkers for prognostic assessment and therapeutic targets of HCC. In this study, highly purified plasma membrane proteins from clinical tissue samples were obtained using a strategy combining sucrose density gradient centrifugation and subsequent phase partition. Using a two-dimensional gel electrophoresis and MALDI-Q-TOF MS/MS-based proteomics approach, we identified 13 plasma membrane-associated proteins that were differentially expressed in HCC and normal liver tissues. Of those, RhoA was one of the most significantly upregulated proteins in HCC, and its overexpression was confirmed using Western blotting. Immunohistochemistry suggested a link between RhoA expression and poor differentiation and clinicopathologic stage. Suppression of RhoA expression in HepG2 and Hep3B cells by RNA interference led to significant inhibition of cell growth, induction of apoptosis, and a decrease in migration. Our data suggest that RhoA may serve as a potential biomarker and an attractive therapeutic target for HCC.
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Affiliation(s)
- Lantu Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, People's Republic of China.
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17
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Liu Z, Ma Y, Yang J, Qin H. Upregulated and Downregulated Proteins in Hepatocellular Carcinoma: A Systematic Review of Proteomic Profiling Studies. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:61-71. [PMID: 20726783 DOI: 10.1089/omi.2010.0061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Zhihua Liu
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yanlei Ma
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jianjun Yang
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Huanlong Qin
- Evidence-Based Medicine Group, Department of Surgery, the Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, People's Republic of China
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18
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Sun S, Poon RTP, Lee NP, Yeung C, Chan KL, Ng IOL, Day PJR, Luk JM. Proteomics of hepatocellular carcinoma: serum vimentin as a surrogate marker for small tumors (<or=2 cm). J Proteome Res 2010; 9:1923-30. [PMID: 20121168 DOI: 10.1021/pr901085z] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Small hepatocellular carcinomas (HCCs) can be effectively cured by surgery with good clinical outcomes. However, the conventional AFP marker is ineffective in detecting small tumors. Here we employed a proteomic profiling approach to identify a candidate marker for HCC (<or=2 cm) in tumor tissues and then evaluate its clinical feasibility in patients' sera. The study was divided into 2 phases. (i) Biomarker discovery: we collected 76 frozen liver tissues (40 HCC and 36 controls) for proteomics profiling. Candidate protein markers were identified by MALDI-TOF/TOF and confirmed by immunoblot and qPCR. (ii) Clinical evaluation: Selected biomarker was tested by ELISA for sensitivity and specificity using serum samples from a separate cohort of 152 subjects (88 HCC and 64 controls). Vimentin was found significantly overexpressed in HCC, in particular the small-size subgroup (<or=2 cm) with p < 0.01. When tested in the serum samples, vimentin level was significantly higher in small tumors than the non-neoplastic controls (AUC = 0.69 and p < 0.01). Further analysis suggested that elevated circulating vimentin level could detect small HCC at 40.91% sensitivity and 87.50% specificity. Moreover, vimentin was found to be superior to serum AFP assayed at different cut-offs in detecting small tumors. When combined with AFP, the detection sensitivity and specificity could be further enhanced to 58.77 and 98.15%, respectively. In conclusion, serum vimentin is a potential surrogate marker, either alone or in combination with AFP, for detection of small HCCs.
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Affiliation(s)
- Stella Sun
- Department of Surgery, University of Hong Kong, Hong Kong, China
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19
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Lee NPY, Cheung ST, Poon RTP, Fan ST, Luk JM. Genomic and proteomic biomarkers for diagnosis and prognosis of hepatocellular carcinoma. Biomark Med 2010; 1:273-84. [PMID: 20477402 DOI: 10.2217/17520363.1.2.273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Hepatocellular carcinoma is one of the most deadly liver malignancies found worldwide, with hepatitis virus infection being the prominent risk factor for this lesion. Patients with hepatocellular carcinoma are usually first diagnosed when in the advanced stage; thus, long-term clinical outcomes are poor and patients have limited treatment options. Currently, surveillance of hepatocellular carcinoma relies upon serological testing of alpha-fetoprotein levels and hepatic ultrasonography, which have low sensitivity and specificity, and are sometimes operator-dependent, respectively. Therefore, discovery of new biomarkers for early and accurate detection of hepatocellular carcinoma would be of great clinical value. Genomic and proteomic approaches are two major laboratory platforms for the identification of candidate hepatocellular carcinoma biomarkers based on profiling and validating with tumor and nontumor clinical samples. Frequently, these diagnostic markers have been found in association with genetic aberrations, protein-level alterations, post-translational modifications and immune functions. With the discovery of these biomarkers, earlier detection of hepatocellular carcinoma in high-risk subjects (e.g., cirrhosis and hepatitis carriers) becomes possible, which will enable clinicians to offer patients better clinical management and more effective treatment modalities.
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Affiliation(s)
- Nikki P Y Lee
- The University of Hong Kong, Department of Surgery and Center for Cancer Research, Queen Mary Hospital, Pokfulam, Hong Kong, PR China
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20
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Pleguezuelo M, Lopez-Sanchez LM, Rodriguez-Ariza A, Montero JL, Briceno J, Ciria R, Muntane J, de la Mata M. Proteomic analysis for developing new biomarkers of hepatocellular carcinoma. World J Hepatol 2010; 2:127-35. [PMID: 21160983 PMCID: PMC2998961 DOI: 10.4254/wjh.v2.i3.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 01/14/2010] [Accepted: 01/21/2010] [Indexed: 02/06/2023] Open
Abstract
AIM To identify new markers of hepatocellular carcinoma (HCC) using a proteomic analysis. METHODS Patients with liver cirrhosis of the three most frequent etiologies: hepatitis C virus, hepatitis B virus and alcoholic liver disease, were included in the study. The samples were analysed by 2D-electrophoresis in order to determine the differential protein expression. The proteins were separated according to the charge in immobilized pH 3-10 gradient strips and then by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Proteins of interest were excised, digested with trypsin and the resulting peptides were separated and identified. RESULTS Three differentially expressed apolipoproteins (Apo) were identified based on the protein profile using proteomic techniques: Apo-A1, Apo-A4 and Apo-E. Apo-A4 levels were significantly lower in HCC than in non-HCC patients regardless of etiology (P < 0.01). Multivariate logistic regression showed that Apo-A4 and Apo-A1 were the only independent factors related to HCC diagnosis (P < 0.05). The receiver operating characteristic (ROC) curve including both Apo-A4 and Apo-A1 showed an area under the ROC of 0.944 (P < 0.001), a sensitivity of 0.89 and a specificity of 0.81 for diagnosis of HCC. CONCLUSION Apo-A4 and Apo-A1 may be used clinically as biomarkers of HCC with a high sensibility and specificity. These findings may provide additional insights into the mechanism of HCC development and progression.
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Affiliation(s)
- Maria Pleguezuelo
- Maria Pleguezuelo, Ruben Ciria, Liver Research Unit and Academic Department of Surgery, Reina Sofia University Hospital, Avda Menendez Pidal s/n, Cordoba 14004, Spain
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21
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Cabibbo G, Craxì A. Needle track seeding following percutaneous procedures for hepatocellular carcinoma. World J Hepatol 2009; 1:62-6. [PMID: 21160966 PMCID: PMC2999258 DOI: 10.4254/wjh.v1.i1.62] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 09/08/2009] [Accepted: 09/15/2009] [Indexed: 02/06/2023] Open
Abstract
Neoplastic seeding may arise after diagnostic or therapeutic percutaneous procedures for hepatocellular carcinoma. The true incidence of seeding with hepatocellular carcinoma is difficult to assess precisely, but a significant risk of seeding exists and is greater when performing diagnostic biopsy as compared to therapeutic percutaneous procedures [radiofrequency ablation, radiofrequency ablation (RFA); percutaneous ethanol injection, Percutaneous ethanol injection (PEI)]. Whenever liver transplantation is feasible, diagnostic needle biopsies should be avoided, but RFA and PEI are often needed as "bridge" treatments. The role of adjuvant treatments in reducing the incidence of seeding following RFA or PEI requires further evaluation.
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Affiliation(s)
- Giuseppe Cabibbo
- Giuseppe Cabibbo, Antonio Craxì, Cattedra di Gastroenterologia, Dipartimento Biomedico di Medicina Interna e Specialstica, University of Palermo, Palermo 90127, Italy
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22
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Shariff MIF, Cox IJ, Gomaa AI, Khan SA, Gedroyc W, Taylor-Robinson SD. Hepatocellular carcinoma: current trends in worldwide epidemiology, risk factors, diagnosis and therapeutics. Expert Rev Gastroenterol Hepatol 2009; 3:353-67. [PMID: 19673623 DOI: 10.1586/egh.09.35] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide and, owing to changes in the prevalence of the two major risk factors, hepatitis B virus and hepatitis C virus, its overall incidence remains alarmingly high in the developing world and is steadily rising across most of the developed world. Early diagnosis remains the key to effective treatment and there have been recent advances in both the diagnosis and therapy of HCC, which have made important impacts on the disease. This review outlines the epidemiological trends, risk factors, diagnostic developments and novel therapeutics for HCC, both in the developing and developed world.
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Affiliation(s)
- Mohamed I F Shariff
- Liver Unit, Faculty of Medicine, Imperial College London, St Mary's Hospital, 10th Floor QEQM Building, South Wharf Road, London W2 1NY, UK.
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23
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Codarin E, Renzone G, Poz A, Avellini C, Baccarani U, Lupo F, di Maso V, Crocè SL, Tiribelli C, Arena S, Quadrifoglio F, Scaloni A, Tell G. Differential Proteomic Analysis of Subfractioned Human Hepatocellular Carcinoma Tissues. J Proteome Res 2009; 8:2273-84. [DOI: 10.1021/pr8009275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Erika Codarin
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Giovanni Renzone
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Alessandra Poz
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Claudio Avellini
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Umberto Baccarani
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Francesco Lupo
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Vittorio di Maso
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Saveria Lory Crocè
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Claudio Tiribelli
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Simona Arena
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Franco Quadrifoglio
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Andrea Scaloni
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
| | - Gianluca Tell
- Department of Biomedical Sciences and Technologies, University of Udine, 33100 Udine, Italy, Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy, Department of Clinical Pathology, University of Udine, 33100 Udine, Italy, Department of Surgery & Transplantation, University of Udine, 33100 Udine, Italy, Azienda Ospedaliero Universitaria, Molinette, 10100 Torino, Italy, and Centro Studi Fegato, AREA Science Park, 34012 Trieste, Italy
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Analysis of Low-Abundance Differential Proteins in Plasma from Hepatocellular Carcinomas Patients by Multidimensional Chromatography-Tandem Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2009. [DOI: 10.1016/s1872-2040(08)60094-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Beretta L. Comparative analysis of the liver and plasma proteomes as a novel and powerful strategy for hepatocellular carcinoma biomarker discovery. Cancer Lett 2009; 286:134-9. [PMID: 19232462 DOI: 10.1016/j.canlet.2009.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The extraordinary developments made in the past decade in proteomic technologies, in particular in mass spectrometry, have enabled investigators to consider designing studies to search for diagnostic and therapeutic biomarkers by scanning complex proteome samples. We developed a method based on extensive fractionation of intact proteins, to comprehensively and quantitatively profile the liver and plasma proteomes in health and disease. We have applied this method to samples collected from patients with early hepatocellular carcinoma (HCC) and from patients with liver cirrhosis as well as to samples collected from three mouse models of HCC. This method allowed for the identification of proteins that differ in expression levels in liver tissue or in plasma with disease progression from liver fibrosis, cirrhosis or steatohepatitis to HCC. The comparative analysis of the liver and plasma proteomes generated from human and mouse specimens, constitutes a novel and powerful strategy for HCC biomarker discovery.
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Affiliation(s)
- Laura Beretta
- Molecular Diagnostics Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center (M5-A864), 1100 Fairview Avenue North Seattle, WA 98109, USA.
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26
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Pleguezuelo M, Germani G, Marelli L, Xiruochakis E, Misseri M, Manousou P, Arvaniti V, Burroughs AK. Evidence-based diagnosis and locoregional therapy for hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2008; 2:761-84. [PMID: 19090737 DOI: 10.1586/17474124.2.6.761] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Early identification of hepatocellular carcinoma (HCC) is crucial to improving the results of therapy and for patients to be eligible for liver transplantation. Recent advances in noninvasive imaging technology include various techniques of harmonic ultrasound, new ultrasound contrast agents, multislice helical computed tomography and rapid high-quality magnetic resonance. The imaging diagnosis relies on the hallmark of arterial hypervascularity with portal venous washout. Since the use of better radiological techniques has improved the accuracy of noninvasive diagnosis, the role of liver biopsy in the diagnosis of HCC has declined. With recent advances in genomics and proteomics, a great number of potential markers have been identified and developed as new candidate markers for HCC. Locoregional therapies currently constitute the best options for early nonsurgical treatment of HCC. Percutaneous ethanol injection shows similar results to resection surgery for single tumors less than 3 cm in diameter. Radiofrequency ablation is superior to percutaneous ethanol injection in terms of local recurrence. Transarterial chemoembolization is currently the most common approach for the management of HCC without curative options since it improves patient survival, but the optimal embolizing agent, length of interval between sessions and whether the chemotherapeutic agent has any effect have not yet been determined. Combining transarterial chemoembolization with antiangiogenic agents, as well as with other techniques, such as radiofrequency ablation, may improve the results. Injection of radioisotopes such as yttrium-90, via the hepatic artery, may be particularly useful in patients with portal vein thrombosis. Comparisons with other transarterial techniques are needed.
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Affiliation(s)
- Maria Pleguezuelo
- The Royal Free Sheila Sherlock Liver Centre, Royal Free Hospital, Pond Street, London, NW3 2QG, UK.
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27
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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. [DOI: 10.1002/pmic.200800322] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Looi KS, Nakayasu ES, Diaz RAD, Tan EM, Almeida IC, Zhang JY. Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma. J Proteome Res 2008; 7:4004-12. [PMID: 18672925 DOI: 10.1021/pr800273h] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many studies have demonstrated that intracellular proteins, which are involved in carcinogenesis, can provoke autoantibody responses. Therefore, autoantibodies can be used clinically for cancer detection and for proteomic analysis in identification of tumor-associated antigens (TAAs) that are potentially involved in malignant transformation. Liver cancer, especially hepatocellular carcinoma (HCC), is one of the most common tumors in the world. The majority of people with HCC will die within 1 year of its detection. This high case fatality rate can partially be attributed to a lack of diagnostic methods that allow early detection. In the present study, sera from 20 patients with HCC, 30 patients with chronic hepatitis (CH), and 30 patients with liver cirrhosis (LC) as well as sera from 10 normal individuals were used in a proteomic approach to identify HCC-related TAAs. Thirty-four immunoreactive protein spots were excised from the two-dimensional gel electrophoresis (2DE), digested with trypsin, and subsequently analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Of 34 immunoreactive protein spots, 28 were identified. Seventeen of them were not only reactive with serum antibodies in HCC but also with antibodies in pre-HCC conditions, and 11 were only reactive with serum antibodies in HCC but not with antibodies in pre-HCC conditions. In the subsequent analysis, two representative proteins, HSP60 and HSP70, were selected as examples for the validation purpose. The results from immunoassay were consistent with the data from proteomic analysis, supporting our hypothesis that proteins identified with autoantibodies that have been present in precancer conditions may be not appropriate to use as TAA markers in cancer detection.
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Affiliation(s)
- Kok Sun Looi
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA
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Midorikawa Y, Sugiyama Y, Aburatani H. Screening of liver-targeted drugs. Expert Opin Drug Discov 2008; 3:643-54. [DOI: 10.1517/17460441.3.6.643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Saffroy R, Pham P, Reffas M, Takka M, Lemoine A, Debuire B. New perspectives and strategy research biomarkers for hepatocellular carcinoma. Clin Chem Lab Med 2008; 45:1169-79. [PMID: 17635075 DOI: 10.1515/cclm.2007.262] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Cirrhosis caused by hepatitis B virus, hepatitis C virus or chronic alcohol intake is associated with major risk. Systematic screening for HCC of asymptomatic patients with cirrhosis is needed for earlier detection of small tumors requiring treatment (liver transplantation, surgical resection, percutaneous techniques). The recommended screening strategy among cirrhotic patients is based on regular liver ultrasonography associated with serum alpha-fetoprotein (AFP) assay. As the performance of AFP is not satisfactory, additional tumoral markers are proposed (des-gamma-carboxyprothrombin, glycosylated AFP-L3 fraction). Currently, diagnosis of HCC in cirrhotic patients includes non-invasive tests (imaging after contrast administration, AFP assay); diagnostic biopsy is performed when imaging is limited. After treatment, tumor recurrence is assessed by regular follow-up (AFP assay and imaging). Despite the lack of accurate markers, recent developments in genomic and proteomic approaches will allow the discovery of new biomarkers for primary tumors, as well as for recurrence. This review summarizes the current state of biomarkers for screening, diagnosis and follow-up of HCC, and highlights new perspectives in the field.
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Affiliation(s)
- Raphaël Saffroy
- Service de Biochimie, Biologie Moléculaire et Toxicologie, Hôpital Universitaire Paul Brousse, Université Paris-Sud, UMR-S602, Villejuif, INSERM, Villejuif, France.
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31
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Abstract
Proteomics is the study of proteins and their interactions in a cell. With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. Because proteome reflects more accurately on the dynamic state of a cell, tissue, or organism, much is expected from proteomics to yield better disease markers for diagnosis and therapy monitoring. The advent of proteomics technologies for global detection and quantitation of proteins creates new opportunities and challenges for those seeking to gain greater understanding of diseases. High-throughput proteomics technologies combining with advanced bioinformatics are extensively used to identify molecular signatures of diseases based on protein pathways and signaling cascades. Mass spectrometry plays a vital role in proteomics and has become an indispensable tool for molecular and cellular biology. While the potential is great, many challenges and issues remain to be solved, such as mining low abundant proteins and integration of proteomics with genomics and metabolomics data. Nevertheless, proteomics is the foundation for constructing and extracting useful knowledge to biomedical research. In this review, a snapshot of contemporary issues in proteomics technologies is discussed.
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Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China.
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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: 44] [Impact Index Per Article: 2.6] [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.
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Affiliation(s)
- Stella Sun
- Department of Surgery, LKS Faculty of Medicine, Jockey Club Clinical Research Center, The University of Hong Kong, Pokfulam, Hong Kong
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33
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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: 194] [Impact Index Per Article: 11.4] [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.
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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
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Affiliation(s)
- Wei Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, P.R. China
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Stigliano R, Marelli L, Yu D, Davies N, Patch D, Burroughs AK. Seeding following percutaneous diagnostic and therapeutic approaches for hepatocellular carcinoma. What is the risk and the outcome? Seeding risk for percutaneous approach of HCC. Cancer Treat Rev 2007; 33:437-47. [PMID: 17512669 DOI: 10.1016/j.ctrv.2007.04.001] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 03/30/2007] [Accepted: 04/03/2007] [Indexed: 02/06/2023]
Abstract
BACKGROUND Tumour biopsy is usually considered mandatory for patient management by oncologists. Currently percutaneous ablation is used therapeutically for cirrhotic patients with small hepatocellular carcinoma (HCC), not suitable for resection or waiting for liver transplantation. However malignant seeding is a recognized complication of both diagnostic and therapeutic procedures in patients with HCC. Although percutaneous therapy whether with or without biopsy of a suspected HCC nodule may minimize the risk of seeding, this has not been confirmed. AIM To evaluate the risk of seeding, defined as new neoplastic disease occurring outside the liver capsule, either in the subcutaneous tissue or peritoneal cavity following needle biopsy and/or local ablation therapy (LAT). METHODS A literature search resulted in 179 events in 99 articles between January 1983 and February 2007: 66 seedings followed liver biopsy, 26 percutaneous ethanol injection (PEI), 1 microwave, 22 radiofrequency ablation (RFA), and 64 after combined biopsy and percutaneous treatment (5 microwave; 33 PEI; 26 RFA). RESULTS In 41 papers specifying the total number of patients biopsied and/or treated, the median risk of seeding was 2.29% (range 0-11%) for biopsy group; 1.4% (1.15-1.85%) for PEI when used with biopsy and 0.61% (0-5.56%) for RFA without biopsy, 0.95% (0-12.5%) for RFA with biopsy and 0.72% (0-10%) for liver nodules (including non-HCC nodules) biopsied and ablated. CONCLUSION Risk of seeding with HCC is substantial and appears greater with using diagnostic biopsy alone compared to therapeutic percutaneous procedures. This risk is particularly relevant for patients being considered for liver transplantation.
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Affiliation(s)
- R Stigliano
- Liver Transplantation and Hepatobiliary Medicine Unit, Royal Free Hospital, Pond Street, NW3 2QG London, UK.
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35
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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: 0.4] [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.
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36
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Kanmura S, Uto H, Kusumoto K, Ishida Y, Hasuike S, Nagata K, Hayashi K, Ido A, Stuver SO, Tsubouchi H. Early diagnostic potential for hepatocellular carcinoma using the SELDI ProteinChip system. Hepatology 2007; 45:948-56. [PMID: 17393466 DOI: 10.1002/hep.21598] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED Early detection of HCC increases the potential for curative treatment and improves survival. To facilitate early detection of HCC, this study sought to identify novel diagnostic markers of HCC using surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF/MS) ProteinChip technology. Serum samples were obtained from 153 patients with or without HCC, all of whom had been diagnosed with HCV-associated chronic liver disease. To identify proteins associated with HCC, serum samples were analyzed using SELDI-TOF/MS. We constructed an initial decision tree for the correct diagnosis of HCC using serum samples from patients with (n = 35) and without (n = 44) HCC. Six protein peaks were selected to construct a decision tree using this first group. The efficacy of the decision tree was then assessed using a second group of patients with (n = 29) and without (n = 33) HCC. The sensitivity and specificity of this decision tree for the diagnosis of HCC were 83% and 76%, respectively. For a third group, we analyzed sera from seven patients with HCC obtained before the diagnosis of HCC by ultrasonography (US) and from five patients free of HCC for the past 3 years. Use of these diagnostic markers predicted the diagnosis of HCC in six of these seven patients before HCC was clinically apparent without any false positives. CONCLUSION Serum profiling using the SELDI ProteinChip system is useful for the early detection and prediction of HCC in patients with chronic HCV infection.
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Affiliation(s)
- Shuji Kanmura
- Division of Gastroenterology and Hematology, Department of Internal Medicine, University of Miyazaki, Miyazaki, Japan
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37
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Wright LM, Kreikemeier JT, Fimmel CJ. A concise review of serum markers for hepatocellular cancer. ACTA ACUST UNITED AC 2007; 31:35-44. [PMID: 17293059 DOI: 10.1016/j.cdp.2006.11.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2006] [Indexed: 02/08/2023]
Abstract
BACKGROUND The rising incidence of hepatocellular cancer in the US and worldwide has sparked a renewed interest in HCC serum markers. HCC typically develops in patients with chronic liver disease and cirrhosis. It is in these target populations that serum markers are most urgently needed. Unfortunately, the currently available markers lack sensitivity and specificity. A number of novel candidate markers have recently been introduced. METHODS We performed a review of the literature (2001-2006) of traditional and novel serum markers for hepatocellular cancer. RESULTS Several promising new HCC markers have been identified over the past 5 years. They include single proteins, complex proteomics features, and tumor-specific autoantibodies. The excitement about the new markers is tempered by the realization that none of them have yet met the most stringent criteria defined by the Early Detection Research Network (EDRN). CONCLUSION A new generation of HCC serum markers awaits validation in properly controlled clinical studies.
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Affiliation(s)
- Lorinda M Wright
- Division of Gastroenterology, Hepatology and Nutrition, Loyola University, Chicago, 2160 South First Avenue, Maywood, IL 60153, USA
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38
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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: 2.2] [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.
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Affiliation(s)
- Yasuhiro Kuramitsu
- Department of Biochemistry and Biomolecular Recognition, Yamaguchi University School of Medicine, Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan.
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39
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Kraljevic S, Sedic M, Scott M, Gehrig P, Schlapbach R, Pavelic K. Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view? Cancer Treat Rev 2006; 32:619-29. [PMID: 17069979 DOI: 10.1016/j.ctrv.2006.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Revised: 09/05/2006] [Accepted: 09/07/2006] [Indexed: 02/05/2023]
Abstract
Regardless of continuous advances in technology and expansion of the knowledge in the field of genomic information, cancer still remains one of the leading causes of death in developed countries for many reasons, including non-selectiveness of commonly used anti-cancer drugs that often influence non-specific rather than tumour-specific targets. As cancer cells are characterized by the ability to divide and multiply in an uncontrolled manner whereby a set of specific proteins modulate cell division processes, proteomics seems to be a suitable tool for seeking out molecular mediators of anti-cancer drugs action and resistance, thus improving chemotherapy outcome. This review will focus on the recent knowledge of the molecular mechanisms involved in the anti-cancer drugs response revealed by the proteomics tools. In addition, we will touch upon the effects of "gene drugs" with p53 and p21(waf1/cip1) genes on the protein complement of tumour cells assessed by the two-dimensional gel electrophoresis combined with mass spectrometry. Such studies could substantially contribute to further drug optimization prior to its clinical use and represent an important but still small step in the long way of drug discovery. However, fluctuations in protein expression, distribution, posttranslational modifications, interactions, functions and compartmentalization make it difficult to use exclusively expression proteomics data without putting it in broader biological context. Thus, the challenge today is to shift from the identification of drug response and disease biomarkers to more time-consuming process of revealing the biochemical mechanism that connects a specific protein with a disease or cellular response to a drug.
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Affiliation(s)
- Sandra Kraljevic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Bijenicka Cesta 54, 10002 Zagreb, Croatia.
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40
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Teufelhofer O, Parzefall W, Elbling L, Kainzbauer E, Grasl-Kraupp B, Zielinski C, Schulte-Hermann R, Gerner C. Divide and conquer: Rat liver tissue proteomics based on the analysis of purified constituents. Electrophoresis 2006; 27:4112-20. [PMID: 17054093 DOI: 10.1002/elps.200600017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Comparative proteome data of normal and diseased tissue samples are difficult to interpret. Proteins detected in tissues are derived from different cell types and blood constituents. Pathologic or toxicant-induced aberrations may affect the proteome profile of tissues in several ways since different cell types may respond in very different and highly specific manners. The aim of this study was to analyze the proteome profiles of purified rat liver primary cells and of blood plasma in comparison to liver whole tissue. Moreover, we investigated alterations of these profiles induced by the liver toxicant N-nitrosomorpholine (NNM) used as a model compound. Whole liver samples, pure hepatocytes and Kupffer cells as well as blood plasma were obtained from saline- or NNM-treated rats. Proteins were separated by 2-D PAGE and their amounts were estimated by fluorography. Selected proteins were identified by MS analysis of tryptic digests. Among them we identified proteins exclusively expressed in the analysed constituents. Several of these proteins were assigned in the proteome profile of whole-tissue homogenates. Furthermore, we identified several proteins that were modified, up-regulated or down-regulated due to NNM treatment in total liver homogenates. Some of these protein alterations were specifically detected in primary cells isolated from NNM-treated rats. Thus, we demonstrated the successful assignment of NNM-induced proteome alterations in rat liver to the cell type of origin. The currently applied approach may help to better understand pathologic processes at a whole-tissue level.
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Affiliation(s)
- Olga Teufelhofer
- Internal Medicine Clinic I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
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41
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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: 3.1] [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.
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Affiliation(s)
- J T Feng
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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42
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Berzsenyi MD, Roberts SK, Beard MR. Genomics of Hepatitis B and C Infections: Diagnostic and Therapeutic Applications of Microarray Profiling. Antivir Ther 2006. [DOI: 10.1177/135965350601100515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microarray profiling offers many potential advances in diagnostic and therapeutic intervention in human disease because of its unparalleled ability to conduct high-throughput analysis of gene expression. However, limitations of this technique relate in part to issues regarding the various methodologies and experimental designs as well as difficulties in the interpretation of results. Despite this, microarray profiling has led to a better understanding of the molecular pathogenesis of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. Key events in clearance and the development of chronicity of HCV have been identified that may prove to have a role in the development of future treatments. In addition, pharmacogenomic studies of interferon-based treatment for chronic HCV and HBV have provided mechanistic insights into the therapeutic action of interferons. These advances have implications with respect to the development of improved therapeutic agents. New biomarkers for cancer screening and gene profiles with prognostic value for survival have also been developed for hepatocellular carcinoma, which frequently complicates chronic viral hepatitis. Thus, microarray profiling offers enormous potential for improvements in antiviral therapy and our understanding of blood-borne viral hepatitis.
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Affiliation(s)
- Mark D Berzsenyi
- Department of Gastroenterology, Alfred Hospital, Victoria, Australia
| | - Stuart K Roberts
- Department of Gastroenterology, Alfred Hospital, Victoria, Australia
| | - Michael R Beard
- Infectious Diseases Laboratories and Hanson Institute, Institute of Medical and Veterinary Science, Adelaide, South Australia
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, South Australia, Australia
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43
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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: 64] [Impact Index Per Article: 3.6] [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.
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Affiliation(s)
- Nicolas Chignard
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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44
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Azad NS, Rasool N, Annunziata CM, Minasian L, Whiteley G, Kohn EC. Proteomics in clinical trials and practice: present uses and future promise. Mol Cell Proteomics 2006; 5:1819-29. [PMID: 16737951 DOI: 10.1074/mcp.r600008-mcp200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of clinical proteomics is a promising new field that has the potential to have many applications, including the identification of biomarkers and monitoring of disease, especially in the field of oncology. Expression proteomics evaluates the cellular production of proteins encoded by a particular gene and exploits the differential expression and post-translational modifications of proteins between healthy and diseased states. These biomarkers may be applied towards early diagnosis, prognosis, and prediction of response to therapy. Functional proteomics seeks to decipher protein-protein interactions and biochemical pathways involved in disease biology and targeted by newer molecular therapeutics. Advanced spectrometry technologies and new protein array formats have improved these analyses and are now being applied prospectively in clinical trials. Further advancement of proteomics technology could usher in an era of personalized molecular medicine, where diseases are diagnosed at earlier stages and where therapies are more effective because they are tailored to the protein expression of a patient's malignancy.
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Affiliation(s)
- Nilofer S Azad
- Laboratory of Pathology, Molecular Signaling Section, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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45
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Casiano CA, Mediavilla-Varela M, Tan EM. Tumor-associated antigen arrays for the serological diagnosis of cancer. Mol Cell Proteomics 2006; 5:1745-59. [PMID: 16733262 PMCID: PMC2790463 DOI: 10.1074/mcp.r600010-mcp200] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The recognition that human tumors stimulate the production of autoantibodies against autologous cellular proteins called tumor-associated antigens (TAAs) has opened the door to the possibility that autoantibodies could be exploited as serological tools for the early diagnosis and management of cancer. Cancer-associated autoantibodies are often driven by intracellular proteins that are mutated, modified, or aberrantly expressed in tumor cells and hence are regarded as immunological reporters that could help uncover molecular events underlying tumorigenesis. Emerging evidence suggests that each type of cancer might trigger unique autoantibody signatures that reflect the nature of the malignant process in the affected organ. The advent of novel genomic, proteomic, and high throughput approaches has accelerated interest in the serum autoantibody repertoire in human cancers for the discovery of candidate TAAs. The use of individual anti-TAA autoantibodies as diagnostic or prognostic tools has been tempered by their low frequency and heterogeneity in most human cancers. However, TAA arrays comprising several antigens significantly increase this frequency and hold great promise for the early detection of cancer, monitoring cancer progression, guiding individualized therapeutic interventions, and identification of novel therapeutic targets. Our recent studies suggest that the implementation of TAA arrays in screening programs for the diagnosis of prostate cancer and other cancers should be preceded by the optimization of their sensitivity and specificity through the careful selection of the most favorable combinations of TAAs.
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Affiliation(s)
- Carlos A Casiano
- Center for Health Disparities Research and Department of Biochemistry and Microbiology, Loma Linda University School of Medicine, California 92350, USA.
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Santamaría E, Muñoz J, Fernandez-Irigoyen J, Sesma L, Mora MI, Berasain C, Lu SC, Mato JM, Prieto J, Avila MA, Corrales FJ. Molecular Profiling of Hepatocellular Carcinoma in Mice with a Chronic Deficiency of HepaticS-Adenosylmethionine: Relevance in Human Liver Diseases. J Proteome Res 2006; 5:944-53. [PMID: 16602702 DOI: 10.1021/pr050429v] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
S-adenosylmethionine arises as a central molecule in the preservation of liver homeostasis as a chronic hepatic deficiency results in spontaneous development of steatohepatitis and hepatocellular carcinoma. In the present work, we have attempted a comprehensive analysis of proteins associated with hepatocarcinogenesis in MAT1A knock out mice using a combination of two-dimensional electrophoresis and mass spectrometry, to then apply the resulting information to identify hallmarks of human HCC. Our results suggest the existence of individual-specific factors that might condition the development of preneoplastic lesions. Proteomic analysis allowed the identification of 151 differential proteins in MAT1A-/- mice tumors. Among all differential proteins, 27 changed in at least 50% of the analyzed tumors, and some of these alterations were already detected months before the development of HCC in the KO liver. The expression level of genes coding for 13 of these proteins was markedly decreased in human HCC. Interestingly, seven of these genes were also found to be down-regulated in a pretumoral condition such as cirrhosis, while depletion of only one marker was assessed in less severe liver disorders.
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Affiliation(s)
- Enrique Santamaría
- Division of Hepatology and Gene Therapy, CIMA, University of Navarra, 31008 Pamplona, Spain
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Luk JM, Lam CT, Siu AFM, Lam BY, Ng IOL, Hu MY, Che CM, Fan ST. Proteomic profiling of hepatocellular carcinoma in Chinese cohort reveals heat-shock proteins (Hsp27, Hsp70, GRP78) up-regulation and their associated prognostic values. Proteomics 2006; 6:1049-57. [PMID: 16400691 DOI: 10.1002/pmic.200500306] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
To facilitate the identification of candidate molecular biomarkers that are linked to the pathogenesis of hepatocellular carcinoma (HCC), we investigated protein-expression profiles of 146 tissue specimens including 67 pairs of tumors and adjacent non-tumors resected from HCC patients as well as 12 normal livers by 2-DE. Among the 1800 spots displayed in the liver proteome, a total of 90 protein species were found to be significantly different between the three groups (P < 0.05). Three of the top candidate markers up-regulated in HCC, with high receiver operating characteristic (ROC) curves, were identified by MS/MS analysis and belonged to the chaperone members: heat-shock protein (Hsp)27, Hsp70 and glucose-regulated protein (GRP)78. Over-expression of these chaperone proteins in HCC tissues was confirmed by Western blotting and immunohistochemistry. In correlation with clinico-pathological parameters, expression of Hsp27 was linked to alpha-fetoprotein level (P = 0.007) whereas up-regulation of GRP78 was associated with tumor venous infiltration (P = 0.035). No significant association of Hsp70 with any pathologic features was observed. The present HCC proteome analysis revealed that in response to the stressful cancerous microenvironment, tumor cells strived to increase the expression of chaperone proteins for cyto-protective function and to enhance tumor growth and metastasis.
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Affiliation(s)
- John M Luk
- Centre for the Study of Liver Disease and Department of Surgery, The University of Hong Kong, Hong Kong SAR, P. R. China.
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Horn A, Kreusch S, Bublitz R, Hoppe H, Cumme GA, Schulze M, Moore T, Ditze G, Rhode H. Multidimensional proteomics of human serum using parallel chromatography of native constituents and microplate technology. Proteomics 2006; 6:559-70. [PMID: 16342237 DOI: 10.1002/pmic.200500142] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A versatile, multidimensional, and non-denaturing proteome separation procedure using microplate technology is presented, yielding a digitized image of proteome composition. In the first dimension, the sample under study is separated into 96 fractions by size exclusion chromatography (SEC). In the second dimension, the fractions of the first dimension are transferred by the liquid-handling device CyBi-Well (CyBio AG, Jena, Germany) to 96 parallel anion exchange chromatography columns. In this way the proteins are conserved in their native states and are distributed in 2400 liquid fractions with high recovery rates and sufficient reproducibility. The resulting fractions are subjected to protein quantitation and identification. Spectrophotometrical and immunological methods and enzyme activity measurements are used for quantitation. To identify proteins, the fractions are subjected to MALDI-MS, and their tryptic digests to both MALDI- and LC-ESI-MS/MS. All preparation steps except the first are applied in parallel to sets of multiples of 96 samples. The procedure may be refined by adding more separation steps and may be adapted to various protein amounts and to various proteomes. Moreover, the method offers the opportunity to investigate functional protein complexes. The method was applied to separate the normal human serum proteome. Within 255 fractions exhibiting the highest protein concentrations, 742 proteins were identified by LC-ESI-MS/MS peptide sequence tags.
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Affiliation(s)
- Anton Horn
- Institute of Biochemistry, Friedrich Schiller University, Medical Faculty, Jena, Germany
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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
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50
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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